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Nuclear RIPK1 promotes chromatin remodeling to mediate inflammatory response

Abstract

RIPK1 is a master regulator of multiple cell death pathways, including apoptosis and necroptosis, and inflammation. Importantly, activation of RIPK1 has also been shown to promote the transcriptional induction of proinflammatory cytokines in cells undergoing necroptosis, in animal models of amyotrophic lateral sclerosis (ALS) and Alzheimer’s disease (AD), and in human ALS and AD. Rare human genetic carriers of non-cleavable RIPK1 variants (D324V and D324H) exhibit distinct symptoms of recurrent fevers and increased transcription of proinflammatory cytokines. Multiple RIPK1 inhibitors have been advanced into human clinical trials as new therapeutics for human inflammatory and neurodegenerative diseases, such as ALS and AD. However, it is unclear whether and how RIPK1 kinase activity directly mediates inflammation independent of cell death as the nuclear function of RIPK1 has not yet been explored. Here we show that nuclear RIPK1 is physically associated with the BAF complex. Upon RIPK1 activation, the RIPK1/BAF complex is recruited by specific transcription factors to active enhancers and promoters marked by H3K4me1 and H3K27ac. Activated nuclear RIPK1 mediates the phosphorylation of SMARCC2, a key component of the BAF complex, to promote chromatin remodeling and the transcription of specific proinflammatory genes. Increased nuclear RIPK1 activation and RIPK1/BAF-mediated chromatin-remodeling activity were found in cells expressing non-cleavable RIPK1, and increased enrichment of activated RIPK1 on active enhancers and promoters was found in an animal model and human pathological samples of ALS. Our results suggest that RIPK1 kinase serves as a transcriptional coregulator in nucleus that can transmit extracellular stimuli to the BAF complex to modulate chromatin accessibility and directly regulate the transcription of specific genes involved in mediating inflammatory responses.

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Fig. 1: Activated RIPK1 can be found in nucleus.
Fig. 2: RIPK1 is a transcriptional co-activator associated with multiple transcription factors and BAF complex.
Fig. 3: Inhibition of RIPK1 kinase activity disrupts genome-wide DNA accessibility by repressing the co-occupancy of SMARCC2 and BRG1.
Fig. 4: Nuclear RIPK1 modulates nucleosome-remodeling activity by mediating the phosphorylation of SMARCC2.
Fig. 5: Nuclear RIPK1 promotes transcription by mediating the phosphorylation of SMARCC2.
Fig. 6: Genome-wide analysis of the transcriptional targets of RIPK1 and BAF complex in ALS patients and ALS mouse model.
Fig. 7: A model of RIPK1 kinase activity-dependent transcriptional activation by regulating chromatin-modeling activity.

Data availability

ATAC-seq, RNA-seq and CUT&Tag data have been deposited in the GEO database (http://www.ncbi.nlm.nih.gov/geo/) with an accession number GSE179018. All the codes used in the analysis are available upon request.

References

  1. Mifflin, L., Ofengeim, D. & Yuan, J. Receptor-interacting protein kinase 1 (RIPK1) as a therapeutic target. Nat. Rev. Drug Discov. 19, 553–571 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  2. Ito, Y. et al. RIPK1 mediates axonal degeneration by promoting inflammation and necroptosis in ALS. Science 353, 603–608 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  3. Ofengeim, D. et al. RIPK1 mediates a disease-associated microglial response in Alzheimer’s disease. Proc. Natl. Acad. Sci. USA 114, E8788–E8797 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  4. Zhu, K. et al. Necroptosis promotes cell-autonomous activation of proinflammatory cytokine gene expression. Cell Death Dis. 9, 500 (2018).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  5. Lalaoui, N. et al. Mutations that prevent caspase cleavage of RIPK1 cause autoinflammatory disease. Nature 577, 103–108 (2020).

    CAS  PubMed  Article  Google Scholar 

  6. Tao, P. et al. A dominant autoinflammatory disease caused by non-cleavable variants of RIPK1. Nature 577, 109–114 (2020).

