Harnessing the tissue and plasma lncRNA-peptidome to discover peptide-based cancer biomarkers

Proteome-centric studies, although have identified numerous lncRNA-encoded polypeptides, lack differential expression analysis of lncRNA-peptidome across primary tissues, cell lines and cancer states. We established a computational-proteogenomic workflow involving re-processing of publicly available...

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Bibliographic Details
Published in:Scientific reports 2019-08, Vol.9 (1), p.12322-17, Article 12322
Main Authors: Chakraborty, Sajib, Andrieux, Geoffroy, Hasan, A. M. Mahmudul, Ahmed, Musaddeque, Hosen, Md. Ismail, Rahman, Tania, Hossain, M. Anwar, Boerries, Melanie
Format: Article
Language:English
Subjects:
631/114/1314
631/114/2784
631/67/2195
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Adenocarcinoma
Adenocarcinoma - blood
Adenocarcinoma - genetics
Biomarkers
Biomarkers, Tumor - blood
Biomarkers, Tumor - genetics
Cancer
Cell Line
Colon
Colonic Neoplasms - blood
Colonic Neoplasms - genetics
Computer applications
Epithelium
Humanities and Social Sciences
Humans
Male
multidisciplinary
Neoplasms - blood
Neoplasms - genetics
Organ Specificity
Peptides
Peptides - blood
Plasma
Polypeptides
Prognosis
Prostate cancer
Prostatic Neoplasms - blood
Prostatic Neoplasms - genetics
Proteogenomics
Proteome - metabolism
Proteomes
RNA, Long Noncoding - blood
Science
Science (multidisciplinary)
Tissues
Tumor cell lines
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Summary:Proteome-centric studies, although have identified numerous lncRNA-encoded polypeptides, lack differential expression analysis of lncRNA-peptidome across primary tissues, cell lines and cancer states. We established a computational-proteogenomic workflow involving re-processing of publicly available LC-MS/MS data, which facilitated the identification of tissue-specific and universally expressed (UExp) lncRNA-polypeptides across 14 primary human tissues and 11 cell lines. The utility of lncRNA-peptidome as cancer-biomarkers was investigated by re-processing LC-MS/MS data from 92 colon-adenocarcinoma (COAD) and 30 normal colon-epithelium tissues. Intriguingly, a significant upregulation of five lncRNA UExp-polypeptides in COAD tissues was observed. Furthermore, clustering of the UExp-polypeptides led to the classification of COAD patients that coincided with the clinical stratification, underlining the prognostic potential of the UExp-polypeptides. Lastly, we identified differential abundance of the UExp-polypeptides in the plasma of prostate-cancer patients highlighting their potential as plasma-biomarker. The analysis of lncRNA-peptidome may pave the way to identify effective tissue/plasma biomarkers for different cancer types.
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-019-48774-1