Topic Editors

Dr. Aristotelis Chatziioannou
Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation (NHRF), 11635 Athens, Greece
Prof. Dr. Yudong Zhang
School of Computer Science, University of Leicester, Leicester LE1 7RH, UK

Big Data in Healthcare, Bioinformatics and Precision Medicine

Abstract submission deadline
30 October 2022
Manuscript submission deadline
31 December 2022
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42240

Topic Information

Dear Colleagues,

A great challenge regarding the big data in healthcare, bioinformatics and precision medicine is the extraction of insightful, actionable knowledge from the streams of omics data related to patients that can be translated into effective therapies tailored to the molecular characteristics of the actual, biological state of an individual. In the context of host-related, genetic background vulnerabilities, or dysregulation of commensal microbiome promoting pathogenic infections, the role of comorbidities may now be examined through the manifold exploitation of diverse sequencing technologies.

These fascinating developments integrate a broad spectrum of experimental high-throughput techniques, such as microarrays, various next-generation sequencing (NGS) technologies, NMR, LC/GC–MS, etc. These technologies, applicable simultaneously to the same biospecimen, generate datasets of unprecedented molecular resolution that can be complemented by various types of imaging data, biosignals, or clinical records.

Crucial is the deployment of powerful, big data and analytic techniques alongside the maturation of the experimental arm, sculpting the profile of Big Data in Healthcare, Bioinformatics, and Precision Medicine, through:

  • Advancements in multi-omic integration
  • Molecular network modeling/visualization
  • Machine/deep learning techniques in omics
  • Advancing/optimizing in the utilization and integration of biomedical ontologies
  • Intelligent pharmacogenomic analysis
  • Nanotechnological applications/nanosensor systems

This Topic aims to collect the fruits of research in these and other areas relevant to Big Data in Healthcare, Bioinformatics and Precision Medicine. The submission of papers with solid connections to multi-omic integration, big data analytic pipelines, health monitoring/diagnostic applications is strongly encouraged.

Dr. Aristotelis Chatziioannou
Prof. Dr. Yudong Zhang
Topic Editors

Keywords

  • multi-omics
  • translational studies on tumors
  • tumor detection and segmentation
  • histopathological diagnosis
  • biomedical ontologies
  • semantic network modeling
  • biomedical deep learning
  • intelligent pharmacogenomics
  • integrative bioinformatics
  • biomedical big data interpretation
  • network-driven interpretation
  • deep learning
  • machine learning
  • artificial intelligence
  • image processing
  • personalized medicine
  • bioinformatics
  • health informatics
  • computational biology

Participating Journals

Journal Name Impact Factor CiteScore Launched Year First Decision (median) APC
Applied Sciences
applsci
2.838 3.7 2011 17.4 Days 2300 CHF Submit
Biology
biology
5.168 2.8 2012 16.7 Days 2000 CHF Submit
Genes
genes
4.141 5.0 2010 17.1 Days 2400 CHF Submit
Journal of Personalized Medicine
jpm
3.508 1.8 2011 20.1 Days 2000 CHF Submit
Cancers
cancers
6.575 5.8 2009 17.4 Days 2400 CHF Submit

Published Papers (73 papers)

