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| Status |
Public on Jan 30, 2023 |
| Title |
RNA-seq profiling of salivary transcriptome reveals potential diagnostic RNAs and oral microbial dysbiosis in oral squamous cell carcinoma |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
Background:
The differential abundance of cell-free RNAs in bodily fluids is emerging as a promising tool for the non-invasive molecular diagnosis of cancer. Human saliva is considered a promising source of non-invasive biomarkers of diagnostic value for oral cancer detection. This study aims to identify diagnostic potent salivary RNAs in oral squamous cell carcinoma (OSCC)-patients by RNA-Sequencing.
Method:
Unstimulated saliva was collected from 5 normal control (NC) individuals and 9 OSCC patients (PS) with prior consent and ethical committee approvals. Total RNA isolated from cell-free saliva (CFS) supernatant was used to prepare small RNA libraries and sequenced on the Ion Torrent S5 platform. The sequencing reads were aligned to the human genome (hg19) using Bowtie 2, and the differential expression analysis was performed using RUVSeq and DESeq2. Mapped reads were screened across miRBase (v22) annotations for miRNAs and Gencode (v19) annotation for other RNAs. Reads were quantified by the Featurecount (v1.4.6) module of the R-package. The microbial-RNA enrichment analysis was determined using the One Codex platform.
Result:
RNA-sequencing detected protein-coding transcripts (PCTs), long-intergenic RNAs (lincRNAs), microRNAs (miRNAs), small nuclear RNAs (snRNAs), transfer RNAs (tRNAs) and pseudogenes from the saliva of PS and HC samples. Transcriptome analyses revealed 89 PCTs, 18 lincRNAs and 6 miRNAs differentially expressed between PS and HC with a log2fold change ≥ 1 or ≤ -1 and p-value < 0.05. Gene ontology and pathway enrichment analyses indicated a significant correlation of the identified PCTs and miRNAs to various cancer-related pathways that may have implications in the pathogenesis of OSCC. Interestingly, unmapped non-human reads aligned to the microbial reference genomes. Further analyses of these microbial sequence reads revealed a significant microbial dysbiosis differentiating PS from HC. Metabolic pathways and functional analysis of the identified microbial phylotypes showed gene ontologies associated with inflammation, cell proliferation, ROS generation, and a range of metabolic processes.
Conclusion:
We report novel panels of differentially expressed PCTs, miRNAs and lincRNAs distinguishing PS from HC. Importantly, our results also provide evidence for oral microbial dysbiosis that appears to have pathological implications in OSCC. Summarily, this study provides a comprehensive landscape of salivary RNAs that can be exploited as non-invasive biomarkers for OSCC detection.
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| Overall design |
Cell free salivary transcriptome profiling among 5 normal controls and 9 oral squamous cell carcinoma patients.
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| Contributor(s) |
Saproo S, Ahuja G, Sarkar SS, Dass G, Konyak CW, Tayal J, Mehta A, Naidu S, Gautam V |
| Citation(s) |
36703917 |
| Submission date |
Jun 03, 2021 |
| Last update date |
Jan 31, 2023 |
| Contact name |
srivatsava naidu |
| E-mail(s) |
srivatsava.naidu@iitrpr.ac.in
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| Organization name |
indian institute of technology ropar
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| Department |
biomedical engineering
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| Lab |
non-coding RNAs lab
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| Street address |
bhara phool
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| City |
ropar |
| State/province |
punjab |
| ZIP/Postal code |
140001 |
| Country |
India |
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| Platforms (1) |
| GPL17303 |
Ion Torrent Proton (Homo sapiens) |
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| Samples (28)
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| Relations |
| BioProject |
PRJNA734811 |
| SRA |
SRP322426 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE176077_LincRNA_matrix_file.txt.gz |
40.1 Kb |
(ftp)(http) |
TXT |
| GSE176077_One_Codex_PS_Results.xlsx |
2.1 Mb |
(ftp)(http) |
XLSX |
| GSE176077_One_Codex_Results_HC.xlsx |
56.0 Kb |
(ftp)(http) |
XLSX |
| GSE176077_Protein_coding_matrix_file.txt.gz |
160.3 Kb |
(ftp)(http) |
TXT |
| GSE176077_Total_transcripts_matrix_file.txt.gz |
306.1 Kb |
(ftp)(http) |
TXT |
| GSE176077_miRNA_matrix_file.txt.gz |
18.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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