    CAS  PubMed  Article  Google Scholar 

  7. Hargreaves, D. C. & Crabtree, G. R. ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. Cell Res. 21, 396–420 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  8. Sokpor, G., Xie, Y., Rosenbusch, J. & Tuoc, T. Chromatin remodeling BAF (SWI/SNF) complexes in neural development and disorders. Front. Mol. Neurosci. 10, 243 (2017).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  9. Ho, L. & Crabtree, G. R. Chromatin remodelling during development. Nature 463, 474–484 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  10. Heintzman, N. D. et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39, 311–318 (2007).

    CAS  PubMed  Article  Google Scholar 

  11. Creyghton, M. P. et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl. Acad. Sci. USA 107, 21931–21936 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  12. Ofengeim, D. et al. Activation of necroptosis in multiple sclerosis. Cell Rep. 10, 1836–1849 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  13. Li, X. et al. Ubiquitination of RIPK1 regulates its activation mediated by TNFR1 and TLRs signaling in distinct manners. Nat. Commun. 11, 6364 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  14. Degterev, A. et al. Identification of RIP1 kinase as a specific cellular target of necrostatins. Nat. Chem. Biol. 4, 313–321 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  15. Wallach, D., Kang, T. B., Dillon, C. P. & Green, D. R. Programmed necrosis in inflammation: Toward identification of the effector molecules. Science 352, aaf2154 (2016).

    PubMed  Article  CAS  Google Scholar 

  16. Zhang, X., Dowling, J. P. & Zhang, J. RIPK1 can mediate apoptosis in addition to necroptosis during embryonic development. Cell Death Dis. 10, 245 (2019).

    PubMed  PubMed Central  Article  Google Scholar 

  17. Newton, K. et al. Cleavage of RIPK1 by caspase-8 is crucial for limiting apoptosis and necroptosis. Nature 574, 428–431 (2019).

    CAS  PubMed  Article  Google Scholar 

  18. Najafov, A. et al. BRAF and AXL oncogenes drive RIPK3 expression loss in cancer. PLoS Biol. 16, e2005756 (2018).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  19. Najafov, A., Chen, H. & Yuan, J. Necroptosis and cancer. Trends Cancer 3, 294–301 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  20. Local, A. et al. Identification of H3K4me1-associated proteins at mammalian enhancers. Nat. Genet. 50, 73–82 (2018).

    CAS  PubMed  Article  Google Scholar 

  21. Rada-Iglesias, A. et al. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470, 279–283 (2011).

    CAS  PubMed  Article  Google Scholar 

  22. Henikoff, S., Henikoff, J. G., Kaya-Okur, H. S. & Ahmad, K. Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation. Elife 9, e63274 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  23. Kaya-Okur, H. S. et al. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat. Commun. 10, 1930 (2019).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  24. Zhou, Y. et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat. Commun. 10, 1523 (2019).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  25. Xu, D. et al. TBK1 suppresses RIPK1-driven apoptosis and inflammation during development and in aging. Cell 174, 1477–1491.e19 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  26. Song, F., Chiang, P., Wang, J., Ravits, J. & Loeb, J. A. Aberrant neuregulin 1 signaling in amyotrophic lateral sclerosis. J. Neuropathol. Exp. Neurol. 71, 104–115 (2012).

    CAS  PubMed  Article  Google Scholar 

  27. Cheng, D. et al. The genome-wide transcriptional regulatory landscape of ecdysone in the silkworm. Epigenet. Chromatin 11, 48 (2018).

    Article  CAS  Google Scholar 

  28. Herrera-Uribe, J. et al. Changes in H3K27ac at gene regulatory regions in porcine alveolar macrophages following LPS or polyIC exposure. Front. Genet. 11, 817 (2020).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  29. Chiu, I. M. et al. A neurodegeneration-specific gene-expression signature of acutely isolated microglia from an amyotrophic lateral sclerosis mouse model. Cell Rep. 4, 385–401 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  30. Iurlaro, M. et al. Mammalian SWI/SNF continuously restores local accessibility to chromatin. Nat. Genet. 53, 279–287 (2021).

