KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-mouse/human p1253 | Epicypher | SKU: 13-2015 |
| p53 (1C12) Mouse mAb | Cell Signaling | #2524 |
| anti-mouse/human p53 | Leica Biosystems | P53-DO7-L-CE |
| anti-mouse CD16/32;clone 93 | BioLegend | Cat# 101330;AB_2561482 |
| anti-mouse CD25 (APC-Cy7);clone PC61 | BioLegend | Cat# 102026;AB_830745 |
| anti-mouse CD279 (PD-1) (BV605);clone 29F.1A12 | BioLegend | Cat# 135220;AB_2562616 |
| anti-mouse CD3 (eFluor 450);clone 17A2 | eBioscience | Cat# 48-0032-80;AB_1272229 |
| anti-mouse CD366 (TIM3) (PE-Cy7);clone RMT3-23 | eBioscience | Cat# 25-5870-82;AB_2573483 |
| anti-mouse CD4 (BUV737);clone RM4-5 | BD Biosciences | Cat# 612844;AB_2732918 |
| anti-mouse CD45 (BUV395);clone 30-F11 | BD Biosciences | Cat# 564279;AB_2651134 |
| anti-mouse CD62L (BV711);clone MEL-14 | BioLegend | Cat# 104445;AB_2564215 |
| anti-mouse CD69 (APC);clone H1.2F3 | BioLegend | Cat# 104513;AB_492844 |
| anti-mouse CD8a (BV605);clone 53-6.7 | BioLegend | Cat# 100744;AB_2562609 |
| anti-mouse FoxP3 (PerCP-Cy5.5);clone FJK-16s | eBioscience | Cat# 45-5773-80;AB_914349 |
| anti-mouse/human CD11b (PE/Dazzle 594);clone M1/70 | BioLegend | Cat# 101255;AB_2563647 |
| anti-mouse/human CD44 (PE);clone IM7 | BioLegend | Cat# 103023;AB_493686 |
| anti-mouse/human Gzmb (AF700);clone QA16A02 | BioLegend | Cat# 372221;AB_2728388 |
| anti-mouse/human TCF1 (AF488);clone C63D9 | Cell Signaling Technology | Cat# 6444S |
| anti-Ly-6G (clone 18A) PerCP/Cyanine5.5 | BioLegend | Cat# 127615 |
| anti-CD90.2 (clone 30-H12) FITC | BioLegend | Cat# 105306 |
| anti-CX3CR1 (clone SA011F11) BV650 | BioLegend | Cat# 14903 |
| anti-NK1.1 (clone PK136) BV605 | BioLegend | Cat# 108753 |
| anti-Folate Receptor 2 (clone 10/FR2) APC | BioLegend | Cat# 153305 |
| anti-I-A/I-E (clone M5/114.15.2) BV711 | BioLegend | Cat# 107643 |
| anti-CD206 (clone C068C2) PE/Cyanine7 | BioLegend | Cat# 141719 |
| anti-CD64 (clone X54-5/7.1) PE/Dazzle | BioLegend | Cat# 139319 |
| anti-Ly6C (clone HK1.4) BV785 | BioLegend | Cat# 128041 |
| Streptavidin-PE | BioLegend | Cat# 405203 |
| anti-TIM-4 (clone RMT4-54) BV421 | BD Biosciences | Cat# 744874 |
| anti-CD200R3 (clone Ba13) BUV805 | BD Biosciences | Cat# 752653 |
| anti-CD45 (clone 30-F11) BUV395 | BD Biosciences | Cat# 565967 |
| anti-Siglec-F (clone E50-2440) APC-R700 | BD Biosciences | Cat# 565183 |
| anti-FCeR1a (clone MAR-1) BV750 | BD Biosciences | Cat# 751756 |
| anti-CD19 (clone 1D3) BUV615 | BD Biosciences | Cat# 751213 |
| anti-CD11c (clone N418) BUV737 | BD Biosciences | Cat# 749039 |
| anti-CD103 (clone M290) BUV563 | BD Biosciences | Cat# 741261 |
| anti-CD11b (clone M1/70) APC-eFluor 780 | Invitrogen | Cat# 47-0112-80 |
| anti-CD16/CD32 (clone 2.4G2) | Bio X Cell | Cat# BP0307 |
| Lyve1 Biotin (clone ALY7) 13-0443-82 | Thermo Scientific | Cat# |
| anti-CD8 alpha, clone: YTS169.4 | Abcam | Cat# ab22378 |
| anti-Neutrophil | Abcam | Cat# ab2557 |
| anti-Arginase-1 | Cell Signaling Technology | Cat# 93668T |
| VECTASHIELD Vibrance® Antifade Mounting Medium | VECTOR Laboratories | Cat# H-1700 |
