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PTIR1 acts as a suppressor of immunoproteasome and promotes cancer immune resistance [TILs 10x scRNA-seq]

ABSTRACT: PTIR1 acts as a suppressor of immunoproteasome and promotes cancer immune resistance [TILs 10x scRNA-seq]

PROVIDER: PRJNA823649 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18642984.fastq.gz	Fastqsanger.gz
	SRR18642985.fastq.gz	Fastqsanger.gz
	SRR18642986.fastq.gz	Fastqsanger.gz
	SRR18642987.fastq.gz	Fastqsanger.gz
	SRR18642988.fastq.gz	Fastqsanger.gz

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PTIR1 acts as a suppressor of immunoproteasome and promotes cancer immune resistance

Project description:PTIR1 acts as a suppressor of immunoproteasome and promotes cancer immune resistance

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PTIR1 acts as a suppressor of immunoproteasome and promotes cancer immune resistance [TILs 10x scRNA-seq]

Project description:Cancer cells evade host immune surveillance by virtue of poor immunogenicity. We identify a novel oncogene that acts as a promotor of tumor immune resistance, designated as PTIR1. Tumor-intrinsic PTIR1 is induced by RNA splicing and highly correlated with poor outcome of patients with cancer.

2025-04-05 | GSE200190 | GEO

PTIR1 acts as a suppressor of immunoproteasome and promotes cancer immune resistance

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Immunoproteasome dysfunction augments alternative polarization of alveolar macrophages

Project description:The proteasome is a central regulatory hub for intracellular signaling by degrading numerous signaling mediators. Immunoproteasomes are specialized types of proteasomes known to be involved in shaping adaptive immune responses, but their role for innate immune signaling is elusive. Here, we analyzed immunoproteasome function for polarization of alveolar macrophages which are highly specialized tissue macrophages of the alveolar surface of the lung. Classical activation (M1 polarization) of primary alveolar macrophages by LPS/IFNÎ³ transcriptionally induced all three immunoproteasome subunits LMP2, LMP7, and MECL-1. In contrast, IL-4 triggered alternative (M2) activation was accompanied by posttranscriptional upregulation of LMP2 and LMP7. Accordingly, immunoproteasome activity increased in M1 cells, and to some extent under M2 conditions. Analyzing the polarization capability from LMP7 deficient mice revealed no effect on the LPS/IFNÎ³ triggered M1 profile, but uncovered a distorted M2 profile for IL-4 stimulated LMP7-/- alveolar macrophages as characterized by increased M2 marker gene expression and CCL17 cytokine release. This shift in immunoproteasome-dependent M2 polarization was accompanied by amplified AKT/STAT6 activation and IRF4 expression in LMP7-/- alveolar macrophages. IL-13 stimulation of LMP7 deficient cells induced a similar M2 skewed profile and IL4RÎ± protein expression was generally elevated in LMP7-/- alveolar macrophages, indicating that amplified IL4R signaling in immunoproteasome defective cells may contribute to augmented M2 polarization. Importantly, treatment with an LMP7-specific proteasome inhibitor recapitulated the findings of genetic LMP7 inactivation. Our results thus suggest a novel role of immunoproteasome function for regulating innate immune function of macrophages by limiting IL4R expression and signaling. Expression data of M0 and M2 macrophages derived from Lmp7 k.o. and control animals

2016-06-29 | E-GEOD-72000 | biostudies-arrayexpress

Caffeine modulates immunoproteasome activity and content in colorectal adenocarcinoma cells

