Biomarkers in Lung Cancer

A special issue of Cancers (ISSN 2072-6694). This special issue belongs to the section "Cancer Biomarkers".

Deadline for manuscript submissions: closed (31 May 2021) | Viewed by 37485

Special Issue Editor


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Guest Editor
Direttore UOC Oncologia Medica 2, Istituto Nazionale Tumori "Regina Elena", Via Elio Chianesi 53, 00144 Roma, Italy
Interests: epidermal growth factor receptor (EGFR); anaplastic lymphoma kinase (ALK); non-small-cell lung carcinoma (NSCLC); PDL1

Special Issue Information

Dear Colleagues,

Lung cancer is the most frequently diagnosed cancer, and the leading cause of cancer-related death worldwide. Non-small cell lung cancer (NSCLC) represents approximately 85% of all cases and includes lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Small-cell lung cancer (SCLC) accounts for most of the remaining lung cancer diagnoses. Lung cancer is a very complex and heterogeneous disease, and its clinical course is determined by patient characteristics and cancer-specific features ranging from the histologic subtype to peculiar genetic alterations at a somatic level. The treatment of locally advanced and metastatic lung cancer is often challenging and relies on systemic agents. Chemotherapy has represented the mainstay of lung cancer treatment for many decades. However, the recent innovation in biotechnologies has on one hand allowed for a more granular dissection of the disease at a biomolecular and genomic level, and on the other hand has permitted the development of a plethora of targeted therapeutic agents. This ongoing complex process is encompassing all cancers and is the basis of the precision medicine concept in oncology.

Lung cancer is the pioneer disease in this context, with the identification of EGFR mutations as a driver factor in advanced LUAD, conferring sensibility for treatment with specific tyrosine kinase inhibitors (TKIs), which have significantly improved clinical outcomes. Subsequently, additional actionable alterations were identified, particularly enriched in LUAD, such as ALK or ROS1 fusions. More recently, the paradigm has further evolved with the identification of a variety of agnostic genomic driver alterations in cancer, such as BRAF V600E, METex14, KRASG12C, and ERBB2 mutations and NTRK and RET fusions. Ongoing clinical trials are testing the clinical activity of specific target agents on lung cancer patients affected by tumors harboring such genomic alterations, with promising results. Innovative technologies allow for the detection of these somatic genomic alterations at the tumor tissue level, but also at the serum level, after a liquid biopsy. Nevertheless, the detection of a specific targetable mutation does not always translate into effectiveness of the relative target agent. In fact, a relevant subset of LUAD patients do not benefit from treatment with TKIs, even in the presence of actionable mutations. Therefore, a deeper understanding of the context in which these genomic alterations occur is necessary. Moreover, while targetable aberrations are fairly common in LUAD, they have not been identified in LUSC and SCLC. Thus, scientific investigation to specifically explore for the presence of driver and actionable alterations in these two additional subsets of lung cancer is a current unmet need.

Another major development that has taken place in recent years, involving all of the histologic subtypes of lung cancer to a different degree, is the efficient employment of anti-cancer immunotherapy. The inhibition of the PD-1/PD-L1 checkpoint has emerged as the leading path in this process. However, a valid universal biomarker predicting the efficacy of immune checkpoint inhibitors (ICIs) is lacking. The immunohistochemical quantification of PD-L1 expression has shown some predictive value for ICI activity, but a stronger standardization of the method is necessary. Another potential predictive biomarker of ICI efficacy that has been suggested is a high tumor mutational burden (TMB), but evidence in this regard is controversial and not mature enough to drive decisions in NSCLC. For instance, recent data allude to a reduced benefit from ICI in tumors harboring mutations in specific genes, such as KEAP1 and STK11, despite high TMB. Presumably, the current view on TMB needs to be better defined in the wider context of genomic instability.

Hence, the identification of new predictive biomarkers able to anticipate efficacy or resistance to a specific lung cancer treatment is a current priority for the scientific community. A predictive biomarker plays the important role of the matching factor between our ability to obtain a refined classification of lung cancer subtypes at a molecular level and the increasing availability of new targeted agents and immunotherapy options.

Investigation into new biomarkers can be performed at the tumor tissue level, or by measuring and qualifying specific factors in the serum. At a biological level, biomarkers can be represented by the expression of definite proteins, specific alterations in blood count, distinct transcriptional and/or genetic alterations, or even peculiar epigenetic events. Cancer-related biomarkers can be found at a tumor tissue level, or even on liquid biopsy, in which additional factors such as circulating tumor cells, exosomes, microRNAs, and cell-free DNA can be detected and further analyzed.

