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Data Science in Cancer Genomics and Precision Medicine: 2nd Edition

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

Deadline for manuscript submissions: 20 December 2025 | Viewed by 3121

Special Issue Editor

Special Issue Information

Dear Colleagues,

This is a continuation to our series on the hot topic of “Data Science in Cancer Genomics and Precision Medicine”. We have already published a successful Special Issue, receiving interesting contributions and stimulating discussions (https://www.mdpi.com/journal/ijms/special_issues/Genomics_Medicine).

Data science in cancer genomics represents a new interdisciplinary field that applies statistics and next-generation sequencing (NGS) technologies to understand alterations in the genome of cancer cells. The data generated by these technologies are often termed “multi-omics data” and can include information on DNA, RNA, proteins, and epigenetic modifications. The use of data science in cancer genomics allows us to better understand the molecular basis of different cancers and exploit this information to match each patient with the most appropriate molecular targeted therapy, widely known as “precision medicine”. While traditional chemotherapy and radiation treatments target cellular processes that are common to both healthy and cancerous cells, precision medicine specifically directs newly developed treatments to cancer cells based on their underlying molecular profile.

This Special Issue of the International Journal of Molecular Sciences focuses on the research field of cancer genomics and precision medicine and welcomes both original research articles and review papers that deal with the molecular mechanisms underlying modifications in human cancer cells.

Dr. Apostolos Zaravinos
Guest Editor

Manuscript Submission Information

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Keywords

  • cancer genomics
  • big data
  • tumor immunology
  • translational oncology
  • precision medicine
  • next-generation sequencing
  • omics
  • cancer genomic datasets

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Published Papers (2 papers)

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Research

18 pages, 1440 KB  
Article
Pathway-Specific Genomic Alterations in Pancreatic Cancer Across Populations at Risk
by Cecilia Monge, Brigette Waldrup, Francisco G. Carranza, Sophia Manjarrez and Enrique Velazquez-Villarreal
Int. J. Mol. Sci. 2025, 26(16), 7695; https://doi.org/10.3390/ijms26167695 - 8 Aug 2025
Viewed by 410
Abstract
Pancreatic cancer (PC) is a highly aggressive malignancy with increasing incidence and poor survival. Hispanic/Latino (H/L) patients, despite having a lower overall incidence than Non-Hispanic White (NHW) patients, are often diagnosed younger and at more advanced stages, leading to worse outcomes. The molecular [...] Read more.
Pancreatic cancer (PC) is a highly aggressive malignancy with increasing incidence and poor survival. Hispanic/Latino (H/L) patients, despite having a lower overall incidence than Non-Hispanic White (NHW) patients, are often diagnosed younger and at more advanced stages, leading to worse outcomes. The molecular mechanisms underlying these disparities remain unclear. This study characterizes mutations in key oncogenic pathways—TP53, WNT, PI3K, TGF-Beta, and RTK/RAS—among H/L and NHW patients using publicly available datasets. We analyzed genomic data from 4248 PC patients (407 H/L; 3841 NHW), comparing mutation frequencies across pathways. Chi-squared tests assessed group differences, and Kaplan–Meier analysis evaluated survival outcomes by pathway alterations. TGF-Beta pathway mutations were less common in H/L patients (18.4% vs. 24.4%, p = 8.6 × 10−3), with notable differences in SMAD2 (1.5% vs. 0.4%, p = 6.3 × 10−3) and SMAD4 (15% vs. 19.9%, p = 0.02). While overall differences in other pathways were not statistically significant, several genes showed borderline significance, including ERBB4, ALK, HRAS, RIT1 (RTK/RAS), and CTNNB1 (WNT). No significant survival differences were observed in H/L patients, but NHW patients with TP53 alterations showed borderline survival associations. This study reveals ethnicity-specific pathway alterations in PC, with SMAD2, ERBB4, ALK, and CTNNB1 mutations being more frequent in H/L patients, while SMAD4 and PI3K alterations had prognostic value in NHW patients. These findings indicate the importance of incorporating ethnicity-specific molecular profiling into precision oncology for PC. Full article
(This article belongs to the Special Issue Data Science in Cancer Genomics and Precision Medicine: 2nd Edition)
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27 pages, 12788 KB  
Article
A Multi-Omics Analysis of a Mitophagy-Related Signature in Pan-Cancer
by Nora Agir, Ilias Georgakopoulos-Soares and Apostolos Zaravinos
Int. J. Mol. Sci. 2025, 26(2), 448; https://doi.org/10.3390/ijms26020448 - 7 Jan 2025
Cited by 2 | Viewed by 1672
Abstract
Mitophagy, an essential process within cellular autophagy, has a critical role in regulating key cellular functions such as reproduction, metabolism, and apoptosis. Its involvement in tumor development is complex and influenced by the cellular environment. Here, we conduct a comprehensive analysis of a [...] Read more.
Mitophagy, an essential process within cellular autophagy, has a critical role in regulating key cellular functions such as reproduction, metabolism, and apoptosis. Its involvement in tumor development is complex and influenced by the cellular environment. Here, we conduct a comprehensive analysis of a mitophagy-related gene signature, composed of PRKN, PINK1, MAP1LC3A, SRC, BNIP3L, BECN1, and OPTN, across various cancer types, revealing significant differential expression patterns associated with molecular subtypes, stages, and patient outcomes. Pathway analysis revealed a complex interplay between the expression of the signature and potential effects on the activity of various cancer-related pathways in pan-cancer. Immune infiltration analysis linked the mitophagy signature with certain immune cell types, particularly OPTN with immune infiltration in melanoma. Methylation patterns correlated with gene expression and immune infiltration. Mutation analysis also showed frequent alterations in PRKN (34%), OPTN (21%), PINK1 (28%), and SRC (15%), with implications for the tumor microenvironment. We also found various correlations between the expression of the mitophagy-related genes and sensitivity in different drugs, suggesting that targeting this signature could improve therapy efficacy. Overall, our findings underscore the importance of mitophagy in cancer biology and drug resistance, as well as its potential for informing treatment strategies. Full article
(This article belongs to the Special Issue Data Science in Cancer Genomics and Precision Medicine: 2nd Edition)
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