Rigual, M. D. M., Sanchez Sanchez, P. & Djouder, N. Is liver regeneration key in hepatocellular carcinoma development? Trends Cancer 9, 140–157 (2023).
Martini, T., Naef, F. & Tchorz, J. S. Spatiotemporal metabolic liver zonation and consequences on pathophysiology. Annu. Rev. Pathol. 18, 439–466 (2023).
Gordillo, M., Evans, T. & Gouon-Evans, V. Orchestrating liver development. Development 142, 2094–2108 (2015).
Wang, B. et al. Self-renewing diploid Axin2+ cells fuel homeostatic renewal of the liver. Nature 524, 180–185 (2015).
Sun, T. et al. AXIN2+ pericentral hepatocytes have limited contributions to liver homeostasis and regeneration. Cell Stem Cell 26, 97–107 (2020).
May, S. et al. Absent expansion of AXIN2+ hepatocytes and altered physiology in Axin2CreERT2 mice challenges the role of pericentral hepatocytes in homeostatic liver regeneration. J. Hepatol. 78, 1028–1036 (2023).
Chen, F. et al. Broad distribution of hepatocyte proliferation in liver homeostasis and regeneration. Cell Stem Cell 26, 27–33 (2020).
Matsumoto, T. et al. In vivo lineage tracing of polyploid hepatocytes reveals extensive proliferation during liver regeneration. Cell Stem Cell 26, 34–47 (2020).
Wei, Y. et al. Liver homeostasis is maintained by midlobular zone 2 hepatocytes. Science 371, eabb1625 (2021).
He, L. et al. Proliferation tracing reveals regional hepatocyte generation in liver homeostasis and repair. Science 371, eabc4346 (2021).
Ben-Moshe, S. et al. Spatial sorting enables comprehensive characterization of liver zonation. Nat. Metab. 1, 899–911 (2019).
Herranz-Montoya, I., Park, S. & Djouder, N. A comprehensive analysis of prefoldins and their implication in cancer. iScience 24, 103273 (2021).
Tummala, K. S. et al. Inhibition of de novo NAD+ synthesis by oncogenic URI causes liver tumorigenesis through DNA damage. Cancer Cell 26, 826–839 (2014).
Xu, J. et al. A spatiotemporal atlas of mouse liver homeostasis and regeneration. Nat. Genet. 56, 953–969 (2024).
MacParland, S. A. et al. Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations. Nat. Commun. 9, 4383 (2018).
Chaves-Perez, A. et al. URI is required to maintain intestinal architecture during ionizing radiation. Science 364, eaaq1165 (2019).
Schuler, M. et al. Efficient temporally controlled targeted somatic mutagenesis in hepatocytes of the mouse. Genesis 39, 167–172 (2004).
Nivison-Smith, L. et al. Retinal amino acid neurochemistry of the southern hemisphere lamprey, Geotria australis. PLoS ONE 8, e58406 (2013).
Mitchell, C. & Willenbring, H. A reproducible and well-tolerated method for 2/3 partial hepatectomy in mice. Nat. Protoc. 3, 1167–1170 (2008).
He, Y. et al. Glutamine synthetase deficiency in murine astrocytes results in neonatal death. Glia 58, 741–754 (2010).
Bellisle, F. et al. Monosodium glutamate as a palatability enhancer in the European diet. Physiol. Behav. 49, 869–873 (1991).
Celestino, M. et al. Differential effects of sodium chloride and monosodium glutamate on kidney of adult and aging mice. Sci. Rep. 11, 481 (2021).
Heymann, F. & Tacke, F. Immunology in the liver–from homeostasis to disease. Nat. Rev. Gastroenterol. Hepatol. 13, 88–110 (2016).
Gras, G. et al. EAAT expression by macrophages and microglia: still more questions than answers. Amino Acids 42, 221–229 (2012).
Krenkel, O. & Tacke, F. Liver macrophages in tissue homeostasis and disease. Nat. Rev. Immunol. 17, 306–321 (2017).
Lachmann, A. et al. ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics 26, 2438–2444 (2010).
Selak, M. A. et al. Succinate links TCA cycle dysfunction to oncogenesis by inhibiting HIF-α prolyl hydroxylase. Cancer Cell 7, 77–85 (2005).
Koivunen, P. et al. Inhibition of hypoxia-inducible factor (HIF) hydroxylases by citric acid cycle intermediates: possible links between cell metabolism and stabilization of HIF. J. Biol. Chem. 282, 4524–4532 (2007).
Hewitson, K. S. et al. Structural and mechanistic studies on the inhibition of the hypoxia-inducible transcription factor hydroxylases by tricarboxylic acid cycle intermediates. J. Biol. Chem. 282, 3293–3301 (2007).
Ryan, H. E. et al. Hypoxia-inducible factor-1α is a positive factor in solid tumor growth. Cancer Res. 60, 4010–4015 (2000).
Clausen, B. E. et al. Conditional gene targeting in macrophages and granulocytes using LysMcre mice. Transgenic Res. 8, 265–277 (1999).
Annunziato, S., Sun, T. & Tchorz, J. S. The RSPO-LGR4/5-ZNRF3/RNF43 module in liver homeostasis, regeneration, and disease. Hepatology 76, 888–899 (2022).
Boulter, L. et al. Macrophage-derived Wnt opposes Notch signaling to specify hepatic progenitor cell fate in chronic liver disease. Nat. Med. 18, 572–579 (2012).
CZI Cell Science Program et al. CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data. Nucleic Acids Res. https://doi.org/10.1093/nar/gkae1142 (2023).