From a functional point of view, it is very common for a predictive biomarker to be strictly connected to the targetable and altered biological mechanism that conferred a growth advantage to the cancer cells. Nevertheless, as evidence has shown, the functionality aspect alone is not sufficient for the identification of a predictive biomarker. Moreover, there is a possibility that a multiparametric combination of biomarkers into compound classifiers could synergistically improve their final predictive potential. This aspect highlights the importance of biomarker "post-processing" and opens a new window on the possibility to employ proteomic, transcriptomic, and next-generation genomic sequencing data produced by innovative high-throughput technologies in order to predict treatment outcomes. The analysis of "big data" utilizing emerging artificial intelligence algorithms could make this feasible. Most importantly, such complex classifiers could also offer some potential predictive value for other lung cancer histologic subtypes besides LUAD, such as LUSC and SCLC.

Prof. Dr. Federico Cappuzzo
Guest Editor

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Keywords

  • lung cancer
  • Non-small cell lung cancer (NSCLC)
  • lung adenocarcinoma (LUAD)
  • lung squamous cell carcinoma (LUSC)
  • biomarker
  • tyrosine kinase inhibitors (TKIs)
  • PD-1/PD-L1

Published Papers (13 papers)

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16 pages, 7763 KiB  
Article
The Association of Annexin A1 and Chemosensitivity to Osimertinib in Lung Cancer Cells
by Min-Chun Chuang, Jr-Hau Lung, Yi-Chuan Chen, Yu-Ching Lin, Ya-Chin Li and Ming-Szu Hung
Cancers 2021, 13(16), 4106; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers13164106 - 15 Aug 2021
Cited by 6 | Viewed by 2684
Abstract
Annexin A1 (ANXA1) has been reported to promote tumor growth and resistance to chemotherapy drugs in lung cancer cells. In this study, we focused on the association of ANXA1 and chemosensitivity with a third generation epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI), Osimertinib, [...] Read more.
Annexin A1 (ANXA1) has been reported to promote tumor growth and resistance to chemotherapy drugs in lung cancer cells. In this study, we focused on the association of ANXA1 and chemosensitivity with a third generation epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI), Osimertinib, in lung cancer cells with EGFR mutations. The overexpression of ANXA1 was observed in the lung cancer cells studied. The downregulation of ANXA1 with small interference RNA (siRNA) decreased the growth of lung cancer cells. In lung cancer cells with EGFR mutations, the knockdown of ANXA1 increased the chemosensitivity to Osimertinib, and decreased the tumorigenesis, invasion and migration of lung cancer cells. Further study showed that the knockdown of ANXA1 inhibited the phosphorylation of EGFR and down-stream Akt pathways and promoted apoptosis in lung cancer cells treated with Osimertinib. A mice xenograft lung cancer model was established in our study and showed that ANXA1 siRNA enhanced the effects of Osimertinib in vivo. Our study results showed that ANXA1 plays critical roles in chemosensitivity to EGFR-TKI in lung cancer cells with the EGFR mutation. Our efforts may be used in the development of lung cancer treatment strategies in the future. Full article
(This article belongs to the Special Issue Biomarkers in Lung Cancer)
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17 pages, 1805 KiB  
Article
Plasma Based Protein Signatures Associated with Small Cell Lung Cancer
by Johannes F. Fahrmann, Hiroyuki Katayama, Ehsan Irajizad, Ashish Chakraborty, Taketo Kato, Xiangying Mao, Soyoung Park, Eunice Murage, Leona Rusling, Chuan-Yih Yu, Yinging Cai, Fu Chung Hsiao, Jennifer B. Dennison, Hai Tran, Edwin Ostrin, David O. Wilson, Jian-Min Yuan, Jody Vykoukal and Samir Hanash
Cancers 2021, 13(16), 3972; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers13163972 - 06 Aug 2021
Cited by 3 | Viewed by 2464
Abstract
Small-cell-lung cancer (SCLC) is associated with overexpression of oncogenes including Myc family genes and YAP1 and inactivation of tumor suppressor genes. We performed in-depth proteomic profiling of plasmas collected from 15 individuals with newly diagnosed early stage SCLC and from 15 individuals before [...] Read more.
Small-cell-lung cancer (SCLC) is associated with overexpression of oncogenes including Myc family genes and YAP1 and inactivation of tumor suppressor genes. We performed in-depth proteomic profiling of plasmas collected from 15 individuals with newly diagnosed early stage SCLC and from 15 individuals before the diagnosis of SCLC and compared findings with plasma proteomic profiles of 30 matched controls to determine the occurrence of signatures that reflect disease pathogenesis. A total of 272 proteins were elevated (area under the receiver operating characteristic curve (AUC) ≥ 0.60) among newly diagnosed cases compared to matched controls of which 31 proteins were also elevated (AUC ≥ 0.60) in case plasmas collected within one year prior to diagnosis. Ingenuity Pathway analyses of SCLC-associated proteins revealed enrichment of signatures of oncogenic MYC and YAP1. Intersection of proteins elevated in case plasmas with proteomic profiles of conditioned medium from 17 SCLC cell lines yielded 52 overlapping proteins characterized by YAP1-associated signatures of cytoskeletal re-arrangement and epithelial-to-mesenchymal transition. Among samples collected more than one year prior to diagnosis there was a predominance of inflammatory markers. Our integrated analyses identified novel circulating protein features in early stage SCLC associated with oncogenic drivers. Full article
