Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency

Stem Cells

Volumn 33, Issue 2, 2015, Pages 367-377

  Kushwaha, Ritu ^a   Jagadish, Nirmala ^a   Kustagi, Manjunath ^a   Tomishima, Mark J ^a   Mendiratta, Geetu ^a   Bansal, Mukesh ^a   Kim, Hyunjae R ^a   Sumazin, Pavel ^a   Alvarez, Mariano J ^a   Lefebvre, Celine ^a   Villagrasa Gonzalez, Patricia ^a   Viale, Agnes ^a   Korkola, James E ^a   Houldsworth, Jane ^a   Feldman, Darren R ^a   Bosl, George J ^a   Califano, Andrea ^a,b   Chaganti, R S K ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

Biomathematical modeling; Differentiation; Embryonal carcinoma; Embryonic stem cells; Gene expression; Pluripotent stem cells

Indexed keywords

OCTAMER TRANSCRIPTION FACTOR 4; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR NANOG; TRANSCRIPTION FACTOR SOX2; TUMOR PROTEIN;

ADULT; ALGORITHM; ARTICLE; CELL LINEAGE; DOWN REGULATION; EMBRYO DEVELOPMENT; EMBRYONIC STEM CELL; GENE EXPRESSION PROFILING; GENE SILENCING; GENETIC ASSOCIATION; GERM CELL TUMOR; HUMAN; HUMAN CELL; IN VITRO STUDY; IN VIVO STUDY; MALE; PLURIPOTENT STEM CELL; RISK ASSESSMENT; BIOLOGICAL MODEL; GENETICS; METABOLISM; NEOPLASM; PATHOLOGY; TUMOR CELL LINE;

ADULT; ALGORITHMS; CELL LINE, TUMOR; HUMANS; MALE; MODELS, BIOLOGICAL; NEOPLASM PROTEINS; NEOPLASMS, GERM CELL AND EMBRYONAL; PLURIPOTENT STEM CELLS; TRANSCRIPTION FACTORS;

EID: 84921633624     PISSN: 10665099     EISSN: 15494918     Source Type: Journal    
DOI: 10.1002/stem.1870     Document Type: Article

References (60)