Grant, C. E., Bailey, T. L. & Noble, W. S. FIMO: scanning for occurrences of a given motif. Bioinformatics 27, 1017–1018 (2011).
Azzolin, L. et al. YAP/TAZ incorporation in the beta-catenin destruction complex orchestrates the Wnt response. Cell 158, 157–170 (2014).
Robanus-Maandag, E. C. et al. A new conditional Apc-mutant mouse model for colorectal cancer. Carcinogenesis 31, 946–952 (2010).
Brault, V. et al. Inactivation of the β-catenin gene by Wnt1-Cre-mediated deletion results in dramatic brain malformation and failure of craniofacial development. Development 128, 1253–1264 (2001).
Zhang, N. et al. The Merlin/NF2 tumor suppressor functions through the YAP oncoprotein to regulate tissue homeostasis in mammals. Dev. Cell 19, 27–38 (2010).
Zhou, Y. & Danbolt, N. C. Glutamate as a neurotransmitter in the healthy brain. J. Neural Transm. 121, 799–817 (2014).
Nair, A. B. & Jacob, S. A simple practice guide for dose conversion between animals and human. J. Basic Clin. Pharm. 7, 27–31 (2016).
Qvartskhava, N. et al. Hyperammonemia in gene-targeted mice lacking functional hepatic glutamine synthetase. Proc. Natl Acad. Sci. USA 112, 5521–5526 (2015).
Garrido, A. et al. Histone acetylation of bile acid transporter genes plays a critical role in cirrhosis. J. Hepatol. https://doi.org/10.1016/j.jhep.2021.12.019 (2021).
Lau, A. & Tymianski, M. Glutamate receptors, neurotoxicity and neurodegeneration. Pflugers Arch. 460, 525–542 (2010).
Bhushan, B. et al. TCPOBOP-induced hepatomegaly and hepatocyte proliferation are attenuated by combined disruption of MET and EGFR signaling. Hepatology 69, 1702–1718 (2019).
Fukuchi, T. et al. Effects of portal-systemic shunt following 90% partial hepatectomy in rats. J. Surg. Res. 89, 126–131 (2000).
Myronovych, A. et al. Role of platelets on liver regeneration after 90% hepatectomy in mice. J. Hepatol. 49, 363–372 (2008).
Ramachandran, P. et al. Resolving the fibrotic niche of human liver cirrhosis at single-cell level. Nature 575, 512–518 (2019).
Ma, L. et al. Tumor cell biodiversity drives microenvironmental reprogramming in liver cancer. Cancer Cell 36, 418–430 (2019).
Tummala, K. S. et al. Hepatocellular carcinomas originate predominantly from hepatocytes and benign lesions from hepatic progenitor cells. Cell Rep. 19, 584–600 (2017).
Gomes, A. L. et al. Metabolic inflammation-associated IL-17A causes non-alcoholic steatohepatitis and hepatocellular carcinoma. Cancer Cell 30, 161–175 (2016).
Cramer, T. et al. HIF-1α is essential for myeloid cell-mediated inflammation. Cell 112, 645–657 (2003).
Li, W. et al. Monocyte-derived Kupffer cells dominate in the Kupffer cell pool during liver injury. Cell Rep. 42, 113164 (2023).
Shi, C. & Pamer, E. G. Monocyte recruitment during infection and inflammation. Nat. Rev. Immunol. 11, 762–774 (2011).
Zwicker, C., Bujko, A. & Scott, C. L. Hepatic macrophage responses in inflammation, a function of plasticity, heterogeneity or both? Front. Immunol. 12, 690813 (2021).
Kistner, A. et al. Doxycycline-mediated quantitative and tissue-specific control of gene expression in transgenic mice. Proc. Natl Acad. Sci. USA 93, 10933–10938 (1996).
Fawal, M. A., Brandt, M. & Djouder, N. MCRS1 binds and couples rheb to amino acid-dependent mTORC1 activation. Dev. Cell 33, 67–82 (2015).
Dupre, A. et al. Associating portal embolization and artery ligation to induce rapid liver regeneration in staged hepatectomy. Br. J. Surg. 102, 1541–1550 (2015).
Okabe, H. et al. Percentage of future liver remnant volume before portal vein embolization influences the degree of liver regeneration after hepatectomy. J. Gastrointest. Surg. 17, 1447–1451 (2013).
Teijeiro, A. et al. Inhibition of the IL-17A axis in adipocytes suppresses diet-induced obesity and metabolic disorders in mice. Nat. Metab. 3, 496–512 (2021).
Buren, S. et al. Regulation of OGT by URI in response to glucose confers c-MYC-dependent survival mechanisms. Cancer Cell 30, 290–307 (2016).
Djouder, N. et al. S6K1-mediated disassembly of mitochondrial URI/PP1gamma complexes activates a negative feedback program that counters S6K1 survival signaling. Mol. Cell 28, 28–40 (2007).
Bueno Batista, M. et al. Disrupting hierarchical control of nitrogen fixation enables carbon-dependent regulation of ammonia excretion in soil diazotrophs. PLoS Genet. 17, e1009617 (2021).
Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).
Andreatta, M. & Carmona, S. J. UCell: robust and scalable single-cell gene signature scoring. Comput. Struct. Biotechnol. J. 19, 3796–3798 (2021).
Zhang, P. et al. Epigenomic analysis reveals a dynamic and context-specific macrophage enhancer landscape associated with innate immune activation and tolerance. Genome Biol. 23, 136 (2022).