(This article belongs to the Special Issue Biomarkers in Lung Cancer)
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14 pages, 2286 KiB  
Article
Targeted Next-Generation Sequencing Analysis Predicts the Recurrence in Resected Lung Adenocarcinoma Harboring EGFR Mutations
by In Ae Kim, Jae Young Hur, Hee Joung Kim, Song Am Lee, Jae Joon Hwang, Wan Seop Kim and Kye Young Lee
Cancers 2021, 13(14), 3632; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers13143632 - 20 Jul 2021
Cited by 4 | Viewed by 2319
Abstract
Targeted NGS, widely applied to identify driver oncogenes in advanced lung adenocarcinoma, may also be applied to resected early stage cancers. We investigated resected EGFR-mutated lung adenocarcinoma mutation profiles to evaluate prognostic impacts. Tissues from 131 patients who had complete resection of [...] Read more.
Targeted NGS, widely applied to identify driver oncogenes in advanced lung adenocarcinoma, may also be applied to resected early stage cancers. We investigated resected EGFR-mutated lung adenocarcinoma mutation profiles to evaluate prognostic impacts. Tissues from 131 patients who had complete resection of stage I–IIIA EGFR-mutated lung adenocarcinoma were analyzed by targeted NGS for 207 cancer-related genes. Recurrence free survival (RFS) was estimated according to genetic alterations using the Kaplan–Meier method and Cox proportional regression analysis. The relapse rate was 25.2% (33/131). Five-year RFS of stages IA, IB, II, and IIIA were 82%, 75%, 35%, and 0%, respectively (p < 0.001). RFS decreased with the number of co-mutations (p = 0.025). Among co-mutations, the CTNNB1 mutation was associated with short RFS in a multivariate analysis (hazard ratio: 5.4, 95% confidence interval: 2.1–14.4; p = 0.001). TP53 mutations were associated with short RFS in stage IB–IIIA (p = 0.01). RFS was shorter with EGFR exon 19 deletion (19-del) than with mutation 21-L858R in stage IB–IIIA tumors (p = 0.008). Among 19-del subtypes, pL747_P753delinS (6/56, 8.9%) had shorter RFS than pE746_A750del (39/56, 69.6%), the most frequent subtype (p = 0.004). Full article
(This article belongs to the Special Issue Biomarkers in Lung Cancer)
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15 pages, 1051 KiB  
Article
Interrelations between Patients’ Clinicopathological Characteristics and Their Association with Response to Immunotherapy in a Real-World Cohort of NSCLC Patients
by Ana Callejo, Joan Frigola, Patricia Iranzo, Caterina Carbonell, Nely Diaz, David Marmolejo, Juan David Assaf, Susana Cedrés, Alex Martinez-Marti, Alejandro Navarro, Nuria Pardo, Ramon Amat and Enriqueta Felip
Cancers 2021, 13(13), 3249; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers13133249 - 29 Jun 2021
Cited by 8 | Viewed by 2498
Abstract
Immune checkpoint inhibitors (ICIs) have transformed non-small cell lung cancer (NSCLC) treatment. Unfortunately, only some patients benefit from these therapies. Thus, certain clinicopathological characteristics of the patients have been proposed as biomarkers of ICIs response. We assembled a retrospective cohort of 262 NSCLC [...] Read more.
Immune checkpoint inhibitors (ICIs) have transformed non-small cell lung cancer (NSCLC) treatment. Unfortunately, only some patients benefit from these therapies. Thus, certain clinicopathological characteristics of the patients have been proposed as biomarkers of ICIs response. We assembled a retrospective cohort of 262 NSCLC patients treated with ICIs, compiled relevant clinicopathological characteristics, and studied their associations with treatment outcome using Cox proportional-hazards survival models. Additionally, we investigated the interrelations between clinicopathological features and devised a method to create a compendium associated with ICIs response by selecting those that provide non-redundant information. In multivariate analyses, ECOG performance status (hazard ratio (HR) 1.37 (95% CI 1.11 to 1.68), p < 0.005), LDH (HR 1.24 (95% CI 1.03 to 1.48), p = 0.02)) and PD-L1 negativity were associated with decreased progression-free survival (PFS) (HR 1.92 (95% CI 1.03 to 3.58), p = 0.04), whereas presentation of immune-related adverse events (irAEs) (HR 0.35 (95% CI 0.22 to 0.55, p < 0.005) or females (HR 0.52 (95% CI 0.33 to 0.80, p < 0.005) had longer PFS. Additionally, numerous clinicopathological indicators were found to be interrelated. Thus, we searched for features that provide non-redundant information, and found the combination of LDH levels, irAEs, and gender to have a better association with ICIs treatment response (cross-validated c-index = 0.66). We concluded that several clinicopathological features showed prognostic value in our real-world cohort. However, some are interrelated, and compendiums of features should therefore consider these interactions. Joint assessment of LDH, irAEs, and gender may be a good prognostic compendium. Full article
(This article belongs to the Special Issue Biomarkers in Lung Cancer)
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17 pages, 3099 KiB  
Article
Plasma Proteomic Analysis in Non-Small Cell Lung Cancer Patients Treated with PD-1/PD-L1 Blockade
by Mohamed Eltahir, Johan Isaksson, Johanna Sofia Margareta Mattsson, Klas Kärre, Johan Botling, Martin Lord, Sara M. Mangsbo and Patrick Micke
Cancers 2021, 13(13), 3116; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers13133116 - 22 Jun 2021
Cited by 18 | Viewed by 2906
Abstract
Checkpoint inhibitors have been approved for the treatment of non-small cell lung cancer (NSCLC). However, only a minority of patients demonstrate a durable clinical response. PD-L1 scoring is currently the only biomarker measure routinely used to select patients for immunotherapy, but its predictive [...] Read more.