1. Marson A, Levine SS, Cole MF, et al. Connecting micro RNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 2008; 134: 521-533.
2. Jaenisch R, Young R,. Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell 2008; 132: 567-582.
3. Schuettengruber B, Cavalli G,. Recruitment of polycomb group complexes and their role in the dynamic regulation of cell fate choice. Development 2009; 136: 3531-3542.
4. Young RA,. Control of embryonic stem cell state. Cell 2011; 144: 940-954.
5. Loh KM, Lim B,. A precarious balance: Pluripotency factors as lineage specifiers. Cell Stem Cell 2011; 8: 363-369.
6. Shu J, Wu C, Wu Y, et al. Induction of pluripotency in mouse somatic cells with lineage specifiers. Cell 2013; 153: 963-975.
7. Carro MS, Lim WK, Alvarez MJ, et al. The transcriptional network for mesenchymal transformation of brain tumors. Nature 2010; 463: 318-325.
8. Ravasi T, Suzuki H, Cannistraci CV, et al. An atlas of combinatorial transcriptional regulation in mouse and man. Cell 2010; 140: 744-752.
9. Della Gatta G, Palomero T, Perez-Garcia A, et al. Reverse engineering of TLX oncogenic transcriptional networks identifies RUNX1 as tumor suppressor in T-ALL. Nat Med 2012; 18: 436-440.
10. Basso K, Margolin AA, Stolovitzky G, et al. Reverse engineering of regulatory networks in human B cells. Nat Genet 2005; 37: 382-390.
11. Basso K, Saito M, Sumazin P, et al. Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells. Blood 2010; 115: 975-984.
12. Palomero T, Lim WK, Odom DT, et al. NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth. Proc Natl Acad Sci USA 2006; 103: 18261-18266.
13. Lim WK, Lyashenko E, Califano A,. Master regulators used as breast cancer metastasis classifier. Pac Symp Biocomp 2009; 14: 504-515.
14. Margolin AA, Palomero T, Sumazin P, et al. ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes. Proc Natl Acad Sci USA 2009; 106: 244-249.
15. Zhao X, D' Arca D, Lim WK, et al. The N-Myc-DLL3 cascade is suppressed by the ubiquitin ligase Huwe1 to inhibit proliferation and promote neurogenesis in the developing brain. Dev Cell 2009; 17: 210-221.
16. Lefebvre C, Rajbhandari P, Alvarez MJ, et al. A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Mol Syst Biol 2010; 6: 377-386.
17. Cadeiras M, von Bayern M, Sinha A, et al. Drawing networks of rejection-A systems biological approach to the identification of candidate genes in heart transplantation. J Cell Mol Med 2011; 15: 949-956.
18. Sperger JM, Chen X, Draper JS, et al. Gene expression patterns in human embryonic stem cells and human pluripotent germ cell tumors. Proc Natl Acad Sci USA 2003; 100: 13350-13355.
19. Ulbright TM,. Germ cell neoplasms of the testis. Am J Surg Pathol 1993; 17: 1075-1091.
20. Chaganti RS, Houldsworth J,. Genetics and biology of adult human male germ cell tumors. Cancer Res 2000; 60: 1475-1482.
21. Korkola JE, Houldsworth J, Dobrzynski D, et al. Gene expression-based classification of nonseminomatous male germ cell tumors. Oncogene 2005; 24: 5101-5107.
22. Korkola JE, Houldsworth J, Chadalavada RS, et al. Down-regulation of stem cell genes, including those in a 200-kb gene cluster at 12p1331, is associated with in vivo differentiation of human male germ cell tumors. Cancer Res 2006; 66: 820-827.
23. Korkola JE, Houldsworth J, Feldman DR, et al. Identification and validation of a gene expression signature that predicts outcome in adult men with germ cell tumors. J Clin Oncol 2009; 27: 5240-5247.
24. Houldsworth J, Heath SC, Bosl GJ, et al. Expression profiling of lineage differentiation in pluripotential human embryonal carcinoma cells. Cell Growth Differ 2002; 13: 257-264.
25. Schmidt D, Wilson MD, Spyrou C, et al. ChIP-seq: Using high-throughput sequencing to discover protein-DNA interactions. Methods 2009; 48: 240-248.
26. Gautier L, Cope L, Bolstad BM, et al. affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004; 3: 307-315.
27. Margolin AA, Wang K, Lim WK, et al. Reverse engineering cellular networks. Nat Protoc 2006; 1: 662-671.
28. Liu G, Loraine AE, Shigeta R, et al. NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res 2003; 31: 82-86.
29. Subramanian A, Tamayo P, Mootha V, et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005; 102: 15545-15550.
30. Anscombe FJ,. The validity of comparative experiments. J R Stat Society Series A (Gen) 1948; 111: 181-211.
31. Pearson K,. On Lines and Planes of Closest Fit to Systems of Points in Space (PDF) Philos Mag 1901; 2: 559-572.
