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Multiome analysis (ATAC + Gene Expression (GEX)) of SUN1 knockout and control CT26 tumors grown in syngeneic mouse model

ABSTRACT: T cell infiltration is essential for immune checkpoint inhibitors to be effective in treating solid cancers. Through a bioinformatic pipeline, we identified a target gene SUN1 that might relate to modulating immune cell infiltration and immune response. Thus, we generated one Sun1_knockout CT26 cell line (Sun1_KO) using CRISPR-Cas9. By performing multiome single nuclei sequencing using tumors grown in syngeneic model, we set out to understand how mouse Sun1 can affect the regulatory network in tumor cells in vivo.

ORGANISM(S): Mus musculus

PROVIDER: GSE262237 | GEO | 2024/03/29

REPOSITORIES: GEO

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RNA-Seq analysis of SUN1 knockout and control CT26 cells and tumors

Project description:T cell infiltration is essential for immune checkpoint inhibitors to be effective in treating solid cancers. Through a bioinformatic pipeline, we identified a target gene SUN1 that might relate to modulating immune cell infiltration and immune response. Thus, we generated one Sun1_knockout CT26 cell line (Sun1_KO) and two control CT26 cell lines (Sun1_Control) using CRISPR-Cas9. By performing RNA-seq on cultured cells, tumors grown in syngeneic model, and purified tumor cells from tumors grown in syngeneic model, we set out to understand how mouse Sun1 can affect immune-related pathways and immune cell infiltration and anti-PD1 efficacy in BALB/c mice.

2024-03-29 | GSE250602 | GEO

Multiome analysis (ATAC + Gene Expression (GEX)) of SUN1 knockout and control CT26 tumors grown in syngeneic mouse model

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RNA-Seq analysis of SUN1 knockout and control CT26 cells and tumors

Project description:RNA-Seq analysis of SUN1 knockout and control CT26 cells and tumors

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Spatially resolved multiomics of human cardiac niches - Multiome GEX

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Plasmodium berghei SUN1 and allantoicase interaction proteomics

Project description:SUN1 was identified in a screen for fertility genes in Plasmodium berghei. To understand its role, SUN1 was tagged with an HA tag at the endogenous locus, and SUN1 interacting proteins were characterised by affinity purification followed by mass spectrometry. This led to the identification of allantoicase as a SUN1-associated protein. Subsequent affinity interaction proteomics of HA-tagged allantoicase confirmed the interaction between these two proteins.

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Requirement for Sun1 in the expression of meiotic reproductive genes and piRNA

Project description:The inner nuclear envelope (NE) proteins interact with the nuclear lamina and participate in the architectural compartmentalization of chromosomes. The association of NE proteins with DNA contributes to the spatial rearrangement of chromosomes and their gene expression. Sun1 is an inner nuclear membrane (INM) protein that locates to telomeres and anchors chromosome movement in the prophase of meiosis. Here, we have created Sun1-/- mice and found that these mice are born and grow normally but are reproductively infertile. Detailed molecular analyses showed that Sun1-/- P14 testes are repressed for the expression of reproductive genes and have no detectable piRNA. These findings raise a heretofore unrecognized role of Sun1 in the selective gene expression of coding and non-coding RNAs needed for gemetogenesis. Total RNA was isolated from E14.5 mouse embryonic fibroblasts (MEFs) and and day 9 and 14 mouse whole testes. cDNA samples from paired (same parents) wt (Cy3-labled) and Sun1-/- (Cy5-labled) mice were mixed and hybridized.

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RNA sequencing data of CT26-shppp2r1a and CT26-scr samples

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Depletion of Sun1/2 Induces Heterochromatin Accrual in MSCs

Project description:Mesenchyal Stem Cells (MSCs) differentiation into multiple lineages, such as osteocytes and adipocytes, has been shown to be regulated by mechanical signals. The Linker of the Nucleoskeleton and Cytoskeleton (LINC) complex has been shown to be required for mechanical signal transduction, regulation of MSCs differentiation, and nuclear integrity. The LINC complex is made of Nesprins and Sun proteins. Nesprin proteins associate with the cytoskeleton on the outer nuclear membrane and Sun proteins are bound to the inner nuclear membrane where they bind to inner nuclear proteins and chromatin. We investigated the role of the Sun1/2 in regulating the inner nuclear functions of chromatin organization and adipogenic differentiation independently of the LINC complex function. We show that depletion of Sun1/2 increased nuclear area and perimeter, and decreased circularity. Expression of a dominant-negative KASH (dnKASH) domain targeting the SUN domain on Sun proteins inhibiting Nesprin-SUN association resulting a loss of Nesprin localization to the nuclear envelope decreased nuclear area and circularity. Adipogenesis was inhibited during Sun1/2 depletion while dnKASH expression accelerated adipgoenesis. RNA-seq data showed decreased adipogensis and increased immune response during Sun1/2 depletion. dnKASH responded oppositely with increased adipogenic gene expression and decreased immune response. We also observed increased H3K9me3 levels, increased H3K9me3 foci count, and enrichment on Adipoq during Sun1/2 depletion. No increase of H3K9me3 levels, foci count, or increased H3K9me3 enrichment on Adipoq was found during dnKASH expression. We conclude that physically decoupling of the LINC complex via dnKASH accelerates adipogenesis and that Sun1/2 regulates chromatin organization and adipogenesis independently of the LINC complex function.

2022-07-13 | GSE193505 | GEO

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Project description:TCR variable regions transcripts of three CT26-shppp2r1a samples and three CT26-scr samples

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Project description:PI3K inhibitors with differential selectivity to distinct PI3K isoforms have been tested extensively in clinical trials, largely to target tumor epithelial cells. PI3K signaling also regulates the immune system and inhibition of PI3Kdelta modulate the tumor immune microenvironment of pre-clinical mouse tumor models by relieving T-regs-mediated immunosuppression. While PI3K inhibitors as a class and PI3Ka/d specifically are associated with immune-related side effects. However, the impact of mixed PI3K inhibitors in tumor immunology is under-explored. Here we examine the differential effects of AZD8835 a dual PI3Ka/d inhibitor specifically on the tumor immune microenvironment using syngeneic CT26 mice. CT-26 (5x10^6 cells/mouse) tumor cells were implanted subcutaneously (s.c.) in the left flank of female Balb/c and C57/Bl6 mice, respectively. AZD8835 was dosed at 50mg/kg twice daily in at 2days on/ 5 days off schedule for times indicated in figures or 25mg/kg BID daily. At end of study tumor tissues were then transferred into the gentleMACS C Tube containing RPMI. Tumor samples were processed using the mouse tumor dissociation kit from Miltenyi Biotec. Cells were liberated from tumors for downstream application using a mouse tumor dissociation kit and octodissociator (Miltenyi) according to manufacturer’s instructions. For RNA sequencing, total RNA was extracted using the RNeasy 96 Qiacube HT Kit (Qiagen), quality validated using nanodrop and Quantit RNA Assay Kit (Thermo Fisher), and submitted for TrueSeq Stranded mRNA library preparation, following the manufacturer’s instructions (Illumina). Resulting libraries were sequenced on the HiSeq4000 System.

2019-01-08 | E-MTAB-7386 | biostudies-arrayexpress

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