Checkpoint inhibitors have been approved for the treatment of non-small cell lung cancer (NSCLC). However, only a minority of patients demonstrate a durable clinical response. PD-L1 scoring is currently the only biomarker measure routinely used to select patients for immunotherapy, but its predictive accuracy is modest. The aim of our study was to evaluate a proteomic assay for the analysis of patient plasma in the context of immunotherapy. Pretreatment plasma samples from 43 NSCLC patients who received anti-PD-(L)1 therapy were analyzed using a proximity extension assay (PEA) to quantify 92 different immune oncology-related proteins. The plasma protein levels were associated with clinical and histopathological parameters, as well as therapy response and survival. Unsupervised hierarchical cluster analysis revealed two patient groups with distinct protein profiles associated with high and low immune protein levels, designated as “hot” and “cold”. Further supervised cluster analysis based on T-cell activation markers showed that higher levels of T-cell activation markers were associated with longer progression-free survival (PFS) (p < 0.01). The analysis of single proteins revealed that high plasma levels of CXCL9 and CXCL10 and low ADA levels were associated with better response and prolonged PFS (p < 0.05). Moreover, in an explorative response prediction model, the combination of protein markers (CXCL9, CXCL10, IL-15, CASP8, and ADA) resulted in higher accuracy in predicting response than tumor PD-L1 expression or each protein assayed individually. Our findings demonstrate a proof of concept for the use of multiplex plasma protein levels as a tool for anti-PD-(L)1 response prediction in NSCLC. Additionally, we identified protein signatures that could predict the response to anti-PD-(L)1 therapy. Full article
(This article belongs to the Special Issue Biomarkers in Lung Cancer)
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13 pages, 2448 KiB  
Article
Splenic Volume as a Surrogate Marker of Immune Checkpoint Inhibitor Efficacy in Metastatic Non Small Cell Lung Cancer
by Loïck Galland, Julie Lecuelle, Laure Favier, Cléa Fraisse, Aurélie Lagrange, Courèche Kaderbhai, Caroline Truntzer and François Ghiringhelli
Cancers 2021, 13(12), 3020; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers13123020 - 16 Jun 2021
Cited by 10 | Viewed by 2229
Abstract
Monoclonal antibodies targeting PD1/PD-L1 are game changers in advanced non-small cell lung cancer (NSCLC), but biomarkers are lacking. We previously reported the prognostic role of splenic volume in digestive cancer and its correlation with the presence of immunosuppressive cells. The aim of this [...] Read more.
Monoclonal antibodies targeting PD1/PD-L1 are game changers in advanced non-small cell lung cancer (NSCLC), but biomarkers are lacking. We previously reported the prognostic role of splenic volume in digestive cancer and its correlation with the presence of immunosuppressive cells. The aim of this study was to evaluate the prognostic role of splenic volume in NSCLC patients treated with immune checkpoint inhibitors (ICIs). We conducted a retrospective study of 276 patients receiving ICIs for advanced NSCLC in the Georges François Leclerc Cancer Center. The association between splenic volume at baseline and at two months of therapy and progression-free survival (PFS) during ICI treatment or overall survival (OS) from ICI initiation was evaluated using univariate and multivariable Cox analyses. Splenic volume during treatment and the change in splenic volume were associated with poor PFS (respectively p = 0.02 and p = 0.001) and with OS (respectively p < 1.10−3 and p < 1.10−3). Baseline splenic volume at the first evaluation was also associated with poor OS (p = 0.001). LDH rate and dNLR were positively correlated with splenic volume, as well as with its evolution. After the adjustment of clinical variables, splenic volumes remained a predictive marker of immunotherapy efficacy. Splenic volume is a prognostic biomarker in patients with advanced NSCLC treated with ICIs. Full article
(This article belongs to the Special Issue Biomarkers in Lung Cancer)
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12 pages, 796 KiB  
Article
Comparison of Resistance Spectra after First and Second Line Osimertinib Treatment Detected by Liquid Biopsy
by Balázs Jóri, Stefanie Schatz, Len Kaller, Bettina Kah, Julia Roeper, Hayat O. Ramdani, Linda Diehl, Petra Hoffknecht, Christian Grohé, Frank Griesinger, Markus Tiemann, Lukas C. Heukamp and Markus Falk
Cancers 2021, 13(12), 2861; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers13122861 - 08 Jun 2021
Cited by 11 | Viewed by 3110
Abstract
Since 2009, several first, second, and third generation EGFR tyrosine kinase inhibitors (TKI) have been approved for targeted treatment of EGFR mutated metastatic non-small lung cancer (NSCLC). A vast majority of patients is improving quickly on treatment; however, resistance is inevitable and typically [...] Read more.
