Dissecting engineered cell types and enhancing cell fate conversion via Cellnet

Cell

Volumn 158, Issue 4, 2014, Pages 889-902

  Morris, Samantha A ^a,b,c   Cahan, Patrick ^a,b,c   Li, Hu ^d   Zhao, Anna M ^a,b,c   San Roman, Adrianna K ^b,e   Shivdasani, Ramesh A ^b,e   Collins, James J ^f   Daley, George Q ^a,b,c  

^a BOSTON CHILDREN S HOSPITAL   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c HARVARD STEM CELL INSTITUTE   (United States)

^d MAYO GRADUATE SCHOOL   (United States)

^e DANA FARBER CANCER INSTITUTE   (United States)

^f Boston University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALBUMIN; CCAAT ENHANCER BINDING PROTEIN ALPHA; EBF1 PROTEIN; HEPATOCYTE NUCLEAR FACTOR 3ALPHA; HEPATOCYTE NUCLEAR FACTOR 4ALPHA; KRUPPEL LIKE FACTOR 4; KRUPPEL LIKE FACTOR 5; NLRC5 PROTEIN; POU2AF1 PROTEIN; STAT1 PROTEIN; TRANSCRIPTION FACTOR CDX2; TRANSCRIPTION FACTOR FOXP1; TRANSCRIPTION FACTOR POU; TRANSCRIPTION FACTOR TBX6; UNCLASSIFIED DRUG; UVOMORULIN; ESTRADIOL; LOW DENSITY LIPOPROTEIN;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; B LYMPHOCYTE; CELL ENGINEERING; CELL FATE; CELL POPULATION; COLITIS; COLON; ENDODERM; FIBROBLAST; GENE REGULATORY NETWORK; HEMATOPOIETIC STEM CELL; IN VITRO STUDY; INTESTINE EPITHELIUM; LIVER; LIVER CELL; MACROPHAGE; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; STEM CELL; ADULT; CELL FUNCTION; CELL STRUCTURE; CELL TYPE; CONTROLLED STUDY; FLOW CYTOMETRY; GENE EXPRESSION; PHAGOCYTOSIS; UPREGULATION; ANIMAL; CYTOLOGY; METABOLISM; PROCEDURES; STANDARDS; SYSTEMS BIOLOGY;

ANIMALS; B-LYMPHOCYTES; CELL ENGINEERING; GENE REGULATORY NETWORKS; MACROPHAGES; MICE; SYSTEMS BIOLOGY;

EID: 84908431507     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2014.07.021     Document Type: Article

References (40)

