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| Status |
Public on Oct 09, 2024 |
| Title |
Mutant-p53 stimulates Cxcl1 Expression from Distal Enhancers to Suppress Immune Response to Pancreatic Cancer [CUT&RUN] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer without effective treatments. It is characterized by activating KRAS mutations and p53 alterations. However, how these mutations alter cell-intrinsic gene programs to influence the immune landscape of the tumor microenvironment (TME) remains poorly understood. Here, we demonstrate that p53R172H enhances tumor growth, establishes a suppressive TME by inducing immune evasion, and blunts the effectiveness of immune checkpoint inhibitors (ICIs). We discovered that the oncogenic function of p53R172H is mediated by upregulation of the immunosuppressive chemokine Cxcl1. Mechanistically, we show that p53R172H binds to the distal enhancers of the Cxcl1 gene and increases enhancer activity and Cxcl1 expression. NF-kB also occupies Cxcl1 enhancers, and p53R172H binds these enhancers in an NF-kB-dependent manner, suggesting a role of NF-kB in commuting p53R172H to the Cxcl1 enhancers. Our findings elucidate how a common mutation in a critical tumor-suppressor gene exploits enhancers to modulate chemokine gene expression and foster an immunosuppressive TME in PDAC that undermines the efficacy of ICI.
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| Overall design |
To investigate the role of p53R172H in pancreatic ductal adenocarcinoma (PDAC), we generated isogenic Trp53-/- PDAC cells (KrasG12D/+; Trp53-/-) using CRISPR-Cas9. We compared transcriptional programs via RNA-seq and PRO-seq, exonic mutations using Exome-seq, and genome occupancy with CUT&RUN between Trp53R172H/- and isogenic and syngenic Trp53-/- cells, as well as Trp53-/- cells with ectopically expressed p53R172H.
We orthotopically implanted the PDAC cells into the pancreas of mice and evaluated tumor growth, size, and the immune landscape. We further treated the mice with immune checkpoint inhibitors and monitored their survival.
To explore the role of Cxcl1 and its enhancers, we generated Cxcl1-/- cells and Cxcl1 enhancer knockout cells. We then assessed gene expression, immune profiling, and the response to immune checkpoint inhibitors in these models.
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| Contributor(s) |
Mahat DB, Kumra H, Castro SA, Metcalf E, Nguyen K, Morisue R, Ho WW, Chen I, Sullivan B, Yim LK, Singh A, Fu J, Waterton S, Cheng Y, Moiso E, Chauhan V, Moura Silva H, Spranger S, Jain RK, Sharp PA |
| Citation(s) |
39257788 |
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| Submission date |
Aug 18, 2024 |
| Last update date |
Oct 10, 2024 |
| Contact name |
Dig B Mahat |
| E-mail(s) |
mahat@mit.edu, dbm222@cornell.edu
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| Phone |
4436153053
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| Organization name |
Massachusetts Institute of Technology
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| Department |
Koch Institute for Integrative Cancer Research
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| Lab |
Phillip A. Sharp
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| Street address |
Koch Institute, MIT, 500 Main St, Building 76, #417
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (20)
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| Relations |
| BioProject |
PRJNA1149458 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE275108_RAW.tar |
1.4 Gb |
(http)(custom) |
TAR (of BEDGRAPH) |
SRA Run Selector |
| Raw data are available in SRA |
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