An epigenetic program established by gene – environment interactions initiates pancreatic carcinogenesis [ATAC-seq]

Description: Summary from GEO:

"Damaged tissues have increased risk of cancer development through poorly understood mechanisms. For example, 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 tumor models, we show that the combination of Kras mutation and tissue damage promotes a functionally relevant chromatin state in the pancreatic epithelium that distinguishes neoplastic transformation from normal regeneration and is inherited throughout malignant evolution. This cancer-associated epigenetic state emerges remarkably fast, involves chromatin accessibility changes not induced by pancreatic injury alone, and contributes to the early activation of neoplasia specific genes that define advanced human pancreatic cancer. Among the genes activated by injury-facilitated chromatin reprogramming are a series of known and novel cancer-related factors, including the alarmin cytokine IL33, which cooperates with mutant Kras in driving neoplastic transformation in the absence of tissue damage. 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 cooperation between genetics and environmental cues in cancer initiation."

Overall design from GEO:

"Characterization of the chromatin accessibility profiles of lineage-traced pancreatic epithelial cells isolated directly by FACS-sorting (mKate2+ or GFP+) from normal, regenerating, early neoplastic and malignant murine pancreatic tissues: To compare the effects of tissue injury in mutant Kras-expressing or Kras wild-type pancreatic epithelial cells, cells were sorted from KC;RIK (p48-Cre;RIK;LSLKrasG12D) or C;RIK (p48-Cre;RIK) male mice treated with caerulein or PBS (vehicle control) at 5 weeks of age, using littermates when possibe. To characterize invasive disease, pancreatic ductal adenocarcinoma (PDAC) cells were isolated from cancer lesions arising in autochthonous transgenic models (KPflC;RIK (p48Cre;RIK;LSL-KrasG12D;p53fl/+) or in immunocompetent mice upon orthotopic transplantation of pre-malignant Kras-mutated;p53-null pancreatic organoids. 3-6 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 #: GSE132440

Access via BioProject

Accession #: PRJNA548087

Access via SRA

Accession #: SRP200963
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): TAR, TXT, BW
Dataset Size: 14.4 MB (TXT), 14.9 GB (TAR)

Data Catalog Record Updated: 2023-10-16