Since 2009, several first, second, and third generation EGFR tyrosine kinase inhibitors (TKI) have been approved for targeted treatment of EGFR mutated metastatic non-small lung cancer (NSCLC). A vast majority of patients is improving quickly on treatment; however, resistance is inevitable and typically occurs after one year for TKI of the first and second generation. Osimertinib, a third generation TKI, has recently been approved for first line treatment in the palliative setting and is expected to become approved for the adjuvant setting as well. Progression-free survival (PFS) under osimertinib is superior to its predecessors but its spectrum of resistance alterations appears significantly more diverse compared to first and second generation EGFR TKI. As resistance mechanisms to osimertinib are therapeutically targetable in some cases, it is important to comprehensively test for molecular alterations in the relapse scenario. Liquid biopsy may be advantageous over tissue analysis as it has the potential to represent tumor heterogeneity and clonal diversification. We have previously shown high concordance of hybrid capture (HC) based next generation sequencing (NGS) in liquid biopsy versus solid tumor biopsies. In this study, we now present real-word data from 56 patients with metastatic NSCLC that were tested by liquid biopsy at the time of disease progression on mostly second line treated osimertinib treatment. We present examples of single and multiple TKI resistance mechanisms, including mutations in multiple pathways, copy number changes and rare fusions of RET, ALK, FGFR3 and BRAF. In addition, we present the added value of HC based NGS to reveal polyclonal resistance development at the DNA level encoding multiple EGFR C797S and PIK3CA mutations. Full article
(This article belongs to the Special Issue Biomarkers in Lung Cancer)
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13 pages, 1547 KiB  
Article
Serum Metabolite Profiles in Participants of Lung Cancer Screening Study; Comparison of Two Independent Cohorts
by Piotr Widłak, Karol Jelonek, Agata Kurczyk, Joanna Żyła, Magdalena Sitkiewicz, Edoardo Bottoni, Giulia Veronesi, Joanna Polańska and Witold Rzyman
Cancers 2021, 13(11), 2714; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers13112714 - 31 May 2021
Cited by 10 | Viewed by 2465
Abstract
Serum metabolome is a promising source of molecular biomarkers that could support early detection of lung cancer in screening programs based on low-dose computed tomography. Several panels of metabolites that differentiate lung cancer patients and healthy individuals were reported, yet none of them [...] Read more.
Serum metabolome is a promising source of molecular biomarkers that could support early detection of lung cancer in screening programs based on low-dose computed tomography. Several panels of metabolites that differentiate lung cancer patients and healthy individuals were reported, yet none of them were validated in the population at high-risk of developing cancer. Here we analyzed serum metabolome profiles in participants of two lung cancer screening studies: MOLTEST-BIS (Poland, n = 369) and SMAC-1 (Italy, n = 93). Three groups of screening participants were included: lung cancer patients, individuals with benign pulmonary nodules, and those without any lung alterations. Concentrations of about 400 metabolites (lipids, amino acids, and biogenic amines) were measured by a mass spectrometry-based approach. We observed a reduced level of lipids, in particular cholesteryl esters, in sera of cancer patients from both studies. Despite several specific compounds showing significant differences between cancer patients and healthy controls within each study, only a few cancer-related features were common when both cohorts were compared, which included a reduced concentration of lysophosphatidylcholine LPC (18:0). Moreover, serum metabolome profiles in both noncancer groups were similar, and differences between cancer patients and both groups of healthy participants were comparable. Large heterogeneity in levels of specific metabolites was observed, both within and between cohorts, which markedly impaired the accuracy of classification models: The overall AUC values of three-state classifiers were 0.60 and 0.51 for the test (MOLTEST) and validation (SMAC) cohorts, respectively. Therefore, a hypothetical metabolite-based biomarker for early detection of lung cancer would require adjustment to lifestyle-related confounding factors that putatively affect the composition of serum metabolome. Full article
(This article belongs to the Special Issue Biomarkers in Lung Cancer)
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13 pages, 1505 KiB  
Article
Clinical Application of Next-Generation Sequencing of Plasma Cell-Free DNA for Genotyping Untreated Advanced Non-Small Cell Lung Cancer
by Maria Gabriela O. Fernandes, Natália Cruz-Martins, Conceição Souto Moura, Susana Guimarães, Joana Pereira Reis, Ana Justino, Maria João Pina, Adriana Magalhães, Henrique Queiroga, José Carlos Machado, Venceslau Hespanhol and José Luis Costa
Cancers 2021, 13(11), 2707; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers13112707 - 30 May 2021
Cited by 7 | Viewed by 2809
Abstract
Background: Analysis of circulating tumor DNA (ctDNA) has remarkable potential as a non-invasive lung cancer molecular diagnostic method. This prospective study addressed the clinical value of a targeted-gene amplicon-based plasma next-generation sequencing (NGS) assay to detect actionable mutations in ctDNA in patients with [...] Read more.
Background: Analysis of circulating tumor DNA (ctDNA) has remarkable potential as a non-invasive lung cancer molecular diagnostic method. This prospective study addressed the clinical value of a targeted-gene amplicon-based plasma next-generation sequencing (NGS) assay to detect actionable mutations in ctDNA in patients with newly diagnosed advanced lung adenocarcinoma. Methods: ctDNA test performance and concordance with tissue NGS were determined, and the correlation between ctDNA findings, clinical features, and clinical outcomes was evaluated in 115 patients with paired plasma and tissue samples. Results: Targeted-gene NGS-based ctDNA and NGS-based tissue analysis detected 54 and 63 genomic alterations, respectively; 11 patients presented co-mutations, totalizing 66 hotspot mutations detected, 51 on both tissue and plasma, 12 exclusively on tissue, and 3 exclusively on plasma. NGS-based ctDNA revealed a diagnostic performance with 81.0% sensitivity, 95.3% specificity, 94.4% PPV, 83.6% NPV, test accuracy of 88.2%, and Cohen’s Kappa 0.764. PFS and OS assessed by both assays did not significantly differ. Detection of ctDNA alterations was statistically associated with metastatic disease (p = 0.013), extra-thoracic metastasis (p = 0.004) and the number of organs involved (p = 0.010). Conclusions: This study highlights the potential use of ctDNA for mutation detection in newly diagnosed NSCLC patients due to its high accuracy and correlation with clinical outcomes. Full article