Project description:Proteasomes hydrolyze most intracellular proteins. Immunoproteasome is a specific form of proteasome implicated in inflammation, cancer and autoimmune diseases. Modulation of immunoproteasome activity and content is a promising direction for the management of socially important pathologies. Using previously obtained reporter colorectal cancer cell lines, we tested how various commonly used compounds including ibuprofen, acetylsalicylic acid, vitamin C, caffeine and others, affect immunoproteasome expression. Methods: Immunoproteasome subunit expression was assessed by flow cytometry, qPCR and Western blot. Proteasome activity was tested using fluorogenic substrates and the activity probe. Transcriptome analysis was performed to identify patterns of gene expression changes. Results: Among the tested compounds caffeine was the only drug that revealed modest reduction in quantity of immunoproteasomes. The effect of caffeine on immunoproteasomes varied between cell lines and was stronger as a result of prolonged treatment. The reduction of immunoproteasome content in cells treated with caffeine coincided with decreased expression of immunoproteasome subunits and downregulation of Nrf3 transcription factor and a PAC4 proteasome assembly chaperone. Moreover, decreased expression of immunoproteasome subunits in cells treated with caffeine coincided with the reduction of oxidative stress levels. Caffeine did not affect the degradation of immunoproteasomes by autophagy. Conclusions: Modulation of immunoproteasome expression by caffeine might help to optimize existing and develop novel strategies for the treatment of colorectal cancer and several autoimmune diseases.

2024-10-22 | GSE279800 | GEO

Immunoproteasome dysfunction augments alternative polarization of alveolar macrophages

Project description:The proteasome is a central regulatory hub for intracellular signaling by degrading numerous signaling mediators. Immunoproteasomes are specialized types of proteasomes known to be involved in shaping adaptive immune responses, but their role for innate immune signaling is elusive. Here, we analyzed immunoproteasome function for polarization of alveolar macrophages which are highly specialized tissue macrophages of the alveolar surface of the lung. Classical activation (M1 polarization) of primary alveolar macrophages by LPS/IFNγ transcriptionally induced all three immunoproteasome subunits LMP2, LMP7, and MECL-1. In contrast, IL-4 triggered alternative (M2) activation was accompanied by posttranscriptional upregulation of LMP2 and LMP7. Accordingly, immunoproteasome activity increased in M1 cells, and to some extent under M2 conditions. Analyzing the polarization capability from LMP7 deficient mice revealed no effect on the LPS/IFNγ triggered M1 profile, but uncovered a distorted M2 profile for IL-4 stimulated LMP7-/- alveolar macrophages as characterized by increased M2 marker gene expression and CCL17 cytokine release. This shift in immunoproteasome-dependent M2 polarization was accompanied by amplified AKT/STAT6 activation and IRF4 expression in LMP7-/- alveolar macrophages. IL-13 stimulation of LMP7 deficient cells induced a similar M2 skewed profile and IL4Rα protein expression was generally elevated in LMP7-/- alveolar macrophages, indicating that amplified IL4R signaling in immunoproteasome defective cells may contribute to augmented M2 polarization. Importantly, treatment with an LMP7-specific proteasome inhibitor recapitulated the findings of genetic LMP7 inactivation. Our results thus suggest a novel role of immunoproteasome function for regulating innate immune function of macrophages by limiting IL4R expression and signaling.

2016-06-29 | GSE72000 | GEO

The small protein YjiS acts as a virulence suppressor in Salmonella Typhimurium

Project description:The small protein YjiS acts as a virulence suppressor in Salmonella Typhimurium

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Targeting an alternate Wilms Tumor Antigen-1 peptide bypasses immunoproteasome dependency

Project description:scRNAseq reveals immune evasion from engineered T cell receptor gene therapy by acquisition of immunoproteasome deficiency in acute myeloid leukemia

2022-09-30 | GSE190501 | GEO

Transcriptomic profile of Traf6-deficient CD8+ TILs

Project description:Transcriptomic profile of sorted CD8+ TILs from Rag1-/- mice 4 days after transferred. Each group has two replicates.

2023-12-06 | GSE222539 | GEO

RNA-seq of T in PBMC and TILs

Project description:Purpose: Transcriptome profiling (RNA-seq) was used to compare the expression differences between T in PBMC and TILs Methods:Paired TILs and T in PBMC cells were sorted from fresh patient blood and tumor samples. Then the mRNA were sequeced using xTen platform. The sequence reads that passed quality filters were analyzed. Results: by extract mRNA from tumor infiltrated T cells from ovarian cancer patient sample and T cells from patient bllod samples, we compared the different expressed genes from TIL and T in blood. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to T cell exhausetion. Conclusions: We conclude that T in PBMC and TILs share different transcriptome characterization.

2022-12-18 | GSE157936 | GEO

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