An epigenetic program established by gene – environment interactions initiates pancreatic carcinogenesis [Set2]

Description: Summary from GEO:

"Damaged tissues have increased risk of cancer development through poorly understood mechanisms. In the pancreas, tissue damage collaborates with activating mutations in the Kras oncogene to dramatically accelerate the formation of early neoplastic lesions and ultimately pancreatic cancer. By integrating genomics, single-cell chromatin assays and spatiotemporally-controlled functional perturbations in autochthonous mouse models, we show that the combination of Kras mutation and tissue damage promotes a unique chromatin state in the pancreatic epithelium that distinguishes neoplastic transformation from normal regeneration and is selected for throughout malignant evolution. This cancer-associated epigenetic state emerges within 48 hours of pancreatic injury, and involves large-scale chromatin accessibility changes that contribute to the early dysregulation of genes defining human pancreatic cancer. Among the genes most rapidly activated by tissue damage in the pre-malignant pancreatic epithelium is the alarmin cytokine IL33, which cooperates with mutant Kras in unleashing the epigenetic remodeling program of early neoplasia and neoplastic transformation in the absence of injury. Collectively, our study demonstrates how gene-environment interactions can rapidly produce gene regulatory programs that dictate early neoplastic commitment and provides a molecular framework for understanding the interplay between genetics and environmental cues in cancer initiation."

Overall design from GEO:

"Identification of the transcriptional changes induced upon doxycycline (dox)-inducible Brd4 knockdown in either wild-type or mutant Kras bulk pancreatic epithelial cells triggered to undergo regenerative (Injury condition) or proneoplastic (Kras*+Injury condition) transitions, respectively: Brd4-suppressed vs Brd4-expressing pancreatic epithelial cells were FACS-sorted (mKate2+;GFP+) from pancreata from p48Cre;RIK;TRE-GFP-shRNA (Kras wild-type) or p48Cre;RIK;TRE-GFP-shRNA;LSL-KrasG12D (Kras mutant) mice (harbouring Brd4 shRNA -1448, 552- or control Renilla shRNA -713-) at day 2 after treatment with caerulein. Brd4-expressing (shRen) pancreatic epithelial cells FACS-sorted from p48Cre;RIK;TRE-GFP-shRNA (Kras wild-type) mice which were placed on dox diet but not subjected to caerulein treatment served as additional control to pinpoint caerulein- and mutant Kras-specific effects. 3 biological replicates (independent mice) were used per experimental condition."

Subject of Study

Mus musculus

Subject(s)

Carcinogenesis

Chromatin Immunoprecipitation Sequencing

OncoTree Cancer Type(s)

Pancreatic Adenocarcinoma

Access via GEO

Accession #: GSE132329

Access via BioProject

Accession #: PRJNA547617

Access via SRA

Accession #: SRP200686
Access Restrictions: Free to All
Access Instructions: The NCBI Gene Expression Omnibus, SRA and BioProject databases provide open access to these files.
Associated Publications: Alonso-Curbelo D, Ho Y, Burdziak C, Maag J, Morris J, Chandwani R, Chen H, Tsanov K, Barriga F, Luan W, Tasdemir N, Livshits G, Azizi E, Chun J, Wilkinson J, Mazutis L, Leach S, Koche R, Pe’er D, Lowe S. A gene–environment-induced epigenetic program initiates tumorigenesis. Nature. 2021; 590(7847):642-648.
Equipment Used: Illumina HiSeq 2500
High throughput sequencing system
Dataset Format(s): CSV
Dataset Size: 1.7 MB

Data Catalog Record Updated: 2023-10-16