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Resetting the transcription factor network reverses terminal chronic hepatic failure
Open accessAbstract
The cause of organ failure is enigmatic for many degenerative diseases, including end-stage liver disease. Here, using a CCl4-induced rat model of irreversible and fatal hepatic failure, which also exhibits terminal changes in the extracellular matrix, we demonstrated that chronic injury stably reprograms the critical balance of transcription factors and that diseased and dedifferentiated cells can be returned to normal function by re-expression of critical transcription factors, a process similar to the type of reprogramming that induces somatic cells to become pluripotent or to change their cell lineage. Forced re-expression of the transcription factor HNF4α induced expression of the other hepatocyte-expressed transcription factors; restored functionality in terminally diseased hepatocytes isolated from CCl4-treated rats; and rapidly reversed fatal liver failure in CCl4-treated animals by restoring diseased hepatocytes rather than replacing them with new hepatocytes or stem cells. Together, the results of our study indicate that disruption of the transcription factor network and cellular dedifferentiation likely mediate terminal liver failure and suggest reinstatement of this network has therapeutic potential for correcting organ failure without cell replacement.
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“previous reports indicated that MPH dedifferentiation could only be partially inhibited when using combined inhibition of multiple dedifferentiating signaling pathways (Sun et al, 2019; Xiang et al, 2019) or through forced expression of supra‐physiologic amounts of the Hep‐ID TF HNF4A (Nishikawa et al, 2015; Tafaleng et al, 2021; Yang et al, 2021).”
From An extended transcription factor regulatory network controls hepatocyte identity (2023) · cites this paper as Nishikawa et al, 2015
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Cites
Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors
Takahashi, K., Tanabe, K., Ohnuki, M., Narita, M., Ichisaka, T., Tomoda, K., & Yamanaka, S. (2007) · Cell · doi:10.1016/j.cell.2007.11.019 · Cited by 20,221
TopHat: discovering splice junctions with RNA-Seq
Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,682
Chapter 4 Preparation of Isolated Rat Liver Cells
Seglen, P. O. (1976) · Methods in cell biology · doi:10.1016/s0091-679x(08)61797-5 · Cited by 5,297
HIGH-YIELD PREPARATION OF ISOLATED RAT LIVER PARENCHYMAL CELLS
Berry, M. N., & Friend, D. S. (1969) · The Journal of Cell Biology · doi:10.1083/jcb.43.3.506 · Cited by 4,407
Telomere measurement by quantitative PCR
Cawthon, R. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.10.e47 · Cited by 3,538
Schuppan, D., & Afdhal, N. H. (2008) · The Lancet · doi:10.1016/s0140-6736(08)60383-9 · Cited by 2,089
Liver fibrosis – from bench to bedside
Friedman, S. L. (2003) · Journal of Hepatology · doi:10.1016/s0168-8278(02)00429-4 · Cited by 1,780
Pancreatic β Cell Dedifferentiation as a Mechanism of Diabetic β Cell Failure
Talchai, C., Xuan, S., Lin, H. V., Sussel, L., & Accili, D. (2012) · Cell · doi:10.1016/j.cell.2012.07.029 · Cited by 1,415
Hayhurst, G. P., Lee, Y.-H., Lambert, G., Ward, J. M., & Gonzalez, F. J. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.4.1393-1403.2001 · Cited by 1,107
Sladek, F. M., Zhong, W. M., Lai, E., & Darnell, J. E. (1990) · Genes & Development · doi:10.1101/gad.4.12b.2353 · Cited by 1,027
Management of Cirrhosis and Ascites
Ginès, P., Cárdenas, A., Arroyo, V., & Rodés, J. (2004) · New England Journal of Medicine · doi:10.1056/nejmra035021 · Cited by 768
