Methylation changes at the GNAS imprinted locus in pancreatic cystic neoplasms are important for the diagnosis of malignant cysts

Sandra Faias; Marlene Duarte; Luísa Pereira; Paula Chaves; Marília Cravo; Antonio Dias Pereira; Cristina Albuquerque

doi:10.4251/wjgo.v12.i9.1056

Methylation changes at the GNAS imprinted locus in pancreatic cystic neoplasms are important for the diagnosis of malignant cysts

World J Gastrointest Oncol. 2020 Sep 15;12(9):1056-1064. doi: 10.4251/wjgo.v12.i9.1056.

Authors

Sandra Faias¹, Marlene Duarte², Luísa Pereira³, Paula Chaves⁴, Marília Cravo⁵, Antonio Dias Pereira¹, Cristina Albuquerque²

Affiliations

¹ Department of Gastroenterology, Instituto Português de Oncologia de Lisboa Francisco Gentil, EPE, Lisboa 1099-023, Portugal.
² Unidade de Investigação em Patobiologia Molecular (UIPM), Instituto Português de Oncologia de Lisboa Francisco Gentil, EPE, Lisboa 1099-023, Portugal.
³ Centro de Matemática e Aplicações (CMA-UBI), Universidade da Beira Interior, Covilhã 6200-506, Portugal.
⁴ Faculty of Health Sciences, University of Beira Interior, Covilhã 6200-506, Portugal.
⁵ Department of Gastroenterology, Hospital Beatriz Ângelo, Loures 2674-514, Portugal.

Abstract

Background: Guanine nucleotide-binding protein, alpha stimulating (GNAS) mutations are characteristic of intraductal papillary mucinous neoplasms (IPMNs). Pancreatic ductal adenocarcinomas (PDACs) harboring GNAS mutations originate in IPMNs. GNAS is a complex imprinted locus that produces five transcripts regulated by differential methylated regions, NESP55, GNASAS, GNASXL, GNAS1A, and GNAS.

Aim: To evaluate if methylation changes in the differential methylated regions of GNAS locus contributed to malignant progression of pancreatic cysts.

Methods: GNAS locus methylation was analyzed in archival pancreatic cyst fluid (PCF) obtained by endoscopic ultrasound with fine-needle aspiration by methylation specific-multiplex ligation dependent probe amplification. Results were normalized and analyzed using Coffalyser.Net software.

Results: Fifty-two PCF samples obtained by endoscopic ultrasound with fine-needle aspiration and previously characterized for KRAS and GNAS mutations were studied. The final diagnoses were surgical (11) and clinicopathological (41), including 30 benign cysts, 14 pre-malignant cyst, and eight malignant cysts. Methylation changes at NESP55, GNASAS, GNAS1A, and especially GNASXL were more frequent in malignant cysts, and NESP55 and GNASAS were useful for diagnosis. A combined variable defined as "GNAS locus methylation changes" was significantly associated with malignancy (6/8 malignant cysts and only 2/20 benign cysts) and improved classification. Hypermethylation in both maternally (NESP55) and paternally (GNASXL) derived promoters was found in 3/3 PDACs.

Conclusion: This is the first study to identify methylation changes in the GNAS locus, improving the diagnosis of malignant pancreatic cysts and suggesting a role in progression to PDAC.

Keywords: Biomarker; GNAS locus; Intraductal papillary mucinous neoplasms; Methylation; Pancreas cyst; Pancreatic neoplasm.