32. Mantel N, Haenszel W,. Statistical aspects of the analysis of data from retrospective studies of disease. J Natl Cancer Inst 1959; 22: 719-748.
33. Niwa H, Miyazaki J, Smith AG,. Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells. Nat Genet 2000; 24: 372-376.
34. Mitsui K, Tokuzawa Y, Itoh H, et al. The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell 2003; 113: 631-642.
35. Chazaud C, Yamanaka Y, Pawson T, et al. Early lineage segregation between epiblast and primitive endoderm in mouse blastocysts through the Grb2-MAPK pathway. Dev Cell 2006; 10: 615-624.
36. Ivanova N, Dobrin R, Lu R, et al. Dissecting self-renewal in stem cells with RNA interference. Nature 2006; 442: 533-538.
37. Wang Z, Oron E, Nelson B, et al. Distinct lineage specification roles for NANOG, OCT4, and SOX2 in human embryonic stem cells. Cell Stem Cell 2012; 10: 440-454.
38. Okuda A, Fukushima A, Nishimoto M, et al. UTF1, a novel transcriptional coactivator expressed in pluripotent embryonic stem cells and extra-embryonic cells. EMBO J 1998; 17: 2019-2032.
39. Loh YH, Wu Q, Chew JL, et al. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet 2006; 4: 431-440.
40. Nishimoto M, Katano M, Yamagishi T, et al. In vivo function and evolution of the eutherian-specific pluripotency marker UTF1. PLoS One 2013; 8: e68119.
41. Chen X, Xu H, Yuan P, et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008; 33: 1106-1117.
42. van den Berg DL, Snoek T, Mullin NP, et al. An Oct4-centered protein interaction network in embryonic stem cells. Cell Stem Cell 2010; 6: 369-381.
43. Sumazin P, Yang X, Chiu HS, et al. An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell 2011; 147: 370-381.
44. Mani KM, Lefebvre C, Wang K, et al. A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Mol Syst Biol 2008; 4: 169-177.
45. Zhao Y, Yin X, Qin H, et al. Two supporting factors greatly improve the efficiency of human iPSC generation Cell Stem Cell 2008; 3: 475-479.
46. Chia NY, Chan YS, Feng B, et al. A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Nature 2010; 468: 316-320.
47. Ma Z, Swigut T, Valouev A, et al. Sequence-specific regulator Prdm14 safeguards mouse ESCs from entering extraembryonic endoderm fates. Nat Struct Mol Biol 2011; 18: 120-127.
48. Jia J, Zheng X, Hu G, et al. Regulation of pluripotency and self- renewal of ESCs through epigenetic-threshold modulation and mRNA pruning. Cell 2012; 151: 576-589.
49. Chan YS, Göke J, Lu X, et al. A PRC2-dependent repressive role of PRDM14 in human embryonic stem cells and induced pluripotent stem cell reprogramming. Stem Cells 2012; 31: 682-692.
50. Grabole N, Tischler J, Hackett JA, et al. Prdm14 promotes germline fate and naive pluripotency by repressing FGF signaling and DNA methylation. EMBO Rep 2013; 14: 629-637.
51. Yamaji M, Ueda J, Hayashi K, et al. PRDM14 ensures naive pluripotency through dual regulation of signaling and epigenetic pathways in mouse embryonic stem cells. Cell Stem Cell 2013; 12: 368-382.
52. Ye S, Li P, Tong C, et al. Embryonic stem cell self-renewal pathways converge on the transcription factor Tfcp2l1. EMBO J 2013; 32: 2548-2560.
53. Fischedick G, Klein DC, Wu G, et al. Zfp296 is a novel, pluripotent-specific reprogramming factor. PLoS One 2012; 7: e34645.
54. Juárez-Moreno K, Erices R, Beltran AS, et al. Breaking through an epigenetic wall: Re-activation of Oct4 by KRAB-containing designer zinc finger transcription factors. Epigenetics 2013; 8 164-176.
55. Ji Q, Fischer LA, Brown R C, et al. Engineered zinc-finger transcription factors activate OCT4 (POU5F1), SOX2, KLF4, c-MYC (MYC) and miR302/367. Nucleic Acids Res 2014; 42: 6158-6167.
56. Oh S, Shin S, Janknecht R,. ETV1, 4 and 5: An oncogenic subfamily of ETS transcription factors. Biochim Biophys Acta 2012; 1826: 1-12.
57. Nishioka N, Yamamoto S, Kiyonari H, et al. Tead4 is required for specification of trophectoderm in pre-implantation mouse embryos. Mech Dev 2008; 125: 270-283.
58. Gao H, Wu X, Sun, Y, et al. Suppression of homeobox transcription factor VentX promotes expansion of human hematopoietic stem/multipotent progenitor cells. J Biol Chem 2012; 287: 29979-29987.
59. Jung M, Peterson H, Chavez L, et al. A data integration approach to mapping OCT4 gene regulatory networks operative in embryonic stem cells and embryonal carcinoma cells. PLoS One 2010; 5: e10709.
60. Scerbo P, Girardot F, Vivien C, et al. Ventx factors function as Nanog-like guardians of developmental potential in Xenopus. PLoS One 2012; 7: e36855.