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Article
Head and Neck Cancer Types and Risks of Cervical–Cranial Vascular Complications within 5 Years after Radiation Therapy
J. Pers. Med. 2022, 12(7), 1060; https://doi.org/10.3390/jpm12071060 - 29 Jun 2022
Abstract
Background and purpose: to investigate the frequency of cervical–cranial vascular complications soon after radiation therapy (RT) and identify differences among patients with various types of head and neck cancer (HNC). Methods: We enrolled 496 patients with HNC who had received their final RT [...] Read more.
Background and purpose: to investigate the frequency of cervical–cranial vascular complications soon after radiation therapy (RT) and identify differences among patients with various types of head and neck cancer (HNC). Methods: We enrolled 496 patients with HNC who had received their final RT dose in our hospital. These patients underwent carotid duplex ultrasound (CDU) for monitoring significant carotid artery stenosis (CAS). Brain imaging were reviewed to detect vertebral, intracranial artery stenosis, or preexisted CAS before RT. Primary outcome was significant CAS at the internal or common carotid artery within first 5 years after RT. We categorized the patients into nasopharyngeal carcinoma (NPC) and non-NPC groups and compared the cumulative occurrence of significant CAS between the groups using Kaplan–Meier and Cox-regression analyses. Results: Compared to the NPC group, the non-NPC group had a higher frequency of significant CAS (12.7% vs. 2.0%) and were more commonly associated with significant CAS after adjusting the covariates (Adjusted hazard ratio: 0.17, 95% confident interval: 0.05–0.57) during the follow-up period. All the non-NPC subtypes (oral cancer/oropharyngeal, hypopharyngeal, and laryngeal cancers) were associated with higher risks of significant CAS than the NPC group (p < 0.001 respectively). Conclusion: Significant CAS was more frequently noted within 5 years of RT among the patients with non-NPC HNC than among the patients with NPC. Scheduled carotid artery surveillance and vascular risk monitoring should be commenced earlier for patients with non-NPC HNC. By contrast, vascular surveillance could be deferred to 5 years after RT completion in NPC patients. Full article
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Article
Characterization of the Oncogenic Potential of Eukaryotic Initiation Factor 4A1 in Lung Adenocarcinoma via Cell Cycle Regulation and Immune Microenvironment Reprogramming
Biology 2022, 11(7), 975; https://0-doi-org.brum.beds.ac.uk/10.3390/biology11070975 - 28 Jun 2022
Abstract
Lung adenocarcinoma (LUAD) is a common type of lung cancer. Although the diagnosis and treatment of LUAD have significantly improved in recent decades, the survival for advanced LUAD is still poor. It is necessary to identify more targets for developing potential agents against [...] Read more.
Lung adenocarcinoma (LUAD) is a common type of lung cancer. Although the diagnosis and treatment of LUAD have significantly improved in recent decades, the survival for advanced LUAD is still poor. It is necessary to identify more targets for developing potential agents against LUAD. This study explored the dysregulation of translation initiation factors, specifically eukaryotic initiation factors 4A1 (EIF4A1) and EIF4A2, in developing LUAD, as well as their underlying mechanisms. We found that the expression of EIF4A1, but not EIF4A2, was higher in tumor tissue and associated with poor clinical outcomes in LUAD patients. Elevated expression of EIF4H with poor prognosis may potentiate the oncogenic role of EIF4A1. Functional enrichment analysis revealed that upregulation of EIF4A1 was related to cell cycle regulation and DNA repair. The oncogenic effect of EIF4A1 was further elucidated by Gene Set Variation Analysis (GSVA). The GSVA score of the gene set positively correlated with EIF4A1 was higher in tumors and significantly associated with worse survival. In the meantime, gene set enrichment analysis (GSEA) also indicated that elevated EIF4A1 expression in LUAD patients was associated with a decreased infiltration score for immune cells by reducing anticancer immune cell types and recruiting immunosuppressive cells. Consistent with the results, the GSVA score of genes whose expression was negatively correlated with EIF4A1 was lower in the tumor tissue of LUAD cases with worse clinical outcomes and was strongly associated with the disequilibrium of anti-cancer immunity by recruiting anticancer immune cells. Based on the results from the present study, we hypothesize that the dysregulation of EIF4A1 might be involved in the pathophysiology of LUAD development by promoting cancer growth and changing the tumor immune microenvironment. This can be used to develop potential diagnostic biomarkers or therapeutic targets for LUAD. Full article
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Article
Development of Machine Learning Models Predicting Estimated Blood Loss during Liver Transplant Surgery
J. Pers. Med. 2022, 12(7), 1028; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12071028 - 23 Jun 2022
Abstract
The incidence of major hemorrhage and transfusion during liver transplantation has decreased significantly over the past decade, but major bleeding remains a common expectation. Massive intraoperative hemorrhage during liver transplantation can lead to mortality or reoperation. This study aimed to develop machine learning [...] Read more.
The incidence of major hemorrhage and transfusion during liver transplantation has decreased significantly over the past decade, but major bleeding remains a common expectation. Massive intraoperative hemorrhage during liver transplantation can lead to mortality or reoperation. This study aimed to develop machine learning models for the prediction of massive hemorrhage and a scoring system which is applicable to new patients. Data were retrospectively collected from patients aged >18 years who had undergone liver transplantation. These data included emergency information, donor information, demographic data, preoperative laboratory data, the etiology of hepatic failure, the Model for End-stage Liver Disease (MELD) score, surgical history, antiplatelet therapy, continuous renal replacement therapy (CRRT), the preoperative dose of vasopressor, and the estimated blood loss (EBL) during surgery. The logistic regression model was one of the best-performing machine learning models. The most important factors for the prediction of massive hemorrhage were the disease etiology, activated partial thromboplastin time (aPTT), operation duration, body temperature, MELD score, mean arterial pressure, serum creatinine, and pulse pressure. The risk-scoring system was developed using the odds ratios of these factors from the logistic model. The risk-scoring system showed good prediction performance and calibration (AUROC: 0.775, AUPR: 0.753). Full article
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Article
Characterization of Immune-Based Molecular Subtypes and Prognostic Model in Prostate Adenocarcinoma
Genes 2022, 13(6), 1087; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13061087 - 18 Jun 2022
Abstract
Prostate adenocarcinoma (PRAD), also named prostate cancer, the most common visceral malignancy, is diagnosed in male individuals. Herein, in order to obtain immune-based subtypes, we performed an integrative analysis to characterize molecular subtypes based on immune-related genes, and further discuss the potential features [...] Read more.
Prostate adenocarcinoma (PRAD), also named prostate cancer, the most common visceral malignancy, is diagnosed in male individuals. Herein, in order to obtain immune-based subtypes, we performed an integrative analysis to characterize molecular subtypes based on immune-related genes, and further discuss the potential features and differences between identified subtypes. Simultaneously, we also construct an immune-based risk model to assess cancer prognosis. Our findings showed that the two subtypes, C1 and C2, could be characterized, and the two subtypes showed different characteristics that could clearly describe the heterogeneity of immune microenvironments. The C2 subtype presented a better survival rate than that in the C1 subtype. Further, we constructed an immune-based prognostic model based on four screened abnormally expressed genes, and they were selected as predictors of the robust prognostic model (AUC = 0.968). Our studies provide reference for characterization of molecular subtypes and immunotherapeutic agents against prostate cancer, and the developed robust and useful immune-based prognostic model can contribute to cancer prognosis and provide reference for the individualized treatment plan and health resource utilization. These findings further promote the development and application of precision medicine in prostate cancer. Full article
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Article
Potential Cancer Risk in Patients with Rheumatoid Arthritis: A Longitudinal Korean Population-Based Analysis
J. Pers. Med. 2022, 12(6), 965; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12060965 - 13 Jun 2022
Abstract
The potential link between rheumatoid arthritis (RA) and cancer incidence needs to be validated due to inconsistent results between Asian and Western countries. We explored the long-term association of RA with the overall and organ-specific cancer incidence using nationwide population data. This longitudinal [...] Read more.
The potential link between rheumatoid arthritis (RA) and cancer incidence needs to be validated due to inconsistent results between Asian and Western countries. We explored the long-term association of RA with the overall and organ-specific cancer incidence using nationwide population data. This longitudinal follow-up study (2002–2015) included 3070 patients with RA and 12,280 controls (1:4 propensity score-matched for sex, age, residence, and income) from the Korean National Health Insurance Service-Health Screening Cohort database. A Cox proportional hazard model estimated the hazard ratio for malignancy following adjusting for covariates. Despite the similar overall cancer incidence between RA and control groups, differences in the incidence of organ-specific cancers were noted: the RA group had a 1.63-fold greater likelihood for lung cancer (95% confidence interval 1.11–2.40). In the sex-stratified subgroup analyses, the male RA patients exhibited higher odds of lung and thyroid cancer but a lower probability for colorectal cancer; no such associations were detected in either female patients with RA or age subgroups. In summary, the higher likelihood for lung cancer in Korean RA patients, especially thyroid and lung cancer in male RA patients, seems to be characteristic, which needs to be carefully monitored. Full article
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Article
Bioinformatic Prioritization and Functional Annotation of GWAS-Based Candidate Genes for Primary Open-Angle Glaucoma
Genes 2022, 13(6), 1055; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13061055 - 13 Jun 2022
Abstract
Background: Primary open-angle glaucoma (POAG) is the most prevalent glaucoma subtype, but its exact etiology is still unknown. In this study, we aimed to prioritize the most likely ‘causal’ genes and identify functional characteristics and underlying biological pathways of POAG candidate genes. Methods: [...] Read more.
Background: Primary open-angle glaucoma (POAG) is the most prevalent glaucoma subtype, but its exact etiology is still unknown. In this study, we aimed to prioritize the most likely ‘causal’ genes and identify functional characteristics and underlying biological pathways of POAG candidate genes. Methods: We used the results of a large POAG genome-wide association analysis study from GERA and UK Biobank cohorts. First, we performed systematic gene-prioritization analyses based on: (i) nearest genes; (ii) nonsynonymous single-nucleotide polymorphisms; (iii) co-regulation analysis; (iv) transcriptome-wide association studies; and (v) epigenomic data. Next, we performed functional enrichment analyses to find overrepresented functional pathways and tissues. Results: We identified 142 prioritized genes, of which 64 were novel for POAG. BICC1, AFAP1, and ABCA1 were the most highly prioritized genes based on four or more lines of evidence. The most significant pathways were related to extracellular matrix turnover, transforming growth factor-β, blood vessel development, and retinoic acid receptor signaling. Ocular tissues such as sclera and trabecular meshwork showed enrichment in prioritized gene expression (>1.5 fold). We found pleiotropy of POAG with intraocular pressure and optic-disc parameters, as well as genetic correlation with hypertension and diabetes-related eye disease. Conclusions: Our findings contribute to a better understanding of the molecular mechanisms underlying glaucoma pathogenesis and have prioritized many novel candidate genes for functional follow-up studies. Full article
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Article
Bioinformatics and Experimental Analyses Reveal NFIC as an Upstream Transcriptional Regulator for Ischemic Cardiomyopathy
Genes 2022, 13(6), 1051; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13061051 - 13 Jun 2022
Abstract
Ischemic cardiomyopathy (ICM) caused by coronary artery disease always leads to myocardial infarction and heart failure. Identification of novel transcriptional regulators in ICM is an effective method to establish new diagnostic and therapeutic strategies. In this study, we used two RNA-seq datasets and [...] Read more.
Ischemic cardiomyopathy (ICM) caused by coronary artery disease always leads to myocardial infarction and heart failure. Identification of novel transcriptional regulators in ICM is an effective method to establish new diagnostic and therapeutic strategies. In this study, we used two RNA-seq datasets and one microarray dataset from different studies, including 25 ICM and 21 non-failing control (NF) samples of human left ventricle tissues for further analysis. In total, 208 differentially expressed genes (DEGs) were found by combining two RNA-seq datasets with batch effects removed. GO and KEGG analyses of DEGs indicated that the response to wounding, positive regulation of smooth muscle contraction, chromatin, PI3K-Akt signaling pathway, and transporters pathways are involved in ICM. Simple Enrichment Analysis found that NFIC-binding motifs are enriched in promoter regions of downregulated genes. The Gene Importance Calculator further proved that NFIC is vital. NFIC and its downstream genes were verified in the validating microarray dataset. Meanwhile, in rat cardiomyocyte cell line H9C2 cells, two genes (Tspan1 and Hopx) were confirmed, which decreased significantly along with knocking down Nfic expression. In conclusion, NFIC participates in the ICM process by regulating TSPAN1 and HOPX. NFIC and its downstream genes may be marker genes and potential diagnostic and therapeutic targets for ICM. Full article
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Article
PhenGenVar: A User-Friendly Genetic Variant Detection and Visualization Tool for Precision Medicine
J. Pers. Med. 2022, 12(6), 959; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12060959 - 12 Jun 2022
Abstract
Precision medicine has been revolutionized by the advent of high-throughput next-generation sequencing (NGS) technology and development of various bioinformatic analysis tools for large-scale NGS big data. At the population level, biomedical studies have identified human diseases and phenotype-associated genetic variations using NGS technology, [...] Read more.
Precision medicine has been revolutionized by the advent of high-throughput next-generation sequencing (NGS) technology and development of various bioinformatic analysis tools for large-scale NGS big data. At the population level, biomedical studies have identified human diseases and phenotype-associated genetic variations using NGS technology, such as whole-genome sequencing, exome sequencing, and gene panel sequencing. Furthermore, patients’ genetic variations related to a specific phenotype can also be identified by analyzing their genomic information. These breakthroughs paved the way for the clinical diagnosis and precise treatment of patients’ diseases. Although many bioinformatics tools have been developed to analyze the genetic variations from the individual patient’s NGS data, it is still challenging to develop user-friendly programs for clinical physicians who do not have bioinformatics programing skills to diagnose a patient’s disease using the genomic data. In response to this demand, we developed a Phenotype to Genotype Variation program (PhenGenVar), which is a user-friendly interface for monitoring the variations in a gene of interest for molecular diagnosis. This allows for flexible filtering and browsing of variants of the disease and phenotype-associated genes. To test this program, we analyzed the whole-genome sequencing data of an anonymous person from the 1000 human genome project data. As a result, we were able to identify several genomic variations, including single-nucleotide polymorphism, insertions, and deletions in specific gene regions. Therefore, PhenGenVar can be used to diagnose a patient’s disease. PhenGenVar is freely accessible and is available at our website. Full article
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Article
Development of a Machine Learning Model to Predict Non-Durable Response to Anti-TNF Therapy in Crohn’s Disease Using Transcriptome Imputed from Genotypes
J. Pers. Med. 2022, 12(6), 947; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12060947 - 09 Jun 2022
Abstract
Almost half of patients show no primary or secondary response to monoclonal anti-tumor necrosis factor α (anti-TNF) antibody treatment for inflammatory bowel disease (IBD). Thus, the exact mechanisms of a non-durable response (NDR) remain inadequately defined. We used our genome-wide genotype data to [...] Read more.
Almost half of patients show no primary or secondary response to monoclonal anti-tumor necrosis factor α (anti-TNF) antibody treatment for inflammatory bowel disease (IBD). Thus, the exact mechanisms of a non-durable response (NDR) remain inadequately defined. We used our genome-wide genotype data to impute expression values as features in training machine learning models to predict a NDR. Blood samples from various IBD cohorts were used for genotyping with the Korea Biobank Array. A total of 234 patients with Crohn’s disease (CD) who received their first anti-TNF therapy were enrolled. The expression profiles of 6294 genes in whole-blood tissue imputed from the genotype data were combined with clinical parameters to train a logistic model to predict the NDR. The top two and three most significant features were genetic features (DPY19L3, GSTT1, and NUCB1), not clinical features. The logistic regression of the NDR vs. DR status in our cohort by the imputed expression levels showed that the β coefficients were positive for DPY19L3 and GSTT1, and negative for NUCB1, concordant with the known eQTL information. Machine learning models using imputed gene expression features effectively predicted NDR to anti-TNF agents in patients with CD. Full article
