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Integrative Omics Approaches to Decipher Cancer Signaling
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Integrative Omics Approaches to Decipher Cancer Signaling

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (30 November 2022) | Viewed by 10791

Special Issue Editors

Dr. Yashwanth Subbannayya

E-Mail Website
Guest Editor
Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
Interests: Systems Biology; Cancer Biology; Innate Immunity; Signaling pathways; Proteomics
Dr. Sanjiban Chakrabarty

E-Mail Website
Guest Editor
Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
Interests: Functional Genomics

Special Issue Information

Dear Colleagues,

Over the last few decades, omics-based high-throughput approaches have enabled researchers to unravel some of the molecular mechanisms of cancer in unprecedented detail. Vast amounts of omics datasets deposited into cancer-specific public repositories have enabled rapid developments in cancer-based diagnostics, prognostics, and therapies. The integration of multi-omics datasets will allow deciphering and modeling mechanisms of tumorigenesis, cancer heterogeneity, drug resistance, cancer recurrence, and cancer patients’ survival.

This Special Issue on “Integrative Omics Approaches to Decipher Cancer Signaling” will focus on studies that integrate multi-omics data on cancer and thereby identify, characterize, and validate mechanisms of cancer signaling. We welcome original papers and reviews on this emerging area of cancer biology. Original articles describing at least two omics-based approaches applied to study patient samples or in vitro models, as well as studies developing logical models of tumor-specific processes using deposited or original multi-omics findings are encouraged.

Dr. Yashwanth Subbannayya
Dr. Sanjiban Chakrabarty
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • cancer biology
  • omics data
  • multi-omics
  • data integration
  • Systems biology
  • tumor microenvironment
  • therapeutics
  • proteogenomics
  • personalized medicine
  • logical modeling

Published Papers (4 papers)

