ArticleNPJ genomic medicine2021
Pan-cancer analysis of transcripts encoding novel open-reading frames (nORFs) and their potential biological functions.
Article in NPJ genomic medicine, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 49 citations in OpenAlex.
- Bioinformatic Tools for Non-bioinformaticians: A Roadmap to Study Unknown Microprotein Sequences.Methods in molecular biology (Clifton, N.J.) · 2026Article
- ECM-based molecular subtypes define prognostic, EMT status, and therapeutic diversity in IDH-mutant gliomas.NPJ precision oncology · 2025Article
- Eukaryotic Microproteins.Annual review of biochemistry · 2025Review
- Identification of Small Open Reading Frame-encoded Proteins in the Human Genome.Genomics, proteomics & bioinformatics · 2025Article
- Noncanonical microprotein regulation of immunity.Molecular therapy : the journal of the American Society of Gene Therapy · 2024Review
- Review
- Leveraging a disulfidptosis‑related lncRNAs signature for predicting the prognosis and immunotherapy of glioma.Cancer cell international · 2023Article
- Microproteins-Discovery, structure, and function.Proteomics · 2023Review
- What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome?Molecular & cellular proteomics : MCP · 2023Article
- Shining a light on the dark proteome: Non-canonical open reading frames and their encoded miniproteins as a new frontier in cancer biology.Protein science : a publication of the Protein Society · 2023Review
- Intrinsically disordered proteins and conformational noise: The hypothesis a decade later.iScience · 2023Review
- What can Ribo-seq and proteomics tell us about the non-canonical proteome?bioRxiv : the preprint server for biology · 2023Article
- Review
- Evolutionary origins and interactomes of human, young microproteins and small peptides translated from short open reading frames.Molecular cell · 2023Article
- Proteoforms expand the world of microproteins and short open reading frame-encoded peptides.iScience · 2023Review
- Proteogenomic Analysis of Breast Cancer Transcriptomic and Proteomic Data, Using De Novo Transcript Assembly: Genome-Wide Identification of Novel Peptides and Clinical Implications.Molecular & cellular proteomics : MCP · 2022Article
- Novel open reading frames in human accelerated regions and transposable elements reveal new leads to understand schizophrenia and bipolar disorder.Molecular psychiatry · 2022Article
- Prognostic Model and Nomogram Construction and Validation With an Autophagy-Related Gene Signature in Low-Grade Gliomas.Frontiers in genetics · 2022Article
- Unveiling a Ghost Proteome in the Glioblastoma Non-Coding RNAs.Frontiers in cell and developmental biology · 2021Review
- Evolutionary divergence of novel open reading frames in cichlids speciation.Scientific reports · 2020Article
Corrections and comments
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Authors and funding
17 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Uncharacterized and unannotated open-reading frames, which we refer to as novel open reading frames (nORFs), may sometimes encode peptides that remain unexplored for novel therapeutic opportunities. To our knowledge, no systematic identification and characterization of transcripts encoding nORFs or their translation products in cancer, or in any other physiological process has been performed. We use our curated nORFs database (nORFs.org), together with RNA-Seq data from The Cancer Genome Atlas (TCGA) and Genotype-Expression (GTEx) consortiums, to identify transcripts containing nORFs that are expressed frequently in cancer or matched normal tissue across 22 cancer types. We show nORFs are subject to extensive dysregulation at the transcript level in cancer tissue and that a small subset of nORFs are associated with overall patient survival, suggesting that nORFs may have prognostic value. We also show that nORF products can form protein-like structures with post-translational modifications. Finally, we perform in silico screening for inhibitors against nORF-encoded proteins that are disrupted in stomach and esophageal cancer, showing that they can potentially be targeted by inhibitors. We hope this work will guide and motivate future studies that perform in-depth characterization of nORF functions in cancer and other diseases.
Identifiers
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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.