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Article
Risk of Infertility in Males with Obstructive Sleep Apnea: A Nationwide, Population-Based, Nested Case-Control Study
J. Pers. Med. 2022, 12(6), 933; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12060933 - 05 Jun 2022
Abstract
Obstructive sleep apnea (OSA) yields intermittent hypoxia, hypercapnia, and sleep fragmentation. OSA is associated with chronic medical conditions such as cardiovascular diseases, metabolic syndrome, and neurocognitive dysfunction. However, the risk of infertility in OSA remains unclear due to limited data and lack of [...] Read more.
Obstructive sleep apnea (OSA) yields intermittent hypoxia, hypercapnia, and sleep fragmentation. OSA is associated with chronic medical conditions such as cardiovascular diseases, metabolic syndrome, and neurocognitive dysfunction. However, the risk of infertility in OSA remains unclear due to limited data and lack of long-term population-based studies. The study aims to assess the risk of infertility in obstructive sleep apnea (OSA) by means of a population-based cohort study. The data was utilized from the Taiwan National Health Insurance Research Database (NHIRD) to conduct a population-based cohort study (1997–2013). Compared with the Non-OSA group, the male with OSA and surgery group has the OR (odds ratio) of infertility of 2.70 (95% CI, 1.46–4.98, p = 0.0015), but no significance exists in females with OSA. When the data was stratified according to age and gender, some associations in the specific subgroups were significant. Respectively, males aged 20–35 years old and aged 35–50 years old with a history of OSA and surgery both had a positive association with infertility. (aOR: 3.19; 95% CI, 1.18–8.66, p = 0.0227; aOR: 2.57; 95% CI, 1.18–5.62 p = 0.0176). Male patients with OSA suffer from reduced fertility, but no significant difference was noted in females with OSA. The identification of OSA as a risk factor for male infertility will aid clinicians to optimize long-term medical care. Furthermore, more studies will be encouraged to clarify the effect of OSA on female fertility. Full article
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Article
The Therapeutic Potential of ADAMTS8 in Lung Adenocarcinoma without Targetable Therapy
J. Pers. Med. 2022, 12(6), 902; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12060902 - 30 May 2022
Abstract
Lung cancer is well known for its high mortality worldwide. The treatment for advanced lung cancer needs more attention to improve its survival time. A disintegrin and metallopeptidase with thrombospondin motifs 8 (ADAMTS8) has been linked to several cancer types. However, its role [...] Read more.
Lung cancer is well known for its high mortality worldwide. The treatment for advanced lung cancer needs more attention to improve its survival time. A disintegrin and metallopeptidase with thrombospondin motifs 8 (ADAMTS8) has been linked to several cancer types. However, its role in lung cancer is worthy of deep investigation to promote novel drug development. This study took advantage of RNA-seq and bioinformatics to verify the role that ADAMTS8 plays in lung cancer. The functional assays suggested that ADAMTS8 mediates invasion and metastasis when expressed at a low level, contributing to poor overall survival (OS). The expression of ADAMTS8 was under the regulation of GATA Binding Protein 1 (GATA1) and executed its pathologic role through Thrombospondin Type 1 Domain Containing 1 (THSD1) and ADAMTS Like 2 (ADAMTSL2). To define the impact of ADAMTS8 in the lung cancer treatment strategy, this study further grouped lung cancer patients in the TCGA database into mutated epidermal growth factor receptor (EGFR)/wild-type EGFR and programmed death ligand 1 (PD-L1) high/low groups. Importantly, the expression of ADAMTS8 was correlated positively with the recruitment of anticancer NKT cells and negatively with the infiltration of immunosuppressive Treg and exhausted T cells. The results indicated that lung cancer patients with higher ADAMTS8 levels among wild-type EGFR or low PD-L1 groups survive longer than those with lower levels do. This study indicates that ADAMTS8 might be a treatment option for patients with lung adenocarcinoma who lack efficient targeted or immunotherapies. Full article
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Article
MDMF: Predicting miRNA–Disease Association Based on Matrix Factorization with Disease Similarity Constraint
J. Pers. Med. 2022, 12(6), 885; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12060885 - 27 May 2022
Abstract
MicroRNAs (miRNAs) have drawn enormous attention owing to their significant roles in various biological processes, as well as in the pathogenesis of human diseases. Therefore, predicting miRNA–disease associations is a pivotal task for the early diagnosis and better understanding of disease pathogenesis. To [...] Read more.
MicroRNAs (miRNAs) have drawn enormous attention owing to their significant roles in various biological processes, as well as in the pathogenesis of human diseases. Therefore, predicting miRNA–disease associations is a pivotal task for the early diagnosis and better understanding of disease pathogenesis. To date, numerous computational frameworks have been proposed to identify potential miRNA–disease associations without escalating the costs and time required for clinical experiments. In this regard, I propose a novel computational framework (MDMF) for identifying potential miRNA–disease associations using matrix factorization with a disease similarity constraint. To evaluate the performance of MDMF, I calculated the area under the ROC curve (AUCs) in the framework of global and local leave-one-out cross-validation (LOOCV). In conclusion, MDMF achieved reliable AUC values of 0.9147 and 0.8905 for global and local LOOCV, respectively, which was a significant improvement upon the previous methods. Additionally, case studies were conducted on two major human cancers (breast cancer and lung cancer) to validate the effectiveness of MDMF. Comprehensive experimental results demonstrate that MDMF not only discovers miRNA–disease associations efficiently but also deciphers the underlying roles of miRNAs in the pathogenesis of diseases at a system level. Full article
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Article
Advanced Molecular Characterisation in Relapsed and Refractory Paediatric Acute Leukaemia, the Key for Personalised Medicine
J. Pers. Med. 2022, 12(6), 881; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12060881 - 27 May 2022
Abstract
Relapsed and refractory (R/r) disease in paediatric acute leukaemia remains the first reason for treatment failure. Advances in molecular characterisation can ameliorate the identification of genetic biomarkers treatment strategies for this disease, especially in high-risk patients. The purpose of this study was to [...] Read more.
Relapsed and refractory (R/r) disease in paediatric acute leukaemia remains the first reason for treatment failure. Advances in molecular characterisation can ameliorate the identification of genetic biomarkers treatment strategies for this disease, especially in high-risk patients. The purpose of this study was to analyse a cohort of R/r children diagnosed with acute lymphoblastic (ALL) or myeloid (AML) leukaemia in order to offer them a targeted treatment if available. Advanced molecular characterisation of 26 patients diagnosed with R/r disease was performed using NGS, MLPA, and RT-qPCR. The clinical relevance of the identified alterations was discussed in a multidisciplinary molecular tumour board (MTB). A total of 18 (69.2%) patients were diagnosed with B-ALL, 4 (15.4%) with T-ALL, 3 (11.5%) with AML and 1 patient (3.8%) with a mixed-phenotype acute leukaemia (MPL). Most of the patients had relapsed disease (88%) at the time of sample collection. A total of 17 patients (65.4%) were found to be carriers of a druggable molecular alteration, 8 of whom (47%) received targeted therapy, 7 (87.5%) of them in addition to hematopoietic stem cell transplantation (HSCT). Treatment response and disease control were achieved in 4 patients (50%). In conclusion, advanced molecular characterisation and MTB can improve treatment and outcome in paediatric R/r acute leukaemias. Full article
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Article
The French Early Breast Cancer Cohort (FRESH): A Resource for Breast Cancer Research and Evaluations of Oncology Practices Based on the French National Healthcare System Database (SNDS)
Cancers 2022, 14(11), 2671; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers14112671 - 27 May 2022
Abstract
Background: Breast cancer (BC) is the most frequent cancer and the leading cause of cancer-related death in women. The French National Cancer Institute has created a national cancer cohort to promote cancer research and improve our understanding of cancer using the National Health [...] Read more.
Background: Breast cancer (BC) is the most frequent cancer and the leading cause of cancer-related death in women. The French National Cancer Institute has created a national cancer cohort to promote cancer research and improve our understanding of cancer using the National Health Data System (SNDS) and amalgamating all cancer sites. So far, no detailed separate data are available for early BC. Objectives: To describe the creation of the French Early Breast Cancer Cohort (FRESH). Methods: All French women aged 18 years or over, with early-stage BC newly diagnosed between 1 January 2011 and 31 December 2017, treated by surgery, and registered in the general health insurance coverage plan were included in the cohort. Patients with suspected locoregional or distant metastases at diagnosis were excluded. BC treatments (surgery, chemotherapy, targeted therapy, radiotherapy, and endocrine therapy), and diagnostic procedures (biopsy, cytology, and imaging) were extracted from hospital discharge reports, outpatient care notes, or pharmacy drug delivery data. The BC subtype was inferred from the treatments received. Results: We included 235,368 patients with early BC in the cohort (median age: 60 years). The BC subtype distribution was as follows: luminal (80.2%), triple-negative (TNBC, 9.5%); HER2+ (10.3%), or unidentifiable (n = 44,388, 18.9% of the cohort). Most patients underwent radiotherapy (n = 200,685, 85.3%) and endocrine therapy (n = 165,655, 70.4%), and 38.3% (n = 90,252) received chemotherapy. Treatments and care pathways are described. Conclusions: The FRESH Cohort is an unprecedented population-based resource facilitating future large-scale real-life studies aiming to improve care pathways and quality of care for BC patients. Full article
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Article
Loss of CHGA Protein as a Potential Biomarker for Colon Cancer Diagnosis: A Study on Biomarker Discovery by Machine Learning and Confirmation by Immunohistochemistry in Colorectal Cancer Tissue Microarrays
Cancers 2022, 14(11), 2664; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers14112664 - 27 May 2022
Abstract
Background. The incidence of colorectal cancers has been constantly increasing. Although the mortality has slightly decreased, it is far from satisfaction. Precise early diagnosis for colorectal cancer has been a great challenge in order to improve patient survival. Patients and Methods. We started [...] Read more.
Background. The incidence of colorectal cancers has been constantly increasing. Although the mortality has slightly decreased, it is far from satisfaction. Precise early diagnosis for colorectal cancer has been a great challenge in order to improve patient survival. Patients and Methods. We started with searching for protein biomarkers based on our colorectal cancer biomarker database (CBD), finding differential expressed genes (GEGs) and non-DEGs from RNA sequencing (RNA-seq) data, and further predicted new biomarkers of protein–protein interaction (PPI) networks by machine learning (ML) methods. The best-selected biomarker was further verified by a receiver operating characteristic (ROC) test from microarray and RNA-seq data, biological network, and functional analysis, and immunohistochemistry in the tissue arrays from 198 specimens. Results. There were twelve proteins (MYO5A, CHGA, MAPK13, VDAC1, CCNA2, YWHAZ, CDK5, GNB3, CAMK2G, MAPK10, SDC2, and ADCY5) which were predicted by ML as colon cancer candidate diagnosis biomarkers. These predicted biomarkers showed close relationships with reported biomarkers of the PPI network and shared some pathways. An ROC test showed the CHGA protein with the best diagnostic accuracy (AUC = 0.9 in microarray data and 0.995 in RNA-seq data) among these candidate protein biomarkers. Furthermore, immunohistochemistry examination on our colon cancer tissue microarray samples further confirmed our bioinformatical prediction, indicating that CHGA may be used as a potential biomarker for early diagnosis of colon cancer patients. Conclusions. CHGA could be a potential candidate biomarker for diagnosing earlier colon cancer in the patients. Full article
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Article
Construction and Validation of a Tumor Microenvironment-Based Scoring System to Evaluate Prognosis and Response to Immune Checkpoint Inhibitor Therapy in Lung Adenocarcinoma Patients
Genes 2022, 13(6), 951; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13060951 - 26 May 2022
Abstract
Background: Lung cancer is among the most dangerous malignant tumors to human health. Lung adenocarcinoma (LUAD) accounts for about 40% of all lung cancers. Accumulating evidence suggests that the tumor microenvironment (TME) is a crucial regulator of carcinogenesis and therapeutic efficacy in LUAD. [...] Read more.
Background: Lung cancer is among the most dangerous malignant tumors to human health. Lung adenocarcinoma (LUAD) accounts for about 40% of all lung cancers. Accumulating evidence suggests that the tumor microenvironment (TME) is a crucial regulator of carcinogenesis and therapeutic efficacy in LUAD. However, the impact of tumor microenvironment-related signatures (TMERSs) representing the TME characteristics on the prognosis and therapeutic outcome of LUAD patients remains to be further explored. Materials and methods: Gene expression files and clinical information of 1630 LUAD samples and 275 samples with immunotherapy information from different databases such as The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and Cancer Research Institute (CRI) iAtlas were downloaded and analyzed. Three hundred tumor microenvironment-related signatures (TMERS) based on a comprehensive collection of marker genes were quantified by single sample gene set enrichment analysis (ssGSEA), and then eight significant signatures were selected to construct the tumor microenvironment-related signature score (TMERSscore) by performing Least Absolute Shrinkage and Selection Operator (LASSO)-Cox analysis. Results: In this study, we constructed a TME-based prognostic stratification model for patients with LUAD and validated it in several external datasets. Furthermore, the TMERSscore was found to be positively correlated with tumor malignancy and a high TMERSscore predicted a poor prognosis. Moreover, the TMERSscore of responders treated with Immune Checkpoint Inhibitor (ICI) therapies was significantly lower than that of non-responders, and the TMERSscore was positively correlated with the tumor immune dysfunction and exclusion (TIDE) score, implying that a low TMERSscore predicts a better response to ICI treatment and may provide independent and incremental predictive value over current biomarkers. Conclusions: Overall, we constructed a TMERSscore that can be used for LUAD patient prognosis stratification as well as ICI therapeutic efficacy evaluation, supportive results from independent external validation sets showed its robustness and effectiveness. Full article
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Article
DNA Hypermethylation and a Specific Methylation Spectrum on the X Chromosome in Turner Syndrome as Determined by Nanopore Sequencing
J. Pers. Med. 2022, 12(6), 872; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12060872 - 26 May 2022
Abstract
The molecular genetic mechanism of Turner syndrome (TS) still leaves much to be discovered. Methods: TS (45X0) patients and age-matched controls (46XX and 46XY) were selected. The nanopore sequencing combined with trio-whole exome sequencing (trio-WES) were used for the first time to investigate [...] Read more.
The molecular genetic mechanism of Turner syndrome (TS) still leaves much to be discovered. Methods: TS (45X0) patients and age-matched controls (46XX and 46XY) were selected. The nanopore sequencing combined with trio-whole exome sequencing (trio-WES) were used for the first time to investigate TS. Results: Thirteen TS (45X0) patients and eight controls were enrolled. Trio-WES analysis did not find any pathogenetic or likely pathogenic variants except X chromosome (chrX) deletion. The average methylation levels and patterns of chrX in 45X0 and 46XY were similar, and significantly higher than in 46XX (p = 2.22 × 10−16). Both hyper-methylation and hypo-methylation were detected in the CpG island (CGI), CGI_shore, promoter, genebody, and PAR1-region, while in the transposon element inactivation regions of the chrX and hypermethylation were predominant. A total of 125 differentially methylated genes were identified in 45X0 compared to 46XX, including 8 and 117 hypermethylated and hypomethylated genes, respectively, with the enrichment terms of mitophagy, regulation of DNA-binding transcription factor activity, etc. Conclusions: The results suggest that the methylation profile in patients with TS might be determined by the number of X chromosomes; the patterns of methylation in TS were precisely associated with the maintenance of genomic stability and improvement of gene expression. Differentially methylated genes/pathways might reveal the potential epigenetic modulation and lead to better understanding of TS. Full article
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Article
Distinct Phenotypes of Kidney Transplant Recipients in the United States with Limited Functional Status as Identified through Machine Learning Consensus Clustering
J. Pers. Med. 2022, 12(6), 859; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12060859 - 25 May 2022
Abstract
Background: There have been concerns regarding increased perioperative mortality, length of hospital stay, and rates of graft loss in kidney transplant recipients with functional limitations. The application of machine learning consensus clustering approach may provide a novel understanding of unique phenotypes of functionally [...] Read more.