| Chemicals, peptides, and recombinant proteins | ||
| Fixable Viability Dye eFluor 506 | eBioscience | Cat# 65-0866-18 |
| Fixable Viability Dye eFluor 780 | eBioscience | Cat# 65-0865-14 |
| DMEM | Gibco | Cat# 11995 |
| Heat-inactivated fetal bovine serum | Tissue Culture Biologics | Cat# 101HI |
| Tissue culture-treated 10 cm plates | Corning | Cat# CLS430167 |
| Trypsin-EDTA | Gibco | Cat# 25200 |
| α-PD-1 | BioXcell | Cat# BE0146 |
| α-CTLA4 | BioXcell | Cat# 9D9 |
| Collagenase IV | Thermo Scientific | Cat# 17104019 |
| DNase I, Grade II, from bovine pancreas | Sigma-Aldrich | Cat# 10104159001 |
| Liberase TL Research Grade | Sigma-Aldrich | Cat# 05401020001 |
| Lipofectamine 2000 transfection reagent | Thermo Scientific | Cat# 18324012 |
| PureFection | System Bioscience | Cat# LV750A |
| T4 Polynucleotide Kinase | New England Biolabs | Cat# M0201 |
| Tango Buffer | Thermo Scientific | Cat# BY5 |
| FastDigest BbsI restriction enzyme | Thermo Scientific | Cat# FD1014 |
| T7 DNA Ligase | New England Biolabs | Cat# M0318 |
| Alkaline Phosphatase | Thermo Scientific | Cat# EF0654 |
| ACK Lysing Buffer | Thermo Scientific | Cat# A1049201 |
| Plasmid-Safe ATP-Dependent DNase | Biosearch Technologies | Cat# E3101K |
| QIAprep Spin Miniprep Kit | Qiagen | Cat# 27104 |
| S.O.C. Medium | Thermo Scientific | Cat# 15544034 |
| Carbenicillin Disodium Salt | Thermo Scientific | Cat# 10177012 |
| anti-mouse CXCL1 | Leinco Technologies | Cat# K125 |
| anti-mouse CCL2 | Bio-Techne | Cat# MAB479 |
| Recombinant Mouse CXCL1 | Bio-Techne | Cat# 453-KC |
| Recombinant Mouse CCL2 | Bio-Techne | Cat# 452-M2 |
| anti-Mouse CXCL1- Biotin | Leinco Technologies | Cat# K124 |
| anti-Mouse CXCL1- Biotin | Bio-Techne | Cat# BAF479 |
| HRP Streptavidin | BioLegend | Cat# 405210 |
| TMB Substrate Solution | BioLegend | Cat# 421101 |
| Tissue-Tek® O.C.T. Compound | Sakura Finetek | Cat# 62550 |
| Antigen Unmasking Solution | VECTOR Laboratories | Cat# H-3300 |
| Stop Solution | BioLegend | Cat# 423001 |
| Critical commercial assays | ||
| FoxP3 Transcription Factor Staining Buffer Set | eBioscience | Cat# 00-5523-00 |
| Chemically competent Stbl3 E. coli cells | Thermo Scientific | Cat# C737303 |
| One Shot TOP10 Chemically Competent E. coli cells | Thermo Scientific | Cat# C404006 |
| Cytofix/Cytoperm Fixation/Permeabilization buffer | BD Biosciences | Cat# 554714 |
| Precision Count Beads | BioLegend | Cat# 424902 |
| UltraComp eBeads Compensation Beads | Invitrogen | Cat# 01-2222-42 |
| Mouse Cytokine Array C3 | RayBiotech | Cat# AAM-CYT-3 |
| Mouse LIX/ CXCL5 ELISA kit | Thermo Scientific | Cat# EMCXCL5 |
| 96-well ELISA plates | BioLegend | Cat# 423501 |
| RNeasy Mini Kit | Qiagen | Cat# 74104 |
| High-Capacity cDNA Reverse Transcription Kit | Applied Biosystems | Cat# 4368814 |
| Power SYBR Green PCR Master Mix | Applied Biosystems | Cat# 4368577 |
| ChIC/CUT&RUN Kit | EpiCypher | Cat# 14-1048 |
| TPCA-1 | Selleckchem | Cat# S2824 |
| Deposited data | ||
| RNA-seq | This study | GSE275105 Secure token: ujstwuygpfsbpkz |