Liver Regeneration after Partial Hepatectomy
Michalopoulos, G. K. (2010) · The American Journal of Pathology · doi:10.2353/ajpath.2010.090675 · Cited by 713
Grimm, D., Lee, J. S., Wang, L., Desai, T., Akache, B., Storm, T. A., & Kay, M. A. (2008) · Journal of Virology · doi:10.1128/jvi.00254-08 · Cited by 696
Assessment of the prognosis of cirrhosis: Child–Pugh versus MELD
Durand, F., & Valla, D. C. (2004) · Journal of Hepatology · doi:10.1016/j.jhep.2004.11.015 · Cited by 668
Parviz, F., Matullo, C., Garrison, W. D., Savatski, L., Adamson, J. W., Ning, G., Kaestner, K. H., Rossi, J. M., Zaret, K. S., & Duncan, S. A. (2003) · Nature Genetics · doi:10.1038/ng1175 · Cited by 588
Self-citationLaconi, E., Oren, R., Mukhopadhyay, D. K., Hurston, E., Laconi, S., Pani, P., Dabeva, M. D., & Shafritz, D. A. (1998) · American Journal Of Pathology · doi:10.1016/s0002-9440(10)65574-5 · Cited by 381
Mecanismos de lesión hepatocelular
Muntané, J., González, R., Ranchal, I., Collado, J. A., Lopez-Sanchez, L. M., Herencia, C., Rodríguez‐Ariza, A., Muñoz-Castañeda, J. R., & de la Mata, M. (2007) · Revista Española de Enfermedades Digestivas · doi:10.4321/s1130-01082007000700007 · Cited by 350
Techniques and Basic Experiments for the Study of Brain and Behavior
(1976) · Elsevier eBooks · doi:10.1016/c2013-0-04439-8 · Cited by 345
Direct Lineage Conversion of Terminally Differentiated Hepatocytes to Functional Neurons
Marro, S. G., Pang, Z. P., Yang, N., Tsai, M.-C., Qu, K., Chang, H. Y., Südhof, T. C., & Wernig, M. (2011) · Cell stem cell · doi:10.1016/j.stem.2011.09.002 · Cited by 343
Mechanisms of Liver Injury. III. Oxidative stress in the pathogenesis of hepatitis C virus
Choi, J., & Ou, J.-H. J. (2006) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00522.2005 · Cited by 310
Kyrmizi, I., Hatzis, P., Katrakili, N., Tronche, F., Gonzalez, F. J., & Talianidis, I. (2006) · Genes & Development · doi:10.1101/gad.390906 · Cited by 285
Regulation of Hepatocyte Nuclear Factor 4α-mediated Transcription
Gonzalez, F. J. (2008) · Drug Metabolism and Pharmacokinetics · doi:10.2133/dmpk.23.2 · Cited by 199
Core transcriptional regulatory circuitry in human hepatocytes
Odom, D. T., Dowell, R. D., Jacobsen, E. S., Nekludova, L., Rolfe, A., Danford, T., Gifford, D. K., Fraenkel, E., Bell, G. I., & Young, R. A. (2006) · Molecular Systems Biology · doi:10.1038/msb4100059 · Cited by 197
Ageing, telomeres, senescence, and liver injury
Hoare, M., Das, T., & Alexander, G. (2010) · Journal of Hepatology · doi:10.1016/j.jhep.2010.06.009 · Cited by 184
Bolotin, E., Liao, H., Ta, T. C., Yang, C., Hwang‐Verslues, W. W., Evans, J. R., Jiang, T., & Sladek, F. M. (2009) · Hepatology · doi:10.1002/hep.23357 · Cited by 174
Hepatocyte nuclear factor 4α attenuates hepatic fibrosis in rats
Yue, H.-Y., Yin, C., Jl, H., Zeng, X. Y., Chen, Y., Zhong, W. H., Hu, P.-F., Deng, X., Tan, Y.-X., Zhang, J.-P., et al. (2009) · Gut · doi:10.1136/gut.2008.174904 · Cited by 160
Hepatocyte transplantation in rats with decompensated cirrhosis
Kobayashi, N., Ito, M., Nakamura, J., Cai, J., Gao, C., Hammel, J. M., & Fox, I. J. (2000) · Hepatology · doi:10.1053/he.2000.5636 · Cited by 137
Self-citationPonnazhagan, S., Mukherjee, P., Yöder, M. C., Wang, X.-S., Zhou, S. Z., Kaplan, J. M., Wadsworth, S. C., & Srivastava, A. (1997) · Gene · doi:10.1016/s0378-1119(96)00576-8 · Cited by 125
Treatment of cirrhosis and liver failure in rats by hepatocyte xenotransplantation
Nagata, H., Ito, M., Cai, J., Edge, A. S. B., Platt, J. L., & Fox, I. J. (2003) · Gastroenterology · doi:10.1053/gast.2003.50065 · Cited by 125
