Barnett, K. C., Li, S., Liang, K. & Ting, J. P. A. 360 degrees view of the inflammasome: mechanisms of activation, cell death, and diseases. Cell 186, 2288–2312 (2023).
Google Scholar
Green, D. R. Caspases and their substrates. Cold Spring Harb. Perspect. Biol. 14, a041012 (2022).
Google Scholar
Kesavardhana, S., Malireddi, R. K. S. & Kanneganti, T. D. Caspases in cell death, inflammation, and pyroptosis. Annu. Rev. Immunol. 38, 567–595 (2020).
Google Scholar
Eckhart, L. & Fischer, H. Caspase-5: structure, pro-inflammatory activity and evolution. Biomolecules 14, 520 (2024).
Google Scholar
Herrmann, B. I., Grayczyk, J. P. & Brodsky, I. E. Collab or cancel? Bacterial influencers of inflammasome signaling. Annu. Rev. Microbiol. 77, 451–477 (2023).
Google Scholar
Ross, C. et al. Inflammatory caspases: toward a unified model for caspase activation by inflammasomes. Annu. Rev. Immunol. 40, 249–269 (2022).
Google Scholar
Gehart, H. & Clevers, H. Tales from the crypt: new insights into intestinal stem cells. Nat. Rev. Gastroenterol. Hepatol. 16, 19–34 (2019).
Google Scholar
Rim, E. Y., Clevers, H. & Nusse, R. The Wnt pathway: from signaling mechanisms to synthetic modulators. Annu. Rev. Biochem. 91, 571–598 (2022).
Google Scholar
Beumer, J. & Clevers, H. Cell fate specification and differentiation in the adult mammalian intestine. Nat. Rev. Mol. Cell Biol. 22, 39–53 (2021).
Google Scholar
Shi, J. et al. Inflammatory caspases are innate immune receptors for intracellular LPS. Nature 514, 187–192 (2014).
Google Scholar
Sander, L. E. et al. Detection of prokaryotic mRNA signifies microbial viability and promotes immunity. Nature 474, 385–389 (2011).
Google Scholar
Moretti, J. et al. Caspase-11 interaction with NLRP3 potentiates the noncanonical activation of the NLRP3 inflammasome. Nat. Immunol. 23, 705–717 (2022).
Google Scholar
Holland, M., Rutkowski, R. & Levin, T. C. Evolutionary dynamics of proinflammatory caspases in primates and rodents. Mol. Biol. Evol. 41, msae220 (2024).
Google Scholar
Uhlen, M. et al. Tissue-based map of the human proteome. Science 347, 1260419 (2015).
Google Scholar
Lin, X. Y., Choi, M. S. & Porter, A. G. Expression analysis of the human caspase-1 subfamily reveals specific regulation of the CASP5 gene by lipopolysaccharide and interferon-gamma. J. Biol. Chem. 275, 39920–39926 (2000).
Google Scholar
Casson, C. N. et al. Human caspase-4 mediates noncanonical inflammasome activation against gram-negative bacterial pathogens. Proc. Natl Acad. Sci. USA 112, 6688–6693 (2015).
Google Scholar
Naseer, N. et al. Salmonella enterica serovar Typhimurium induces NAIP/NLRC4- and NLRP3/ASC-independent, caspase-4-dependent inflammasome activation in human intestinal epithelial cells. Infect. Immun. 90, e0066321 (2022).
Google Scholar
Gao, C. & Chen, Y. G. Dishevelled: The hub of Wnt signaling. Cell Signal 22, 717–727 (2010).
Google Scholar
Sharma, M., Castro-Piedras, I., Simmons, G. E. Jr & Pruitt, K. Dishevelled: a masterful conductor of complex Wnt signals. Cell Signal 47, 52–64 (2018).
Google Scholar
Exconde, P. M. et al. The tetrapeptide sequence of IL-18 and IL-1β regulates their recruitment and activation by inflammatory caspases. Cell Rep. 42, 113581 (2023).
Google Scholar
Nusse, R. & Clevers, H. Wnt/β-catenin signaling, disease, and emerging therapeutic modalities. Cell 169, 985–999 (2017).
Google Scholar
Bankaitis, E. D., Ha, A., Kuo, C. J. & Magness, S. T. Reserve stem cells in intestinal homeostasis and injury. Gastroenterology 155, 1348–1361 (2018).
Google Scholar
Shivdasani, R. A., Clevers, H. & de Sauvage, F. J. Tissue regeneration: reserve or reverse? Science 371, 784–786 (2021).
Google Scholar
Sprangers, J., Zaalberg, I. C. & Maurice, M. M. Organoid-based modeling of intestinal development, regeneration, and repair. Cell Death Differ. 28, 95–107 (2021).
Google Scholar
Xie, G. et al. Zinc finger protein 277 is an intestinal transit-amplifying cell marker and colon cancer oncogene. JCI Insight 7, e150894 (2022).
Google Scholar
Ayyaz, A. et al. Single-cell transcriptomes of the regenerating intestine reveal a revival stem cell. Nature 569, 121–125 (2019).
