دورية أكاديمية
أعرض في EDS

Independent transcriptional patterns reveal biological processes associated with disease-free survival in early colorectal cancer.

التفاصيل البيبلوغرافية
العنوان: Independent transcriptional patterns reveal biological processes associated with disease-free survival in early colorectal cancer.
المؤلفون: Knapen DG; Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands., Hone Lopez S; Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands., de Groot DJA; Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands., de Haan JJ; Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands., de Vries EGE; Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands., Dienstmann R; Oncology Data Science (ODysSey) Group, Vall d'Hebron Institute of Oncology, Universitat Autónoma de Barcelona, Barcelona, Spain., de Jong S; Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands., Bhattacharya A; Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands., Fehrmann RSN; Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands. r.s.n.fehrmann@umcg.nl.
المصدر: Communications medicine [Commun Med (Lond)] 2024 May 03; Vol. 4 (1), pp. 79. Date of Electronic Publication: 2024 May 03.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Nature Portfolio Country of Publication: England NLM ID: 9918250414506676 Publication Model: Electronic Cited Medium: Internet ISSN: 2730-664X (Electronic) Linking ISSN: 2730664X NLM ISO Abbreviation: Commun Med (Lond) Subsets: PubMed not MEDLINE
أسماء مطبوعة: Original Publication: [London] : Nature Portfolio, [2021]-
مستخلص: Background: Bulk transcriptional profiles of early colorectal cancer (CRC) can fail to detect biological processes associated with disease-free survival (DFS) if the transcriptional patterns are subtle and/or obscured by other processes' patterns. Consensus-independent component analysis (c-ICA) can dissect such transcriptomes into statistically independent transcriptional components (TCs), capturing both pronounced and subtle biological processes.
Methods: In this study we (1) integrated transcriptomes (n = 4228) from multiple early CRC studies, (2) performed c-ICA to define the TC landscape within this integrated data set, 3) determined the biological processes captured by these TCs, (4) performed Cox regression to identify DFS-associated TCs, (5) performed random survival forest (RSF) analyses with activity of DFS-associated TCs as classifiers to identify subgroups of patients, and 6) performed a sensitivity analysis to determine the robustness of our results RESULTS: We identify 191 TCs, 43 of which are associated with DFS, revealing transcriptional diversity among DFS-associated biological processes. A prominent example is the epithelial-mesenchymal transition (EMT), for which we identify an association with nine independent DFS-associated TCs, each with coordinated upregulation or downregulation of various sets of genes.
Conclusions: This finding indicates that early CRC may have nine distinct routes to achieve EMT, each requiring a specific peri-operative treatment strategy. Finally, we stratify patients into DFS patient subgroups with distinct transcriptional patterns associated with stage 2 and stage 3 CRC.
(© 2024. The Author(s).)
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فهرسة مساهمة: Local Abstract: [plain-language-summary] While treatments for patients with colorectal cancer have improved, many patients (around 30-50%) have cancers that will eventually relapse and these patients will die due to their disease. Researchers have been studying the genes involved in colorectal cancer to help us understand why some cancers might relapse. However, current methods to do this may miss subtle or hidden patterns in the gene activity related to cancer relapse. To deal with this, we used a special method called consensus-independent component analysis (c-ICA) to dig more deeply into the activity of genes. This helped us to uncover some potential biological processes underpinning colorectal cancer relapse, which ultimately could help researchers to identify better treatments for patients with colorectal cancer.
تواريخ الأحداث: Date Created: 20240503 Latest Revision: 20240507
رمز التحديث: 20240507
مُعرف محوري في PubMed: PMC11068726
DOI: 10.1038/s43856-024-00504-z
PMID: 38702451
قاعدة البيانات: MEDLINE
الوصف
تدمد:2730-664X
DOI:10.1038/s43856-024-00504-z