Background: There have been concerns regarding increased perioperative mortality, length of hospital stay, and rates of graft loss in kidney transplant recipients with functional limitations. The application of machine learning consensus clustering approach may provide a novel understanding of unique phenotypes of functionally limited kidney transplant recipients with distinct outcomes in order to identify strategies to improve outcomes. Methods: Consensus cluster analysis was performed based on recipient-, donor-, and transplant-related characteristics in 3205 functionally limited kidney transplant recipients (Karnofsky Performance Scale (KPS) < 40% at transplant) in the OPTN/UNOS database from 2010 to 2019. Each cluster’s key characteristics were identified using the standardized mean difference. Posttransplant outcomes, including death-censored graft failure, patient death, and acute allograft rejection were compared among the clusters Results: Consensus cluster analysis identified two distinct clusters that best represented the clinical characteristics of kidney transplant recipients with limited functional status prior to transplant. Cluster 1 patients were older in age and were more likely to receive deceased donor kidney transplant with a higher number of HLA mismatches. In contrast, cluster 2 patients were younger, had shorter dialysis duration, were more likely to be retransplants, and were more likely to receive living donor kidney transplants from HLA mismatched donors. As such, cluster 2 recipients had a higher PRA, less cold ischemia time, and lower proportion of machine-perfused kidneys. Despite having a low KPS, 5-year patient survival was 79.1 and 83.9% for clusters 1 and 2; 5-year death-censored graft survival was 86.9 and 91.9%. Cluster 1 had lower death-censored graft survival and patient survival but higher acute rejection, compared to cluster 2. Conclusion: Our study used an unsupervised machine learning approach to characterize kidney transplant recipients with limited functional status into two clinically distinct clusters with differing posttransplant outcomes. Full article
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Article
Risk Factors of Incident Lung Cancer in Patients with Non-Cystic Fibrosis Bronchiectasis: A Korean Population-Based Study
Cancers 2022, 14(11), 2604; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers14112604 - 25 May 2022
Abstract
Background: Patients with non-cystic fibrosis bronchiectasis have an increased risk of lung cancer, followed by higher mortality in this population. Because the risk factors of lung cancer have not been well identified, this study aimed to investigate the risk factors of lung cancer [...] Read more.
Background: Patients with non-cystic fibrosis bronchiectasis have an increased risk of lung cancer, followed by higher mortality in this population. Because the risk factors of lung cancer have not been well identified, this study aimed to investigate the risk factors of lung cancer in individuals with newly diagnosed bronchiectasis. Methods: This cohort study using the Korean National Health Insurance Service database identified 7425 individuals with incident bronchiectasis among those who participated in the health screening exam in 2009. The cohort was followed from baseline to the date of incident: lung cancer, death, or until the end of the study period. We investigated the risk factors of lung cancer in participants with bronchiectasis using the Cox–proportional hazard models. Results: During median 8.3 years of follow-up duration, 1.9% (138/7425) developed lung cancer. In multivariable analyses, significant factors associated with increased risk of incident lung cancer included: males (adjusted hazard ratio [HR] = 3.54, 95% confidence interval [CI] = 2.17–5.79) than females, the overweight (adjusted HR = 1.55, 95% CI = 1.03–2.35) than the normal weight, current smokers (adjusted HR = 3.10, 95% CI = 2.00–4.79) than never smokers, participants living in the rural area (adjusted HR = 2.54, 95% CI = 1.68–3.85) than those living in the metropolitan area. Among comorbidities, chronic obstructive pulmonary disease was associated with an increased risk of lung cancer (adjusted HR = 1.46, 95% CI = 1.01–2.13) in participants with bronchiectasis. In contrast, mild alcohol consumption was associated with reduced risk of lung cancer (adjusted HR = 0.47, 95% CI = 0.29–0.74) in those with bronchiectasis. Conclusion: This Korean population-based study showed that males, current smoking, overweight, living in rural areas, and comorbid chronic obstructive pulmonary disease are associated with increased risk of lung cancer in individuals with bronchiectasis. Full article
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Article
Reassessment of Reliability and Reproducibility for Triple-Negative Breast Cancer Subtyping
Cancers 2022, 14(11), 2571; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers14112571 - 24 May 2022
Abstract
Triple-negative breast cancer (TNBC) is a heterogeneous disease with diverse, often poor prognoses and treatment responses. In order to identify targetable biomarkers and guide personalized care, scientists have developed multiple molecular classification systems for TNBC based on transcriptomic profiling. However, there is no [...] Read more.
Triple-negative breast cancer (TNBC) is a heterogeneous disease with diverse, often poor prognoses and treatment responses. In order to identify targetable biomarkers and guide personalized care, scientists have developed multiple molecular classification systems for TNBC based on transcriptomic profiling. However, there is no consensus on the molecular subtypes of TNBC, likely due to discrepancies in technical and computational methods used by different research groups. Here, we reassessed the major steps for TNBC subtyping, validated the reproducibility of established TNBC subtypes, and identified two more subtypes with a larger sample size. By comparing results from different workflows, we demonstrated the limitations of formalin-fixed, paraffin-embedded samples, as well as batch effect removal across microarray platforms. We also refined the usage of computational tools for TNBC subtyping. Furthermore, we integrated high-quality multi-institutional TNBC datasets (discovery set: n = 457; validation set: n = 165). Performing unsupervised clustering on the discovery and validation sets independently, we validated four previously discovered subtypes: luminal androgen receptor, mesenchymal, immunomodulatory, and basal-like immunosuppressed. Additionally, we identified two potential intermediate states of TNBC tumors based on their resemblance with more than one well-characterized subtype. In summary, we addressed the issues and limitations of previous TNBC subtyping through comprehensive analyses. Our results promote the rational design of future subtyping studies and provide new insights into TNBC patient stratification. Full article
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Article
Gene Expression Monotonicity across Bladder Cancer Stages Informs on the Molecular Pathogenesis and Identifies a Prognostic Eight-Gene Signature
Cancers 2022, 14(10), 2542; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers14102542 - 21 May 2022
Abstract
Despite advancements in molecular classification, tumor stage and grade still remain the most relevant prognosticators used by clinicians to decide on patient management. Here, we leverage publicly available data to characterize bladder cancer (BLCA)’s stage biology based on increased sample sizes, identify potential [...] Read more.
Despite advancements in molecular classification, tumor stage and grade still remain the most relevant prognosticators used by clinicians to decide on patient management. Here, we leverage publicly available data to characterize bladder cancer (BLCA)’s stage biology based on increased sample sizes, identify potential therapeutic targets, and extract putative biomarkers. A total of 1135 primary BLCA transcriptomes from 12 microarray studies were compiled in a meta-cohort and analyzed for monotonal alterations in pathway activities, gene expression, and co-expression patterns with increasing stage (Ta–T1–T2–T3–T4), starting from the non-malignant tumor-adjacent urothelium. The TCGA-2017 and IMvigor-210 RNA-Seq data were used to validate our findings. Wnt, MTORC1 signaling, and MYC activity were monotonically increased with increasing stage, while an opposite trend was detected for the catabolism of fatty acids, circadian clock genes, and the metabolism of heme. Co-expression network analysis highlighted stage- and cell-type-specific genes of potentially synergistic therapeutic value. An eight-gene signature, consisting of the genes AKAP7, ANLN, CBX7, CDC14B, ENO1, GTPBP4, MED19, and ZFP2, had independent prognostic value in both the discovery and validation sets. This novel eight-gene signature may increase the granularity of current risk-to-progression estimators. Full article
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Article
Sex Differences in the Prevalence of Head and Neck Cancers: A 10-Year Follow-Up Study of 10 Million Healthy People
Cancers 2022, 14(10), 2521; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers14102521 - 20 May 2022
Cited by 1
Abstract
Background: Descriptive epidemiologists have repeatedly reported that males are more susceptible to head and neck cancers. However, most published data are those of cross-sectional studies, and no population-based cohort study has yet been published. The aim of this study was to compare the [...] Read more.
Background: Descriptive epidemiologists have repeatedly reported that males are more susceptible to head and neck cancers. However, most published data are those of cross-sectional studies, and no population-based cohort study has yet been published. The aim of this study was to compare the prevalence of head and neck cancers in healthy males with females. Methods: A retrospective cohort study using the Korean National Health Insurance Service database on 9,598,085 individuals who underwent regular health checkups from 1 January to 31 December 2009. We sought head and neck cancers developed during the 10-year follow-up. Results: A total of 10,732 (incidence rate (IR) per 1000 person-years 0.25) individuals were newly diagnosed with head and neck cancer among the 9,598,085 individuals during the 10-year follow-up. The IR was 0.19 in males (8500 affected) and 0.06 in females (2232 affected). Notably, the male–female ratio increased with age below 70 years but decreased thereafter. The male–female difference was most apparent for laryngeal cancer; the male IR was 11-fold higher in the 40 s and 20-fold higher in the 60 s, followed by hypopharyngeal cancer (6.8- and 24.2-fold). Males smoked more and drank more alcohol than females (p < 0.0001 *, p < 0.0001 *). When never-smokers/-drinkers (only) were compared, males remained at a 2.9-fold higher risk of head and neck cancer than females. The hazard ratios for head and neck cancers in males tended to increase in the lower part of the upper aerodigestive tract: larynx (13.9) > hypopharynx (10.9) > oropharynx (4.4) > nasopharynx (2.9) > sinonasal region (1.8) > oral (1.6). Only the salivary gland cancer incidence did not differ between the sexes; the gland is not in the upper aerodigestive tract. Conclusion: Males are much more susceptible to head and neck cancers than females regardless of whether they drink alcohol or smoke tobacco. Sex differences in the incidence of head and neck cancer are most evident in the 60 s in the lower part of the upper aerodigestive tract, such as the larynx and hypopharynx. Full article
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Article
Deep Splicer: A CNN Model for Splice Site Prediction in Genetic Sequences
Genes 2022, 13(5), 907; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13050907 - 19 May 2022
Abstract
Many living organisms have DNA in their cells that is responsible for their biological features. DNA is an organic molecule of two complementary strands of four different nucleotides wound up in a double helix. These nucleotides are adenine (A), thymine (T), guanine (G), [...] Read more.
Many living organisms have DNA in their cells that is responsible for their biological features. DNA is an organic molecule of two complementary strands of four different nucleotides wound up in a double helix. These nucleotides are adenine (A), thymine (T), guanine (G), and cytosine (C). Genes are DNA sequences containing the information to synthesize proteins. The genes of higher eukaryotic organisms contain coding sequences, known as exons and non-coding sequences, known as introns, which are removed on splice sites after the DNA is transcribed into RNA. Genome annotation is the process of identifying the location of coding regions and determining their function. This process is fundamental for understanding gene structure; however, it is time-consuming and expensive when done by biochemical methods. With technological advances, splice site detection can be done computationally. Although various software tools have been developed to predict splice sites, they need to improve accuracy and reduce false-positive rates. The main goal of this research was to generate Deep Splicer, a deep learning model to identify splice sites in the genomes of humans and other species. This model has good performance metrics and a lower false-positive rate than the currently existing tools. Deep Splicer achieved an accuracy between 93.55% and 99.66% on the genetic sequences of different organisms, while Splice2Deep, another splice site detection tool, had an accuracy between 90.52% and 98.08%. Splice2Deep surpassed Deep Splicer on the accuracy obtained after evaluating C. elegans genomic sequences (97.88% vs. 93.62%) and A. thaliana (95.40% vs. 94.93%); however, Deep Splicer’s accuracy was better for H. sapiens (98.94% vs. 97.15%) and D. melanogaster (97.14% vs. 92.30%). The rate of false positives was 0.11% for human genetic sequences and 0.25% for other species’ genetic sequences. Another splice prediction tool, Splice Finder, had between 1% and 3% of false positives for human sequences, while other species’ sequences had around 4% and 10%. Full article
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Article
Radioactive Iodine Treatment for Thyroid Cancer Patients Increases the Risk of Long-Term Gastrointestinal Disorders: A Nationwide Population-Based Cohort Analysis
Cancers 2022, 14(10), 2505; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers14102505 - 19 May 2022
Abstract
(1) Background: The study aimed to investigate the association between radioactive iodine (RAI) treatment and long-term gastrointestinal disorders including ulcers, atrophic gastritis, and secondary malignant neoplasm of the stomach in patients with thyroid cancer. (2) Methods: The data of the study were extracted [...] Read more.
(1) Background: The study aimed to investigate the association between radioactive iodine (RAI) treatment and long-term gastrointestinal disorders including ulcers, atrophic gastritis, and secondary malignant neoplasm of the stomach in patients with thyroid cancer. (2) Methods: The data of the study were extracted from the National Health Insurance Database (NHIRD) of Taiwan between 2000 to 2015. Patients of ages older than 20 with thyroid cancer after thyroidectomy were included and divided into groups with RAI (study cohort) and without RAI (comparison cohort). Multivariate Cox proportional hazards regression analysis and the Kaplan–Meier method were used for statistical analysis. (3) Results: A total of 7250 (with RAI: 5800, without RAI: 1450) patients were included. The Kaplan-Meier analysis revealed a significantly higher cumulative risk for overall gastrointestinal disorders in the group with RAI (log-rank p = 0.034). The risk for gastrointestinal disorders was higher when receiving a cumulative RAI dose higher than 1.11 GBq in the Cox regression analysis. In the subgroup analysis, the risks of gastric and duodenal ulcers are significantly higher in the group with RAI treatment. (4) Conclusions: This study revealed that RAI was associated with an increased risk for long-term gastrointestinal disorders, specifically gastric and duodenal ulcers, in thyroid cancer, especially when the cumulative dose exceeds 1.11 GBq. Full article
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Article
Physiologically-Based Pharmacokinetics Modeling for Hydroxychloroquine as a Treatment for Malaria and Optimized Dosing Regimens for Different Populations
J. Pers. Med. 2022, 12(5), 796; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12050796 - 14 May 2022
Abstract
Malaria is a severe parasite infectious disease with high fatality. As one of the approved treatments of this disease, hydroxychloroquine (HCQ) lacks clinical administration guidelines for patients with special health conditions and co-morbidities. This may result in improper dosing for different populations and [...] Read more.
Malaria is a severe parasite infectious disease with high fatality. As one of the approved treatments of this disease, hydroxychloroquine (HCQ) lacks clinical administration guidelines for patients with special health conditions and co-morbidities. This may result in improper dosing for different populations and lead them to suffer from severe side effects. One of the most important toxicities of HCQ overdose is cardiotoxicity. In this study, we built and validated a physiologically based pharmacokinetic modeling (PBPK) model for HCQ. With the full-PBPK model, we predicted the pharmacokinetic (PK) profile for malaria patients without other co-morbidities under the HCQ dosing regimen suggested by Food and Drug Administration (FDA) guidance. The PK profiles for different special populations were also predicted and compared to the normal population. Moreover, we proposed a series of adjusted dosing regimens for different populations with special health conditions and predicted the concentration-time (C-T) curve of the drug plasma concentration in these populations which include the pregnant population, elderly population, RA patients, and renal impairment populations. The recommended special population-dependent dosage regimens can maintain the similar drug levels observed in the virtual healthy population under the original dosing regimen provided by FDA. Last, we developed mathematic formulas for predicting dosage based on a patient’s body measurements and two indexes of renal function (glomerular filtration rate and serum creatine level) for the pediatric and morbidly obese populations. Those formulas can facilitate personalized treatment of this disease. We hope to provide some advice to clinical practice when taking HCQ as a treatment for malaria patients with special health conditions or co-morbidities so that they will not suffer from severe side effects due to higher drug plasma concentration, especially cardiotoxicity. Full article
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Review
An Umbrella Review of the Evidence of Sex Determination Procedures in Forensic Dentistry
J. Pers. Med. 2022, 12(5), 787; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12050787 - 13 May 2022
Abstract
Sex determination in forensic dentistry is a major step towards postmortem profiling. The most widely recognized method is DNA, yet its application in the dental field of forensic sciences is still impractical. Depending on the conditions of the remains, teeth are often the [...] Read more.