1. N. Barker, J.H. van Es, J. Kuipers, P. Kujala, M. van den Born, M. Cozijnsen, A. Haegebarth, J. Korving, H. Begthel, P.J. Peters, and H. Clevers Identification of stem cells in small intestine and colon by marker gene Lgr5 Nature 449 2007 1003 1007
2. G.M. Bernardo, and R.A. Keri FOXA1: a transcription factor with parallel functions in development and cancer Biosci. Rep. 32 2012 113 130
3. L.H. Bussmann, A. Schubert, T.P. Vu Manh, L. De Andres, S.C. Desbordes, M. Parra, T. Zimmermann, F. Rapino, J. Rodriguez-Ubreva, E. Ballestar, and T. Graf A robust and highly efficient immune cell reprogramming system Cell Stem Cell 5 2009 554 566
4. P. Cahan, H. Li, S.A. Morris, E. Lummertz da Rocha, G.Q. Daley, and J.J. Collins CellNet: Network Biology Applied to Stem Cell Engineering Cell 158 2014 903 915 this issue
5. D.E. Cohen, and D. Melton Turning straw into gold: directing cell fate for regenerative medicine Nat. Rev. Genet. 12 2011 243 252
6. E.H. Davidson, and D.H. Erwin Gene regulatory networks and the evolution of animal body plans Science 311 2006 796 800
7. A. Di Tullio, T.P. Vu Manh, A. Schubert, G. Castellano, R. Månsson, and T. Graf CCAAT/enhancer binding protein alpha (C/EBP(alpha))-induced transdifferentiation of pre-B cells into macrophages involves no overt retrodifferentiation Proc. Natl. Acad. Sci. USA 108 2011 17016 17021
8. R. Feng, S.C. Desbordes, H. Xie, E.S. Tillo, F. Pixley, E.R. Stanley, and T. Graf PU.1 and C/EBPalpha/beta convert fibroblasts into macrophage-like cells Proc. Natl. Acad. Sci. USA 105 2008 6057 6062
9. R.P. Fordham, S. Yui, N.R.F. Hannan, C. Soendergaard, A. Madgwick, P.J. Schweiger, O.H. Nielsen, L. Vallier, R.A. Pedersen, and T. Nakamura et al. Transplantation of expanded fetal intestinal progenitors contributes to colon regeneration after injury Cell Stem Cell 13 2013 734 744
10. J.-D. Fu, N.R. Stone, L. Liu, C.I. Spencer, L. Qian, Y. Hayashi, P. Delgado-Olguin, S. Ding, B.G. Bruneau, and D. Srivastava Direct Reprogramming of Human Fibroblasts toward a Cardiomyocyte-like State Stem Cell Rep. 1 2013 235 247
11. N. Gao, P. White, and K.H. Kaestner Establishment of intestinal identity and epithelial-mesenchymal signaling by Cdx2 Dev. Cell 16 2009 588 599
12. W.D. Garrison, M.A. Battle, C. Yang, K.H. Kaestner, F.M. Sladek, and S.A. Duncan Hepatocyte nuclear factor 4alpha is essential for embryonic development of the mouse colon Gastroenterology 130 2006 1207 1220
13. P. Huang, Z. He, S. Ji, H. Sun, D. Xiang, C. Liu, Y. Hu, X. Wang, and L. Hui Induction of functional hepatocyte-like cells from mouse fibroblasts by defined factors Nature 475 2011 386 389
14. M. Ieda, J.-D. Fu, P. Delgado-Olguin, V. Vedantham, Y. Hayashi, B.G. Bruneau, and D. Srivastava Direct reprogramming of fibroblasts into functional cardiomyocytes by defined factors Cell 142 2010 375 386
15. K. Lins, A. Reményi, A. Tomilin, S. Massa, M. Wilmanns, P. Matthias, and H.R. Schöler OBF1 enhances transcriptional potential of Oct1 EMBO J. 22 2003 2188 2198
16. E. Lujan, S. Chanda, H. Ahlenius, T.C. Südhof, and M. Wernig Direct conversion of mouse fibroblasts to self-renewing, tripotent neural precursor cells Proc. Natl. Acad. Sci. USA 109 2012 2527 2532
17. S. Marro, Z.P. Pang, N. Yang, M.-C. Tsai, K. Qu, H.Y. Chang, T.C. Südhof, and M. Wernig Direct lineage conversion of terminally differentiated hepatocytes to functional neurons Cell Stem Cell 9 2011 374 382
18. B.B. McConnell, A.M. Ghaleb, M.O. Nandan, and V.W. Yang The diverse functions of Krüppel-like factors 4 and 5 in epithelial biology and pathobiology Bioessays 29 2007 549 557
19. S.A. Morris, and G.Q. Daley A blueprint for engineering cell fate: current technologies to reprogram cell identity Cell Res. 23 2013 33 48