(This article belongs to the Special Issue Biomarkers in Lung Cancer)
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14 pages, 754 KiB  
Article
Gene Expression Levels of the Prolyl Hydroxylase Domain Proteins PHD1 and PHD2 but Not PHD3 Are Decreased in Primary Tumours and Correlate with Poor Prognosis of Patients with Surgically Resected Non-Small-Cell Lung Cancer
by Ana Koren, Matija Rijavec, Tomaž Krumpestar, Izidor Kern, Aleksander Sadikov, Tanja Čufer and Peter Korošec
Cancers 2021, 13(10), 2309; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers13102309 - 12 May 2021
Cited by 9 | Viewed by 2030
Abstract
Background: Hypoxia correlates with poor prognosis in several cancer types, including lung cancer. Prolyl hydroxylase domain proteins (PHDs) play a role in cell oxygen sensing, negatively regulating the hypoxia-inducible factor (HIF) pathway. Our study aim was to evaluate PHD1, PHD2 and PHD3 [...] Read more.
Background: Hypoxia correlates with poor prognosis in several cancer types, including lung cancer. Prolyl hydroxylase domain proteins (PHDs) play a role in cell oxygen sensing, negatively regulating the hypoxia-inducible factor (HIF) pathway. Our study aim was to evaluate PHD1, PHD2 and PHD3 mRNA expression levels in primary tumours and normal lungs of non-small-cell lung cancer (NSCLC) patients and to correlate it with selected regulators of HIF signalling, with clinicopathological characteristics and overall survival (OS). Methods: Tumour tissue samples were obtained from 60 patients with surgically resected NSCLC who were treated with radical surgery. In 22 out of 60 cases, matching morphologically normal lung tissue was obtained. PHD1, PHD2 and PHD3 mRNA expressions were measured using RT-qPCR. Results: The PHD1 and PHD2 mRNA levels in primary tumours were significantly decreased compared to those in normal lungs (both p < 0.0001). PHD1 and PHD2 expression in tumours was positively correlated (rs = 0.82; p < 0.0001) and correlated well with HIF pathway downstream genes HIF1A, PKM2 and PDK1. Decreased PHD1 and PHD2 were associated with larger tumour size, higher tumour stage (PHD1 only) and squamous cell carcinoma. Patients with low PHD1 and patients with low PHD2 expression had shorter OS than patients with high PHD1 (p = 0.02) and PHD2 expression (p = 0.01). PHD1 showed borderline independent prognostic values in multivariate analysis (p = 0.06). In contrast, we found no associations between PHD3 expression and any of the observed parameters. Conclusions: Our results show that reduced expression of PHD1 and PHD2 is associated with the development and progression of NSCLC. PHD1 could be further assessed as a prognostic marker in NSCLC. Full article
(This article belongs to the Special Issue Biomarkers in Lung Cancer)
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14 pages, 2122 KiB  
Article
Mass Spectrometry as a Highly Sensitive Method for Specific Circulating Tumor DNA Analysis in NSCLC: A Comparison Study
by Pierre-Jean Lamy, Paul van der Leest, Nicolas Lozano, Catherine Becht, Frédérique Duboeuf, Harry J. M. Groen, Werner Hilgers, Nicolas Pourel, Naomi Rifaela, Ed Schuuring and Catherine Alix-Panabières
Cancers 2020, 12(10), 3002; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers12103002 - 16 Oct 2020
Cited by 20 | Viewed by 4223
Abstract
Plasma-based tumor mutational profiling is arising as a reliable approach to detect primary and therapy-induced resistance mutations required for accurate treatment decision making. Here, we compared the FDA-approved Cobas® EGFR Mutation Test v2 with the UltraSEEK™ Lung Panel on the MassARRAY® [...] Read more.
Plasma-based tumor mutational profiling is arising as a reliable approach to detect primary and therapy-induced resistance mutations required for accurate treatment decision making. Here, we compared the FDA-approved Cobas® EGFR Mutation Test v2 with the UltraSEEK™ Lung Panel on the MassARRAY® System on detection of EGFR mutations, accompanied with preanalytical sample assessment using the novel Liquid IQ® Panel. 137 cancer patient-derived cell-free plasma samples were analyzed with the Cobas® and UltraSEEK™ tests. Liquid IQ® analysis was initially validated (n = 84) and used to determine ccfDNA input for all samples. Subsequently, Liquid IQ® results were applied to harmonize ccfDNA input for the Cobas® and UltraSEEK™ tests for 63 NSCLC patients. The overall concordance between the Cobas® and UltraSEEK™ tests was 86%. The Cobas® test detected more EGFR exon19 deletions and L858R mutations, while the UltraSEEK™ test detected more T790M mutations. A 100% concordance in both the clinical (n = 137) and harmonized (n = 63) cohorts was observed when >10 ng of ccfDNA was used as determined by the Liquid IQ® Panel. The Cobas® and UltraSEEK™ tests showed similar sensitivity in EGFR mutation detection, particularly when ccfDNA input was sufficient. It is recommended to preanalytically determine the ccfDNA concentration accurately to ensure sufficient input for reliable interpretation and treatment decision making. Full article
(This article belongs to the Special Issue Biomarkers in Lung Cancer)
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Review

