Accurate annotation of human protein-coding small open reading frames

Martínez, Thomas F.; Chu, Qian; Donaldson, Cynthia J.; Tan, Dan; Shokhirev, Maxim N.; Saghatelian, Alan

doi:10.1038/s41589-019-0425-0

Cited by 175 publications

(255 citation statements)

References 62 publications

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“…Our extensive MHC-I immunopeptidome proteomics analysis allowed us to validate that nuORFs are translated and presented, and provided ground truth for improving prediction quality. The >6,000 nuORF peptides we identified with stringent criteria as presented on MHC I, have similar biochemical and biophysical characteristics to peptides derived from annotated proteins, and dramatically expand the number of nuORFs detected by mass spectrometry Martinez et al 2019;Ma et al 2016Ma et al , 2014, particularly in primary cancer samples. As 50.6% of nuORFs were detected in more than one MS sample, they are recurrently translated and MHC Ipresented, with identical peptide sequences frequently detected in patient-derived cancer cell lines and in B721.221 mono-allelic cells expressing matching alleles, highlighting the robustness of nuORF prediction and the dependency of MHC I presentation on the HLA allele expressed in a given sample.…”

Section: Discussionmentioning

confidence: 77%

“…These nuORFs are derived from the 5' and 3' untranslated regions (UTRs), overlapping yet outof-frame alternative ORFs in annotated protein-coding genes, long non-coding RNAs (lncRNAs), pseudogenes and other transcripts currently annotated as non-protein coding (Fields et al 2015;Chew et al 2013). Ribo-seq analysis of HEK293T, HeLa-S3, and K562 cell lines and of human fibroblasts infected with HSV-1 and HCMV has identified translated nuORFs that contribute peptides to the MHC I immunopeptidome, suggesting that nuORFs could also have an immunological function Martinez et al 2019). However, a global understanding of the extent to which nuORFs contribute to the immunopeptidomes of healthy and cancer tissues, as well as the diversity and tissue specificity of nuORFs is still lacking.…”

Section: Introductionmentioning

confidence: 99%

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Thousands of novel unannotated proteins expand the MHC I immunopeptidome in cancer

Ouspenskaia

Law

Clauser

et al. 2020

Preprint

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Tumor epitopes -peptides that are presented on surface-bound MHC I proteins -provide targets for cancer immunotherapy and have been identified extensively in the annotated protein-coding regions of the genome. Motivated by the recent discovery of translated novel unannotated open reading frames (nuORFs) using ribosome profiling (Ribo-seq), we hypothesized that cancer-associated processes could generate nuORFs that can serve as a new source of tumor antigens that harbor somatic mutations or show tumor-specific expression. To identify cancer-specific nuORFs, we generated Ribo-seq profiles for 29 malignant and healthy samples, developed a sensitive analytic approach for hierarchical ORF prediction, and constructed a high-confidence database of translated nuORFs across tissues. Peptides from 3,555 unique translated nuORFs were presented on MHC I, based on analysis of an extensive dataset of MHC I-bound peptides detected by mass spectrometry, with >20-fold more nuORF peptides detected in the MHC I immunopeptidomes compared to whole proteomes. We further detected somatic mutations in nuORFs of cancer samples and identified nuORFs with tumor-specific translation in melanoma, chronic lymphocytic leukemia and glioblastoma. NuORFs thus expand the pool of MHC I-presented, tumorspecific peptides, targetable by immunotherapies.

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Section: Discussionmentioning

confidence: 77%

Section: Introductionmentioning

confidence: 99%

Thousands of novel unannotated proteins expand the MHC I immunopeptidome in cancer

Ouspenskaia

Law

Clauser

et al. 2020

Preprint

View full text Add to dashboard Cite

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“…Studies using microarrays, such as the IMI MARCAR Project [22] and Microarray Innovations in Leukemia (MILE) [23], have made great contributions to medical researches. We collected 617462 unique smORFs from SmProt [8], sORFs.org [7] and the study by Thomas et al [9]. Using probe reannotation, we remaped the probes of microarrays to smORFs and estimated smORF RNA expressions (Fig.…”

Section: Smorf Rna Quanti Cation Based On Microarraymentioning

confidence: 99%

“…The CEL les were processed using R package oligo (v1.48.0) [40] and ff (v2. [2][3][4][5][6][7][8][9][10][11][12][13][14]. Package ff was used with default parameters.…”

Section: Microarray Data Processingmentioning

confidence: 99%

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smORFunction: A Tool for Predicting Functions of Small Open Reading Frames and Microproteins

Cui

2020

Preprint

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Background Small open reading frame (smORF) is open reading frame with a length of less than 100 codons. Microproteins, translated from smORFs, have been found to participate in a variety of biological processes such as muscle formation and contraction, cell proliferation, and immune activation. Although previous studies have collected and annotated a large abundance of smORFs, functions of the vast majority of smORFs are still unknown. It is thus increasingly important to develop computational methods to annotate the functions of these smORFs. Results In this study, we collected 617,462 unique smORFs from three studies. The expression of smORF RNAs was estimated by reannotated microarray probes. Using a speed-optimized correlation algorism, the functions of smORFs were predicted by their correlated genes with known functional annotations. After applying our method to 5 known microproteins from literatures, our method successfully predicted their functions. Further validation from the UniProt database showed that at least one function of 202 out of 270 microproteins was predicted. Conclusions We developed a method, smORFunction, to provide function predictions of smORFs/microproteins in at most 265 models generated from 173 datasets, including 48 tissues/cells, 82 diseases (and normal). The tool can be available at http://www.cuilab.cn/smorfunction.

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The Small Open Reading Frame‐Encoded Peptides: Advances in Methodologies and Functional Studies

et al. 2021

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Small open reading frames (sORFs) are an important class of genes with less than 100 codons. They were historically annotated as noncoding or even junk sequences. In recent years, accumulating evidence suggests that sORFs could encode a considerable number of polypeptides, many of which play important roles in both physiology and disease pathology. However, it has been technically challenging to directly detect sORF‐encoded peptides (SEPs). Here, we discuss the latest advances in methodologies for identifying SEPs with mass spectrometry, as well as the progress on functional studies of SEPs.

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Accurate annotation of human protein-coding small open reading frames

Cited by 175 publications

References 62 publications

Thousands of novel unannotated proteins expand the MHC I immunopeptidome in cancer

Thousands of novel unannotated proteins expand the MHC I immunopeptidome in cancer

smORFunction: A Tool for Predicting Functions of Small Open Reading Frames and Microproteins

The Small Open Reading Frame‐Encoded Peptides: Advances in Methodologies and Functional Studies

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