Discovery of potential biomarkers in oral squamous cell carcinoma using next generation sequencing and proteomic technologies / Jesinda Pauline Kerishnan
Oral cancer patients have one of the lowest survival rates in the world due to its poor prognosis. Early detection and diagnosis using more reliable biomarkers will improve the current survival rate of OSCC patients. The present study aims to identify potential molecular biomarkers associated to...
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| Format: | Thesis |
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2018
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| Online Access: | http://studentsrepo.um.edu.my/10332/ http://studentsrepo.um.edu.my/10332/4/jesinda.pdf |
| Summary: | Oral cancer patients have one of the lowest survival rates in the world due to its
poor prognosis. Early detection and diagnosis using more reliable biomarkers will
improve the current survival rate of OSCC patients. The present study aims to identify
potential molecular biomarkers associated to OSCC using a combination of genomics
and proteomics technologies. First, the demographic characteristics of patients were
analysed to identify and determine the suitable cohort for this study. Demographic study
of 208 OSCC patients and 134 non-OSCC controls confirmed that the local female
Indian community that practices betel quid chewing is at the highest risk of developing
OSCC and past exposure to HPV16 infection could contribute to the onset of OSCC. To
identify potential OSCC biomarkers, 12 pairs of gDNA from OSCC and its adjacent
non-malignant tissues were subjected to exome sequencing. The sequencing analysis
identified 50 somatically mutated genes in OSCC of which CASP8, USP40, NOTCH1,
and COL11A1 were further evaluated as candidate biomarkers. These 4 genes were
previously reported in various cancers including the head and neck cancer. However,
the exact association of USP40 and COL11A1 mutations in OSCC were not fully
described. Most of the SNVs identified in these genes were found to be novel in OSCC
and were characterized as deleterious. Finally, genotyping of the candidate genes using
Fluidigm SNP Genotyping in a larger population of 167 OSCC patients successfully
identified USP40 as a promising biomarker for OSCC. In the proteomic study, sera of
25 OSCC patients and 25 healthy controls were subjected to 2-DE and Western blotting,
whereas 6 pairs of extracted proteins from OSCC and its adjacent non-malignant tissues
were subjected to label free LC-MS. A total of 27 differently expressed proteins in
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OSCC were identified. Among these proteins; LRG, A1BG, PRO2044, ACTBM, HBB,
CRNS1, HBA, F8WAH6 and SCND3 were found to be uniquely expressed in OSCC
when compared with other cancers. These proteins may have the potential as specific
biomarkers for OSCC. SYNE1 (Nesprin-1) was the only biomarker identified by both
genomic and proteomic approach. Lastly, functional enrichment and pathway analysis
were also performed on these 77 potential biomarkers using ConsensusPathDB, DAVID
v6.8 and STRING v10.1 to elucidate the biological function and pathways associated
with OSCC. Based on these analyses, the most significant biological function of these
biomarkers in OSCC was its involvement with exosomes in the extracellular region.
Whereas, the most significant pathway identified was the platelet activation, signalling
and aggregation pathway. Findings from both the biological function and pathway
analysis indicate that the identified biomarkers play an important role in cancer
metastasis. In summary, the study had successfully identified a combination of 13 novel
potential biomarkers and further improved our current understanding on the biological
functions and pathways associated with OSCC. However, further studies are required to
validate these biomarkers in a larger cohort and to fully understand the role of these
biomarkers in OSCC. |
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