The epigenetic modifier PBRM1 restricts the basal activity of the innate immune system by repressing retinoic acid‐inducible gene‐I‐like receptor signalling and is a potential prognostic biomarker for colon cancer

Shu, Xing-sheng; Zhao, Yingying; Sun, Yanmei; Zhong, Li-Ye; Cheng, Yingduan; Zhang, Yixiang; Ning, Kaile; Tao, Qian; Wang, Yejun; Ying, Ying

doi:10.1002/path.4986

Cited by 35 publications

(26 citation statements)

References 50 publications

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“…In support of this, a recent CRISPR-Cas9 screen identified PBRM1, along with other PBAF-specific subunits, as resistance factors against T-cell mediated killing (Pan et al, 2018). This is related to a general role for PBRM1 in suppressing the inflammatory response, as PBRM1 deletion also increases innate immunity hyperinflammation in the gut (He et al, 2017;Shu et al, 2017). The general role for PBRM1 in the stress response could relate to PBRM1's role in suppressing inflammation (and T-cell mediated toxicity) through the regulation of homeostasis (Chovatiya and Medzhitov, 2014), although that connection will need to be explored further.…”

Section: Discussionmentioning

confidence: 85%

PBRM1 regulates the stress response in epithelial cells

Porter

Dhiman

Chowdhury

et al. 2018

Preprint

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Polybromo1 (PBRM1) is a chromatin remodeler subunit highly mutated in cancer, particularly renal clear cell carcinoma. PBRM1 is a member of the SWI/SNF subcomplex, PBAF (PBRM1-Brg1/Brm Associated Factors) and is characterized by six tandem bromodomains. Here we establish a role for PBRM1 in epithelial cell maintenance through the expression of genes involved in cell adhesion, metabolism, stress response, and apoptosis. In support of a general role for PBRM1 in stress response and apoptosis, we observe that loss of PBRM1 results in an increase in reactive oxygen species generation and a decrease in cellular viability under stress conditions. We find that loss of PBRM1 promotes cell growth under favorable conditions but is required for cell survival under conditions of cellular stress.

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Section: Discussionmentioning

confidence: 85%

PBRM1 regulates the stress response in epithelial cells

Porter

Dhiman

Chowdhury

et al. 2018

Preprint

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“…The brief analytical pipeline for both platforms including initial quality check, reads filtering, mapping to Arabidopsis genome and subsequent transcriptome-related analysis following the standard procedures has been published previously (Fig. 1 ) [ 27 , 28 ]. The quality assessment and platform comparison will be discussed in the forthcoming sections.…”

Section: Resultsmentioning

confidence: 99%

“…The bioinformatic pipeline was performed as described previously with minor modifications [ 27 , 28 ]. Raw sequencing reads were filtered to get clean reads by using SOAPnuke (v1.5.2, parameters -l 15, -q 0.2, -n 0.05) ( https://github.com/BGI-flexlab/SOAPnuke ).…”

Section: Methodsmentioning

confidence: 99%

Comparative performance of the BGISEQ-500 and Illumina HiSeq4000 sequencing platforms for transcriptome analysis in plants

et al. 2018

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BackgroundThe next-generation sequencing (NGS) technology has greatly facilitated genomic and transcriptomic studies, contributing significantly in expanding the current knowledge on genome and transcriptome. However, the continually evolving variety of sequencing platforms, protocols and analytical pipelines has led the research community to focus on cross-platform evaluation and standardization. As a NGS pioneer in China, the Beijing Genomics Institute (BGI) has announced its own NGS platform designated as BGISEQ-500, since 2016. The capability of this platform in large-scale DNA sequencing and small RNA analysis has been already evaluated. However, the comparative performance of BGISEQ-500 platform in transcriptome analysis remains yet to be elucidated. The Illumina series, a leading sequencing platform in China’s sequencing market, would be a preferable reference to evaluate new platforms.MethodsTo this end, we describe a cross-platform comparative study between BGISEQ-500 and Illumina HiSeq4000 for analysis of Arabidopsis thaliana WT (Col 0) transcriptome. The key parameters in RNA sequencing and transcriptomic data processing were assessed in biological replicate experiments, using aforesaid platforms.ResultsThe results from the two platforms BGISEQ-500 and Illumina HiSeq4000 shared high concordance in both inter- (correlation, 0.88–0.93) and intra-platform (correlation, 0.95–0.98) comparison for gene quantification, identification of differentially expressed genes and alternative splicing events. However, the two platforms yielded highly variable interpretation results for single nucleotide polymorphism and insertion–deletion analysis.ConclusionThe present case study provides a comprehensive reference dataset to validate the capability of BGISEQ-500 enabling it to be established as a competitive and reliable platform in plant transcriptome analysis.Electronic supplementary materialThe online version of this article (10.1186/s13007-018-0337-0) contains supplementary material, which is available to authorized users.

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“…Therefore, IFN‐β identifies the virus RNA and induces the congenital antiviral response . Remarkably, like other innate immune pathways, upon stimulation, RLR signaling is markedly amplified by multiple feed‐forward loops in self‐regulatory or autocrine/paracrine ways . TLRs are usually sensitive to microbial components, DNA, and RNA fragments .…”

Section: The Importance Of the Intestinal Epithelial Barrier And Micrmentioning

confidence: 99%

“…23 Remarkably, like other innate immune pathways, upon stimulation, RLR signaling is markedly amplified by multiple feed-forward loops in self-regulatory or autocrine/paracrine ways. 24 TLRs are usually sensitive to microbial components, DNA, and RNA fragments. 25 TLRs can be located on the cell surface or in the intracellular compartment, with the specific ligand completing the feedback and associated with a specific adaptor that activates the cascade of downstream signals.…”

Section: The Importance Of the Intestinal Epithelial Barrier And Micrmentioning

confidence: 99%

The role of microbiota in the development of colorectal cancer

Dai

Zhang

et al. 2019

Intl Journal of Cancer

104

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Colorectal cancer is the third largest cancer in worldwide and has been proven to be closely related to the intestinal microbiota. Many reports and clinical studies have shown that intestinal microbial behavior may lead to pathological changes in the host intestines. The changes can be divided into epigenetic changes and carcinogenic changes at the gene level, which ultimately promote the production and development of colorectal cancer. This article reviews the pathways of microbial signaling in the intestinal epithelial barrier, the role of microbiota in inflammatory colorectal tumors, and typical microbial carcinogenesis. Finally, by gaining a deeper understanding of the intestinal microbiota, we hope to achieve the goal of treating colorectal cancer using current microbiota technologies, such as fecal microbiological transplantation.

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The epigenetic modifier PBRM1 restricts the basal activity of the innate immune system by repressing retinoic acid‐inducible gene‐I‐like receptor signalling and is a potential prognostic biomarker for colon cancer

Cited by 35 publications

References 50 publications

PBRM1 regulates the stress response in epithelial cells

PBRM1 regulates the stress response in epithelial cells

Comparative performance of the BGISEQ-500 and Illumina HiSeq4000 sequencing platforms for transcriptome analysis in plants

The role of microbiota in the development of colorectal cancer

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