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Series GSE246923 Query DataSets for GSE246923
Status Public on May 01, 2024
Title Opposing tumor cell-intrinsic and -extrinsic roles of the IRF1 transcription factor in anti-tumor immunity
Organisms Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Type I interferons (IFN-I) and IFN- foster antitumor immunity by facilitating T cell responses. Paradoxically, IFNs may promote T cell exhaustion by activating immune checkpoints. The downstream regulators of these responses are incompletely understood. Herein, we describe how Interferon Regulatory Factor 1 (IRF1) orchestrates these opposing effects of IFNs. IRF1 expression in tumors blocked Toll-like receptor and IFN-I-dependent host antitumor immunity by preventing IFN stimulated gene (ISG) programs and effector programs in dendritic cells and T cells. In contrast, expression of IRF1 in the host, but not IRF3 or IFN-, was also required for antitumor immunity to wildtype and Irf1-/- tumors. Mechanistically, tumor cell IRF1 regulated major histocompatibility class I expression and bound uniquely or together with STAT1 at many ISGs, contributing to expression of immunosuppressive but not immunostimulatory ISGs. Overexpression of PD-L1 in Irf1-/- tumors only partially restored tumor growth, suggesting that the negative effects of tumor IRF1 on antitumor immunity are multifactorial. Thus, we identify tumor cell IRF1 expression as a previously unrecognized selective inhibitor of host IFN-I dependent antitumor immunity, while host IRF1 and IFN-I are critical drivers of antitumor immune responses.
 
Overall design Wildtype and IRF1-/- MC 38 cells were stimulated with IFN-y for 2h. Chromatin from 0, and 2h stimlated samples was immunoprecipitated with antibodies against IRF1 or STAT1 followed by NGS library prep and sequencing in Illumina.

Wildtype and IRF1-/- MC 38 cells (mouse colon cancer line) or M238 cells (human melanoma line) were stimulated with IFN-y for 2h or 6h. mRNA from 0, and 2h stimlated samples for MC38 and 0h and 6h stimulated samples for M238 cells were used for RNA-Seq library generation followed by NGS library prep and sequencing in Illumina instrument.

WT and Irf1-/- MC38 tumors (pooled 4-6) from WT and Ifnar-/- mice on day12 were chopped into small pieces (2-4 mm size) before dissociation with Miltenyi's gentle MACS enzyme mix (# 130-096-730) in a Miltenyi GentleMACS Octo Dissociator (Miltenyi Biotec Inc., San Diego, CA) with pre- set 37C_mTDK_1 protocol. After digestion, cells were filtered through 70 uM MACS smart stainer, counted and appropriate number of cells were loaded to target 10,000 cells. Single cell gene expression libraries were created using Chromium Next GEM Single Cell 3' (v3.1 Chemistry) (10x Genomics), Chromium Next GEM Chip G Single Cell Kit (10x Genomics), and Single Index Kit T Set A (10x Genomics) according to the manufacturer's instructions. Sequencing was performed in Illumina Novaseq-6000 instrument at 100 cycle.
 
Contributor(s) Purbey PK, Scumpia PO, Smale ST
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Submission date Nov 02, 2023
Last update date May 01, 2024
Contact name Prabhat Kumar Purbey
E-mail(s) ppurbey@gmail.com
Phone 3102064946
Organization name UCLA
Department MIMG
Lab Stephen T. Smale
Street address 675 Charles E. Young Drive South
City los angeles
State/province California
ZIP/Postal code 90095
Country USA
 
Platforms (3)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (49)
GSM7880907 WT_MC38, IRF1, ChIP-seq, 1
GSM7880908 WT_MC38, IRF1, ChIP-seq, 2
GSM7880909 WT_MC38, IRF1, ChIP-seq, 3
Relations
BioProject PRJNA1035108

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Supplementary file Size Download File type/resource
GSE246923_RAW.tar 6.4 Gb (http)(custom) TAR (of BEDGRAPH, MTX, TSV, TXT)
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Raw data are available in SRA

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