HOXA9 gene promotor methylation and copy number variation of SOX2 and HV2 genes in cell free DNA: A potential diagnostic panel for non-small cell lung cancer

Abstract

Background Most cases of lung cancer are diagnosed at advanced stage. Detection of genetic and epigenetic markers in cell-free DNA (cfDNA) is a promising tool for the diagnosis of lung cancer at an early stage. The aim of this study was to identify non-invasive diagnostic markers in cell free DNA (cfDNA) for non-small cell lung cancer (NSCLC) as it is the most common type of lung cancer. Methods We investigated the cfDNA HOXA9 gene promotor methylation by pyrosequencing. Copy number variation of SOX2 and HV2 genes were detected by real-time PCR in cfDNA extracted from plasma samples of 25 newly diagnosed NSCLC patients and 25 age and sex matched controls. Results Methylation level of HOXA9 was significantly higher in NSCLC patients than controls (p > 0.001). SOX2 showed significantly higher CNV and HV2 showed lower CNV in patients than controls (p > 0.001, p = 0.001 respectively). Receiver Operating Characteristic (ROC) curve analysis for HOXA9 methylation, SOX2 CNV and HV2 CNV showed a discrimination power of 79.4%, 80% and 77.5% respectively and the area under the curve for the combined analysis of the three genes was 0.958 with 88% sensitivity and 100% specificity. Conclusions In this study, we suggest a potentially diagnostic panel that may help in detection of lung cancer with high sensitivity and specificity using cell free DNA. This Panel included HOXA9 gene methylation and the CNV of SOX2 and HV2 genes.

Detection of the DNA methylation of seven genes contribute to the early diagnosis of lung cancer

“…Hulbert et al (Hulbert et al 2017 ) reported that the combination of CDO1 , TAC1 and SOX17 in plasma showed a sensitivity, specificity and AUC of 86%, 78% and 77% in the diagnosis of non-small cell lung cancer with stage I and IIA from the individuals with non-cancer. Abou-Zeid et al (Abou-Zeid et al 2023 ) reported that the methylation level of HOXA9 was significantly higher in NSCLC patients than controls ( P > 0.001). Liu et al (Liu et al 2017 ) used the Mate-analysis through the systematic literature search yielded a total of 33 studies including a total of 4801 subjects (2238 patients with lung cancer and 2563 controls) and covering 32 genes.…”

Identifying the prognosis implication, immunotherapy response prediction value, and potential targeted compound inhibitors of integrin subunit α3 (ITGA3) in human cancers

“…TMB and MSI have emerged as major response-predictive biomarkers for the effectiveness of ICB therapy [ 24 , 25 ]. CNV, as a form of genomic structural variation, has been proven to be involved in the occurrence and development of various cancers and affects the prognosis of patients [ 37 , 38 ], and can also be used in cancer diagnosis [ 39 ]. As an epigenetic modification, DNA methylation often disrupts gene regulation and affects patient prognosis in a variety of cancers [ 40 , 41 ].…”