Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Chakraborty S

PROVIDER: S-EPMC6707329 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

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

Chakraborty Sajib S Andrieux Geoffroy G Hasan A M Mahmudul AMM Ahmed Musaddeque M Hosen Md Ismail MI Rahman Tania T Hossain M Anwar MA Boerries Melanie M

Scientific reports 20190823 1

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-pe ...[more]

PMID: 31444383

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Project description:Long non-coding RNAs (lncRNA) play critical roles in pathogenesis of neurodegenerative diseases. Human plasma carries lncRNAs that are stable in the blood, and their disease-specific profile have made them valuable biomarkers for some diseases. This study reports screening of the plasma levels of 90 lncRNAs in patients with Alzheimer disease (AD) to find out plasma-based AD biomarkers. Total RNA was isolated from plasma samples of 50 AD and 50 matched healthy controls. The plasma samples of 10 advanced AD patients and 10 matched healthy controls were screened for expression levels of 90 lncRNAs using Human LncRNA Profiler qPCR Array Kit (SBI). Based on the profiling results, lncRNAs BC200, NDM29, NEAT1, FAS-AS1 and GAS5-AS1 were selected for further analysis in all samples and their biomarker potency was evaluated by ROC curve analysis. We further surveyed RNAseq data by in silico analysis. We found that the NEAT1 and BC200 levels in the plasma of the AD patients were significantly higher compared with the control group (P=0.0021, p= 0.02, respectively). ROC curve analysis showed that the plasma level of NEAT1 and BC200 discriminated AD patients from healthy controls with sensitivity of 72 % and 60 %, and specificity of 84 % and 91 % respectively. Moreover, NEAT1 discriminated MCI (60 % sensitivity and 91 % specificity) and advanced-AD patients from healthy controls (73 % sensitivity and 71 % specificity). Besides, plasma level of BC200 discriminated the pre-clinical subjects from healthy controls with 83 % sensitivity and 66 % specificity. A positive correlation was also observed between plasma levels of BC200 with the age patients (r = 0.34, p=0.02). In silico RNAseq data analysis showed that a total of 33 lncRNAs were up-regulated but 13 lncRNAs were down-regulated significantly in AD patients compared with the healthy controls. In conclusion, this study elucidated that the plasma levels of lncRNAs NEAT1 and BC200 might be considered as potential blood-based biomarkers for AD development and progression.

Dataset Information

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

Publications

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

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