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Research

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21 pages, 24266 KiB  
Article
Integrative and Comprehensive Pan-Cancer Analysis of Lymphocyte-Specific Protein Tyrosine Kinase in Human Tumors
by Mingwei Han, Yiming Li, Yixiao Guo, Wanwan Zhu and Jianli Jiang
Int. J. Mol. Sci. 2022, 23(22), 13998; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232213998 - 13 Nov 2022
Cited by 4 | Viewed by 1663
Abstract
Lymphocyte-specific protein tyrosine kinase (LCK) is common in a variety of hematologic malignancies but comparatively less common in solid tumors. This study aimed to explore the potential diagnostic and prognostic value of LCK across tumors through integrative and comprehensive pan-cancer analysis, as well [...] Read more.
Lymphocyte-specific protein tyrosine kinase (LCK) is common in a variety of hematologic malignancies but comparatively less common in solid tumors. This study aimed to explore the potential diagnostic and prognostic value of LCK across tumors through integrative and comprehensive pan-cancer analysis, as well as experimental validation. Multiple databases were used to explore the expression, alteration, prognostic value, association with immune infiltration, and potential functional pathways of LCK in pan-cancers. The results were further validated by western blotting and qPCR of patient samples as well as tumor cell lines. High LCK expression typically represents a better prognosis. Notably, drug sensitivity prediction of LCK identified P-529 as a candidate for drug development. Gene Annotations (GO) and KEGG analyses showed significant enrichment of PD-L1 and the T-cell receptor pathway. The results from patient samples and tumor cell lines confirmed these conclusions in LIHC. In conclusion, LCK is differentially expressed in multiple tumors and normal tissues. Further analysis highlighted its association with prognostic implications, pan-cancer genetic alterations, and immune signatures. Our data provide evidence for a diagnostic marker of LCK and the possible use of LCK as a target for the treatment of tumors. Full article
(This article belongs to the Special Issue Integrative Omics Approaches to Decipher Cancer Signaling)
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18 pages, 10455 KiB  
Article
A Novel Role of Arrhythmia-Related Gene KCNQ1 Revealed by Multi-Omic Analysis: Theragnostic Value and Potential Mechanisms in Lung Adenocarcinoma
by Kai-Tun Chang, Hsing-Ju Wu, Chien-Wei Liu, Chia-Ying Li and Hung-Yu Lin
Int. J. Mol. Sci. 2022, 23(4), 2279; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23042279 - 18 Feb 2022
Cited by 6 | Viewed by 1970
Abstract
The early diagnosis, prognostic prediction, and personalized therapy of lung adenocarcinoma (LUAD) remains a challenging issue. KCNQ1 (potassium voltage-gated channel subfamily Q Member 1) is implicated in long QT syndrome (LQTS) and cardiac arrhythmia, while its significance in LUAD remains unclear. In this [...] Read more.
The early diagnosis, prognostic prediction, and personalized therapy of lung adenocarcinoma (LUAD) remains a challenging issue. KCNQ1 (potassium voltage-gated channel subfamily Q Member 1) is implicated in long QT syndrome (LQTS) and cardiac arrhythmia, while its significance in LUAD remains unclear. In this study, we aimed to explore the significance of KCNQ1 in terms of clinical value, tumor immunity, underlying mechanisms, and a precision medicine approach by means of multi-omics analysis. The association of KCNQ1 with LUAD was first explored. Both altered variants and high expression of KCNQ1 in a TCGA-LUAD cohort indicated a favorable outcome. KCNQ1 levels had a negative correlation with tumor proliferation index Ki67 levels. siRNA-knockdown of KCNQ1 promoted the migration ability of lung cancer cells. KCNQ1 levels were decreased in LUAD tissue compared to normal tissue. A receiver operating characteristic (ROC) curve indicated good diagnostic efficiency of KCNQ1. High KCNQ1 is associated with an immunoactive profile of immune infiltration and immunomodulators and is involved in the inhibition of the cell cycle and DNA replication. Lapatinib was identified as a potent drug for LUAD in the context of low KCNQ1. This study unveiled the significance of KCNQ1 in diagnosis and prognosis and provided a corresponding precision medicine strategy for LUAD. Full article
(This article belongs to the Special Issue Integrative Omics Approaches to Decipher Cancer Signaling)
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20 pages, 8462 KiB  
Article
Multi-Omics Reveal the Immunological Role and the Theragnostic Value of miR-216a/GDF15 Axis in Human Colon Adenocarcinoma
by Chun-Bin Tung, Chia-Ying Li and Hung-Yu Lin
Int. J. Mol. Sci. 2021, 22(24), 13636; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222413636 - 20 Dec 2021
Cited by 6 | Viewed by 2634
Abstract
Colon adenocarcinoma (COAD) is the most common type of gastrointestinal cancer and is still the third leading cause of cancer-related mortality worldwide. Accurate screening tools for early diagnosis and prediction of prognosis and precision treatment strategies are urgently required to accommodate the unmet [...] Read more.
Colon adenocarcinoma (COAD) is the most common type of gastrointestinal cancer and is still the third leading cause of cancer-related mortality worldwide. Accurate screening tools for early diagnosis and prediction of prognosis and precision treatment strategies are urgently required to accommodate the unmet medical needs of COAD management. We herein aimed to explore the significance of the microRNA (miR)-216a/growth differentiation factor 15 (GDF15) axis in terms of clinical value, tumor immunity, and potential mechanisms in COAD by using multi-omic analysis. The gene expression levels of miR-216a and GDF15 showed an increase in the COAD group compared to those of the normal group. The expression of miR-216a presented a negative correlation with GDF15 in COAD tumor tissue. The use of an in vitro luciferase reporter assay and bioinformatic prediction revealed that miR-216a-3p acted toward translational inhibition on GDF15 by targeting its 3′untranslated region (UTR) site. High miR-216a expression was associated with decreased overall survival (OS), while the high expression of GDF15 was associated with increased OS. Enriched type 1 T-helper (Th1), enriched regulatory T (Treg), enriched eosinophils, and decreased nature killer T-cells (NKTs) in COAD tumor tissue may play counteracting factors on the tumor-regulatory effects of miR-216a and GDF15. In addition, high GDF15 expression had associations with suppressed immunoinhibitory genes and negative correlations with the infiltration of macrophages and endothelial cells. The enrichment analysis revealed that GDF15 and its co-expression network may be implicated in mitochondrial organization, apoptosis signaling, and endoplasmic reticulum (ER) stress response. The Genomics of Drug Sensitivity in Cancer (GDSC) and Cancer Therapeutics Response Portal (CTRP) analysis identified that Gemcitabine acted as a precision treatment for COAD when GDF15 expression was low. This study supports the miR-216a/GDF15 axis as a diagnostic/prognostic panel for COAD, identifies Th1, Treg, eosinophils, and NKTs as counteracting factors, indicates potential relationships underlying immunomodulation, mitochondrial organization, apoptotic signaling, and ER stress and unveil Gemcitabine as a potential drug for the development of treatment strategy when combined with targeting GDF15. Full article
(This article belongs to the Special Issue Integrative Omics Approaches to Decipher Cancer Signaling)
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Review

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15 pages, 296 KiB  
Review
Recent Multiomics Approaches in Endometrial Cancer
by Dariusz Boroń, Nikola Zmarzły, Magdalena Wierzbik-Strońska, Joanna Rosińczuk, Paweł Mieszczański and Beniamin Oskar Grabarek
Int. J. Mol. Sci. 2022, 23(3), 1237; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23031237 - 22 Jan 2022
Cited by 12 | Viewed by 3762
Abstract
Endometrial cancer is the most common gynecological cancers in developed countries. Many of the mechanisms involved in its initiation and progression remain unclear. Analysis providing comprehensive data on the genome, transcriptome, proteome, and epigenome could help in selecting molecular markers and targets in [...] Read more.
Endometrial cancer is the most common gynecological cancers in developed countries. Many of the mechanisms involved in its initiation and progression remain unclear. Analysis providing comprehensive data on the genome, transcriptome, proteome, and epigenome could help in selecting molecular markers and targets in endometrial cancer. Multiomics approaches can reveal disturbances in multiple biological systems, giving a broader picture of the problem. However, they provide a large amount of data that require processing and further integration prior to analysis. There are several repositories of multiomics datasets, including endometrial cancer data, as well as portals allowing multiomics data analysis and visualization, including Oncomine, UALCAN, LinkedOmics, and miRDB. Multiomics approaches have also been applied in endometrial cancer research in order to identify novel molecular markers and therapeutic targets. This review describes in detail the latest findings on multiomics approaches in endometrial cancer. Full article
(This article belongs to the Special Issue Integrative Omics Approaches to Decipher Cancer Signaling)
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