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

Chatterjee, A.; Bararia, Akash; D, Ganguly; Mondal, Pronoy Kanti; Roy, Paromita; Banerjee, Sudeep; Ghosh, Saswata; Gulati, Sumit; Ghatak, Soumya; Chattopadhay, Bitan Kumar; Basu, P.; Chatterjee, Aniruddha; Sikdar, Nilabja

doi:10.1186/s12935-022-02737-1

Cited by 4 publications

(2 citation statements)

References 56 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The methylation status alteration in cancer cells is also an important point to consider for disease diagnosis. The nature of methylation based alterations discriminates itself from genetic changes based on tumor tissue type specificity, which is crucial in the case of methylation alterations apart from being more pervasive and prevalent in terms of occurrences[ 18 , 19 ]. Aberrant DNA methylation alterations mostly occur in CpG islands and play a vital role in activating tumor suppressor genes and oncogenes, thereby modulating the genome[ 20 - 23 ].…”

Section: Liquid Biopsy and Its Role In Panca Diagnosismentioning

confidence: 99%

Emerging role of non-invasive and liquid biopsy biomarkers in pancreatic cancer

Bararia¹,

Chakraborty²,

Roy³

et al. 2023

World J Gastroenterol

Self Cite

View full text Add to dashboard Cite

A global increase in the incidence of pancreatic cancer (PanCa) presents a major concern and health burden. The traditional tissue-based diagnostic techniques provided a major way forward for molecular diagnostics; however, they face limitations based on diagnosis-associated difficulties and concerns surrounding tissue availability in the clinical setting. Late disease development with asymptomatic behavior is a drawback in the case of existing diagnostic procedures. The capability of cell free markers in discriminating PanCa from autoimmune pancreatitis and chronic pancreatitis along with other precancerous lesions can be a boon to clinicians. Early-stage diagnosis of PanCa can be achieved only if these biomarkers specifically discriminate the non-carcinogenic disease stage from malignancy with respect to tumor stages. In this review, we comprehensively described the non-invasive disease detection approaches and why these approaches are gaining popularity for their early-stage diagnostic capability and associated clinical feasibility.

show abstract

Section: Liquid Biopsy and Its Role In Panca Diagnosismentioning

confidence: 99%

Emerging role of non-invasive and liquid biopsy biomarkers in pancreatic cancer

Bararia¹,

Chakraborty²,

Roy³

et al. 2023

World J Gastroenterol

Self Cite

View full text Add to dashboard Cite

show abstract

“…This scope of global hypomethylation and promoter hypermethylation intensifies as the tumour progresses to metastasis, further amplifying the bimodal characteristics of the tumour DNA methylome [ 9 ]. Growing evidence from recent studies suggests a further defined role for site-specific DNA methylation changes acting as “epigenetic drivers” and potential markers in different cancer types that enable cancer growth [ 10 , 11 , 12 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

Targeted DNA Methylation Editing Using an All-in-One System Establishes Paradoxical Activation of EBF3

Banerjee,

Ajithkumar,

Keestra

et al. 2024

Cancers

Self Cite

View full text Add to dashboard Cite

Cutaneous melanoma is rapidly on the rise globally, surpassing the growth rate of other cancers, with metastasis being the primary cause of death in melanoma patients. Consequently, understanding the mechanisms behind this metastatic process and exploring innovative treatments is of paramount importance. Recent research has shown promise in unravelling the role of epigenetic factors in melanoma progression to metastasis. While DNA hypermethylation at gene promoters typically suppresses gene expression, we have contributed to establishing the newly understood mechanism of paradoxical activation of genes via DNA methylation, where high methylation coincides with increased gene activity. This mechanism challenges the conventional paradigm that promoter methylation solely silences genes, suggesting that, for specific genes, it might actually activate them. Traditionally, altering DNA methylation in vitro has involved using global demethylating agents, which is insufficient for studying the mechanism and testing the direct consequence of gene methylation changes. To investigate promoter hypermethylation and its association with gene activation, we employed a novel approach utilising a CRISPR-SunTag All-in-one system. Here, we focused on editing the DNA methylation of a specific gene promoter segment (EBF3) in melanoma cells using the All-in-one system. Using bisulfite sequencing and qPCR with RNA-Seq, we successfully demonstrated highly effective methylation and demethylation of the EBF3 promoter, with subsequent gene expression changes, to establish and validate the paradoxical role of DNA methylation. Further, our study provides novel insights into the function of the EBF3 gene, which remains largely unknown. Overall, this study challenges the conventional view of methylation as solely a gene-silencing mechanism and demonstrates a potential function of EBF3 in IFN pathway signalling, potentially uncovering new insights into epigenetic drivers of malignancy and metastasis.

show abstract