Dataset Information

Methylation of CALCA and CALCB in Pancreatic Ductal Adenocarcinoma.

ABSTRACT: Calcitonin gene-related peptide (CGRP) plays a diverse and intricate role in chronic low-grade inflammation and is closely related to specific cancers. It includes two subtypes, CALCA (αCGRP) and CALCB (βCGRP), of which αCGRP expression accounts for more than 90%. Here, we show that methylation of CALCA and CALCB in pancreatic ductal adenocarcinoma was significantly higher than that in paracancer. Western blot and immunohistochemistry showed that CGRP, p-AKT, and p-CREB in the tumor tissues were lower than those in the paracarcinoma tissues. In vivo, the expressions of p-AKT and p-CREB in the pancreatic tissues of CALCA-KO rats were also lower than those of wild type. Methylation of CALCA and CALCB is increased in pancreatic adenocarcinoma, and under that condition, p-AKT and p-CREB levels were decreased.

SUBMITTER: Gao F

PROVIDER: S-EPMC8357496 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Methylation of CALCA and CALCB in Pancreatic Ductal Adenocarcinoma.

Gao Feng F Liu Guozhong G Wang Jingwen J Huang Shirong S Ding Fadian F Lian Wei W Lv Xiaoting X Guo Yujia Y Fan Xiangqun X Zhang Sheng S Liu Qicai Q

Oxidative medicine and cellular longevity 20210803

Calcitonin gene-related peptide (CGRP) plays a diverse and intricate role in chronic low-grade inflammation and is closely related to specific cancers. It includes two subtypes, CALCA (αCGRP) and CALCB (βCGRP), of which αCGRP expression accounts for more than 90%. Here, we show that methylation of CALCA and CALCB in pancreatic ductal adenocarcinoma was significantly higher than that in paracancer. Western blot and immunohistochemistry showed that CGRP, p-AKT, and p-CREB in t ...[more]

PMID: 34394823

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Project description:Pancreatic Ductal Adenocarcinoma (PDAC) is an aggressive form of pancreatic cancer that typically manifests itself at an advanced stage and does not respond to most treatment modalities. The survival rate of a PDAC patient is less than 5%, with a median survival of just a couple of months. A better understanding of the molecular pathology of PDAC is needed to guide research for the development of better clinical treatment modalities for PDAC patients. Gene expression studies performed to date have identified different subtypes of PDAC with prognostic and clinical relevance. Subtypes identified to date are highly heterogeneous since pancreatic cancer is heterogeneous cancer. Tumor microenvironment and stroma constitute a major chunk of PDAC and contribute to the heterogeneity. Better subtyping methods are need of the hour for better prognosis and classification of PDAC for future personalized treatment. In this work, we have performed an integrated analysis of DNA methylation and gene expression datasets to provide better mechanistic and molecular insights into Pancreatic cancers, especially PDAC. The use of varied and diverse datasets has provided valuable insights into different cancer types and can play an integral role in revealing the complex nature of underlying biological mechanisms. We performed subtyping of TCGA-PAAD gene expression and methylation datasets into different subtypes using state-of-the-art normalization methods and unsupervised clustering methods that reveal latent hidden factors, leading to additional insights for subtyping. Differential expression and differential methylation were performed for each of the subtypes obtained from clustering. Our analysis gave a consensus of five cluster solution with relevant pathways like MAPK, MET. The five subtypes corresponded to the tumor and stromal subtypes. This analysis helps in distinguishing and identifying different subtypes based on enriched putative genes. These results help propose novel experimentally-verifiable PDAC subtyping and demonstrate that using varied data sets and integrated methods can contribute to disease prognostication and precision medicine in PDAC treatment.

Project description:BackgroundWe have recently constructed a DNA methylation classifier that can discriminate between pancreatic ductal adenocarcinoma (PAAD) liver metastasis and intrahepatic cholangiocarcinoma (iCCA) with high accuracy (PAAD-iCCA-Classifier). PAAD is one of the leading causes of cancer of unknown primary and diagnosis is based on exclusion of other malignancies. Therefore, our focus was to investigate whether the PAAD-iCCA-Classifier can be used to diagnose PAAD metastases from other sites.MethodsFor this scope, the anomaly detection filter of the initial classifier was expanded by 8 additional mimicker carcinomas, amounting to a total of 10 carcinomas in the negative class. We validated the updated version of the classifier on a validation set, which consisted of a biological cohort (n = 3579) and a technical one (n = 15). We then assessed the performance of the classifier on a test set, which included a positive control cohort of 16 PAAD metastases from various sites and a cohort of 124 negative control samples consisting of 96 breast cancer metastases from 18 anatomical sites and 28 carcinoma metastases to the brain.ResultsThe updated PAAD-iCCA-Classifier achieved 98.21% accuracy on the biological validation samples, and on the technical validation ones it reached 100%. The classifier also correctly identified 15/16 (93.75%) metastases of the positive control as PAAD, and on the negative control, it correctly classified 122/124 samples (98.39%) for a 97.85% overall accuracy on the test set. We used this DNA methylation dataset to explore the organotropism of PAAD metastases and observed that PAAD liver metastases are distinct from PAAD peritoneal carcinomatosis and primary PAAD, and are characterized by specific copy number alterations and hypomethylation of enhancers involved in epithelial-mesenchymal-transition.ConclusionsThe updated PAAD-iCCA-Classifier (available at https://classifier.tgc-research.de/ ) can accurately classify PAAD samples from various metastatic sites and it can serve as a diagnostic aid.

Dataset Information

Methylation of CALCA and CALCB in Pancreatic Ductal Adenocarcinoma.

Publications

Methylation of CALCA and CALCB in Pancreatic Ductal Adenocarcinoma.

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