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Gene expression in B16.SIY tumor cells deficient in IFN-g signaling

ABSTRACT: We performed RNASeq on purified tumor cells from wild-type, IFNgR2-, and Jak1-mutant tumors on day 7 after tumor engraftment. To investigate whether IFN-g-insensitive tumor cells showed decreased expression of a negative immune regulatory factor, RNASeq was performed on purified tumor cells from WT, IFNgR2-, and Jak1-mutant tumors on day 7 after tumor engraftment. Compared to wild-type, we found 375 and 305 differentially expressed genes in IFNgR2- and Jak1-mutant tumor cells respectively. 228 of these genes were shared between IFNgR2- and Jak1-mutant tumor cells. Overlapping downregulated genes included those involved in antigen presentation, immune functions, extracellular matrix, ubiquitination, and GTPase activity.RNA sequencing and alignment to gene features were performed by the University of Chicago Genomics Core facility using the Illumina HiSeq platform. Raw read counts were processed by TMM normalization followed by log2 transformation. Genes expressed in fewer than three samples were removed from further analysis. Limma voom was used to identify differentially expressed genes between each mutant cohort and the wild-type cohort with a cutoff fold change > 2 and adjusted p-value < 0.05.

ORGANISM(S): Mus musculus

PROVIDER: GSE125698 | GEO | 2019/03/01

REPOSITORIES: GEO

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Project description:We are studying the natural history, pathogenesis and treatment of patients with WHIM syndrome, an immunodeficiency disorder characterized by warts, hypogammaglobulinemia, recurrent infections and neutropenia usually due to autosomal dominant gain-of-function mutations in chemokine receptor CXCR4. We have identified a patient born with WHIM syndrome and the WHIM mutation CXCR4R334X who has been disease-free for 20 years and who lacks CXCR4R334X in myeloid cells, the cells that drive disease manifestations. She is a genetic and hematopoietic mosaic, since she still has the mutation in lymphoid cells and non-hematopoietic cells. Cytogenetics and microarray analysis revealed that the mechanism of loss of the mutation was deletion of the mutant allele from one copy of chromosome 2. Whole genome sequencing of patient neutrophil and skin fibroblast genomic DNA revealed that the mechanism of deletion was chromothripsis, a process of chromosome shattering resulting in deletions and rearrangements of the non-deleted chromosomal segments. In the patient, this process evidently occurred in a single hematopoietic stem cell (HSC), resulting in deletion of the disease allele CXCR4R334X and one copy of 163 other genes on chromosome 2. This HSC evidently acquired a growth advantage and repopulated the HSC population and the myeloid lineage. Consistent with this, studies using gene targeted mice in competitive bone marrow transplantation experiments revealed that selective Cxcr4 haploinsufficiency (inactivation of one copy of Cxcr4 and not of any other genes) was sufficient to confer a strong engraftment advantage over bone marrow cells from wild type mice as well as bone marrow cells from a mouse model of WHIM syndrome. These results suggest that CXCR4 knockdown may be a useful strategy to enhance bone marrow engraftment in the absence of toxic bone marrow conditioning regimens.

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Gene expression in B16.SIY tumor cells deficient in IFN-g signaling

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