Sex determination in forensic dentistry is a major step towards postmortem profiling. The most widely recognized method is DNA, yet its application in the dental field of forensic sciences is still impractical. Depending on the conditions of the remains, teeth are often the only surviving organ. Some systematic reviews (SRs) have been recently produced; hence this umbrella review critically assesses their level of evidence and provides an overall comprehensive view. An electronic database search was conducted in four databases (PubMed, Cochrane, Web of Science, and LILACS) and three grey search engines up to December 2021, focusing on SRs of sex determination through forensic dentistry procedures. The methodological quality of the SRs was analyzed using the measurement tool to assess SRs criteria (AMSTAR2). Five SRs were included, two of critically low quality and three of low quality. The SRs posited that canines are the most dimorphic teeth; oral tissue remnants are a rich source for sex determination by DNA tracing; and artificial intelligence tools demonstrate high potential in forensic dentistry. The quality of evidence on sex determination using dental approaches was rated as low. Well-designed clinical trials and high standard systematic reviews are essential to corroborate the accuracy of the different procedures of sex determination in forensic dentistry. Full article
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Article
A Novel Cuproptosis-Related Prognostic Gene Signature and Validation of Differential Expression in Clear Cell Renal Cell Carcinoma
Genes 2022, 13(5), 851; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13050851 - 10 May 2022
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most prevalent subtype of renal cell carcinoma, which is characterized by metabolic reprogramming. Cuproptosis, a novel form of cell death, is highly linked to mitochondrial metabolism and mediated by protein lipoylation. However, the clinical impacts [...] Read more.
Clear cell renal cell carcinoma (ccRCC) is the most prevalent subtype of renal cell carcinoma, which is characterized by metabolic reprogramming. Cuproptosis, a novel form of cell death, is highly linked to mitochondrial metabolism and mediated by protein lipoylation. However, the clinical impacts of cuproptosis-related genes (CRGs) in ccRCC largely remain unclear. In the current study, we systematically evaluated the genetic alterations of cuproptosis-related genes in ccRCC. Our results revealed that CDKN2A, DLAT, DLD, FDX1, GLS, PDHA1 and PDHB exhibited differential expression between ccRCC and normal tissues (|log2(fold change)| > 2/3 and p < 0.05). Utilizing an iterative sure independence screening (SIS) method, we separately constructed the prognostic signature of CRGs for predicting the overall survival (OS) and progression-free survival (PFS) in ccRCC patients. The prognostic score of CRGs yielded an area under the curve (AUC) of 0.658 and 0.682 for the prediction of 5-year OS and PFS, respectively. In the Kaplan−Meier survival analysis of OS, a higher risk score of cuproptosis-related gene signature was significantly correlated with worse overall survival (HR = 2.72 (2.01–3.68), log-rank p = 1.76 × 10−7). Patients with a higher risk had a significantly shorter PFS (HR = 2.83 (2.08–3.85), log-rank p = 3.66 × 10−7). Two independent validation datasets (GSE40435 (N = 101), GSE53757 (N = 72)) were collected for meta-analysis, suggesting that CDKN2A (log2(fold change) = 1.46, 95%CI: 1.75–2.35) showed significantly higher expression in ccRCC tissues while DLAT (log2(fold change) = −0.54, 95%CI: −0.93–−0.15) and FDX1 (log2(fold change) = −1.01, 95%CI: −1.61–−0.42) were lowly expressed. The expression of CDKN2A and FDX1 in ccRCC was also significantly associated with immune infiltration levels and programmed cell death protein 1 (PD-1) expression (CDKN2A: r = 0.24, p = 2.14 × 10−8; FDX1: r = −0.17, p = 1.37 × 10−4). In conclusion, the cuproptosis-related gene signature could serve as a potential prognostic predictor for ccRCC patients and may offer novel insights into the cancer treatment. Full article
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Article
A Novel Patient Similarity Network (PSN) Framework Based on Multi-Model Deep Learning for Precision Medicine
J. Pers. Med. 2022, 12(5), 768; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12050768 - 10 May 2022
Abstract
Precision medicine can be defined as the comparison of a new patient with existing patients that have similar characteristics and can be referred to as patient similarity. Several deep learning models have been used to build and apply patient similarity networks (PSNs). However, [...] Read more.
Precision medicine can be defined as the comparison of a new patient with existing patients that have similar characteristics and can be referred to as patient similarity. Several deep learning models have been used to build and apply patient similarity networks (PSNs). However, the challenges related to data heterogeneity and dimensionality make it difficult to use a single model to reduce data dimensionality and capture the features of diverse data types. In this paper, we propose a multi-model PSN that considers heterogeneous static and dynamic data. The combination of deep learning models and PSN allows ample clinical evidence and information extraction against which similar patients can be compared. We use the bidirectional encoder representations from transformers (BERT) to analyze the contextual data and generate word embedding, where semantic features are captured using a convolutional neural network (CNN). Dynamic data are analyzed using a long-short-term-memory (LSTM)-based autoencoder, which reduces data dimensionality and preserves the temporal features of the data. We propose a data fusion approach combining temporal and clinical narrative data to estimate patient similarity. The experiments we conducted proved that our model provides a higher classification accuracy in determining various patient health outcomes when compared with other traditional classification algorithms. Full article
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Article
A Data Science Approach for the Identification of Molecular Signatures of Aggressive Cancers
Cancers 2022, 14(9), 2325; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers14092325 - 07 May 2022
Abstract
The main hallmarks of cancer include sustaining proliferative signaling and resisting cell death. We analyzed the genes of the WNT pathway and seven cross-linked pathways that may explain the differences in aggressiveness among cancer types. We divided six cancer types (liver, lung, stomach, [...] Read more.
The main hallmarks of cancer include sustaining proliferative signaling and resisting cell death. We analyzed the genes of the WNT pathway and seven cross-linked pathways that may explain the differences in aggressiveness among cancer types. We divided six cancer types (liver, lung, stomach, kidney, prostate, and thyroid) into classes of high (H) and low (L) aggressiveness considering the TCGA data, and their correlations between Shannon entropy and 5-year overall survival (OS). Then, we used principal component analysis (PCA), a random forest classifier (RFC), and protein–protein interactions (PPI) to find the genes that correlated with aggressiveness. Using PCA, we found GRB2, CTNNB1, SKP1, CSNK2A1, PRKDC, HDAC1, YWHAZ, YWHAB, and PSMD2. Except for PSMD2, the RFC analysis showed a different list, which was CAD, PSMD14, APH1A, PSMD2, SHC1, TMEFF2, PSMD11, H2AFZ, PSMB5, and NOTCH1. Both methods use different algorithmic approaches and have different purposes, which explains the discrepancy between the two gene lists. The key genes of aggressiveness found by PCA were those that maximized the separation of H and L classes according to its third component, which represented 19% of the total variance. By contrast, RFC classified whether the RNA-seq of a tumor sample was of the H or L type. Interestingly, PPIs showed that the genes of PCA and RFC lists were connected neighbors in the PPI signaling network of WNT and cross-linked pathways. Full article
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Systematic Review
The Effect of Probiotics on Intestinal Tight Junction Protein Expression in Animal  Models: A Meta-Analysis
Appl. Sci. 2022, 12(9), 4680; https://0-doi-org.brum.beds.ac.uk/10.3390/app12094680 - 06 May 2022
Abstract
This study investigates the effect of probiotics supplementation on tight junction protein (TJP) expression in animal models by meta-analysis. We estimated the effect of probiotics administration in an animal inflammatory bowel disease model based on 47 collected articles from the databases, including Sciencedirect, [...] Read more.
This study investigates the effect of probiotics supplementation on tight junction protein (TJP) expression in animal models by meta-analysis. We estimated the effect of probiotics administration in an animal inflammatory bowel disease model based on 47 collected articles from the databases, including Sciencedirect, Pubmed, Scopus, and Google Scholar. The effect size was analyzed with the standardized mean difference, and the heterogeneity of the effect sizes was assessed using Cochran’s Q test. To explain the heterogeneity, moderate analyses, such as meta-ANOVA and meta-regression, were performed using the mixed effects model. Finally, publication bias was assessed using Egger’s linear regression test. Among the evaluated items, zonula occluden (ZO)-1 showed the highest Q statistics value, and the effect sizes of all items were positive with high significance (p < 0.0001). The I2 value of all items reflected high heterogeneity (in excess of 80%). From the results of the meta-ANOVA, the factors of the heterogeneity found in the probiotics strains were investigated. Lactobacillus reuteri was identified as having the greatest effect on claudin and ZO-1 expression. The publication bias was detected by the Egger’s linear regression test, though it revealed that the occludin and ZO-1 had larger sample sizes than the claudin. In sum, this meta-analysis reveals that probiotics are effective at improving TJP expression in a gut environment of inflammatory bowel disease (IBD)-induced animal model. Our findings will interest IBD patients, as they suggest an area warranting future study. Full article
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Article
Secondary Treatment for Men with Localized Prostate Cancer: A Pooled Analysis of PRIAS and ERSPC-Rotterdam Data within the PIONEER Data Platform
J. Pers. Med. 2022, 12(5), 751; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12050751 - 05 May 2022
Abstract
Introduction: Treatment choice for localized prostate cancer is complicated, as each treatment option comes with various pros and cons. It is well established that active surveillance (AS), may be ended with a change to curative treatment at the time of disease progression, but [...] Read more.
Introduction: Treatment choice for localized prostate cancer is complicated, as each treatment option comes with various pros and cons. It is well established that active surveillance (AS), may be ended with a change to curative treatment at the time of disease progression, but it is less clear whether secondary treatment after initial curative treatment is required. As part of the PIONEER project, we quantified the probabilities of treatment change. Methods: A cohort study based on PRIAS and ERSPC-Rotterdam data was conducted. Patients were followed up for 10 years or until the 31st of December 2017. The primary outcome was the incidence of treatment change following initial treatment (i.e., a change to curative treatment following AS or secondary treatment after initial RP/RT). Results: Over a period of 1 to 5 years after initial treatment, the cumulative incidence of treatment change ranged from 3.8% to 42.8% for AS, from 7.6% to 12.1% for radical prostatectomy (RP) and from no change to 5.3% for radiation therapy (RT). While the possibility of treatment change in AS is known, the numbers within a five-year period were substantial. For RP and RT, the rate of change to secondary treatment was lower, but still non-neglectable, with 5 (10)-year incidences up to 12% (20%) and 5% (16%), respectively. Conclusion: This is one of the first studies comparing the incidence of guideline-recommended treatment changes in men receiving different primary treatments (i.e., AS, RT, or RP) for localized prostate cancer (PCa). Full article
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Article
Osteosarcoma-Specific Genes as a Diagnostic Tool and Clinical Predictor of Tumor Progression
Biology 2022, 11(5), 698; https://0-doi-org.brum.beds.ac.uk/10.3390/biology11050698 - 01 May 2022
Abstract
A liquid biopsy is currently an interesting tool for measuring tumor material with the advantage of being non-invasive. The overexpression of vimentin and ezrin genes was associated with epithelial-mesenchymal transition (EMT), a key process in metastasis and progression in osteosarcoma (OS). In this [...] Read more.
A liquid biopsy is currently an interesting tool for measuring tumor material with the advantage of being non-invasive. The overexpression of vimentin and ezrin genes was associated with epithelial-mesenchymal transition (EMT), a key process in metastasis and progression in osteosarcoma (OS). In this study, we identified other OS-specific genes by calculating differential gene expression using the Gene Expression Omnibus (GEO) database, confirmed by using quantitative reverse transcription-PCR (qRT-PCR) to detect OS-specific genes, including VIM and ezrin in the buffy coat, which were obtained from the whole blood of OS patients and healthy donors. Furthermore, the diagnostic model for OS detection was generated by utilizing binary logistic regression with a multivariable fractional polynomial (MFP) algorithm. The model incorporating VIM, ezrin, and COL5A2 genes exhibited outstanding discriminative ability, as determined by the receiver operating characteristic curve (AUC = 0.9805, 95% CI 0.9603, 1.000). At the probability cut-off value of 0.3366, the sensitivity and the specificity of the model for detecting OS were 98.63% (95% CI 90.5, 99.7) and 94.94% (95% CI 87.5, 98.6), respectively. Bioinformatic analysis and qRT-PCR, in our study, identified three candidate genes that are potential diagnostic and prognostic genes for OS. Full article
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Article
Optimal Timing of Cholecystectomy in Secondary Choledocholithiasis Patients Who Underwent Preoperative Endoscopic Retrograde Cholangiopancreatography
Appl. Sci. 2022, 12(9), 4574; https://0-doi-org.brum.beds.ac.uk/10.3390/app12094574 - 30 Apr 2022
Abstract
Secondary choledocholithiasis occurs when stones leave the gallbladder. After therapeutic endoscopic retrograde cholangiopancreatography (ERCP) with stone removal, cholecystectomy should be performed to prevent recurrence. However, the optimal timing for cholecystectomy in secondary choledocholithiasis patients is unclear. The aim of this study was to [...] Read more.
Secondary choledocholithiasis occurs when stones leave the gallbladder. After therapeutic endoscopic retrograde cholangiopancreatography (ERCP) with stone removal, cholecystectomy should be performed to prevent recurrence. However, the optimal timing for cholecystectomy in secondary choledocholithiasis patients is unclear. The aim of this study was to determine the optimal timing for laparoscopic cholecystectomy in patients with secondary choledocholithiasis. In total, 22,996 patients in the Taiwan National Health Insurance Research Database (NHIRD) who underwent laparoscopic cholecystectomy for acute cholecystitis from 1998–2015 were divided into three groups according to whether they underwent surgery as an inpatient (early cholecystectomy (ELC)), within 2 months of admission (intermediate cholecystectomy (ILC)), or 2 months after admission (delayed cholecystectomy (DLC)). The primary outcomes included the recurrence, complication, and mortality rates. After adjusting for confounders, according to the 2013 Tokyo guidelines (cut-off at 2013), a subgroup analysis showed that, compared to the ELC group, the ILC group had lower recurrence, complication, and mortality rates, whereas the DLC group exhibited statistically significantly higher recurrence and mortality rates. In conclusion, the optimal timing of cholecystectomy in secondary choledocholithiasis patients after preoperative ERCP is within 2 months (ILC) after hospital admission. Moreover, ELC is associated with a measurable risk of complications. Full article
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Article
Development and Assessment of the Validity and Reliability of the Short-Form Life Satisfaction Index (LSI-SF) among the Elderly Population
J. Pers. Med. 2022, 12(5), 709; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12050709 - 28 Apr 2022
Abstract
Background: Elderly care should focus on not only prolonging life but also satisfaction with elderly life. Our study investigated the reliability and validity of the Short-Form Life Satisfaction Index (LSI-SF). Method: Data were drawn from the 2015 Taiwan Longitudinal Study on Aging. Internal [...] Read more.
Background: Elderly care should focus on not only prolonging life but also satisfaction with elderly life. Our study investigated the reliability and validity of the Short-Form Life Satisfaction Index (LSI-SF). Method: Data were drawn from the 2015 Taiwan Longitudinal Study on Aging. Internal consistency reliability was used to confirm that the items measured the targeted characteristics. Construct validity was established by confirmatory factor analysis (CFA). Criterion-related validity was examined with the WHO-5 Well-Being Index as an indicator of quality of life. Known-group validity was determined from the difference between frailty stage and quality of life. Results: The high consistency reliability supported the reliability of the LSI-SF. Rigorous CFA validated the construct validity of the LSI-SF. Perfect convergent and discriminant validity supported the validity of the LSI-SF. In addition, there was a significant correlation between the LSI-SF and the WHO-5 Well-Being Index. The LSI-SF appears to be a reliable measure of quality of life in the elderly. We found that frailty status was associated with lower life satisfaction, which supported the known-group validity. Life satisfaction was highest in the non-frailty stage and lowest in the frailty stage. Conclusions: The LSI-SF appears to be a valid and reliable measure of satisfaction with elderly life. Full article
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Article
Role of Metformin in Morbidity and Mortality Associated with Urinary Tract Infections in Patients with Type 2 Diabetes
J. Pers. Med. 2022, 12(5), 702; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12050702 - 28 Apr 2022
Abstract
We conducted this study to compare the morbidity and mortality associated with UTI and sepsis, between metformin users and nonusers in patients with diabetes. As such, 40,774 propensity score-matched metformin users and nonusers were identified from Taiwan’s National Health Insurance Research Database, between [...] Read more.