Google Scholar
Chi, Z. et al. Gasdermin D-mediated metabolic crosstalk promotes tissue repair. Nature 634, 1168–1177 (2024).
Google Scholar
Wong, H. C. et al. Structural basis of the recognition of the dishevelled DEP domain in the Wnt signaling pathway. Nat. Struct. Biol. 7, 1178–1184 (2000).
Google Scholar
Li, V. S. et al. Wnt signaling through inhibition of beta-catenin degradation in an intact Axin1 complex. Cell 149, 1245–1256 (2012).
Google Scholar
Lamkanfi, M. & Dixit, V. M. Inflammasomes and their roles in health and disease. Annu. Rev. Cell Dev. Biol. 28, 137–161 (2012).
Google Scholar
Riedl, S. J. & Salvesen, G. S. The apoptosome: signalling platform of cell death. Nat. Rev. Mol. Cell Biol. 8, 405–413 (2007).
Google Scholar
Shi, J. et al. Cleavage of GSDMD by inflammatory caspases determines pyroptotic cell death. Nature 526, 660–665 (2015).
Google Scholar
Akuma, D. C. et al. Catalytic activity and autoprocessing of murine caspase-11 mediate noncanonical inflammasome assembly in response to cytosolic LPS. eLife 13, e83725 (2024).
Google Scholar
Fodde, R., Smits, R. & Clevers, H. APC, signal transduction and genetic instability in colorectal cancer. Nat. Rev. Cancer 1, 55–67 (2001).
Google Scholar
Zhang, L. & Shay, J. W. Multiple roles of APC and its therapeutic implications in colorectal cancer. J. Natl Cancer Inst. 106, djw332 (2017).
Cancer Genome Atlas, N. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487, 330–337 (2012).
Google Scholar
Guinney, J. et al. The consensus molecular subtypes of colorectal cancer. Nat. Med. 21, 1350–1356 (2015).
Google Scholar
Schwartz, S. Jr et al. Frameshift mutations at mononucleotide repeats in caspase-5 and other target genes in endometrial and gastrointestinal cancer of the microsatellite mutator phenotype. Cancer Res. 59, 2995–3002 (1999).
Google Scholar
Tougeron, D. et al. Tumor-infiltrating lymphocytes in colorectal cancers with microsatellite instability are correlated with the number and spectrum of frameshift mutations. Mod. Pathol. 22, 1186–1195 (2009).
Google Scholar
Smillie, C. S. et al. Intra- and inter-cellular rewiring of the human colon during ulcerative colitis. Cell 178, 714–730 e722 (2019).
Google Scholar
Burclaff, J. et al. A proximal-to-distal survey of healthy adult human small intestine and colon epithelium by single-cell transcriptomics. Cell. Mol. Gastroenterol. Hepatol. 13, 1554–1589 (2022).
Google Scholar
Elmentaite, R. et al. Cells of the human intestinal tract mapped across space and time. Nature 597, 250–255 (2021).
Google Scholar
Flood, B. et al. Altered expression of caspases-4 and -5 during inflammatory bowel disease and colorectal cancer: Diagnostic and therapeutic potential. Clin. Exp. Immunol. 181, 39–50 (2015).
Google Scholar
Steen, C. B., Liu, C. L., Alizadeh, A. A. & Newman, A. M. Profiling cell type abundance and expression in bulk tissues with CIBERSORTx. Methods Mol. Biol. 2117, 135–157 (2020).
Google Scholar
Li, H. et al. Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors. Nat. Genet. 49, 708–718 (2017).
Google Scholar
Triki, M., Lapierre, M., Cavailles, V. & Mokdad-Gargouri, R. Expression and role of nuclear receptor coregulators in colorectal cancer. World J. Gastroenterol. 23, 4480–4490 (2017).
Google Scholar
Beumer, J. et al. High-resolution mRNA and secretome atlas of human enteroendocrine cells. Cell 181, 1291–1306.e1219 (2020).
Google Scholar
Pleguezuelos-Manzano, C. et al. Establishment and culture of human intestinal organoids derived from adult stem cells. Curr. Protoc. Immunol. 130, e106 (2020).
Google Scholar
Haramis, A. P. et al. De novo crypt formation and juvenile polyposis on BMP inhibition in mouse intestine. Science 303, 1684–1686 (2004).
Google Scholar
Moparthi, L. & Koch, S. Wnt signaling in intestinal inflammation. Differentiation 108, 24–32 (2019).
Google Scholar
Kim, D. I. et al. An improved smaller biotin ligase for BioID proximity labeling. Mol. Biol. Cell 27, 1188–1196 (2016).
Google Scholar
Veeman, M. T., Slusarski, D. C., Kaykas, A., Louie, S. H. & Moon, R. T. Zebrafish prickle, a modulator of noncanonical Wnt/Fz signaling, regulates gastrulation movements. Curr. Biol. 13, 680–685 (2003).
Google Scholar
Fuerer, C. & Nusse, R. Lentiviral vectors to probe and manipulate the Wnt signaling pathway. PLoS ONE 5, e9370 (2010).
