β1 integrin signaling governs necroptosis via the chromatin remodeling factor CHD4

Fibrosis, characterized by sustained activation of myofibroblasts and excessive extracellular matrix (ECM) deposition, is known to be associated with chronic inflammation. RIPK3, the central kinase of necroptosis signaling, is upregulated in fibrosis and contributes to the TNF-mediated inflammation. In bile duct ligation-induced liver fibrosis, we found that myofibroblasts are the major cell type expressing RIPK3. Genetic ablation of β1 integrins, the major profibrotic ECM receptors in fibroblasts, not only abolished ECM fibrillogenesis but also blunted RIPK3 expression via an epigenetic mechanism mediated by the chromatin remodeling factor CHD4. While the function of CHD4 has been conventionally linked to NuRD and ChAHP complexes, we found that CHD4 potently repressed a set of genes, including Ripk3, with high locus specificity but independent of either the NuRD or ChAHP complex. Thus, our data uncover that β1 integrin intrinsically links fibrotic signaling to RIPK3-driven inflammation via a novel mode of action of CHD4.

[1]  Tony D. Southall,et al.  NuRD‐independent Mi‐2 activity represses ectopic gene expression during neuronal maturation , 2023, bioRxiv.

[2]  V. Hornung,et al.  Tumor necrosis factor is a necroptosis-associated alarmin , 2022, bioRxiv.

[3]  M. Pellegrini,et al.  Epigenetic silencing of RIPK3 in hepatocytes prevents MLKL-mediated necroptosis from contributing to liver pathologies. , 2022, Gastroenterology.

[4]  Antoine M. van Oijen,et al.  The role of auxiliary domains in modulating CHD4 activity suggests mechanistic commonality between enzyme families , 2022, bioRxiv.

[5]  Frank Y. S. Chuang,et al.  KSHV episome tethering sites on host chromosomes and regulation of latency-lytic switch by CHD4 , 2022, Cell reports.

[6]  J. Wrana,et al.  Myofibroblast YAP/TAZ activation is a key step in organ fibrogenesis , 2022, JCI insight.

[7]  J. Rasko,et al.  Unique protein interaction networks define the chromatin remodelling module of the NuRD complex , 2021, bioRxiv.

[8]  P. Rodrigues,et al.  RIPK3 acts as a lipid metabolism regulator contributing to inflammation and carcinogenesis in non-alcoholic fatty liver disease , 2020, Gut.

[9]  V. Hornung,et al.  C-tag TNF: a reporter system to study TNF shedding , 2020, The Journal of Biological Chemistry.

[10]  J. Qin,et al.  Myofiber necroptosis promotes muscle stem cell proliferation via releasing Tenascin-C during regeneration , 2020, Cell Research.

[11]  André F. Rendeiro,et al.  Structural cells are key regulators of organ-specific immune responses , 2020, Nature.

[12]  Wenjun Yu,et al.  ADNP Controls Gene Expression Through Local Chromatin Architecture by Association With BRG1 and CHD4 , 2020, Frontiers in Cell and Developmental Biology.

[13]  P. Cramer,et al.  Nucleosome-CHD4 chromatin remodeler structure maps human disease mutations , 2020, eLife.

[14]  J. Redondo,et al.  Attenuated Epigenetic Suppression of Muscle Stem Cell Necroptosis Is Required for Efficient Regeneration of Dystrophic Muscles , 2020, Cell reports.

[15]  J. Mackay,et al.  The Nucleosome Remodeling and Deacetylase Complex Has an Asymmetric, Dynamic, and Modular Architecture , 2020, bioRxiv.

[16]  J. Ledford,et al.  A homozygous SFTPA1 mutation drives necroptosis of type II alveolar epithelial cells in patients with idiopathic pulmonary fibrosis , 2019, The Journal of experimental medicine.

[17]  F. Lupu,et al.  The NuRD chromatin-remodeling complex enzyme CHD4 prevents hypoxia-induced endothelial Ripk3 transcription and murine embryonic vascular rupture , 2019, Cell Death & Differentiation.

[18]  J. Mackay,et al.  The stoichiometry and interactome of the Nucleosome Remodeling and Deacetylase (NuRD) complex are conserved across multiple cell lines , 2019, The FEBS journal.

[19]  Matthew C. Canver,et al.  Rational targeting of a NuRD subcomplex guided by comprehensive in situ mutagenesis , 2019, Nature Genetics.