We conducted this study to compare the morbidity and mortality associated with UTI and sepsis, between metformin users and nonusers in patients with diabetes. As such, 40,774 propensity score-matched metformin users and nonusers were identified from Taiwan’s National Health Insurance Research Database, between 1 January 2000 and 31 December 2017. We adopted the Cox proportional hazards model with robust standard error estimates for comparing the risks of UTI, sepsis, and death due to UTI or sepsis, in patients with T2DM. Compared with the nonuse of metformin, the aHRs (95% CI) for metformin use in UTI, recurrent UTI, sepsis, and death due to UTI or sepsis were 1.06 (0.98, 1.15), 1.08 (0.97, 1.2), 1.01 (0.97, 1.06), and 0.58 (0.42, 0.8), respectively. The cumulative incidence of death due to UTI or sepsis was significantly lower in metformin users than in nonusers (p = 0.002). A longer cumulative duration of metformin use had a lower aHR in the risk of death due to UTI or sepsis than metformin nonuse. In patients with T2DM, metformin use showed no significant differences in the risks of UTI, recurrent UTI, or sepsis. However, it was associated with a lower risk of death due to UTI or sepsis than metformin nonuse. Full article
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Article
Human Papillomavirus Infection and the Risk of Erectile Dysfunction: A Nationwide Population-Based Matched Cohort Study
J. Pers. Med. 2022, 12(5), 699; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12050699 - 27 Apr 2022
Cited by 2
Abstract
Background: Male patients with genital warts are known for higher rates of sexual dysfunction. This study was conducted to investigate whether human papillomaviruses (HPV) infection is associated with an increased risk of erectile dysfunction (ED). Methods: Patients aged over 18 with HPV infection [...] Read more.
Background: Male patients with genital warts are known for higher rates of sexual dysfunction. This study was conducted to investigate whether human papillomaviruses (HPV) infection is associated with an increased risk of erectile dysfunction (ED). Methods: Patients aged over 18 with HPV infection (n = 13,296) and propensity score-matched controls (n = 53,184) were recruited from the Longitudinal Health Insurance Database (LHID). The primary endpoint was the diagnosis of ED. Chi-square tests were used to analyze the distribution of demographic characteristics. The Cox proportional hazards regression was used to estimate the hazard ratios (HRs) and 95% confidence intervals (CIs) for the development of ED in both groups, after adjusting for sex, age, relevant comorbidities, co-medication, and surgery. Results: ED developed in 181 patients of the study group. The incidence density of ED was 2.53 per 1000 person-years for the HPV group and 1.51 per 1000 person-years for the non-HPV group, with an adjusted HR (95% CI) of 1.63 (1.37–1.94). In stratification analysis, adjusted HR of diabetes-, chronic obstructive pulmonary disease (COPD-), and stroke-subgroup were 2.39, 2.51, and 4.82, with significant p values for interaction, respectively. Sensitivity analysis yields consistent findings. Conclusions: The patients with HPV infection had a higher risk of subsequent ED in comparison to the non-HPV controls. The mechanism behind such association and its possible role in ED prevention deserves further study in the future. Full article
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Article
A Risk Model of Eight Immune-Related Genes Predicting Prognostic Response to Immune Therapies for Gastric Cancer
Genes 2022, 13(5), 720; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13050720 - 20 Apr 2022
Abstract
Immune checkpoint inhibitor (ICI) treatment is considered as an innovative approach for cancers. Since not every patient responded well to ICI therapy, it is imperative to screen out novel signatures to predict prognosis. Based on 407 gastric cancer (GC) samples retrieved from The [...] Read more.
Immune checkpoint inhibitor (ICI) treatment is considered as an innovative approach for cancers. Since not every patient responded well to ICI therapy, it is imperative to screen out novel signatures to predict prognosis. Based on 407 gastric cancer (GC) samples retrieved from The Cancer Genome Atlas (TCGA), 36 immune-related hub genes were identified by weighted gene co-expression network analysis (WGCNA), and eight of them (RNASE2, CGB5, INHBE, DUSP1, APOA1, CD36, PTGER3, CTLA4) were used to formulate the Cox regression model. The obtained risk score was proven to be significantly correlated with overall survival (OS), consistent with the consequence of the Gene Expression Omnibus (GEO) cohort (n = 433). Then, the relationship between the risk score and clinical, molecular and immune characteristics was further investigated. Results showed that the low-risk subgroup exhibited higher mutation rate, more M1 macrophages, CD8+ and CD4+ T cells infiltrating, more active MHC-I, and bias to “IFN-γ Dominant” immune type, which is consistent with our current understanding of tumor prognostic risk. Furthermore, it is suggested that our model can accurately predict 1-, 2-, and 3-year OS of GC patients, and that it was superior to other canonical models, such as TIDE and TIS. Thus, these eight genes are probably considered as potential signatures to predict prognosis and to distinguish patient benefit from ICI, serving as a guiding individualized immunotherapy. Full article
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Article
Effects of Multi-Omics Characteristics on Identification of Driver Genes Using Machine Learning Algorithms
Genes 2022, 13(5), 716; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13050716 - 19 Apr 2022
Abstract
Cancer is a complex disease caused by genomic and epigenetic alterations; hence, identifying meaningful cancer drivers is an important and challenging task. Most studies have detected cancer drivers with mutated traits, while few studies consider multiple omics characteristics as important factors. In this [...] Read more.
Cancer is a complex disease caused by genomic and epigenetic alterations; hence, identifying meaningful cancer drivers is an important and challenging task. Most studies have detected cancer drivers with mutated traits, while few studies consider multiple omics characteristics as important factors. In this study, we present a framework to analyze the effects of multi-omics characteristics on the identification of driver genes. We utilize four machine learning algorithms within this framework to detect cancer driver genes in pan-cancer data, including 75 characteristics among 19,636 genes. The 75 features are divided into four types and analyzed using Kullback–Leibler divergence based on CGC genes and non-CGC genes. We detect cancer driver genes in two different ways. One is to detect driver genes from a single feature type, while the other is from the top N features. The first analysis denotes that the mutational features are the best characteristics. The second analysis reveals that the top 45 features are the most effective feature combinations and superior to the mutational features. The top 45 features not only contain mutational features but also three other types of features. Therefore, our study extends the detection of cancer driver genes and provides a more comprehensive understanding of cancer mechanisms. Full article
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Article
Update on the Phenotypic and Genotypic Spectrum of KIF11-Related Retinopathy
Genes 2022, 13(4), 713; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13040713 - 18 Apr 2022
Abstract
Background: This study aimed to report the frequency of KIF11-mutations in a large familial exudative vitreoretinopathy (FEVR) population, extend the clinical spectrum of KIF11-associated retinopathy and compare KIF11-associated retinopathy to FEVR with mutations in other genes. Methods: Genetic data collected [...] Read more.
Background: This study aimed to report the frequency of KIF11-mutations in a large familial exudative vitreoretinopathy (FEVR) population, extend the clinical spectrum of KIF11-associated retinopathy and compare KIF11-associated retinopathy to FEVR with mutations in other genes. Methods: Genetic data collected from 696 FEVR families were reviewed. The ocular phenotypes in patients with KIF11 mutations were analyzed and compared with those of FEVR patients with mutations in other genes (FZD4, TSPAN12, LRP5, NDP and JAG1). Results: In a cohort of 696 FEVR families, disease-causing KIF11 mutations were identified in 3.6% of families (25/696). Among 25 KIF11 mutations, 80% (20/25) carried variants of loss of function and 48% (12/25) of variants were de novo. The phenotypes were variable. Compared with FEVR with disease-causing mutations in other genes, chorioretinal dysplasia was observed in 44.2% (31/70) of eyes with KIF11-associated retinopathy and in only 1.3% (1/70) of eyes with FEVR with mutations in other genes (p < 0.01). Increase and straightening of peripheral vessels (ISPV) was observed in 17.1% (12/70) of eyes with KIF11-associated retinopathy, and in 50% (39/78) of eyes with FEVR with mutations in other genes (p < 0.01). Conclusions: The frequency of the KIF11 mutation in FEVR was 3.6% in our database. The manifestation of KIF11-associated retinopathy was variable and different from the phenotype in FEVR caused by other genes. Chorioretinal dysplasia, instead of retinal folds, was the dominant phenotype in KIF11-associated retinopathy. ISPV was rare in KIF11-associated retinopathy. Moreover, our study revealed that most pathogenic KIF11 mutations were de novo. Full article
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Article
Deciphering of Adult Glioma Vulnerabilities through Expression Pattern Analysis of GABA, Glutamate and Calcium Neurotransmitter Genes
J. Pers. Med. 2022, 12(4), 633; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12040633 - 14 Apr 2022
Abstract
Adult infiltrating gliomas are highly aggressive tumors of the central nervous system with a dismal prognosis despite intensive multimodal therapy (chemotherapy and/or radiotherapy). In this study, we studied the expression, methylation and interacting miRNA profiles of GABA-, glutamate- and calcium-related genes in 661 [...] Read more.
Adult infiltrating gliomas are highly aggressive tumors of the central nervous system with a dismal prognosis despite intensive multimodal therapy (chemotherapy and/or radiotherapy). In this study, we studied the expression, methylation and interacting miRNA profiles of GABA-, glutamate- and calcium-related genes in 661 adult infiltrating gliomas available through the TCGA database. Neurotransmitter-based unsupervised clustering identified three established glioma molecular subgroups that parallel major World Health Organization glioma subclasses (IDH-wildtype astrocytomas, IDH-mutant astrocytomas, IDH-mutant oligodendroglioma). In addition, this analysis also defined a novel, neurotransmitter-related glioma subgroup (NT-1), mostly comprised of IDH-mutated gliomas and characterized by the overexpression of neurotransmitter-related genes. Lower expression of neurotransmission-related genes was correlated with increased aggressivity in hypomethylated IDH-wildtype tumors. There were also significant differences in the composition of the tumor inflammatory microenvironment between neurotransmission-based tumor categories, with lower estimated pools of M2-phenotype macrophages in NT-1 gliomas. This multi-omics analysis of the neurotransmission expression landscape of TCGA gliomas—which highlights the existence of neurotransmission-based glioma categories with different expression, epigenetic and inflammatory profiles—supports the existence of operational neurotransmitter signaling pathways in adult gliomas. These findings could shed new light on potential vulnerabilities to exploit in future glioma-targeting drug therapies. Full article
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Article
Association of Permanent Vascular Access Dysfunction with Subsequent Risk of Cardiovascular Disease: A Population-Based Cohort Study
J. Pers. Med. 2022, 12(4), 598; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12040598 - 08 Apr 2022
Abstract
A functional permanent vascular access (VA) is required to perform a successful hemodialysis procedure. Hemodialysis VA dysfunction is a major cause of morbidity and hospitalization in the hemodialysis population. Cardiovascular disease (CVD) is the leading cause of death in patients receiving chronic hemodialysis. [...] Read more.
A functional permanent vascular access (VA) is required to perform a successful hemodialysis procedure. Hemodialysis VA dysfunction is a major cause of morbidity and hospitalization in the hemodialysis population. Cardiovascular disease (CVD) is the leading cause of death in patients receiving chronic hemodialysis. Information about CVD associated with hemodialysis VA dysfunction is unclear. We analyzed the association between dialysis VA dysfunction and the risk of developing CVD in hemodialysis patients. This nationwide population-based cohort study was conducted using data from the National Health Insurance Research Database in Taiwan. One million subjects were sampled from 23 million beneficiaries and data was collected from 2000 to 2013. Patients with end-stage renal disease who had received permanent VA construction and hemodialysis and were aged at least 20 years old from 2000 to 2007 were included in the study population. The primary outcome was CVD, as defined by ICD-9-CM codes 410–414 and 430–437. A total of 197 individuals with permanent VA dysfunction were selected as the test group, and 100 individuals with non-permanent VA dysfunction were selected as the control group. Compared with the control group, the adjusted hazard ratio of CVD for the VA dysfunction group was 3.05 (95% CI: 1.14–8.20). A Kaplan–Meier analysis revealed that the cumulative incidence of CVD was higher in the permanent VA dysfunction group than in the comparison group. Permanent VA dysfunction is significantly associated with an increased risk of subsequent CVD. Full article
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Article
Rhythm Control Better Prevents Dementia than Rate Control Strategies in Patients with Atrial Fibrillation—A Nationwide Cohort Study
J. Pers. Med. 2022, 12(4), 572; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12040572 - 03 Apr 2022
Abstract
Background: Atrial fibrillation (AF) increases the risk of dementia. Whether the pharmacological rhythm control of AF can reduce the risk of dementia compared to the rate control strategy remains unclear. We hypothesize that the rhythm control strategy is better than the rate control [...] Read more.
Background: Atrial fibrillation (AF) increases the risk of dementia. Whether the pharmacological rhythm control of AF can reduce the risk of dementia compared to the rate control strategy remains unclear. We hypothesize that the rhythm control strategy is better than the rate control strategy in preventing dementia. Methods: AF patients aged ≥65 years were identified from the Taiwan National Health Insurance Database. Patients receiving anti-arrhythmic drugs at a cumulative defined daily dose (cDDD) of >30 within the first year of enrollment constituted the rhythm control group. Patients who used rate control medications for a cDDD of >30 constituted the rate control group. A multivariate Cox hazards regression model was used to determine the hazard ratio (HR) for dementia. Results: A total of 3382 AF patients (698 in the rhythm control group; 2684 in the rate control group) were analyzed. During a 4.86 ± 3.38 year follow-up period, 414 dementia events occurred. The rhythm control group had a lower rate of dementia than the rate control group (adjust HR: 0.75, p = 0.031). The rhythm control strategy reduced the risk of dementia particularly in those receiving aspirin (p = 0.03). Conclusions: In patients with AF, pharmacological rhythm control was associated with a lower risk of dementia than rate control over a long-term follow-up period, particularly in patients receiving aspirin treatment. Full article
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Article
Decision Theory versus Conventional Statistics for Personalized Therapy of Breast Cancer
J. Pers. Med. 2022, 12(4), 570; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12040570 - 02 Apr 2022
Abstract
Estrogen and progesterone receptors being present or not represents one of the most important biomarkers for therapy selection in breast cancer patients. Conventional measurement by immunohistochemistry (IHC) involves errors, and numerous attempts have been made to increase precision by additional information from gene [...] Read more.
Estrogen and progesterone receptors being present or not represents one of the most important biomarkers for therapy selection in breast cancer patients. Conventional measurement by immunohistochemistry (IHC) involves errors, and numerous attempts have been made to increase precision by additional information from gene expression. This raises the question of how to fuse information, in particular, if there is disagreement. It is the primary domain of Dempster–Shafer decision theory (DST) to deal with contradicting evidence on the same item (here: receptor status), obtained through different techniques. DST is widely used in technical settings, such as self-driving cars and aviation, and is also promising to deliver significant advantages in medicine. Using data from breast cancer patients already presented in previous work, we focus on comparing DST with classical statistics in this work, to pave the way for its application in medicine. First, we explain how DST not only considers probabilities (a single number per sample), but also incorporates uncertainty in a concept of ‘evidence’ (two numbers per sample). This allows for very powerful displays of patient data in so-called ternary plots, a novel and crucial advantage for medical interpretation. Results are obtained according to conventional statistics (ODDS) and, in parallel, according to DST. Agreement and differences are evaluated, and the particular merits of DST discussed. The presented application demonstrates how decision theory introduces new levels of confidence in diagnoses derived from medical data. Full article
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Article
Incident Rheumatoid Arthritis Following Statin Use: From the View of a National Cohort Study in Korea
J. Pers. Med. 2022, 12(4), 559; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12040559 - 01 Apr 2022
Abstract
Safety issues regarding the potential risk of statins and incident rheumatoid arthritis (RA) have been raised, but the existing data are largely based on Caucasian populations, and continue to have biases and require further validation in Asian populations. Here, we aimed to verify [...] Read more.
