Chiang, J. Y. L. & Ferrell, J. M. Bile acid metabolism in liver pathobiology. Gene Expr. 18, 71–87 (2018).
Ma, Z., de Man, R. A., Kamar, N. & Pan, Q. Chronic hepatitis E: advancing research and patient care. J. Hepatol. 77, 1109–1123 (2022).
Zhao, Y. et al. Mechanistic insight of SARS-CoV-2 infection using human hepatobiliary organoids. Gut 72, 216–218 (2023).
Luxenburger, H. & Thimme, R. SARS-CoV-2 and the liver: clinical and immunological features in chronic liver disease. Gut 72, 1783–1794 (2023).
Wang, Y. et al. SARS-CoV-2 infection of the liver directly contributes to hepatic impairment in patients with COVID-19. J. Hepatol. 73, 807–816 (2020).
Li, X., Fan, C., Tang, J. & Zhang, N. Meta-analysis of liver injury in patients with COVID-19. Medicine 102, e34320 (2023).
Muller, G. et al. Monkeypox virus in liver and spleen of child in Gabon. Lancet 1, 769–770 (1988).
Uphoff, C. C., Pommerenke, C., Denkmann, S. A. & Drexler, H. G. Screening human cell lines for viral infections applying RNA-Seq data analysis. PLoS ONE 14, e0210404 (2019).
Han, Y., Yang, L., Lacko, L. A. & Chen, S. Human organoid models to study SARS-CoV-2 infection. Nat. Methods 19, 418–428 (2022).
Puschhof, J., Pleguezuelos-Manzano, C. & Clevers, H. Organoids and organs-on-chips: insights into human gut-microbe interactions. Cell Host Microbe 29, 867–878 (2021).
Casanova, J. L. & Abel, L. Mechanisms of viral inflammation and disease in humans. Science 374, 1080–1086 (2021).
Merad, M. & Martin, J. C. Pathological inflammation in patients with COVID-19: a key role for monocytes and macrophages. Nat. Rev. Immunol. 20, 355–362 (2020).
Ginhoux, F. & Guilliams, M. Tissue-resident macrophage ontogeny and homeostasis. Immunity 44, 439–449 (2016).
Mosser, D. M. & Edwards, J. P. Exploring the full spectrum of macrophage activation. Nat. Rev. Immunol. 8, 958–969 (2008).
Li, Y. et al. Seasonal coronavirus infections trigger NLRP3 inflammasome activation in macrophages but is therapeutically targetable. Antivir. Res. 216, 105674 (2023).
Paerewijck, O. & Lamkanfi, M. The human inflammasomes. Mol. Asp. Med. 88, 101100 (2022).
Coll, R. C., Schroder, K. & Pelegrin, P. NLRP3 and pyroptosis blockers for treating inflammatory diseases. Trends Pharmacol. Sci. 43, 653–668 (2022).
Marsee, A. et al. Building consensus on definition and nomenclature of hepatic, pancreatic, and biliary organoids. Cell Stem Cell 28, 816–832 (2021).
Cao, X., van den Hil, F. E., Mummery, C. L. & Orlova, V. V. Generation and functional characterization of monocytes and macrophages derived from human induced pluripotent stem cells. Curr. Protoc. Stem Cell Biol. 52, e108 (2020).
Wang, W. et al. The RNA genome of hepatitis E virus robustly triggers an antiviral interferon response. Hepatology 67, 2096–2112 (2018).
Beer, A. et al. Chronic hepatitis E is associated with cholangitis. Liver Int. 39, 1876–1883 (2019).
Li, P. et al. Recapitulating hepatitis E virus-host interactions and facilitating antiviral drug discovery in human liver-derived organoids. Sci. Adv. 8, eabj5908 (2022).
Steiner, S. et al. SARS-CoV-2 biology and host interactions. Nat. Rev. Microbiol. 22, 206–225 (2024).
Guan, J., Fan, Y., Wang, S. & Zhou, F. Functions of MAP3Ks in antiviral immunity. Immunol. Res. 71, 814–832 (2023).
