An atlas of human liver cells reveals heterogeneity and epithelial progenitors
Michalopoulos, G. Okay. & DeFrances, M. C. Regeneration of the liver. Science 276, 60-66 (1997).
Ryerson, A.B. et al. Annual report back to the nation on the state of most cancers, 1975-2012, presenting the growing incidence of liver most cancers. Most cancers 122, 1312-1337 (2016).
Grün, D. & van Oudenaarden, A. Design and evaluation of single-cell sequencing experiments. Cell 163, 799-810 (2015).
Herman, J.S., Sagar and Grün, D. FateID deduce mobile destiny bias in multipotent progenitors from single-cell RNA information. Nat. Strategies 15, 379-386 (2018).
Grün, D. et al. Sequencing of unicellular messenger RNA reveals uncommon varieties of intestinal cells. Nature 525, 251-255 (2015).
Jungermann, Okay. & Kietzmann, T. Zonation of parenchymal and non-parenchymal metabolism within the liver. Annu. Rev Nutr. 16: 179-203 (1996).
Gebhardt, R. Liver metabolic zonation: regulation and implications for liver operate. Pharmacol. Ther. 53, 275-354 (1992).
Kietzmann, T. Metabolic zonation of the liver: the oxygen gradient revisited. Redox Biol. 11, 622-630 (2017).
Halpern, Okay.B. et al. The unicellular spatial reconstruction reveals the worldwide division of labor within the mammalian liver. Nature 542, 352-356 (2017).
MacParland, S.A. et al. Single-cell RNA sequencing of the human liver reveals distinct populations of intrahepatic macrophages. Nat. Widespread. 9, 4383 (2018).
Haghverdi, L., Büttner, M., Wolf, F. A., Buettner, F. & Theis, F. J. Dissemination. The pseudotime robustly reconstructs the branching of the lineage. Nat. Strategies 13, 845-848 (2016).
Strauss, O., Phillips, A., Ruggiero, Okay., and Bartlett A. Dunbar, R. Immunofluorescence identifies distinct subsets of endothelial cells within the human liver. Sci. Rep. 7, 44356 (2017).
Halpern, Okay.B. et al. The pairwise cell sequencing permits the mapping of the spatial gene expression of the endothelial cells of the liver. Nat. Biotechnol. 36, 962-970 (2018).
Raven, A. et al. Cholangiocytes act as facultative hepatic stem cells throughout impaired hepatocyte regeneration. Nature 547, 350-354 (2017).
Michalopoulos, G.Okay., Barua, L. and Bowen, W. C. Transdifferentiation of rat hepatocytes into biliary cells after ligation of the bile ducts and poisonous biliary lesion. Hepatology 41, 535-544 (2005).
Schmelzer, E. et al. Human liver stem cells from fetal and postnatal donors. J. Exp. Med. 204, 1973-1987 (2007).
Turner, R. et al. Biology of human hepatic stem cells and the maturing liver line. Hepatology 53, 1035-1045 (2011).
Grün, D. et al. De novo prediction of stem cell id utilizing unicellular transcriptome information. Cell Stem Cell 19, 266-277 (2016).
Okabe, M. et al. Potential hepatic stem cells reside in regular and injured mouse liver EpCAM + cells. Improvement 136, 1951-1960 (2009).
Cardinale, V. et al. Multipotent stem / progenitor cells in human biliary timber give rise to hepatocytes, cholangiocytes and pancreatic islets. Hepatology 54, 2159-2172 (2011).
Kodama, Y. et al. Hes1 is important for the event of the intrahepatic bile ducts. Gastroenterology 124, A123 (2003).
Sosa-Pineda, B., Wigle, J.T. and Oliver, G. The migration of hepatocytes throughout liver growth requires Prox1. Nat. Broom. 25, 254-255 (2000).
Huch, M. et al. Lengthy-term tradition of secure bipotent stem cells within the genome from grownup human liver. Cell 160, 299-312 (2015).
Betge, J. et al. MUC1, MUC2, MUC5AC and MUC6 in colorectal most cancers: Expression profiles and scientific significance. Virchows Arch. 469, 255-265 (2016).
Park, S.-W. et al. AGR2 disulfide isomerase protein is important for the manufacturing of intestinal mucus. Proc. Natl Acad. Sci. USA 106, 6950-6955 (2009).
Forner, A., Reig, M. and Bruix, J. Hepatocellular carcinoma. Lancet 391, 1301-1314 (2018).
Matkowsky, Okay.A. et al. Aldoketoreductase household 1B10 (AKR1B10) as a biomarker for distinguishing hepatocellular carcinoma from benign hepatic damage. Hum. Pathol. 45, 834-843 (2014).
Rantakari, P. et al. The endothelial protein PLVAP in lymphatics controls the entry of lymphocytes and antigens into the lymph nodes. Nat. Immunol. 16, 386-396 (2015).
Grompe, M. & Strom, S. Mouse with human livers. Gastroenterology 145, 1209-1214 (2013).
Azuma, H. et al. Sturdy growth of human hepatocytes in Fah – / – / Rag2 – / – / Il2rg – / – mice. Nat. Biotechnol. 25, 903-910 (2007).
Uhlén, M. et al. Proteomics. Tissue map of the human proteome. Science 347, 1260419 (2015).
Krieger, S.E. et al. The inhibition of an infection by hepatitis C virus by anti-claudin-1 antibodies includes the neutralization of E2-CD81-claudin-1 combos. Hepatology 51, 1144-1157 (2010).
Lieber, A., Peeters, M.J., Robe, A., Perkins, J. and Kay, M. A. A modified urokinase plasminogen activator induces regeneration of the liver with out bleeding. Hum. Gene Ther. 6, 1029-1037 (1995).
Mailly, L. et al. Elimination of persistent an infection by hepatitis C virus in humanized mice with the help of a monoclonal antibody focusing on claudin-1. Nat. Biotechnol. 33, 549-554 (2015).
Hashimshony, T. et al. CEL-Seq2: Extremely multiplexed, single-cell, extremely delicate monocyte-seq. Genome Biol. 17, 77 (2016).
Li, H. & Durbin, R. Quick and correct lengthy studying alignment with the Burrows-Wheeler transformation. Bioinformatics 26, 589-595 (2010).
D. Grün, L. Kester and A. Oudenaarden, A. Validation of noise fashions for unicellular transcriptomics. Nat. Strategies 11, 637-640 (2014).
Anders, S. & Huber, W. Evaluation of Differential Expression for Sequence Rely Knowledge. Genome Biol. 11, R106 (2010).
Yu, G., Wang, L.-G., Han, Y. & He, Q.-Y. clusterProfiler: an R bundle that compares organic themes amongst clusters of genes. OMICS 16, 284-287 (2012).
Subramanian, A. et al. Gene Enrichment Evaluation: A knowledge-based strategy to decoding genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545-1550 (2005).
Mootha, V.Okay. et al. The PGC-1α delicate genes concerned in oxidative phosphorylation are coordinated in human diabetes. Nat. Broom. 34, 267-273 (2003).
Yu, G. & He, Q. Y. ReactomePA: an R / Bioconductor software program bundle for the evaluation and visualization of the reateome pathway. Mol. Biosyst. 12, 477-479 (2016).
Broutier, L. et al. Tradition and institution of self-regenerating 3D organoids of grownup human and mouse liver and pancreas and their genetic manipulation. Nat. Protocols 11, 1724-1743 (2016).
Aizarani, N. et al. Protocol for sequencing monocellular RNA from cryopreserved hepatic cells. Protoc. Exch. https://doi.org/10.21203/rs.2.9620/v1 (2019).