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Life
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Cancer Genomics and Transcriptomics: Uncovering New Frontiers in Tumor Biology
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Cancer Genomics and Transcriptomics: Uncovering New Frontiers in Tumor Biology

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Genetics and Genomics".

Deadline for manuscript submissions: 14 July 2026 | Viewed by 1800

Special Issue Editors

Dr. Panagiotis Adamopoulos

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Guest Editor
Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
Interests: biochemistry; molecular biology; genomics
Special Issues, Collections and Topics in MDPI journals
Dr. Panagiotis Tsiakanikas

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Guest Editor
Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
Interests: clinical biochemistry; genomics; molecular biology

Special Issue Information

Dear Colleagues,

Cancer genomics and transcriptomics have revolutionized our understanding of tumor biology, revealing the intricate molecular landscapes that drive cancer progression and response to therapy. This Special Issue, titled "Cancer Genomics and Transcriptomics: Uncovering New Frontiers in Tumor Biology", will showcase the latest advancements and emerging trends in these fields, providing a comprehensive overview of how genomic and transcriptomic analyses are reshaping cancer research and treatment. We will explore cutting-edge studies that leverage high-throughput sequencing technologies to dissect the genetic and transcriptomic alterations underpinning various cancer types. Key topics include understanding the functional roles of established oncogenes and tumor suppressor genes, the impacts of non-coding RNAs in cancer, and the influence of somatic mutations on tumor heterogeneity and drug resistance. Furthermore, we will highlight integrative strategies that merge genomics and transcriptomics with other omics data to unravel the complexities of tumor biology and enhance patient stratification. This Special Issue will also address the challenges and opportunities associated with translating genomic and transcriptomic discoveries into clinical practice. By bringing together contributions from leading researchers in the field, this Special Issue will provide insights into the latest methodologies, foster collaborative efforts, and stimulate future research directions. Ultimately, our goal is to advance the development of personalized cancer therapies and enhance our understanding of the molecular mechanisms driving cancer, paving the way for more effective and targeted treatment strategies.

Dr. Panagiotis Adamopoulos
Dr. Panagiotis Tsiakanikas
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 250 words) can be sent to the Editorial Office for assessment.

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. Life 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 2600 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.

Keywords

  • transcriptomic profiling
  • tumor heterogeneity
  • integrative omics
  • non-coding RNAs
  • oncogenes

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Published Papers (2 papers)

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Research

13 pages, 7366 KB  
Article
Dynamics of Postmortem Gene Expression in Normal and Neoplastic Murine Liver
by Evgeny E. Buyko, Ekaterina A. Perina, Danil S. Sobakin, Matvey M. Tsyganov, Dmitry V. Vasilchenko, Sergey V. Vtorushin, Alexander A. Ufandeev, Elena B. Diksas, Olga A. Kaidash, Ekaterina S. Hmelevskaya, Ekaterina V. Parochkina, Igor A. Popov, Vladimir V. Ivanov, Stanislav I. Pekov and Elena V. Udut
Life 2026, 16(4), 683; https://doi.org/10.3390/life16040683 - 16 Apr 2026
Viewed by 449
Abstract
The use of postmortem (autopsy) material in fundamental and applied biomedical research significantly facilitates the collection of biomaterial for statistically robust sample cohorts. However, natural adaptive processes to developing cellular stress in the early postmortem period, caused by oxygen and nutrient deprivation, trigger [...] Read more.
The use of postmortem (autopsy) material in fundamental and applied biomedical research significantly facilitates the collection of biomaterial for statistically robust sample cohorts. However, natural adaptive processes to developing cellular stress in the early postmortem period, caused by oxygen and nutrient deprivation, trigger the activation of numerous genes promoting cell survival under stress. Many of these activated pathways are also crucial for tumor cell survival in vivo, as evidenced by various transcriptomic studies. This study aimed to investigate the potential influence of postmortem interval (PMI) duration on gene expression in normal and tumor tissues. Using a model of chemically induced hepatocellular carcinoma in mouse liver, we comparatively analyzed the dynamics of transcript levels for several genes (BRCA1, BRCA2, CHEK1, CHEK2, ATM, CDK12) in paired samples of normal and tumor tissue over a 24-h PMI using RT-qPCR. In normal tissue, gene expression increased significantly, while tumor tissue demonstrated relative transcriptional stability, with no substantial changes in the studied transcript levels. A critical finding was the observed convergence of expression profiles: initial differences between the tissues were completely eliminated by 24 h PMI. This pattern developed despite formally adequate RNA quality (RQN) and the absence of clear signs of progressive autolysis in histology, indicating the insufficiency of standard quality criteria for detecting postmortem changes. These findings collectively underscore the critical importance of minimizing and controlling PMI during the biobanking of oncological samples for reliable transcriptomic research. Full article
(This article belongs to the Special Issue Cancer Genomics and Transcriptomics: Uncovering New Frontiers in Tumor Biology)
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15 pages, 612 KB  
Article
Inactivation of BAP1 and the Hippo Pathway Characterizes the Genomic Alterations of Peritoneal Mesothelioma
by Maya Samuels, Madi Williams, Angela Hasan, Susan Rafie, Grace S. Saglimbeni, Beau Hsia, Sunil Nair, Sweety Aeilias and Abubakar Tauseef
Life 2026, 16(3), 385; https://doi.org/10.3390/life16030385 - 28 Feb 2026
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Abstract
Background/Objectives: Peritoneal mesothelioma is a rare malignancy characterized by limited therapeutic options and a poor prognosis. Genomic characterization can enhance the understanding of the molecular mechanisms that lead to this disease and can contribute to improved survival outcomes through therapeutic targets. Methods: Analysis [...] Read more.
Background/Objectives: Peritoneal mesothelioma is a rare malignancy characterized by limited therapeutic options and a poor prognosis. Genomic characterization can enhance the understanding of the molecular mechanisms that lead to this disease and can contribute to improved survival outcomes through therapeutic targets. Methods: Analysis was performed using a dataset from the AACR GENIE database (v17.0-public) comprising 204 samples from 192 patients. Data were analyzed to identify patterns in genomic alterations and clinical demographics. Within the GENIE cohort, histologic subtype information was incomplete and inconsistently reported across contributing institutions. Hence, histological subtype genomic analysis was not viable. Results: The most common somatic mutation was found in the BAP1 gene (25.98%). Other common mutations were found in the NF2 (15.19%), TP53 (9.3%) and SETD2 (8.3%) genes. Several pathways were found as potential treatment targets including the chromatin remodeling, Hippo, and p53 signaling pathways. Given the size of our dataset, we were unable to draw significant conclusions about certain demographics. Conclusions: This study presents data that can help draw conclusions on common mutations, mutual exclusivity patterns, and demographics at risk for peritoneal mesothelioma. Genomic analysis of peritoneal mesothelioma may inform possible intervention targets for therapeutic treatment. Full article
(This article belongs to the Special Issue Cancer Genomics and Transcriptomics: Uncovering New Frontiers in Tumor Biology)
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