| PRO-seq | This study | GSE275106 Secure token: ytwtwwqkzvgjtgp |
| Exome-seq | This study | GSE275107 Secure token: sbcrgsaqndcplgx |
| CUT&RUN | This study | GSE275108 Secure token: ctcryaimjtefzav |
| Experimental models: Cell lines | ||
| KrasG12D/+;Trp53R172H/− | Dr. Ashok Saluja lab, University of Miami | N/A |
| KrasG12D/+;Trp53−/− (syngenic) | Dr. Ronald DePinho lab, MD Anderson Cancer Center |
N/A |
| KrasG12D/+;Trp53−/− (isogenic) | This study | N/A |
| KrasG12D/+;Trp53R172H/−;Ccl2−/− | This study | N/A |
| KrasG12D/+;Trp53R172H/−;Ccl2−/−;Cxcl1−/− | This study | N/A |
| KrasG12D/+;Trp53R172H/−;Ccl2−/−;Cxcl5−/− | This study | N/A |
| KrasG12D/+;Trp53R172H/−;Cxcl1−/− | This study | N/A |
| KrasG12D/+;Trp53R172H/−;Cxcl5−/− | This study | N/A |
| KrasG12D/+;Trp53R172H/−;Δe8695 | This study | N/A |
| KrasG12D/+;Trp53R172H/−;Δe8695;Δe8696 | This study | N/A |
| KrasG12D/+;Trp53R172H/−;Δe8696 | This study | N/A |
| KrasG12D/+;Trp53R172H/−;Δe8697 | This study | N/A |
| Experimental models: Organisms/strains | ||
| Mouse: C57BL/6 | Jackson Laboratory | Strain# 000664 |
| Plasmids | ||
| PB-CMV-MCS-EF1α-Puro cDNA cloning and expression vector | System Biosciences | Cat# PB510B-1 |
| Trp53 (NM_011640) Mouse Untagged Clone | Origene | Cat# MC205636 |
| pU6-(BbsI)_CBh-Cas9-T2A-BFP (gift from Ralf Kuehn) | Addgene | Cat# 64323 |
| Oligonucleotides | ||
| See Table_1_Primer_Oligos.xlsx | ||
| Software and algorithms | ||
| FlowJo v10.8.1 | BD Biosciences | https://www.flowjo.com |
| Prism v10.3.0 | Graphpad | https://www.graphpad.com/features |
| CRISPick Design Tool | Broad Institute’s Genetic Perturbation Platform | https://portals.broadinstitute.org/gppx/crispick/public |
| Gene Set Enrichment Analysis (GSEA) | Subramanian et al., 2005 | http://www.broad.mit.edu/gsea/downloads.jsp |
| ImageJ Fiji | ImageJ | https://imagej.net/ij/ |
| QuPath software v.0.5.1 | QuPath | https://qupath.github.io/ |
| Adobe Illustrator CC2023 | Adobe | https://www.adobe.com |
| Bowtie2 v2.2.9 | Langmead et al., 2019 | https://github.com/BenLangmead/bowtie2 |
| Picard v2.8.0 | Broad Institute | https://github.com/broadinstitute/picard |
| SAMtools v0.1.19 | Danecek et al.57 | https://github.com/samtools/samtools |
| R v4.3.3 | R Foundation | https://cran.r-project.org/bin/ |
| DESeq2 v1.40.2 | Love et al.59 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| ggplot2 v3.5.0 | Hadley Wickham | https://cran.r-project.org/web/packages/ggplot2/index.html |
| msigdbr v7.5.1 | Igor Dolgalev | https://cran.r-project.org/web/packages/msigdbr/index.html |
| clusterProfiler v4.8.3 | Yu et al., 2021 | https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html |
| Enrichr | Kuleshov et al., 2016 | http://amp.pharm.mssm.edu/Enrichr/ |
| UCSC Genome Browser | Kent et al. 2002 | https://genome.ucsc.edu/ |
| HOMER (version v4.11.1) | Heinz et al. | http://homer.ucsd.edu/homer/index.html |
| SAMtools (version 1.9) | Danecek et al. | https://www.htslib.org/doc/1.9/samtools.html |
| SEACR | Meers et al. | https://github.com/FredHutch/SEACR?tab=readme-ov-file |