Multi-omics in Oncology: Discovering Novel Biomarkers and Targets

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Cancer Biology".

Deadline for manuscript submissions: closed (31 October 2024) | Viewed by 3921

Special Issue Editor

Special Issue Information

Dear Colleagues,

Cancer is a complex ecosystem shaped by tumor cell heterogeneity, interactions with the tumor microenvironment, and spatiotemporal dynamics. Single-cell assays have revolutionized oncology research, allowing for high-resolution mapping of the tumor immune landscape. Technological advancements have also allowed the measurement of diverse histological patterns, such as genomics, epigenomics, transcriptomics, proteomics, metabolomics, and imaging phenotypes. Integration of single-cell and bulk-level multi-omics data from preclinical models and patient samples offers valuable insights into the functioning of the tumor immune ecosystem and responses to therapy, leading to improved biomarkers and treatments.

Multi-omics-based subtype analysis, combining proteomic, phosphorylated proteomic, and genomic analyses of cancer tissues, could potentially unravel the interconnectedness between cancer signaling and crucial metabolic pathways. Topics of this Special Issue include:

  • Post-translational modifications in cancer biology;
  • Molecular tumor pathology and classification;
  • Cancer biomarkers: screening and diagnosis;
  • Tumor microenvironment.

Dr. Chia-Jung Li
Guest Editor

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Keywords

  • multi-omics
  • cancer signaling
  • biomarkers

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Published Papers (2 papers)

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Research

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20 pages, 3077 KiB  
Article
An Integrated Framework to Identify Prognostic Biomarkers and Novel Therapeutic Targets in Hepatocellular Carcinoma-Based Disabilities
by Md. Okibur Rahman, Asim Das, Nazratun Naeem, Jabeen-E-Tahnim, Md. Ali Hossain, Md. Nur Alam, AKM Azad, Salem A. Alyami, Naif Alotaibi, A. S. Al-Moisheer and Mohammod Ali Moni
Biology 2024, 13(12), 966; https://doi.org/10.3390/biology13120966 - 24 Nov 2024
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Abstract
Hepatocellular carcinoma (HCC) is one of the most prevalent malignant tumors globally, significantly affecting liver functions, thus necessitating the identification of biomarkers and effective therapeutics to improve HCC-based disabilities. This study aimed to identify prognostic biomarkers, signaling cascades, and candidate drugs for the [...] Read more.
Hepatocellular carcinoma (HCC) is one of the most prevalent malignant tumors globally, significantly affecting liver functions, thus necessitating the identification of biomarkers and effective therapeutics to improve HCC-based disabilities. This study aimed to identify prognostic biomarkers, signaling cascades, and candidate drugs for the treatment of HCC through integrated bioinformatics approaches such as functional enrichment analysis, survival analysis, molecular docking, and simulation. Differential expression and functional enrichment analyses revealed 176 common differentially expressed genes from two microarray datasets, GSE29721 and GSE49515, significantly involved in HCC development and progression. Topological analyses revealed 12 hub genes exhibiting elevated expression in patients with higher tumor stages and grades. Survival analyses indicated that 11 hub genes (CCNB1, AURKA, RACGAP1, CEP55, SMC4, RRM2, PRC1, CKAP2, SMC2, UHRF1, and FANCI) and three transcription factors (E2F1, CREB1, and NFYA) are strongly linked to poor patient survival. Finally, molecular docking and simulation identified seven candidate drugs with stable complexes to their target proteins: tozasertib (−9.8 kcal/mol), tamatinib (−9.6 kcal/mol), ilorasertib (−9.5 kcal/mol), hesperidin (−9.5 kcal/mol), PF−562271 (−9.3 kcal/mol), coumestrol (−8.4 kcal/mol), and clofarabine (−7.7 kcal/mol). These findings suggest that the identified hub genes and TFs could serve as valuable prognostic biomarkers and therapeutic targets for HCC-based disabilities. Full article
(This article belongs to the Special Issue Multi-omics in Oncology: Discovering Novel Biomarkers and Targets)
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Review

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20 pages, 1031 KiB  
Review
Current Research on Molecular Biomarkers for Colorectal Cancer in Stool Samples
by Patricio Órdenes, Claudio Carril Pardo, Roberto Elizondo-Vega and Karina Oyarce
Biology 2024, 13(1), 15; https://doi.org/10.3390/biology13010015 - 27 Dec 2023
Cited by 3 | Viewed by 2534
Abstract
Colorectal cancer (CRC) is one of the most diagnosed cancers worldwide, with a high incidence and mortality rate when diagnosed late. Currently, the methods used in healthcare to diagnose CRC are the fecal occult blood test, flexible sigmoidoscopy, and colonoscopy. However, the lack [...] Read more.
Colorectal cancer (CRC) is one of the most diagnosed cancers worldwide, with a high incidence and mortality rate when diagnosed late. Currently, the methods used in healthcare to diagnose CRC are the fecal occult blood test, flexible sigmoidoscopy, and colonoscopy. However, the lack of sensitivity and specificity and low population adherence are driving the need to implement other technologies that can identify biomarkers that not only help with early CRC detection but allow for the selection of more personalized treatment options. In this regard, the implementation of omics technologies, which can screen large pools of biological molecules, coupled with molecular validation, stands out as a promising tool for the discovery of new biomarkers from biopsied tissues or body fluids. This review delves into the current state of the art in the identification of novel CRC biomarkers that can distinguish cancerous tissue, specifically from fecal samples, as this could be the least invasive approach. Full article
(This article belongs to the Special Issue Multi-omics in Oncology: Discovering Novel Biomarkers and Targets)
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