Omics Data Integration: Focusing on Molecular Biomarkers for Cancers and Diseases

Dear Colleagues,

The multi-omics approach has become essential in understanding cancer biology and other severe diseases, offering unprecedented insights into the molecular mechanisms underlying their genesis, progression, and therapeutic responses.

The proteome reflects cellular processes and alterations, identifying biomarkers for early detection and explaining the complex interplay of proteins within cancer cells and their microenvironment. Despite the relatively small number of human genes, alternative splicing and post-translational modifications generate diverse protein isoforms. High-throughput analysis explores protein expression, structures, variants, and functional effects to elucidate pathological mechanisms.

Evaluating the genome and transcriptome is crucial in identifying genetic mutations and variations linked to hereditary and complex diseases, providing insights into the genetic basis of pathologies and revealing how gene regulation alterations contribute to disease development. This analysis aids in early diagnosis, prognosis, and the development of targeted therapies.

Examining the cellular metabolome offers comprehensive insights into biochemical processes and metabolic pathways, identifying biomarkers for early diagnosis and monitoring disease progression. Changes in the metabolite profile can be detected before clinical symptoms become evident.

Integrating genomic, transcriptomic, proteomic, and metabolomic information accelerates translational research, fostering innovation in disease diagnosis, treatment, and prevention. Personalized medicine benefits from omics profiling, tailoring treatments to individuals, enhancing efficacy, and reducing side-effects.

This Special Issue of Biomolecules is dedicated to biomarker discovery based on omics data, with special attention to studies involving multiple high-throughput methods. Interdisciplinary research contributions, including original articles and reviews, are encouraged. Submissions may encompass, but are not limited to, the following areas:

• Biomarker discovery and clinical implications in diagnosis and prognosis;
• Proteomic profiling of tumour heterogeneity and personalized medicine;
• Integration of multi-omics data to unravel complex signalling networks;
• Advancements in mass spectrometry and computational tools;
• Functional proteomics to decipher the roles of specific proteins in disease development;
• Structural proteomics to elucidate new therapeutic approaches;
• Future directions and emerging technologies in omics;
• Single-cell multi-omics approaches;
• Application of multi-omics approaches for personalized medicine.

Join us in advancing knowledge in "Omics Data Integration: Focusing on Molecular Biomarkers for Cancers and Diseases." Your contributions will enhance our understanding of disease biology and pave the way for innovative strategies in diagnosis and treatment.

Sincerely,

Dr. Cinzia Franchin
Guest Editor

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. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). 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.

• omics data analysis
• omics data integration
• biomarker discovery
• bioinformatics
• cancers

Type of Paper: Review

Title: Inflammatory Bowel Diseases and Carcinogenesis: A Proteomic Approach

Abstract: Inflammatory bowel disease (IBD) is a chronic relapsing inflammatory illness of the gastrointestinal tract of unknown etiology. Clinical studies have highlighted a link between IBD and cancers (e.g., intestinal lymphoma, small bowel cancer, colorectal cancer, and cholangiocarcinoma), probably due to the chronic inflammation state and some common therapeutic treatments (e.g., anti-TNF, thiopurines). However, the causes of these correlations are still unknown and several questions are still unsolved. Proteomic techniques have emerged as a crucial tool in investigating the pathophysiology of various diseases including IBD and cancer. In this context, proteomic studies might allow the exploration of pathways involved in IBD pathogenesis identifying potential biomarkers for disease activity, mucosal healing, and tumor progression. The use of proteomic analysis could lead to a deeper understanding of the molecular interactions between IBD and cancer, supporting the development of targeted and personalized therapies. This review aims to present the state of the art in cancer research related to IBD and their therapeutic treatments, obtained through proteomic approaches.