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23 pages, 1035 KiB  
Review
Emerging Lab-on-a-Chip Approaches for Liquid Biopsy in Lung Cancer: Status in CTCs and ctDNA Research and Clinical Validation
by Ângela Carvalho, Gabriela Ferreira, Duarte Seixas, Catarina Guimarães-Teixeira, Rui Henrique, Fernando J. Monteiro and Carmen Jerónimo
Cancers 2021, 13(9), 2101; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers13092101 - 27 Apr 2021
Cited by 14 | Viewed by 4402
Abstract
Despite the intensive efforts dedicated to cancer diagnosis and treatment, lung cancer (LCa) remains the leading cause of cancer-related mortality, worldwide. The poor survival rate among lung cancer patients commonly results from diagnosis at late-stage, limitations in characterizing tumor heterogeneity and the lack [...] Read more.
Despite the intensive efforts dedicated to cancer diagnosis and treatment, lung cancer (LCa) remains the leading cause of cancer-related mortality, worldwide. The poor survival rate among lung cancer patients commonly results from diagnosis at late-stage, limitations in characterizing tumor heterogeneity and the lack of non-invasive tools for detection of residual disease and early recurrence. Henceforth, research on liquid biopsies has been increasingly devoted to overcoming these major limitations and improving management of LCa patients. Liquid biopsy is an emerging field that has evolved significantly in recent years due its minimally invasive nature and potential to assess various disease biomarkers. Several strategies for characterization of circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) have been developed. With the aim of standardizing diagnostic and follow-up practices, microfluidic devices have been introduced to improve biomarkers isolation efficiency and specificity. Nonetheless, implementation of lab-on-a-chip platforms in clinical practice may face some challenges, considering its recent application to liquid biopsies. In this review, recent advances and strategies for the use of liquid biopsies in LCa management are discussed, focusing on high-throughput microfluidic devices applied for CTCs and ctDNA isolation and detection, current clinical validation studies and potential clinical utility. Full article
(This article belongs to the Special Issue Biomarkers in Lung Cancer)
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Other

