Document Details
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Document Type |
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Thesis |
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Document Title |
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GENETIC AND EPIGENETIC SIGNATURES IN SQUAMOUS CELL CARCINOMAS OF THE HEAD AND NECK السمات الجينية واللاجينية للسرطانات التي تنشأ من الخلايا الحرشفية المبطنة لأجزاء الرأس والرقبة |
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Subject |
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Faculty of Sciences |
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Document Language |
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Arabic |
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Abstract |
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Background: In the last few years there has been a growing awareness of squamous cell carcinomas of the head and neck (HNSCC). Worldwide, the HNSCC ranks among the top ten cancers for both mortality and morbidity, affecting around 650,000 new patients each year. In Saudi Arabia, estimated annual numbers of new cancer cases were 39 males and 32 females. Despite the efficiency of therapeutic regimens to treat such disease, significant morbidity remains unacceptably high. Furthermore, compared to cancers of the breast and colon, HNSCC remains less well studied worldwide. Biomarkers for the disease are lacking or remain to be validated across ethnic groups. Therefore, Detection of DNA promoter methylation and genetic mutations in HNSCC Saudi patients from Saudi Arabia adds to the search of is promising biomarkers for early stage cancer detection and cancer progression that may lead to improved treatment outcomes.
Objective: The aim of this study is to profile the genetic and epigenetic alterations in HNSCC patients, also to determine the prevalence of the human papilloma viruses (HPV) and correlate their detection with patients’ clinicopathological parameters as well as to investigate their role as disease biomarkers.
Material and methods: In the present cohort DNA material was extracted from 156 formalin-fixed paraffin-embedded (FFPE) sections from patient with HNSCC and 45 corresponding non-cancerous tissues normal. The samples were retrieved from the National Guard Hospital and King Abdulaziz University Hospital, covering the period from 2005 to 2014. The pertinent’ clinicopathologic data (gender, age, grade, and lymph node status) were taken retrieved from the patients’ records after obtaining the relevant ethical approvals. Methylation patterns in a panel of key genes including RARB, CDKN2A, CDKN2B, SLIT2, RASSF1A, and KL genes were profiled utilizing the semi-quantitative MethyLight assay. Targeted sequencing of 45 patients with oral tongue oral squamous cell carcinoma was performed using Ion Torrent Personal Genome Machine. The Ion AmpliSeq Cancer Hotspot Panel v2 was utilized, targeting 207 regions in 50 genes found to be frequently mutated in cancer. The variants were compared to dbSNP and COSMIC. GP5+/GP6+ oligonucleotides primers-PCR was used as a direct screening method to detect viral DNA (HPV) in 156 HNSCC FFPE blocks.
Results: Interestingly, SLIT2 methylation frequency was the highest (64.6%) followed by RASSF1A (41.3%) then RARB (40.7%), SFRP1 (34.9), KL (30.7%), CKDN2B gene (29.6%) and CKDN2A gene (29.1%). Moreover, our results showed that KL and SFRP1 methylation were more predominant in nasopharyngeal tumors (p=0.001 and p=0.031, respectively). Promoter methylation of KL gene was a frequent event in young female nasopharyngeal cancer patients (p=0.033). Kaplan–Meier analysis showed that patients with moderately differentiated tumors and display SFRP1 methylation have significantly worse overall survival. On the other hand, a better clinical outcome was seen in patients with KL methylation.
The sequencing analysis displays different kinds of missense, nonsense and frameshift mutations in the hotspot regions of the targeted genes. TP53 (64 %) was the highest most frequently mutated gene in OTSCC followed by PIK3CA (36%), CDKN2A (31%), EGFR (24%), APC (22 %), PTEN (22%), VHL (18%), NOTCH1 (16%), FGFR3 (16%) and BRAF (11%).
This study also shows that a total of 11/156 (7%) samples tested were positive for the presence of HPV-DNA and 145/156 (93%) was negative for HPV-DNA. Sanger sequencing method of the positive PCR products was performed to confirm the presence of HPV (type-18). Also, tongue organ was the most organ affected by HPV, especially in the male gender.
Conclusion: the frequent mutations and methylations detected in our cohort could serve as predictive biomarkers for HNSCC either for early detection, prognosis, and treatment response. Furthermore, this study is showing the potential benefit to screen HPV in a large cohort. |
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Supervisor |
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Prof. Dr. Jalaludden Azam.Awlia |
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Thesis Type |
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Doctorate Thesis |
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Publishing Year |
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1439 AH
2018 AD |
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Co-Supervisor |
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Dr. Ashraf Dallol |
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Added Date |
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Wednesday, February 21, 2018 |
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Researchers
| عبير عبدالرحمن السفياني | Alsofyani, Abeer Abdulrahman | Researcher | Doctorate | |
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