[20]  M. Vermeulen,et al.  The Nucleosome Remodelling and Deacetylation complex suppresses transcriptional noise during lineage commitment , 2019, The EMBO journal.

[21]  F. Muntoni,et al.  Necroptosis mediates myofibre death in dystrophin-deficient mice , 2018, Nature Communications.

[22]  Jason D. Buenrostro,et al.  Neutralizing Gatad2a-Chd4-Mbd3/NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency. , 2018, Cell stem cell.

[23]  Xiaodong Wang,et al.  RIP kinases as modulators of inflammation and immunity , 2018, Nature Immunology.

[24]  Samira Kiani,et al.  An enhanced CRISPR repressor for targeted mammalian gene regulation , 2018, Nature Methods.

[25]  M. Bühler,et al.  Activity-dependent neuroprotective protein recruits HP1 and CHD4 to control lineage-specifying genes , 2018, Nature.

[26]  Sandy L. Klemm,et al.  High-throughput chromatin accessibility profiling at single-cell resolution , 2018, bioRxiv.

[27]  Junying Yuan,et al.  Necroptosis promotes cell-autonomous activation of proinflammatory cytokine gene expression , 2018, Cell Death & Disease.

[28]  S. Ryter,et al.  RIPK3 promotes kidney fibrosis via AKT-dependent ATP citrate lyase. , 2018, JCI insight.

[29]  Nicholas A. Sinnott-Armstrong,et al.  An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues , 2017, Nature Methods.

[30]  William T. Sherlock,et al.  A Functional Switch of NuRD Chromatin Remodeling Complex Subunits Regulates Mouse Cortical Development , 2016, Cell reports.

[31]  H. Stunnenberg,et al.  ZMYND8 Co-localizes with NuRD on Target Genes and Regulates Poly(ADP-Ribose)-Dependent Recruitment of GATAD2A/NuRD to Sites of DNA Damage. , 2016, Cell reports.

[32]  S. Friedman,et al.  PAK proteins and YAP-1 signalling downstream of integrin beta-1 in myofibroblasts promote liver fibrosis , 2016, Nature Communications.

[33]  Weihua Li,et al.  Activation of cell-surface proteases promotes necroptosis, inflammation and cell migration , 2016, Cell Research.

[34]  Wei Zhang,et al.  The Nucleosome Remodeling and Deacetylase Complex NuRD Is Built from Preformed Catalytically Active Sub-modules , 2016, Journal of molecular biology.

[35]  Marco Y. Hein,et al.  The Perseus computational platform for comprehensive analysis of (prote)omics data , 2016, Nature Methods.

[36]  R. Fässler,et al.  Integrins synergise to induce expression of the MRTF-A–SRF target gene ISG15 for promoting cancer cell invasion , 2016, Journal of Cell Science.

[37]  A. Thorburn,et al.  Methylation-dependent loss of RIP3 expression in cancer represses programmed necrosis in response to chemotherapeutics , 2015, Cell Research.

[38]  Feng Zhang,et al.  Genome engineering using CRISPR-Cas9 system. , 2015, Methods in molecular biology.

[39]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[40]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[41]  M. Feldmann,et al.  Unraveling the signaling pathways promoting fibrosis in Dupuytren's disease reveals TNF as a therapeutic target , 2013, Proceedings of the National Academy of Sciences.

[42]  Ji Luo,et al.  Mixed lineage kinase domain-like is a key receptor interacting protein 3 downstream component of TNF-induced necrosis , 2012, Proceedings of the National Academy of Sciences.

[43]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[44]  Xiaodong Wang,et al.  Mixed Lineage Kinase Domain-like Protein Mediates Necrosis Signaling Downstream of RIP3 Kinase , 2012, Cell.

[45]  Marcel Martin Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[46]  A. Bradley,et al.  A hyperactive piggyBac transposase for mammalian applications , 2011, Proceedings of the National Academy of Sciences.

[47]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[48]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[49]  Na Zhang,et al.  RIP3, an Energy Metabolism Regulator That Switches TNF-Induced Cell Death from Apoptosis to Necrosis , 2009, Science.

[50]  F. Chan,et al.  Phosphorylation-Driven Assembly of the RIP1-RIP3 Complex Regulates Programmed Necrosis and Virus-Induced Inflammation , 2009, Cell.

[51]  M. Mann,et al.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.

[52]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.