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8 pages, 4375 KiB  
Brief Report
Metabolic Health Together with a Lipid Genetic Risk Score Predicts Survival of Small Cell Lung Cancer Patients
by Lara P. Fernández, María Merino, Gonzalo Colmenarejo, Juan Moreno Rubio, Tais González Pessolani, Guillermo Reglero, Enrique Casado, María Sereno and Ana Ramírez de Molina
Cancers 2021, 13(5), 1112; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers13051112 - 05 Mar 2021
Cited by 2 | Viewed by 1591
Abstract
Small cell lung cancer (SCLC) prognosis is the poorest of all types of lung cancer. Its clinical management remains heterogeneous and therefore, the capability to predict survival would be of great clinical value. Metabolic health (MH) status and lipid metabolism are two relevant [...] Read more.
Small cell lung cancer (SCLC) prognosis is the poorest of all types of lung cancer. Its clinical management remains heterogeneous and therefore, the capability to predict survival would be of great clinical value. Metabolic health (MH) status and lipid metabolism are two relevant factors in cancer prevention and prognosis. Nevertheless, their contributions in SCLC outcome have not yet been analyzed. We analyzed MH status and a transcriptomic panel of lipid metabolism genes in SCLC patients, and we developed a predictive genetic risk score (GRS). MH and two lipid metabolism genes, racemase and perilipin 1, are biomarkers of SCLC survival (HR = 1.99 (CI95%: 1.11–3.61) p = 0.02, HR = 0.36 (CI95%: 0.19–0.67), p = 0.03 and HR = 0.21 (CI95%: 0.09–0.47), respectively). Importantly, a lipid GRS of these genes predict better survival (c-index = 0.691). Finally, in a Cox multivariate regression model, MH, lipid GRS and smoking history are the main predictors of SCLC survival (c-index = 0.702). Our results indicate that the control of MH, lipid gene expression and environmental factors associated with lifestyle is crucial for increased SCLC survival. Here, we propose for the first time, a metabolic precision approach for SCLC patients. Full article
(This article belongs to the Special Issue Biomarkers in Lung Cancer)
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