Title: Salivary DNA methylation biomarker panel to detect head and neck cancer

Abstract

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer in the world based on its mortality, and approximately 900,000 new cases are diagnosed each year with 300,000 deaths per annum. The known major risk factors for the development of SCC include smoking, drinking and human papilloma viral infections. Currently there are no biomarkers to detect HNSCC at an early stage and as a result 5-year survival is less than 50%. DNA promoter hypermethylation of tumour suppressor genes occurs in cancer initiation and progression. In this study, we collected saliva from HNSCC patients and healthy controls and using a sensitive methylation-specific PCR (MSP) assay based on detection of specific CpG hypermethylation events in the promoters of tumour suppressor genes (APC, p14, RASSF1a, DAPK1 and p16), for RASSF1a, DAPK1 and p16, we have demonstrated an overall specificity for this test panel of 73% (53.8-87.2%) for HNSCC patients (n=121) when compared with healthy controls (n=41). In addition, APC and p14 were methylated in a small subset of patients. The DNA methylation of DAPK1, p16 and RASSF1, in the saliva (drool and DNA • SAL™) enabled us to identify individuals with HNSCC at a sensitivity level of 60% (p=0.05 confidence interval 51-68%) and an accuracy of 63% (56-68%), with a Fisher's exact test p=0.002. In conclusion, we demonstrate that salivary DNA methylation biomarkers are clinically useful in detecting head and neck cancer in a non-invasive manner.

Full text

Title: Salivary DNA methylation biomarker panel to detect head and neck cancer
Dmitry A. Ovchinnikov (1), William B Coman (2), Justin J Cooper-White (1,3), Paul D Slowey
(4) and Chamindie Punyadeera (5)(*).
(1) The Australian Institute for Bioengineering and Nanotechnology (2) The School of
Medicine, (3) The School of Chemical Engineering, The University of Queensland, St-Lucia,
Australia (4), Oasis Diagnostics® Corporation, USA and (5)* The University of Queensland
Diamantina Institute, Level 6, TRI, 37 Kent St, Woolloongabba QLD 4102.
Abstract:
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer in the
world based on its mortality, and approximately 900,000 new cases are diagnosed each year
with 300,000 deaths per annum. The known major risk factors for the development of SCC
include smoking, drinking and human papilloma viral infections. Currently there are no
biomarkers to detect HNSCC at an early stage and as a result 5-year survival is less than
50%. DNA promoter hypermethylation of tumour suppressor genes occurs in cancer initiation
and progression. In this study, we collected saliva from HNSCC patients and healthy controls
and using a sensitive methylation-specific PCR (MSP) assay based on detection of specific
CpG hypermethylation events in the promoters of tumour suppressor genes (APC, p14,
RASSF1a, DAPK1 and p16), for RASSF1a, DAPK1 and p16, we have demonstrated an
overall specificity for this test panel of 73% (53.8-87.2%) for HNSCC patients (n=121) when
compared with healthy controls (n=41). In addition, APC and p14 were methylated in a small
subset of patients. The DNA methylation of DAPK1, p16 and RASSF1

, in the saliva (drool
and DNA•SAL™) enabled us to identify individuals with HNSCC at a sensitivity level of
60% (p=0.05 confidence interval 51-68%) and an accuracy of 63% (56-68%), with a Fisher’s
exact test p=0.002. In conclusion, we demonstrate that salivary DNA methylation biomarkers
are clinically useful in detecting head and neck cancer in a non-invasive manner.