Safety issues regarding the potential risk of statins and incident rheumatoid arthritis (RA) have been raised, but the existing data are largely based on Caucasian populations, and continue to have biases and require further validation in Asian populations. Here, we aimed to verify the risk of RA depending on the duration of previous statin use and statin types using a large-scale, nationwide database. This study enrolled 3149 patients with RA and 12,596 matched non-RA participants from the national health insurance database (2002–2015), and investigated their statin prescription histories for two years before the index date. Propensity score overlap-weighted logistic regression was applied after adjusting for multiple covariates. The prior use of any statins and, specifically, the long-term use of lipophilic statins (>365 days) were related to a lower likelihood of developing RA ((odds ratio (OR) = 0.73; 95% confidence intervals (CI) = 0.63–0.85, p < 0.001) and (OR = 0.71; 95% CI = 0.61–0.84, p < 0.001), respectively). Subgroup analyses supported these preventive effects on RA in those with dyslipidemia, independent of sex, age, smoking, alcohol use, hypertension, and hyperglycemia. Hydrophilic statin use or short-term use showed no such associations. Our study suggests that prior statin use, especially long-term lipophilic statin use, appears to confer preventive benefits against RA. Full article
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Article
CT Reconstruction Kernels and the Effect of Pre- and Post-Processing on the Reproducibility of Handcrafted Radiomic Features
J. Pers. Med. 2022, 12(4), 553; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12040553 - 31 Mar 2022
Abstract
Handcrafted radiomics features (HRFs) are quantitative features extracted from medical images to decode biological information to improve clinical decision making. Despite the potential of the field, limitations have been identified. The most important identified limitation, currently, is the sensitivity of HRF to variations [...] Read more.
Handcrafted radiomics features (HRFs) are quantitative features extracted from medical images to decode biological information to improve clinical decision making. Despite the potential of the field, limitations have been identified. The most important identified limitation, currently, is the sensitivity of HRF to variations in image acquisition and reconstruction parameters. In this study, we investigated the use of Reconstruction Kernel Normalization (RKN) and ComBat harmonization to improve the reproducibility of HRFs across scans acquired with different reconstruction kernels. A set of phantom scans (n = 28) acquired on five different scanner models was analyzed. HRFs were extracted from the original scans, and scans were harmonized using the RKN method. ComBat harmonization was applied on both sets of HRFs. The reproducibility of HRFs was assessed using the concordance correlation coefficient. The difference in the number of reproducible HRFs in each scenario was assessed using McNemar’s test. The majority of HRFs were found to be sensitive to variations in the reconstruction kernels, and only six HRFs were found to be robust with respect to variations in reconstruction kernels. The use of RKN resulted in a significant increment in the number of reproducible HRFs in 19 out of the 67 investigated scenarios (28.4%), while the ComBat technique resulted in a significant increment in 36 (53.7%) scenarios. The combination of methods resulted in a significant increment in 53 (79.1%) scenarios compared to the HRFs extracted from original images. Since the benefit of applying the harmonization methods depended on the data being harmonized, reproducibility analysis is recommended before performing radiomics analysis. For future radiomics studies incorporating images acquired with similar image acquisition and reconstruction parameters, except for the reconstruction kernels, we recommend the systematic use of the pre- and post-processing approaches (respectively, RKN and ComBat). Full article
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Review
Update on Multiple Sclerosis Molecular Biomarkers to Monitor Treatment Effects
J. Pers. Med. 2022, 12(4), 549; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12040549 - 31 Mar 2022
Abstract
Multiple sclerosis (MS) is an inflammatory and neurodegenerative disease of the central nervous system characterized by broad inter- and intraindividual heterogeneity. The relapse rate, disability progression, and lesion load assessed through MRI are used to detect disease activity and response to treatment. Although [...] Read more.
Multiple sclerosis (MS) is an inflammatory and neurodegenerative disease of the central nervous system characterized by broad inter- and intraindividual heterogeneity. The relapse rate, disability progression, and lesion load assessed through MRI are used to detect disease activity and response to treatment. Although it is possible to standardize these characteristics in larger patient groups, so far, this has been difficult to achieve in individual patients. Easily detectable molecular biomarkers can be powerful tools, permitting a tailored therapy approach for MS patients. However, only a few molecular biomarkers have been routinely used in clinical practice as the validation process, and their transfer into clinical practice takes a long time. This review describes the characteristics of an ideal MS biomarker, the challenges of establishing new biomarkers, and promising molecular biomarkers from blood or CSF samples used to monitor MS treatment effects in clinical practice. Full article
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Article
Pooled Analysis of Complications with Transvenous ICD Compared to Subcutaneous ICD in Patients with Catecholaminergic Polymorphic Ventricular Arrhythmia
J. Pers. Med. 2022, 12(4), 536; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12040536 - 28 Mar 2022
Abstract
Background: Catecholaminergic polymorphic ventricular tachycardia (CPVT) is associated with arrhythmic events which may lead to sudden cardiac death (SCD). A leading therapy for CPVT besides medical treatment with beta-blockers is the use of an implantable cardioverter-defibrillator (ICD). For this paper we compared data [...] Read more.
Background: Catecholaminergic polymorphic ventricular tachycardia (CPVT) is associated with arrhythmic events which may lead to sudden cardiac death (SCD). A leading therapy for CPVT besides medical treatment with beta-blockers is the use of an implantable cardioverter-defibrillator (ICD). For this paper we compared data from a pooled analysis to get further evidence about the complications of transvenous and subcutaneous ICDs. Methods: We gathered data from a search of PubMed, Web of Science, Cochrane Library and Cinahl. For our analysis, we chose 30 studies with a total number of 784 patients. We compared the data regarding complications caused by different ICD device types. Results: During a mean follow up of 38.9 months for the patients with ICD implantation (n = 337), data showed a complication rate of 101 (30%). A total of 330 (98%) of them received a transvenous-ICD (T-ICD) and 7 (2%) a subcutaneous-ICD (S-ICD). A total of 97 (29.4%) of the T-ICD patients and 4 (57.1%) of the S-ICD patients had at least one complication. Of the 234 complications that occurred in T-ICD patients 152 (65%) were inappropriate shocks due to supraventricular arrhythmias, T/R-wave oversensing or electrode defect, 26 (11.1%) lead fracture/failure, 1 (0.4%) electrode defect, 46 were (19.7%) events of electrical storms, 1 (0.4%) thromboembolic event, 2 (0.8%) cases of endocarditis and 6 (2.6%) infections of the ICD-pocket. Ten (100%) of the complications for the four patients with the S-ICD were an event of an inappropriate shock due to supraventricular arrhythmias, T/R-wave oversensing or electrode defect. Conclusion: Subcutaneous ICDs (S-ICD) show a certain advantage over T-ICDs regarding lead-related complications. Nevertheless, they still show problems with inappropriate shocks and other ICD related complications. Therefore, a case-by-case decision is advised, but the continuous improvement of S-ICD might make it an overall advantageous therapy option in the future. Full article
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Article
Association of Elevated Expression Levels of COL4A1 in Stromal Cells with an Immunosuppressive Tumor Microenvironment in Low-Grade Glioma, Pancreatic Adenocarcinoma, Skin Cutaneous Melanoma, and Stomach Adenocarcinoma
J. Pers. Med. 2022, 12(4), 534; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12040534 - 28 Mar 2022
Abstract
Aberrant expression of collagen type IV alpha chain 1 (COL4A1) can influence tumor cell behavior. To examine the association of COL4A1 expression in the tumor microenvironment (TME) with tumor progression, we performed bioinformatics analyses of The Cancer Genome Atlas RNA sequencing [...] Read more.
Aberrant expression of collagen type IV alpha chain 1 (COL4A1) can influence tumor cell behavior. To examine the association of COL4A1 expression in the tumor microenvironment (TME) with tumor progression, we performed bioinformatics analyses of The Cancer Genome Atlas RNA sequencing and RNA microarray datasets available in public databases and identified upregulated COL4A1 expression in most examined tumor types compared to their normal counterparts. The elevated expression of COL4A1 was correlated with low survival rates of patients with low-grade glioma, pancreatic adenocarcinoma, skin cutaneous melanoma, and stomach adenocarcinoma, thus suggesting its potential use as a biomarker for the poor prognosis of these tumors. However, COL4A1 was mostly expressed in adjacent stromal cells, such as cancer-associated fibroblasts (CAFs) and endothelial cells. Additionally, COL4A1 expression was highly correlated with the signatures of CAFs and endothelial cells in all four tumor types. The expression of marker genes for the infiltration of pro-tumoral immune cells, such as Treg, M2, and TAM, and those of immunosuppressive cytokines exhibited very strong positive correlations with COL4A1 expression. Collectively, our data suggest that COL4A1 overexpression in stromal cells may be a potential regulator of tumor-supporting TME composition associated with poor prognosis. Full article
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Article
In Silico Bioinformatics Followed by Molecular Validation Using Archival FFPE Tissue Biopsies Identifies a Panel of Transcripts Associated with Severe Asthma and Lung Cancer
Cancers 2022, 14(7), 1663; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers14071663 - 25 Mar 2022
Abstract
Severe asthma and lung cancer are both heterogeneous pathological diseases affecting the lung tissue. Whilst there are a few studies that suggest an association between asthma and lung cancer, to the best of our knowledge, this is the first study to identify common [...] Read more.
Severe asthma and lung cancer are both heterogeneous pathological diseases affecting the lung tissue. Whilst there are a few studies that suggest an association between asthma and lung cancer, to the best of our knowledge, this is the first study to identify common genes involved in both severe asthma and lung cancer. Publicly available transcriptomic data for 23 epithelial brushings from severe asthmatics and 55 samples of formalin-fixed paraffin-embedded (FFPE) lung cancer tissue at relatively early stages were analyzed by absolute gene set enrichment analysis (GSEA) in comparison to 37 healthy bronchial tissue samples. The key pathways enriched in asthmatic patients included adhesion, extracellular matrix, and epithelial cell proliferation, which contribute to tissue remodeling. In the lung cancer dataset, the main pathways identified were receptor tyrosine kinase signaling, wound healing, and growth factor response, representing the early cancer pathways. Analysis of the enriched genes derived from the pathway analysis identified seven genes expressed in both the asthma and lung cancer sets: BCL3, POSTN, PPARD, STAT1, MYC, CD44, and FOSB. The differential expression of these genes was validated in vitro in the cell lines retrieved from different lung cancer and severe asthma patients using real-time PCR. The effect of the expression of the seven genes identified in the study on the overall survival of lung cancer patients (n = 1925) was assessed using a Kaplan–Meier plot. In vivo validation performed in the archival biopsies obtained from patients diagnosed with both the disease conditions provided interesting insights into the pathogenesis of severe asthma and lung cancer, as indicated by the differential expression pattern of the seven transcripts in the mixed group as compared to the asthmatics and lung cancer samples alone. Full article
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Article
DeepBiomarker: Identifying Important Lab Tests from Electronic Medical Records for the Prediction of Suicide-Related Events among PTSD Patients
J. Pers. Med. 2022, 12(4), 524; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12040524 - 24 Mar 2022
Abstract
Identifying patients with high risk of suicide is critical for suicide prevention. We examined lab tests together with medication use and diagnosis from electronic medical records (EMR) data for prediction of suicide-related events (SREs; suicidal ideations, attempts and deaths) in post-traumatic stress disorder [...] Read more.
Identifying patients with high risk of suicide is critical for suicide prevention. We examined lab tests together with medication use and diagnosis from electronic medical records (EMR) data for prediction of suicide-related events (SREs; suicidal ideations, attempts and deaths) in post-traumatic stress disorder (PTSD) patients, a population with a high risk of suicide. We developed DeepBiomarker, a deep-learning model through augmenting the data, including lab tests, and integrating contribution analysis for key factor identification. We applied DeepBiomarker to analyze EMR data of 38,807 PTSD patients from the University of Pittsburgh Medical Center. Our model predicted whether a patient would have an SRE within the following 3 months with an area under curve score of 0.930. Through contribution analysis, we identified important lab tests for suicide prediction. These identified factors imply that the regulation of the immune system, respiratory system, cardiovascular system, and gut microbiome were involved in shaping the pathophysiological pathways promoting depression and suicidal risks in PTSD patients. Our results showed that abnormal lab tests combined with medication use and diagnosis could facilitate predicting SRE risk. Moreover, this may imply beneficial effects for suicide prevention by treating comorbidities associated with these biomarkers. Full article
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Article
Inherited and De Novo Variation in Lithuanian Genomes: Introduction to the Analysis of the Generational Shift
Genes 2022, 13(4), 569; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13040569 - 23 Mar 2022
Abstract
Most genetic variants are rare and specific to the population, highlighting the importance of characterizing local population genetic diversity. Many countries have initiated population-based whole-genome sequencing (WGS) studies. Genomic variation within Lithuanian families are not available in the public databases. Here, we describe [...] Read more.
Most genetic variants are rare and specific to the population, highlighting the importance of characterizing local population genetic diversity. Many countries have initiated population-based whole-genome sequencing (WGS) studies. Genomic variation within Lithuanian families are not available in the public databases. Here, we describe initial findings of a high-coverage (an average of 36.27×) whole genome sequencing for 25 trios of the Lithuanian population. Each genome on average carried approximately 4,701,473 (±28,255) variants, where 80.6% (3,787,626) were single nucleotide polymorphisms (SNPs), and the rest 19.4% were indels. An average of 12.45% was novel according to dbSNP (build 150). The WGS structural variation (SV) analysis identified on average 9133 (±85.10) SVs, of which 95.85% were novel. De novo single nucleotide variation (SNV) analysis identified 4417 variants, where 1.1% de novo SNVs were exonic, 43.9% intronic, 51.9% intergenic, and the rest 3.13% in UTR or downstream sequence. Three potential pathogenic de novo variants in the ZSWIM8, CDC42EP1, and RELA genes were identified. Our findings provide useful information on local human population genomic variation, especially for de novo variants, and will be a valuable resource for further genetic studies, and medical implications. Full article
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Article
Sex Differences in Clinical Characteristics and Outcomes of Patients with SARS-CoV-2-Infection Admitted to Intensive Care Units in Austria
J. Pers. Med. 2022, 12(4), 517; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12040517 - 23 Mar 2022
Abstract
Importance: A male predominance is reported in hospitalised patients with COVID-19 alongside a higher mortality rate in men compared to women. Objective: To assess if the reported sex bias in the COVID-19 pandemic is validated by analysis of a subset of patients with [...] Read more.
Importance: A male predominance is reported in hospitalised patients with COVID-19 alongside a higher mortality rate in men compared to women. Objective: To assess if the reported sex bias in the COVID-19 pandemic is validated by analysis of a subset of patients with severe disease. Design: A nationwide retrospective cohort study was performed using the Austrian National COVID Database. We performed a sex-specific Lasso regression to select the covariates best explaining the outcomes of mechanical ventilation and death using variables known before ICU admission. We use logistic regression to construct a sex-specific “risk score” for the outcomes using these variables. Setting: We studied the characteristics and outcomes of patients admitted to intensive care units (ICUs) in Austria. Participants: 5118 patients admitted to the ICU in Austria with a COVID-19 diagnosis in 03/2020–03/2021. Exposures: Demographic and clinical characteristics, vital signs and laboratory tests, comorbidities, and management of patients admitted to ICUs were analysed for possible sex differences. Main outcomes and measures: The aim was to define risk scores for mechanical ventilation and mortality for each sex to provide better sex-sensitive management and outcomes in the future. Results: We found balanced accuracies between 55% and 65% to predict the outcomes. Regarding outcome death, we found that the risk score for pre-ICU variables increases with age, renal insufficiency (f: OR 1.7(2), m: 1.9(2)) and decreases with observance as admission cause (f: OR 0.33(5), m: 0.36(5)). Additionally, the risk score for females also includes respiratory insufficiency (OR 2.4(4)) while heart failure for males only (OR 1.5(1)). Conclusions and relevance: Better knowledge of how sex influences COVID-19 outcomes at ICUs will have important implications for the ongoing pandemic’s clinical care and management strategies. Identifying sex-specific features in individuals with COVID-19 and fatal consequences might inform preventive strategies and public health services. Full article
Article