Broutier, L. et al. Culture and establishment of self-renewing human and mouse adult liver and pancreas 3D organoids and their genetic manipulation. Nat. Protoc. 11, 1724–1743 (2016).
Hamming, I. et al. Tissue distribution of ACE2 protein, the functional receptor for SARS coronavirus. A first step in understanding SARS pathogenesis. J. Pathol. 203, 631–637 (2004).
Shiratori, H. et al. THP-1 and human peripheral blood mononuclear cell-derived macrophages differ in their capacity to polarize in vitro. Mol. Immunol. 88, 58–68 (2017).
Legrand, C. et al. Lactate dehydrogenase (LDH) activity of the cultured eukaryotic cells as marker of the number of dead cells in the medium [corrected]. J. Biotechnol. 25, 231–243 (1992).
Chiang, J. Y. L. & Ferrell, J. M. Bile acid receptors FXR and TGR5 signaling in fatty liver diseases and therapy. Am. J. Physiol. Gastrointest. Liver Physiol. 318, G554–G573 (2020).
Yin, X., Li, X. & Feng, Z. Role of envelopment in the HEV life cycle. Viruses 8, 229 (2016).
Hanafi, N. I., Mohamed, A. S., Sheikh Abdul Kadir, S. H. & Othman, M. H. D. Overview of bile acids signaling and perspective on the signal of ursodeoxycholic acid, the most hydrophilic bile acid, in the heart. Biomolecules 8, 159 (2018).
Li, Y. et al. Hepatitis E virus infection activates NOD-like receptor family pyrin domain-containing 3 inflammasome antagonizing interferon response but therapeutically targetable. Hepatology 75, 196–212 (2022).
Wang, Y. et al. Combating pan-coronavirus infection by indomethacin through simultaneously inhibiting viral replication and inflammatory response. iScience 26, 107631 (2023).
Group, R. C. et al. Dexamethasone in hospitalized patients with Covid-19. N. Engl. J. Med. 384, 693–704 (2021).
Li, P. et al. Clinical features, antiviral treatment, and patient outcomes: a systematic review and comparative analysis of the previous and the 2022 mpox outbreaks. J. Infect. Dis. 228, 391–401 (2023).
Mitja, O. et al. Mpox in people with advanced HIV infection: a global case series. Lancet 401, 939–949 (2023).
Bruhn, P. J., Osterballe, L., Hillingso, J., Svendsen, L. B. & Helgstrand, F. Posttraumatic levels of liver enzymes can reduce the need for CT in children: a retrospective cohort study. Scand. J. Trauma Resusc. Emerg. Med. 24, 104 (2016).
Duarte-Neto, A. N. et al. Main autopsy findings of visceral involvement by fatal mpox in patients with AIDS: necrotising nodular pneumonia, nodular ulcerative colitis, and diffuse vasculopathy. Lancet Infect. Dis. 23, 1218–1222 (2023).
Li, P. et al. Mpox virus infection and drug treatment modelled in human skin organoids. Nat. Microbiol. 8, 2067–2079 (2023).
Li, P. et al. Mpox virus infects and injures human kidney organoids, but responding to antiviral treatment. Cell Discov. 9, 34 (2023).
Li, P. et al. Recapitulating infection, thermal sensitivity and antiviral treatment of seasonal coronaviruses in human airway organoids. eBioMedicine 81, 104132 (2022).
Lamers, M. M. & Haagmans, B. L. SARS-CoV-2 pathogenesis. Nat. Rev. Microbiol. 20, 270–284 (2022).
Vazquez-Armendariz, A. I. et al. Multilineage murine stem cells generate complex organoids to model distal lung development and disease. EMBO J. 39, e103476 (2020).
Vazquez-Armendariz, A. I. & Tata, P. R. Recent advances in lung organoid development and applications in disease modeling. J. Clin. Invest. 133, e170500 (2023).
Recaldin, T. et al. Human organoids with an autologous tissue-resident immune compartment. Nature 633, 165–173 (2024).
Huch, M. et al. Long-term culture of genome-stable bipotent stem cells from adult human liver. Cell 160, 299–312 (2015).