    CAS  PubMed  Article  Google Scholar 

  31. Monaco, C., Nanchahal, J., Taylor, P. & Feldmann, M. Anti-TNF therapy: past, present and future. Int. Immunol. 27, 55–62 (2015).

    CAS  PubMed  Article  Google Scholar 

  32. Bao, X. et al. A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63. Genome Biol. 16, 284 (2015).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  33. Kwon, H., Imbalzano, A. N., Khavari, P. A., Kingston, R. E. & Green, M. R. Nucleosome disruption and enhancement of activator binding by a human SW1/SNF complex. Nature 370, 477–481 (1994).

    CAS  PubMed  Article  Google Scholar 

  34. Ochoa, D. et al. The functional landscape of the human phosphoproteome. Nat. Biotechnol. 38, 365–373 (2020).

    CAS  PubMed  Article  Google Scholar 

  35. Chesi, A. et al. Exome sequencing to identify de novo mutations in sporadic ALS trios. Nat. Neurosci. 16, 851–855 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  36. Machol, K. et al. Expanding the spectrum of BAF-related disorders: de novo variants in SMARCC2 cause a syndrome with intellectual disability and developmental delay. Am. J. Hum. Genet. 104, 164–178 (2019).

    CAS  PubMed  Article  Google Scholar 

  37. Huttlin, E. L. et al. A tissue-specific atlas of mouse protein phosphorylation and expression. Cell 143, 1174–1189 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  38. Tak, P. P. & Firestein, G. S. NF-kappaB: a key role in inflammatory diseases. J. Clin. Invest. 107, 7–11 (2001).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  39. Fiuza, C. et al. Inflammation-promoting activity of HMGB1 on human microvascular endothelial cells. Blood 101, 2652–2660 (2003).

    CAS  PubMed  Article  Google Scholar 

  40. Brown, J. D. et al. NF-kappaB directs dynamic super enhancer formation in inflammation and atherogenesis. Mol. Cell 56, 219–231 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  41. Fontana, M. F. et al. JUNB is a key transcriptional modulator of macrophage activation. J. Immunol. 194, 177–186 (2015).

    CAS  PubMed  Article  Google Scholar 

  42. Schonthaler, H. B., Guinea-Viniegra, J. & Wagner, E. F. Targeting inflammation by modulating the Jun/AP-1 pathway. Ann. Rheum. Dis. 70, i109–i112 (2011).

    CAS  PubMed  Article  Google Scholar 

  43. Qiu, Z. et al. Sp1 is up-regulated in cellular and transgenic models of Huntington disease, and its reduction is neuroprotective. J. Biol. Chem. 281, 16672–16680 (2006).

    CAS  PubMed  Article  Google Scholar 

  44. Ravache, M., Weber, C., Merienne, K. & Trottier, Y. Transcriptional activation of REST by Sp1 in Huntington’s disease models. PLoS One 5, e14311 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  45. Swarup, V. et al. Deregulation of TDP-43 in amyotrophic lateral sclerosis triggers nuclear factor kappaB-mediated pathogenic pathways. J. Exp. Med. 208, 2429–2447 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  46. Frakes, A. E. et al. Microglia induce motor neuron death via the classical NF-kappaB pathway in amyotrophic lateral sclerosis. Neuron 81, 1009–1023 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  47. Ikiz, B. et al. The regulatory machinery of neurodegeneration in in vitro models of amyotrophic lateral sclerosis. Cell Rep. 12, 335–345 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  48. Geng, J. et al. Regulation of RIPK1 activation by TAK1-mediated phosphorylation dictates apoptosis and necroptosis. Nat. Commun. 8, 359 (2017).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  49. Dondelinger, Y. et al. Serine 25 phosphorylation inhibits RIPK1 kinase-dependent cell death in models of infection and inflammation. Nat. Commun. 10, 1729 (2019).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  50. Ishii, K. J. et al. TANK-binding kinase-1 delineates innate and adaptive immune responses to DNA vaccines. Nature 451, 725–729 (2008).