20. R. Nechanitzky, D. Akbas, S. Scherer, I. Györy, T. Hoyler, S. Ramamoorthy, A. Diefenbach, and R. Grosschedl Transcription factor EBF1 is essential for the maintenance of B cell identity and prevention of alternative fates in committed cells Nat. Immunol. 14 2013 867 875
21. F. Parviz, C. Matullo, W.D. Garrison, L. Savatski, J.W. Adamson, G. Ning, K.H. Kaestner, J.M. Rossi, K.S. Zaret, and S.A. Duncan Hepatocyte nuclear factor 4alpha controls the development of a hepatic epithelium and liver morphogenesis Nat. Genet. 34 2003 292 296
22. C.-F. Pereira, B. Chang, J. Qiu, X. Niu, D. Papatsenko, C.E. Hendry, N.R. Clark, A. Nomura-Kitabayashi, J.C. Kovacic, and A. Ma'ayan et al. Induction of a hemogenic program in mouse fibroblasts Cell Stem Cell 13 2013 205 218
23. J. Rodríguez-Ubreva, L. Ciudad, D. Gómez-Cabrero, M. Parra, L.H. Bussmann, A. di Tullio, E.M. Kallin, J. Tegnér, T. Graf, and E. Ballestar Pre-B cell to macrophage transdifferentiation without significant promoter DNA methylation changes Nucleic Acids Res. 40 2012 1954 1968
24. S. Sekiya, and A. Suzuki Direct conversion of mouse fibroblasts to hepatocyte-like cells by defined factors Nature 475 2011 390 393
25. K.L. Sheaffer, and K.H. Kaestner Transcriptional networks in liver and intestinal development Cold Spring Harb. Perspect. Biol. 4 2012 a008284
26. R.I. Sherwood, T.-Y.A. Chen, and D.A. Melton Transcriptional dynamics of endodermal organ formation Dev. Dyn. 238 2009 29 42
27. E.Y. Son, J.K. Ichida, B.J. Wainger, J.S. Toma, V.F. Rafuse, C.J. Woolf, and K. Eggan Conversion of mouse and human fibroblasts into functional spinal motor neurons Cell Stem Cell 9 2011 205 218
28. A.J. Strain Isolated hepatocytes: use in experimental and clinical hepatology Gut 35 1994 433 436
29. M.P. Verzi, H. Shin, H.H. He, R. Sulahian, C.A. Meyer, R.K. Montgomery, J.C. Fleet, M. Brown, X.S. Liu, and R.A. Shivdasani Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2 Dev. Cell 19 2010 713 726
30. M.P. Verzi, H. Shin, A.K. San Roman, X.S. Liu, and R.A. Shivdasani Intestinal master transcription factor CDX2 controls chromatin access for partner transcription factor binding Mol. Cell. Biol. 33 2013 281 292
31. T. Vierbuchen, and M. Wernig Direct lineage conversions: unnatural but useful? Nat. Biotechnol. 29 2011 892 907
32. T. Vierbuchen, A. Ostermeier, Z.P. Pang, Y. Kokubu, T.C. Südhof, and M. Wernig Direct conversion of fibroblasts to functional neurons by defined factors Nature 463 2010 1035 1041
33. H. Willenbring A simple code for installing hepatocyte function Cell Stem Cell 9 2011 89 91
34. B. Yu, Z.-Y. He, P. You, Q.-W. Han, D. Xiang, F. Chen, M.-J. Wang, C.-C. Liu, X.-W. Lin, and U. Borjigin et al. Reprogramming fibroblasts into bipotential hepatic stem cells by defined factors Cell Stem Cell 13 2013 328 340
35. + stem cell Nat. Med. 18 2012 618 623
36. K.S. Zaret, and J.S. Carroll Pioneer transcription factors: establishing competence for gene expression Genes Dev. 25 2011 2227 2241
37. Q. Zhou, D.D. Price, K.L. Dreher, B. Pronold, C.S. Callam, J. Sharma, and G.N. Verne Localized colonic stem cell transplantation enhances tissue regeneration in murine colitis J. Cell. Mol. Med. 16 2012 1900 1915
38. B. Barneda-Zahonero, L. Román-González, O. Collazo, H. Rafati, A.B.M.M.K. Islam, L.H. Bussmann, A. di Tullio, L. De Andres, T. Graf, and N. López-Bigas et al. HDAC7 is a repressor of myeloid genes whose downregulation is required for transdifferentiation of pre-B cells into macrophages PLoS Genet. 9 2013 e1003503
39. J. Dauffy, G. Mouchiroud, and R.P. Bourette The interferon-inducible gene, Ifi204, is transcriptionally activated in response to M-CSF, and its expression favors macrophage differentiation in myeloid progenitor cells J. Leukoc. Biol. 79 2006 173 183
40. M.W. Pfaffl A new mathematical model for relative quantification in real-time RT-PCR Nucleic Acids Res. 29 2001 e45