Roos, F. J. M. et al. Human branching cholangiocyte organoids recapitulate functional bile duct formation. Cell Stem Cell 29, 776–794.e713 (2022).
Castejon-Ramirez, S., Pennington, J., Beene, H., Hysmith, N. & Ost, S. A case of neonatal monkeypox treated with oral tecovirimat. Pediatrics https://doi.org/10.1542/peds.2023-061198 (2023).
Yakubovsky, M. et al. Mpox presenting as proctitis in men who have sex with men. Clin. Infect. Dis. 76, 528–530 (2023).
Arfi, V. et al. Characterization of the early steps of infection of primary blood monocytes by human immunodeficiency virus type 1. J. Virol. 82, 6557–6565 (2008).
MacParland, S. A. et al. Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations. Nat. Commun. 9, 4383 (2018).
Hakim, M. S. et al. The global burden of hepatitis E outbreaks: a systematic review. Liver Int. 37, 19–31 (2017).
Davis, H. E., McCorkell, L., Vogel, J. M. & Topol, E. J. Long COVID: major findings, mechanisms and recommendations. Nat. Rev. Microbiol. 21, 133–146 (2023).
Wong, A. C. et al. Serotonin reduction in post-acute sequelae of viral infection. Cell 186, 4851–4867.e4820 (2023).
Pan, Q. et al. Mobilization of hepatic mesenchymal stem cells from human liver grafts. Liver Transpl. 17, 596–609 (2011).
Ettayebi, K. et al. Replication of human noroviruses in stem cell-derived human enteroids. Science 353, 1387–1393 (2016).
Reese, V. C., Oropeza, C. E. & McLachlan, A. Independent activation of hepatitis B virus biosynthesis by retinoids, peroxisome proliferators, and bile acids. J. Virol. 87, 991–997 (2013).
Chhatwal, P. et al. Bile acids specifically increase hepatitis C virus RNA-replication. PLoS ONE 7, e36029 (2012).
Lloyd, G., Atkinson, T. & Sutton, P. M. Effect of bile salts and of fusidic acid on HIV-1 infection of cultured cells. Lancet 1, 1418–1421 (1988).
Winkler, E. S. et al. The intestinal microbiome restricts alphavirus infection and dissemination through a bile acid-type I IFN signaling axis. Cell 182, 901–918 e918 (2020).
Luo, L. et al. Chenodeoxycholic acid from bile inhibits influenza A virus replication via blocking nuclear export of viral ribonucleoprotein complexes. Molecules 23, 3315 (2018).
Kong, F., Saif, L. J. & Wang, Q. Roles of bile acids in enteric virus replication. Anim. Dis. 1, 2 (2021).
Haselow, K. et al. Bile acids PKA-dependently induce a switch of the IL-10/IL-12 ratio and reduce proinflammatory capability of human macrophages. J. Leukoc. Biol. 94, 1253–1264 (2013).
Arbel, R. et al. Nirmatrelvir use and severe Covid-19 outcomes during the Omicron surge. N. Engl. J. Med. 387, 790–798 (2022).
Desai, A. N. et al. Compassionate use of tecovirimat for the treatment of monkeypox infection. JAMA 328, 1348–1350 (2022).
Arias, C. A., Miller, W. R., Olsen, R., Gollihar, J. & Armstrong, A. The response of mpox-associated inflammatory syndrome to steroid therapy. Lancet Infect. Dis. 23, e323–e324 (2023).
de Almeida, L. et al. Identification of immunomodulatory drugs that inhibit multiple inflammasomes and impair SARS-CoV-2 infection. Sci. Adv. 8, eabo5400 (2022).
Malireddi, R. K. S. et al. Inflammatory cell death, PANoptosis, screen identifies host factors in coronavirus innate immune response as therapeutic targets. Commun. Biol. 6, 1071 (2023).
Gautam, A. et al. Necroptosis blockade prevents lung injury in severe influenza. Nature 628, 835–843 (2024).
Pan, Q. Host response to hepatitis E virus. Data Archiving and Networked Services https://doi.org/10.17026/LS/W57FUZ (2024).