Self-citationMechanism for reduced drug clearance in patients with cirrhosis
Pessayre, D., Lebrec, D., Descatoire, V., Martinot-Peignoux, M., & Benhamou, J. (1978) · Gastroenterology · doi:10.1016/0016-5085(78)90297-4 · Cited by 123
Sladek, F. M., & Seidel, S. D. (2001) · Elsevier eBooks · doi:10.1016/b978-012146160-7/50010-x · Cited by 122
In situ detection of oxidative DNA damage, 8-hydroxydeoxyguanosine, in chronic human liver disease
Kitada, T., Seki, S., Iwai, S., Yamada, T., Sakaguchi, H., & Wakasa, K. (2001) · Journal of Hepatology · doi:10.1016/s0168-8278(01)00171-4 · Cited by 118
Mitochondria in Chronic Liver Disease
Grattagliano, I., Russmann, S., Diogo, C. V., Bonfrate, L., Oliveira, P. J., Wang, D. Q. ‐., & Portincasa, P. (2011) · Current Drug Targets · doi:10.2174/138945011795528877 · Cited by 116
Nuclear receptors and genetic disease
Burris, T. P., & McCabe, E. R. B. (2001) · Cited by 115
Molecular Pathology of Liver Diseases
Nelson, J. E., Trinder, D., & Kowdley, K. V. (2010) · Molecular pathology library · doi:10.1007/978-1-4419-7107-4 · Cited by 105
The role of capillarization in hepatic failure: Studies in carbon tetrachloride-induced cirrhosis
Martínez‐Hernández, A., & Martinez, J. (1991) · Hepatology · doi:10.1002/hep.1840140519 · Cited by 105
Limaye, P. B., Alarcón, G., Walls, A. L., Nalesnik, M. A., Michalopoulos, G. K., Demetris, A. J., & Ochoa, E. R. (2008) · Laboratory Investigation · doi:10.1038/labinvest.2008.56 · Cited by 94
The development of the hepatic megalocytosis of chronic pyrrolizidine alkaloid poisoning.
Jago, M. V. (1969) · PubMed Central · Cited by 73
The microenvironment in hepatocyte regeneration and function in rats with advanced cirrhosis
Liu, L., Yannam, G. R., Nishikawa, T., Yamamoto, T., Basma, H., Ito, R., Nagaya, M., Dutta‐Moscato, J., Stolz, D. B., Duan, F., et al. (2011) · Hepatology · doi:10.1002/hep.24815 · Cited by 72
Self-citationBerasain, C., Herrero, J.-I., García–Trevijano, E. R., Avila, M. A., Esteban, J. I., Mato, J. M., & Prìeto, J. (2003) · Hepatology · doi:10.1053/jhep.2003.50269 · Cited by 64
Heart repair by cardiac reprogramming
Nam, Y., Song, K., & Olson, E. N. (2013) · Nature Medicine · doi:10.1038/nm.3147 · Cited by 59
Peterson, J. E. (1965) · The Journal of Pathology and Bacteriology · doi:10.1002/path.1700890117 · Cited by 59
Krähenbühl, S. (1993) · Pharmacology & Therapeutics · doi:10.1016/0163-7258(93)90020-e · Cited by 44
Lechel, A., Manns, M. P., & Rudolph, K. L. (2004) · Journal of Hepatology · doi:10.1016/j.jhep.2004.06.010 · Cited by 44
Bureš, J., Burešová, O., & Huston, J. P. (1976) · Elsevier eBooks · doi:10.1016/b978-0-444-41502-8.50006-5 · Cited by 38
Update on liver transplantation: indications, organ allocation, and long-term care.
Lopez, P. M., & Martin, P. (2006) · PubMed · Cited by 33
GenPlay, a multipurpose genome analyzer and browser
Lajugie, J., & Bouhassira, E. E. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr309 · Cited by 23
Evidence of the Intact Hepatocyte Theory in Alcoholic Cirrhosis
Vaubourdolle, M., Eschwège, V., Guechot, J., Ballet, F., Jaillon, P., GIBOUDEAU, J., & Poupon, R. Y. (1989) · Scandinavian Journal of Gastroenterology · doi:10.3109/00365528909093076 · Cited by 12
Transcriptional Control of Hepatocyte Differentiation
Locker, J. D. (2010) · Molecular pathology library · doi:10.1007/978-1-4419-7107-4_14 · Cited by 3
Self-citation
Flagged first, then by citations
Research works printed but not linked: 2
- Lopez, 2006, Mt Sinai J Med., 73, 1056
- Jago, 1969, Am J Pathol., 56, 405
Cited by
Sorted by citations
Delivery of oligonucleotides to the liver with GalNAc: From research to registered therapeutic drug.
