ArticleLife science alliance2019
Reference-free transcriptome exploration reveals novel RNAs for prostate cancer diagnosis.
Article in Life science alliance, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 26 citations in OpenAlex.
- PROCA11 early activation fuels prostate cancer neuroendocrine traits by regulating cell survival and migration.iScience · 2025Article
- Reference-free RNA profiling predicts triple negative breast cancer chemoresistance to neoadjuvant treatment.NAR cancer · 2025Article
- RAD51-AS1 inhibits the migration and invasion of prostate cancer cells by up-regulating RARA to activate ZYX transcription.Discover oncology · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- Highly sensitive deep panel sequencing of 27 HPV genotypes in prostate cancer biopsies results in very low detection rates and indicates that HPV is not a major etiological driver of this malignancy.Infectious agents and cancer · 2024Article
- An Atlas of Accessible Chromatin in Advanced Prostate Cancer Reveals the Epigenetic Evolution during Tumor Progression.Cancer research · 2024Article
- Integrative analysis of ultra-deep RNA-seq reveals alternative promoter usage as a mechanism of activating oncogenic programmes during prostate cancer progression.Nature cell biology · 2024Article
- Exploring the enigma: history, present, and future of long non-coding RNAs in cancer.Discover oncology · 2024Review
- The Genomic and Epigenomic Landscape of Double-Negative Metastatic Prostate Cancer.Cancer research · 2023Article
- Pro-tumorigenic role of lnc-ZNF30-3 as a sponge counteracting miR-145-5p in prostate cancer.Biology direct · 2023Article
- RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing.Genome biology · 2022Article
- Urinary extracellular vesicles contain mature transcriptome enriched in circular and long noncoding RNAs with functional significance in prostate cancer.Journal of extracellular vesicles · 2022Article
- Overexpression of Nucleolin and Associated Genes in Prostate Cancer.International journal of molecular sciences · 2022Article
- Microbiota of the prostate tumor environment investigated by whole-transcriptome profiling.Genome medicine · 2022Article
- Article
- Long non-coding RNA FER1L4 inhibits prostate cancer progression via sponging miR-92a-3p and upregulation of FBXW7.Cancer cell international · 2020Article
- A Gleason score-related outcome model for human prostate cancer: a comprehensive study based on weighted gene co-expression network analysis.Cancer cell international · 2020Article
Corrections and comments
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Authors and funding
14 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The use of RNA-sequencing technologies held a promise of improved diagnostic tools based on comprehensive transcript sets. However, mining human transcriptome data for disease biomarkers in clinical specimens are restricted by the limited power of conventional reference-based protocols relying on unique and annotated transcripts. Here, we implemented a blind reference-free computational protocol, DE-kupl, to infer yet unreferenced RNA variations from total stranded RNA-sequencing datasets of tissue origin. As a bench test, this protocol was powered for detection of RNA subsequences embedded into putative long noncoding (lnc)RNAs expressed in prostate cancer. Through filtering of 1,179 candidates, we defined 21 lncRNAs that were further validated by NanoString for robust tumor-specific expression in 144 tissue specimens. Predictive modeling yielded a restricted probe panel enabling more than 90% of true-positive detections of cancer in an independent The Cancer Genome Atlas cohort. Remarkably, this clinical signature made of only nine unannotated lncRNAs largely outperformed PCA3, the only used prostate cancer lncRNA biomarker, in detection of high-risk tumors. This modular workflow is highly sensitive and can be applied to any pathology or clinical application.
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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.