    CAS  PubMed  Article  Google Scholar 

  51. Sato, S. et al. Essential function for the kinase TAK1 in innate and adaptive immune responses. Nat. Immunol. 6, 1087–1095 (2005).

    CAS  PubMed  Article  Google Scholar 

  52. Gagnon, K. T., Li, L., Janowski, B. A. & Corey, D. R. Analysis of nuclear RNA interference in human cells by subcellular fractionation and Argonaute loading. Nat. Protoc. 9, 2045–2060 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  53. Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367–1372 (2008).

    CAS  PubMed  Article  Google Scholar 

  54. Si, W. et al. Dysfunction of the reciprocal feedback loop between GATA3- and ZEB2-nucleated repression programs contributes to breast cancer metastasis. Cancer Cell 27, 822–836 (2015).

    CAS  PubMed  Article  Google Scholar 

  55. Li, W. et al. The FOXN3-NEAT1-SIN3A repressor complex promotes progression of hormonally responsive breast cancer. J. Clin. Invest. 127, 3421–3440 (2017).

    PubMed  PubMed Central  Article  Google Scholar 

  56. Iwase, S. et al. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell 128, 1077–1088 (2007).

    CAS  PubMed  Article  Google Scholar 

  57. Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357–359 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  58. Meers, M. P., Tenenbaum, D. & Henikoff, S. Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling. Epigenet. Chromatin 12, 42 (2019).

    Article  CAS  Google Scholar 

  59. Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  60. Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  61. Ramirez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, W160–W165 (2016).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  62. Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  63. Patro, R., Duggal, G., Love, M. I., Irizarry, R. A. & Kingsford, C. Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods 14, 417–419 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  64. Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  65. Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213–1218 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  66. Buenrostro, J. D., Wu, B., Chang, H. Y. & Greenleaf, W. J. ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr. Protoc. Mol. Biol. 109, 21.29.1–21.29.9 (2015).

    Article  Google Scholar 

  67. Zhang, Y. et al. Corepressor protein CDYL functions as a molecular bridge between polycomb repressor complex 2 and repressive chromatin mark trimethylated histone lysine 27. J. Biol. Chem. 286, 42414–42425 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  68. Nott, A. et al. Brain cell type-specific enhancer-promoter interactome maps and disease-risk association. Science 366, 1134–1139 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  69. McQuin, C. et al. CellProfiler 3.0: Next-generation image processing for biology. PLoS Biol. 16, e2005970 (2018).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

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Acknowledgements

We thank Dr. Kevin Struhl for critical reading of this manuscript. We thank Dr. Jianke Zhang of Thomas Jefferson University, for Ripk1D325A/D325A/Ripk3−/− MEFs, Dr. Matthew Frosch of Harvard Neuropathology Services for providing post-mortem human spinal cord pathological samples, Dr. Jennifer Walters at the Harvard Medical School Nikon microscope facility for assistance with fluorescence microscopy, Dr. Gary Kasof of Cell Signaling Technology for developing p-S306 SMARCC2 antibody and Prof. Jiahuai Han of Xiamen University for providing Ripk1D325A/D325A MEFs during revision. This work was supported in part by the National Natural Science Foundation of China (82188101, 21837004 and 91849204), and the National Natural Science Youth Foundation of China (31701210).

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J.Y. and W.L. contributed to the conception of this project. J.Y. supervised the work. W.L. designed and performed experiments and interpreted data. B.S., C.Z., H.W., M.-M.Z., H.Z., M.G.N., D.X., V.J.M., Z.H. made contributions to the specific data acquisition. J.R. provided the patient samples. J.Y. and W.L. drafted and edited the paper. L.M. and J.R. edited the paper.

Corresponding authors

Correspondence to Wanjin Li or Junying Yuan.

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J.Y. is a consultant for Sanofi. The other authors declare that they have no competing financial interests.

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Li, W., Shan, B., Zou, C. et al. Nuclear RIPK1 promotes chromatin remodeling to mediate inflammatory response. Cell Res 32, 621–637 (2022). https://doi.org/10.1038/s41422-022-00673-3

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