Debacker, A. J., Voutila, J., Catley, M., Blakey, D., & Habib, N. (2020) · Molecular Therapy · doi:10.1016/j.ymthe.2020.06.015 · Cited by 424
Tillman, E. J., & Rolph, T. (2020) · Frontiers in Endocrinology · doi:10.3389/fendo.2020.601290 · Cited by 214
Direct Reprogramming of Hepatic Myofibroblasts into Hepatocytes In Vivo Attenuates Liver Fibrosis
Song, G., Pacher, M., Balakrishnan, A., Yuan, Q., Tsay, H.-C., Yang, D., Reetz, J., Brandes, S., Dai, Z., Pützer, B. M., et al. (2016) · Cell Stem Cell · doi:10.1016/j.stem.2016.01.010 · Cited by 208
Argemí, J., Latasa, M. U., Atkinson, S. R., Blokhin, I. O., Massey, V. L., Gue, J. P., Cabezas, J., Lozano, J. J., Booven, D. V., Bell, A. W., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-11004-3 · Cited by 195
Self-citationDesai, S. S., Tung, J. C., Zhou, V. X., Grenert, J. P., Malato, Y., Rezvani, M., Español‐Suñer, R., Willenbring, H., Weaver, V. M., & Chang, T. T. (2016) · Hepatology · doi:10.1002/hep.28450 · Cited by 185
Metadata
- Authors
- Nishikawa, T., Bell, A., Brooks, J. M., Setoyama, K., Melis, M., Han, B., Fukumitsu, K., Handa, K., Tian, J., Kaestner, K. H., Vodovotz, Y., Locker, J., Soto-Gutierrez, A., & Fox, I. J.
- Affiliations
- University of Pittsburgh (US)
- University of Pennsylvania (US)
- Venue
- Journal of Clinical Investigation
- Published
- 2015-03-16
- Volume
- 125
- Issue
- 4
- Pages
- 1533-1544
- ISSN
- 0021-9738 (ISSN-L)
- PMC
- PMC4396487
- OpenAlex
- W2051063852
- Cited by
- 124
- References
- 49
- Citations by year
- 2026: 4 · 2025: 12 · 2024: 15 · 2023: 13 · 2022: 12 · 2021: 17 · 2020: 11 · 2019: 8 · 2018: 9 · 2017: 5 · 2016: 11 · 2015: 5
- FWCI
- 5.93
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Journal of Clinical Investigation (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- U.S. Department of Defense (W81XWH-11-1-, W81XWH, W81XWH1110803)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK099320, R01DK48794, DK099257, R01DK099257, P01DK049210, R01DK048794)
- Topics
- Health Sciences › Medicine › Hepatology › Liver physiology and pathology
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Pharmacology › Drug-Induced Hepatotoxicity and Protection
- Health Sciences › Medicine › Surgery › Tissue Engineering and Regenerative Medicine
- Keywords
- end-stage liver disease, transcriptional regulatory networks, HNF4α, hepatocyte dedifferentiation, cellular reprogramming, carbon tetrachloride-induced liver injury, extracellular matrix
- MeSH terms
- Dependovirus, Animals, Carbon Tetrachloride Poisoning, Cells, Cultured, Gene Expression Regulation, Genetic Vectors, Liver Cirrhosis, Experimental, Male, Rats, Inbred Lew, Recombinant Fusion Proteins, Transcription Factors, Transduction, Genetic, Genetic Therapy, Down-Regulation, Liver Failure, Disease Progression, Gene Expression Profiling, CCAAT-Enhancer-Binding Protein-alpha, Hepatocytes, PPAR alpha, Rats, Hepatocyte Nuclear Factor 1-alpha, Hepatocyte Nuclear Factor 3-beta, Hepatocyte Nuclear Factor 4, Gene Regulatory Networks, Cell Dedifferentiation, Transcriptome
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