Identification of Genetic Risk Factors of Severe COVID-19 Using Extensive Phenotypic Data: A Proof-of-Concept Study in a Cohort of Russian Patients
Genes 2022, 13(3), 534; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13030534 - 17 Mar 2022
Abstract
The COVID-19 pandemic has drawn the attention of many researchers to the interaction between pathogen and host genomes. Over the last two years, numerous studies have been conducted to identify the genetic risk factors that predict COVID-19 severity and outcome. However, such an [...] Read more.
The COVID-19 pandemic has drawn the attention of many researchers to the interaction between pathogen and host genomes. Over the last two years, numerous studies have been conducted to identify the genetic risk factors that predict COVID-19 severity and outcome. However, such an analysis might be complicated in cohorts of limited size and/or in case of limited breadth of genome coverage. In this work, we tried to circumvent these challenges by searching for candidate genes and genetic variants associated with a variety of quantitative and binary traits in a cohort of 840 COVID-19 patients from Russia. While we found no gene- or pathway-level associations with the disease severity and outcome, we discovered eleven independent candidate loci associated with quantitative traits in COVID-19 patients. Out of these, the most significant associations correspond to rs1651553 in MYH14p = 1.4 × 10−7), rs11243705 in SETX (p = 8.2 × 10−6), and rs16885 in ATXN1 (p = 1.3 × 10−5). One of the identified variants, rs33985936 in SCN11A, was successfully replicated in an independent study, and three of the variants were found to be associated with blood-related quantitative traits according to the UK Biobank data (rs33985936 in SCN11A, rs16885 in ATXN1, and rs4747194 in CDH23). Moreover, we show that a risk score based on these variants can predict the severity and outcome of hospitalization in our cohort of patients. Given these findings, we believe that our work may serve as proof-of-concept study demonstrating the utility of quantitative traits and extensive phenotyping for identification of genetic risk factors of severe COVID-19. Full article
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Article
De Novo Transcriptome Analysis Reveals Putative Genes Involved in Anthraquinone Biosynthesis in Rubia yunnanensis
Genes 2022, 13(3), 521; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13030521 - 16 Mar 2022
Abstract
Rubia yunnanensis Diels (R. yunnanensis), a Chinese perennial plant, is well-known for its medicinal values such as rheumatism, contusion, and anemia. It is rich in bioactive anthraquinones, but the biosynthetic pathways of anthraquinones in R. yunnanensis remain unknown. To investigate genes [...] Read more.
Rubia yunnanensis Diels (R. yunnanensis), a Chinese perennial plant, is well-known for its medicinal values such as rheumatism, contusion, and anemia. It is rich in bioactive anthraquinones, but the biosynthetic pathways of anthraquinones in R. yunnanensis remain unknown. To investigate genes involved in anthraquinone biosynthesis in R. yunnanensis, we generated a de novo transcriptome of R. yunnanensis using the Illumina HiSeq 2500 sequencing platform. A total of 636,198 transcripts were obtained, in which 140,078 transcripts were successfully annotated. A differential gene expression analysis identified 15 putative genes involved in anthraquinone biosynthesis. Additionally, the hairy roots of R. yunnanensis were treated with 200 µM Methyl Jasmonate (MeJA). The contents of six bioactive anthraquinones and gene expression levels of 15 putative genes were measured using ultra performance liquid chromatography coupled with mass spectrometry (UPLC-MS/MS) and real-time quantitative polymerase chain reaction (RT-qPCR), respectively. The results showed that the expressions levels for 11 of the 15 genes and the contents of two of six anthraquinones significantly increased by MeJA treatment. Pearson’s correlation analyses indicated that the expressions of 4 of the 15 putative genes were positively correlated with the contents of rubiquinone (Q3) and rubiquinone-3-O-β-d-xylopranosyl-(1→6)-β-d-glucopyranoside (Q20). This study reported the first de novo transcriptome of R. yunnanensis and shed light on the anthraquinone biosynthesis and genetic information for R. yunnanensis. Full article
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Article
Association between Spinal Cord Injury and Alcohol Dependence: A Population-Based Retrospective Cohort Study
J. Pers. Med. 2022, 12(3), 473; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12030473 - 16 Mar 2022
Abstract
Spinal cord injury (SCI) is a devastating disorder. Alcohol abuse has been recognized as hindering SCI patients from rehabilitation, thus leading to longer length of days and poorer prognosis. This article aimed to investigate the association between spinal cord injury (SCI) and alcohol [...] Read more.
Spinal cord injury (SCI) is a devastating disorder. Alcohol abuse has been recognized as hindering SCI patients from rehabilitation, thus leading to longer length of days and poorer prognosis. This article aimed to investigate the association between spinal cord injury (SCI) and alcohol dependence. Data were derived from the National Health Insurance Research Database (NHIRD). The incidence of alcohol dependence between SCI and non-SCI groups was compared. Other possible risk factors were also analyzed. Patients (N = 5670) with SCI from 2000 to 2009 were initially assessed for eligibility. After propensity score matching, 5639 first-time SCI survivors were included. The Cox proportional hazard regression model was used to assess differences in the incidence of alcohol dependence syndrome. Based on the adjusted hazard ratios (HR), the SCI group had a higher hazard for alcohol dependence syndrome compared to the non-SCI group (adjusted HR: 1.39, 95% CI: 1.03~1.86, p = 0.0305). The injury level did not have an impact on the incidence of alcohol dependence syndrome. A higher incidence of alcohol dependence syndrome was related to male patients, lower insurance levels, higher Deyo’s CCI, and psychiatric OPD times. A lower incidence of alcohol dependence syndrome was related to elder age. The incidence of alcohol dependence increased after the occurrence of SCI and was also related to age, sex, monthly income, comorbidities, and psychiatric problems. The injury level did not affect the incidence of alcohol dependence after SCI. Full article
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Article
RNA-Seq Reveals Differentially Expressed Genes Associated with High Fiber Quality in Abaca (Musa textilis Nee)
Genes 2022, 13(3), 519; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13030519 - 15 Mar 2022
Abstract
Despite the importance of and current demand for abaca (Musa textilis Nee) fiber, there has been limited study that capitalizes on RNA-seq to identify candidate genes associated with high fiber quality and bunchy top virus (AbBTV) resistance. Three varieties (Abuab, Inosa, and [...] Read more.
Despite the importance of and current demand for abaca (Musa textilis Nee) fiber, there has been limited study that capitalizes on RNA-seq to identify candidate genes associated with high fiber quality and bunchy top virus (AbBTV) resistance. Three varieties (Abuab, Inosa, and Tangongon), one wild banana variety (Musa balbisiana Colla) Pacol, and two developed backcrosses (Abuab × Pacol BC2 and BC3) were grown at the Institute of Plant Breeding (IPB), Laguna, Philippines. The pseudostems of 3-month-old suckers of each genotype were sampled for RNA-seq. Datasets were analyzed for differential expression (DE) implementing various model frameworks, including pairwise, genotypic and non-DE models. Results indicate that Abuab and BC3 induce the highest proportion (70%) of abaca-specific genes. Gene ontology (GO) enrichment analysis showed several genes associated with cellulose synthase activity, callose synthase, ß-glucosidase activity, glucan biosynthetic process, etc. KEGG pathway analysis showed several genes encoding for enzymes involved in the lignin biosynthetic pathway. Analysis using genotypic DE (GDE) between abaca bunchy top virus (AbBTV)-resistant and -susceptible groups revealed genes such as pathogenesis-related protein and NBS-LRR. As the genotypes were not infected with the pathogen, these genes are yet to be confirmed for their roles in disease resistance and are an interesting subject for further investigation. Full article
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Article
Screening the Significant Hub Genes by Comparing Tumor Cells, Normoxic and Hypoxic Glioblastoma Stem-like Cell Lines Using Co-Expression Analysis in Glioblastoma
Genes 2022, 13(3), 518; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13030518 - 15 Mar 2022
Abstract
Glioblastoma multiforme (GBM) is categorized by rapid malignant cellular growth in the central nervous system (CNS) tumors. It is one of the most prevailing primary brain tumors, particularly in human male adults. Even though the combination therapy comprises surgery, chemotherapy, and adjuvant therapies, [...] Read more.
Glioblastoma multiforme (GBM) is categorized by rapid malignant cellular growth in the central nervous system (CNS) tumors. It is one of the most prevailing primary brain tumors, particularly in human male adults. Even though the combination therapy comprises surgery, chemotherapy, and adjuvant therapies, the survival rate is on average 14.6 months. Glioma stem cells (GSCs) have key roles in tumorigenesis, progression, and counteracting chemotherapy and radiotherapy. In our study, firstly, the gene expression dataset GSE45117 was retrieved and differentially expressed genes (DEGs) were spotted. The co-expression network analysis was employed on DEGs to find the significant modules. The most significant module resulting from co-expression analysis was the turquoise module. The turquoise module related to the tumor cells, hypoxia, normoxic treatments of glioblastoma tumor (GBT), and GSCs were screened. Sixty-one common genes in the turquoise module were selected generated through the co-expression analysis and protein–protein interaction (PPI) network. Moreover, the GO and KEGG pathway enrichment results were studied. Twenty common hub genes were screened by the NetworkAnalyst web instrument constructed on the PPI network through the STRING database. After survival analysis via the Kaplan–Meier (KM) plotter from The Cancer Genome Atlas (TCGA) database, we identified the five most significant hub genes strongly related to the progression of GBM. We further observed these five most significant hub genes also up-regulated in another GBM gene expression dataset. The protein–protein interaction (PPI) network of the turquoise module genes was constructed and a KEGG pathway enrichments study of the turquoise module genes was performed. The VEGF signaling pathway was emphasized because of the strong link with GBM. A gene–disease association network was further constructed to demonstrate the information of the progression of GBM and other related brain neoplasms. All hub genes assessed through this study would be potential markers for the prognosis and diagnosis of GBM. Full article
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Article
Next-Generation Sequencing in Lung Cancer Patients: A Comparative Approach in NSCLC and SCLC Mutational Landscapes
J. Pers. Med. 2022, 12(3), 453; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12030453 - 13 Mar 2022
Abstract
Background: Lung cancer remains one of the most diagnosed malignancies, being the second most diagnosed cancer, while still being the leading cause of cancer-related deaths. Late diagnosis remains a problem, alongside the high mutational burden encountered in lung cancer. Methods: We assessed the [...] Read more.
Background: Lung cancer remains one of the most diagnosed malignancies, being the second most diagnosed cancer, while still being the leading cause of cancer-related deaths. Late diagnosis remains a problem, alongside the high mutational burden encountered in lung cancer. Methods: We assessed the genetic profile of cancer genes in lung cancer using The Cancer Genome Atlas (TCGA) datasets for mutations and validated the results in a separate cohort of 32 lung cancer patients using tumor tissue and whole blood samples for next-generation sequencing (NGS) experiments. Another separate cohort of 32 patients was analyzed to validate some of the molecular alterations depicted in the NGS experiment. Results: In the TCGA analysis, we identified the most commonly mutated genes in each lung cancer dataset, with differences among the three histotypes analyzed. NGS analysis revealed TP53, CSF1R, PIK3CA, FLT3, ERBB4, and KDR as being the genes most frequently mutated. We validated the c.1621A>C mutation in KIT. The correlation analysis indicated negative correlation between adenocarcinoma and altered PIK3CA (r = −0.50918; p = 0.0029). TCGA survival analysis indicated that NRAS and IDH2 (LUAD), STK11 and TP53 (LUSC), and T53 (SCLC) alterations are correlated with the survival of patients. Conclusions: The study revealed differences in the mutational landscape of lung cancer histotypes. Full article
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Article
Gene Network Analysis for Osteoporosis, Sarcopenia, Diabetes, and Obesity in Human Mesenchymal Stromal Cells
Genes 2022, 13(3), 459; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13030459 - 03 Mar 2022
Abstract
The systemic gene interactions that occur during osteoporosis and their underlying mechanisms remain to be determined. To this end, mesenchymal stromal cells (MSCs) were analyzed from bone marrow samples collected from healthy individuals (n = 5) and patients with osteoporosis (n [...] Read more.
The systemic gene interactions that occur during osteoporosis and their underlying mechanisms remain to be determined. To this end, mesenchymal stromal cells (MSCs) were analyzed from bone marrow samples collected from healthy individuals (n = 5) and patients with osteoporosis (n = 5). A total of 120 osteoporosis-related genes were identified using RNA-sequencing (RNA-seq) and Ingenuity Pathway Analysis (IPA) software. In order to analyze these genes, we constructed a heatmap of one-way hierarchical clustering and grouped the gene expression patterns of the samples. The MSCs from one control participant showed a similar expression pattern to that observed in the MSCs of three patients with osteoporosis, suggesting that the differentiating genes might be important genetic determinants of osteoporosis. Then, we selected the top 38 genes based on fold change and expression, excluding osteoporosis-related genes from the control participant. We identified a network among the top 38 genes related to osteoblast and osteoclast differentiation, bone remodeling, osteoporosis, and sarcopenia using the Molecule Activity Predictor program. Among them, 25 genes were essential systemic genes involved in osteoporosis. Furthermore, we identified 24 genes also associated with diabetes and obesity, among which 10 genes were involved in a network related to bone and energy metabolism. The study findings may have implications for the treatment and prevention of osteoporosis. Full article
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Article
Association of Metabolic Parameter Variability with Esophageal Cancer Risk: A Nationwide Population-Based Study
J. Pers. Med. 2022, 12(3), 375; https://0-doi-org.brum.beds.ac.uk/10.3390/jpm12030375 - 01 Mar 2022
Abstract
Introduction: Certain metabolic parameters increase the risk of esophageal cancer. This study investigated the association between the variability in metabolic parameters and esophageal cancer incidence using large nationally representative data. Methods: Using the health checkup and claims data provided by the Korean National [...] Read more.
Introduction: Certain metabolic parameters increase the risk of esophageal cancer. This study investigated the association between the variability in metabolic parameters and esophageal cancer incidence using large nationally representative data. Methods: Using the health checkup and claims data provided by the Korean National Health Insurance Service (NHIS), we included 8,376,233 subjects who underwent NHIS-provided health checkups between 2009 and 2010 (index year) and two or more health checkups within five years before the index year. Hazard ratios (HRs) and 95% confidence intervals (CIs) for esophageal cancer were obtained using Cox proportional hazards models according to the quartiles of variability of each metabolic parameter: fasting blood glucose (FBG), weight, systolic blood pressure (SBP), and total cholesterol (TC) as well as a cumulative number of high-variability parameters. Results: A total of 6,455 cases of esophageal cancer occurred during a mean (±SD) follow-up of 8.8 (±1.1) years. The following metabolic parameters were used, with an adjusted HR and 95% CI: FBG (1.11, 1.03–1.18), weight (1.15, 1.07–1.23), SBP (1.08, 1.01–1.16), and TC (1.23, 1.15–1.32). The risk of esophageal cancer was higher in the highest quartile of variability than the lower quartiles. The risk of esophageal cancer gradually increased with a greater number of high-variability parameters: 1.08 (1.02–1.15), 1.22 (1.14–1.31), and 1.33 (1.21–1.46) for 1, 2, and 3–4 high-variability parameters (vs. none). Conclusions: A high variability of metabolic parameters was associated with an increased esophageal cancer risk. Further studies are needed to replicate our findings in other populations. Full article
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Article
Identification of Immune Markers in Dilated Cardiomyopathies with Heart Failure by Integrated Weighted Gene Coexpression Network Analysis
Genes 2022, 13(3), 393; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13030393 - 22 Feb 2022
Abstract
Dilated cardiomyopathy (DCM), a heterogeneous cardiomyopathy, is a major cause of heart failure and heart transplant. Currently, immunotherapy is believed to be an effective treatment method for DCM. However, individual differences are so obvious that the clinical effect is not satisfactory. In order [...] Read more.
Dilated cardiomyopathy (DCM), a heterogeneous cardiomyopathy, is a major cause of heart failure and heart transplant. Currently, immunotherapy is believed to be an effective treatment method for DCM. However, individual differences are so obvious that the clinical effect is not satisfactory. In order to find immune-related biomarkers of DCM to guide treatment and improve clinical efficacy, we downloaded a GSE120895 dataset from the Gene Expression Omnibus (GEO) database using CIBERSORT and WGCNA algorithms in RStudio and visualizing the protein–protein interaction (PPI) network for key modules by Cytoscape, and finally obtained six hub genes. A GSE17800 dataset was downloaded from the GEO dataset to verify the diagnostic values of hub genes, MYG1, FLOT1, and ATG13, which were excellent. Our study revealed unpublished potential immune mechanisms, biomarkers, and therapeutic targets of DCM. Full article
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