Google Scholar
Sanjana, N. E., Shalem, O. & Zhang, F. Improved vectors and genome-wide libraries for CRISPR screening. Nat. Methods 11, 783–784 (2014).
Google Scholar
Lim, K. L. et al. Parkin mediates nonclassical, proteasomal-independent ubiquitination of synphilin-1: implications for Lewy body formation. J. Neurosci. 25, 2002–2009 (2005).
Google Scholar
Viladomiu, M. et al. IgA-coated E. coli enriched in Crohn’s disease spondyloarthritis promote TH17-dependent inflammation. Sci. Transl. Med. 9, eaaf9655 (2017).
Google Scholar
Sato, T. et al. Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett’s epithelium. Gastroenterology 141, 1762–1772 (2011).
Google Scholar
Barker, N. et al. Identification of stem cells in small intestine and colon by marker gene Lgr5. Nature 449, 1003–1007 (2007).
Google Scholar
National Research Council of the National Academies. Guide for the Care and Use of Laboratory Animals, 8th Edn (The National Academies Press, 2011).
Jadhav, U. et al. Dynamic reorganization of chromatin accessibility signatures during dedifferentiation of secretory precursors into Lgr5+ intestinal stem cells. Cell Stem Cell 21, 65–77.e65 (2017).
Google Scholar
Tabula Muris, C. et al. Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. Nature 562, 367–372 (2018).
Google Scholar
Capdevila, C. et al. Time-resolved fate mapping identifies the intestinal upper crypt zone as an origin of Lgr5+ crypt base columnar cells. Cell 187, 3039–3055.e3014 (2024).
Google Scholar
Boucher, D. et al. Caspase-1 self-cleavage is an intrinsic mechanism to terminate inflammasome activity. J. Exp. Med. 215, 827–840 (2018).
Google Scholar
Faleiro, L., Kobayashi, R., Fearnhead, H. & Lazebnik, Y. Multiple species of CPP32 and Mch2 are the major active caspases present in apoptotic cells. EMBO J. 16, 2271–2281 (1997).
Google Scholar
Dominguez Conde, C. et al. Cross-tissue immune cell analysis reveals tissue-specific features in humans. Science 376, eabl5197 (2022).
Google Scholar
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Google Scholar
Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-seq data with or without a reference genome. BMC Bioinformatics 12, 323 (2011).
Google Scholar
Gulati, G. S. et al. Single-cell transcriptional diversity is a hallmark of developmental potential. Science 367, 405–411 (2020).
Google Scholar
Chen, E. Y. et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics 14, 128 (2013).
Google Scholar
Xie, Z. et al. Gene set knowledge discovery with Enrichr. Curr. Protoc. 1, e90 (2021).
Google Scholar
Liu, Y. et al. Comparative molecular analysis of gastrointestinal adenocarcinomas. Cancer Cell 33, 721–735.e728 (2018).
Google Scholar
Newman, A. M. et al. Determining cell type abundance and expression from bulk tissues with digital cytometry. Nat. Biotechnol. 37, 773–782 (2019).
Google Scholar
Funk, M. C. et al. Aged intestinal stem cells propagate cell-intrinsic sources of inflammaging in mice. Dev. Cell 58, 2914–2929.e2917 (2023).
Google Scholar
Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).
Google Scholar
Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).
Google Scholar
Stecher, G., Tamura, K. & Kumar, S. Molecular Evolutionary Genetics Analysis (MEGA) for macOS. Mol. Biol. Evol. 37, 1237–1239 (2020).
Google Scholar
Jones, D. T., Taylor, W. R. & Thornton, J. M. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8, 275–282 (1992).
Google Scholar
Felsenstein, J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791 (1985).
Google Scholar
Peled, M. et al. Affinity purification mass spectrometry analysis of PD-1 uncovers SAP as a new checkpoint inhibitor. Proc. Natl Acad. Sci. USA 115, E468–E477 (2018).
Google Scholar
Stirling, D. R. et al. CellProfiler 4: improvements in speed, utility and usability. BMC Bioinformatics 22, 433 (2021).
Google Scholar
Vincent, L. Granulometries and opening trees. Fundam. Inf. 41, 57–90 (2000).
Hepworth, M. R. et al. Immune tolerance. Group 3 innate lymphoid cells mediate intestinal selection of commensal bacteria-specific CD4+ T cells. Science 348, 1031–1035 (2015).
Google Scholar
Longman, R. S. et al. CX3CR1+ mononuclear phagocytes support colitis-associated innate lymphoid cell production of IL-22. J. Exp. Med. 211, 1571–1583 (2014).
Google Scholar
Kobayashi, T. et al. The Shigella OspC3 effector inhibits caspase-4, antagonizes inflammatory cell death, and promotes epithelial infection. Cell Host Microbe 13, 570–583 (2013).
Google Scholar
Liu, X. et al. Inflammasome-activated gasdermin D causes pyroptosis by forming membrane pores. Nature 535, 153–158 (2016).
Google Scholar
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