ArticleProceedings of the National Academy of Sciences of the United States of America2015
Systematic transcriptome analysis reveals tumor-specific isoforms for ovarian cancer diagnosis and therapy.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed, 74 citations in OpenAlex.
- Use of comprehensive genomic profiling to direct point-of-care management of patients with gynecologic cancers.Gynecologic oncology · 2016Trial
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- FGFRL1: Structure, Molecular Function, and Involvement in Human Disease.Current issues in molecular biology · 2025Review
- Rubidium ions as a novel therapeutic approach for glioblastoma.Scientific reports · 2025Article
- Deciphering FOXM1 regulation: implications for stemness and metabolic adaptations in glioblastoma.Medical oncology (Northwood, London, England) · 2025Article
- CanISO: a database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris).BMC genomics · 2023Article
- RNA-Based Strategies for Cancer Therapy: In Silico Design and Evaluation of ASOs for Targeted Exon Skipping.International journal of molecular sciences · 2023Article
- Integrative analysis of histone acetyltransferase KAT2A in human cancer.Cancer biomarkers : section A of Disease markers · 2023Article
- RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing.Genome biology · 2022Article
- Comprehensive characterization of the alternative splicing landscape in ovarian cancer reveals novel events associated with tumor-immune microenvironment.Bioscience reports · 2022Article
- An integrated brain-specific network identifies genes associated with neuropathologic and clinical traits of Alzheimer's disease.Briefings in bioinformatics · 2022Article
- Predicting the Lung Adenocarcinoma and Its Biomarkers by Integrating Gene Expression and DNA Methylation Data.Frontiers in genetics · 2022Article
- FOXM1: A Multifunctional Oncoprotein and Emerging Therapeutic Target in Ovarian Cancer.Cancers · 2021Review
- Multimodal detection of protein isoforms and nucleic acids from low starting cell numbers.Lab on a chip · 2021Article
- Tubulin Beta 2C Chain (TBB2C), a Potential Marker of Ovarian Cancer, an Insight from Ovarian Cancer Proteome Profile.ACS omega · 2021Article
- Identification and Analysis of An Epigenetically Regulated Five-lncRNA Signature Associated With Outcome and Chemotherapy Response in Ovarian Cancer.Frontiers in cell and developmental biology · 2021Article
- Characterization of the Potential Role of NTPCR in Epithelial Ovarian Cancer by Integrating Transcriptomic and Metabolomic Analysis.Frontiers in genetics · 2021Article
- An AFM-Based Nanomechanical Study of Ovarian Tissues with Pathological Conditions.International journal of nanomedicine · 2020Article
- Identification of a Sixteen-gene Prognostic Biomarker for Lung Adenocarcinoma Using a Machine Learning Method.Journal of Cancer · 2020Article
- scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data.Genome biology · 2019Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
Tumor-specific molecules are needed across diverse areas of oncology for use in early detection, diagnosis, prognosis and therapy. Large and growing public databases of transcriptome sequencing data (RNA-seq) derived from tumors and normal tissues hold the potential of yielding tumor-specific molecules, but because the data are new they have not been fully explored for this purpose. We have developed custom bioinformatic algorithms and used them with 296 high-grade serous ovarian (HGS-OvCa) tumor and 1,839 normal RNA-seq datasets to identify mRNA isoforms with tumor-specific expression. We rank prioritized isoforms by likelihood of being expressed in HGS-OvCa tumors and not in normal tissues and analyzed 671 top-ranked isoforms by high-throughput RT-qPCR. Six of these isoforms were expressed in a majority of the 12 tumors examined but not in 18 normal tissues. An additional 11 were expressed in most tumors and only one normal tissue, which in most cases was fallopian or colon. Of the 671 isoforms, the topmost 5% (n = 33) ranked based on having tumor-specific or highly restricted normal tissue expression by RT-qPCR analysis are enriched for oncogenic, stem cell/cancer stem cell, and early development loci--including ETV4, FOXM1, LSR, CD9, RAB11FIP4, and FGFRL1. Many of the 33 isoforms are predicted to encode proteins with unique amino acid sequences, which would allow them to be specifically targeted for one or more therapeutic strategies--including monoclonal antibodies and T-cell-based vaccines. The systematic process described herein is readily and rapidly applicable to the more than 30 additional tumor types for which sufficient amounts of RNA-seq already exist.
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