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Cancer Cell International
Published in: Cancer Cell International 1/2022

Open Access 01-12-2022 | Pancreatic Cancer | Research

DNA methylome in pancreatic cancer identified novel promoter hyper-methylation in NPY and FAIM2 genes associated with poor prognosis in Indian patient cohort

Authors: Ankita Chatterjee, Akash Bararia, Debopriyo Ganguly, Pronoy Kanti Mondal, Paromita Roy, Sudeep Banerjee, Shibajyoti Ghosh, Sumit Gulati, Supriyo Ghatak, Bitan Kumar Chattopadhay, Priyadarshi Basu, Aniruddha Chatterjee, Nilabja Sikdar

Published in: Cancer Cell International | Issue 1/2022

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Abstract

Background

Pancreatic ductal adenocarcinoma (PDAC) is one of the leading cancers worldwide and has a poor survival, with a 5-year survival rate of only 8.5%. In this study we investigated altered DNA methylation associated with PDAC severity and prognosis.

Methods

Methylome data, generated using 450 K bead array, was compared between paired PDAC and normal samples in the TCGA cohort (n = 9) and our Indian cohort (n = 7). The total Indian Cohort (n = 75) was split into cohort 1 (n = 7), cohort 2 (n = 22), cohort 3 (n = 26) and cohort 4 (n = 20).Validation of differential methylation (6 selected CpG loci) and associated gene expression for differentially methylated genes (10 selected gDMs) were carried out in separate validation cohorts, using MSP, RT-PCR and IHC correlations between methylation and gene expression were observed in TCGA, GTEx cohorts and in validation cohorts. Kaplan–Meier survival analysis was done to study differential prognosis, during 2–5 years of follow-up.

Results

We identified 156 DMPs, mapped to 91 genes (gDMs), in PDAC; 68 (43.5%) DMPs were found to be differentially methylated both in TCGA cohort and our cohort, with significant concordance at hypo- and hyper-methylated loci. Enrichments of “regulation of ion transport”, “Interferon alpha/beta signalling”, “morphogenesis and development” and “transcriptional dysregulation” pathways were observed among 91 gDMs. Hyper-methylation of NPY and FAIM2 genes with down-regulated expression in PDAC, were significantly associated with poor prognosis in the Indian patient cohort.

Conclusions

Ethnic variations among populations may determine the altered epigenetic landscape in the PDAC patients of the Indian cohort. Our study identified novel differentially methylated genes (mainly NPY and FAIM2) and also validated the previously identified differentially methylated CpG sites associated with PDAC cancer patient’s survival. Comparative analysis of our data with TCGA and CPTAC cohorts showed that both NPY and FAIM2 hyper-methylation and down-regulations can be novel epigenetically regulated genes in the Indian patient population, statistically significantly associated with poor survival and advanced tumour stages.
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Metadata
Title
DNA methylome in pancreatic cancer identified novel promoter hyper-methylation in NPY and FAIM2 genes associated with poor prognosis in Indian patient cohort
Authors
Ankita Chatterjee
Akash Bararia
Debopriyo Ganguly
Pronoy Kanti Mondal
Paromita Roy
Sudeep Banerjee
Shibajyoti Ghosh
Sumit Gulati
Supriyo Ghatak
Bitan Kumar Chattopadhay
Priyadarshi Basu
Aniruddha Chatterjee
Nilabja Sikdar
Publication date
01-12-2022
Publisher
BioMed Central
Published in
Cancer Cell International / Issue 1/2022
Electronic ISSN: 1475-2867
DOI
https://doi.org/10.1186/s12935-022-02737-1

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