ArticleCancer research2024
Transcriptomic Profiling of Plasma Extracellular Vesicles Enables Reliable Annotation of the Cancer-Specific Transcriptome and Molecular Subtype.
Article in Cancer research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers, 1 of them a synthesis that pooled it.
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Who cites it
14 citing papers in PubMed, 1 synthesis or guideline pooled it, 17 citations in OpenAlex.
- Deep representation learning for temporal inference in cancer omics: a systematic literature review.Briefings in bioinformatics · 2026Pooled it
- Phase 1/2 trial of encorafenib, cetuximab, and nivolumab in microsatellite stable BRAFCancer cell · 2025Trial
- Neoantigen Targeting as a Novel Approach for Therapy-Resistant Tumors.Molecular diagnosis & therapy · 2026Review
- Artificial intelligence models: transforming early diagnosis and precise treatment of gastrointestinal cancers.Molecular cancer · 2026Review
- Deconvolution Methods to Link Multi-Omics Data to Cell Type-Specific Extracellular Vesicle Abundances.Proteomics · 2026Review
- Extracellular vesicle biomarkers: current status and future perspectives as novel tools in liquid biopsy.Frontiers in immunology · 2026Review
- Harnessing plasma transcriptomics for non-invasive cancer biomarker identification: a comprehensive review.Discover oncology · 2025Review
- Toward Precision Chemotherapy for Pancreatic Cancer Guided by Transcriptomic Signatures.United European gastroenterology journal · 2025Review
- Early cancer diagnosisWorld journal of gastrointestinal oncology · 2025Article
- Evaluation of Exosome-derived Small RNAs as Potential Biomarkers for Pancreatic Ductal Adenocarcinoma Using Next-generation Sequencing.Annals of laboratory medicine · 2025Article
- Tumor heterogeneity in retinoblastoma: a literature review.Cancer metastasis reviews · 2025Review
- Transcriptomic analysis of circulating extracellular vesicles during the perioperative period of Fontan and Glenn surgery.NPJ cardiovascular health · 2024Article
- Review
- Mechanisms of Resistance to Oncogenic KRAS Inhibition in Pancreatic Cancer.Cancer discovery · 2024Article
Corrections and comments
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Authors and funding
18 authors at 3 institutions in 1 country.
Funding
Abstract
Longitudinal monitoring of patients with advanced cancers is crucial to evaluate both disease burden and treatment response. Current liquid biopsy approaches mostly rely on the detection of DNA-based biomarkers. However, plasma RNA analysis can unleash tremendous opportunities for tumor state interrogation and molecular subtyping. Through the application of deep learning algorithms to the deconvolved transcriptomes of RNA within plasma extracellular vesicles (evRNA), we successfully predicted consensus molecular subtypes in patients with metastatic colorectal cancer. Analysis of plasma evRNA also enabled monitoring of changes in transcriptomic subtype under treatment selection pressure and identification of molecular pathways associated with recurrence. This approach also revealed expressed gene fusions and neoepitopes from evRNA. These results demonstrate the feasibility of using transcriptomic-based liquid biopsy platforms for precision oncology approaches, spanning from the longitudinal monitoring of tumor subtype changes to the identification of expressed fusions and neoantigens as cancer-specific therapeutic targets, sans the need for tissue-based sampling. SIGNIFICANCE: The development of an approach to interrogate molecular subtypes, cancer-associated pathways, and differentially expressed genes through RNA sequencing of plasma extracellular vesicles lays the foundation for liquid biopsy-based longitudinal monitoring of patient tumor transcriptomes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.