#PAGE_PARAMS# #ADS_HEAD_SCRIPTS# #MICRODATA#

An Integrated Cell Purification and Genomics Strategy Reveals Multiple Regulators of Pancreas Development


Discovery of specific pancreas developmental regulators has accelerated in recent years. In contrast, the global regulatory programs controlling pancreas development are poorly understood compared to other organs or tissues like heart or blood. Decoding this regulatory logic may accelerate development of replacement organs from renewable sources like stem cells, but this goal requires identification of regulators and assessment of their functions on a global scale. To address this important challenge for pancreas biology, we combined purification of normal and mutant cells with genome-scale methods to generate and analyze expression profiles from developing pancreas cells. Our work revealed regulatory gene sets governing development of pancreas progenitor cells and their progeny. Our integrative approach nominated multiple pancreas developmental regulators, including suspected risk genes for human diabetes, which we validated by phenotyping mutant mice on a scale not previously reported. Selection of these candidate regulators was unbiased; thus it is remarkable that all were essential for pancreatic islet development. Thus, our studies provide a new heuristic resource for identifying genetic functions underlying pancreas development and diseases like diabetes mellitus.


Vyšlo v časopise: An Integrated Cell Purification and Genomics Strategy Reveals Multiple Regulators of Pancreas Development. PLoS Genet 10(10): e32767. doi:10.1371/journal.pgen.1004645
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004645

Souhrn

Discovery of specific pancreas developmental regulators has accelerated in recent years. In contrast, the global regulatory programs controlling pancreas development are poorly understood compared to other organs or tissues like heart or blood. Decoding this regulatory logic may accelerate development of replacement organs from renewable sources like stem cells, but this goal requires identification of regulators and assessment of their functions on a global scale. To address this important challenge for pancreas biology, we combined purification of normal and mutant cells with genome-scale methods to generate and analyze expression profiles from developing pancreas cells. Our work revealed regulatory gene sets governing development of pancreas progenitor cells and their progeny. Our integrative approach nominated multiple pancreas developmental regulators, including suspected risk genes for human diabetes, which we validated by phenotyping mutant mice on a scale not previously reported. Selection of these candidate regulators was unbiased; thus it is remarkable that all were essential for pancreatic islet development. Thus, our studies provide a new heuristic resource for identifying genetic functions underlying pancreas development and diseases like diabetes mellitus.


Zdroje

1. PradoCL, Pugh-BernardAE, ElghaziL, Sosa-PinedaB, SusselL (2004) Ghrelin cells replace insulin-producing beta cells in two mouse models of pancreas development. Proceedings of the National Academy of Sciences of the United States of America 101: 2924–2929.

2. LynnFC, SmithSB, WilsonME, YangKY, NekrepN, et al. (2007) Sox9 coordinates a transcriptional network in pancreatic progenitor cells. Proceedings of the National Academy of Sciences of the United States of America 104: 10500–10505.

3. SeymourPA, FreudeKK, TranMN, MayesEE, JensenJ, et al. (2007) SOX9 is required for maintenance of the pancreatic progenitor cell pool. Proceedings of the National Academy of Sciences of the United States of America 104: 1865–1870.

4. JonssonJ, CarlssonL, EdlundT, EdlundH (1994) Insulin-promoter-factor 1 is required for pancreas development in mice. Nature 371: 606–609.

5. KrappA, KnoflerM, LedermannB, BurkiK, BerneyC, et al. (1998) The bHLH protein PTF1-p48 is essential for the formation of the exocrine and the correct spatial organization of the endocrine pancreas. Genes & development 12: 3752–3763.

6. KoppJL, DuboisCL, SchafferAE, HaoE, ShihHP, et al. (2011) Sox9+ ductal cells are multipotent progenitors throughout development but do not produce new endocrine cells in the normal or injured adult pancreas. Development 138: 653–665.

7. BenitezCM, GoodyerWR, KimSK (2012) Deconstructing pancreas developmental biology. Cold Spring Harbor perspectives in biology 4 doi: 10.1101/cshperspect.a012401

8. ShihHP, WangA, SanderM (2013) Pancreas Organogenesis: From Lineage Determination to Morphogenesis. Annual review of cell and developmental biology

9. ArdaHE, BenitezCM, KimSK (2013) Gene regulatory networks governing pancreas development. Developmental cell 25: 5–13.

10. NovershternN, SubramanianA, LawtonLN, MakRH, HainingWN, et al. (2011) Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell 144: 296–309.

11. McKinney-FreemanS, CahanP, LiH, LacadieSA, HuangHT, et al. (2012) The transcriptional landscape of hematopoietic stem cell ontogeny. Cell stem cell 11: 701–714.

12. ScearceLM, BrestelliJE, McWeeneySK, LeeCS, MazzarelliJ, et al. (2002) Functional genomics of the endocrine pancreas: the pancreas clone set and PancChip, new resources for diabetes research. Diabetes 51: 1997–2004.

13. GuG, WellsJM, DombkowskiD, PrefferF, AronowB, et al. (2004) Global expression analysis of gene regulatory pathways during endocrine pancreatic development. Development 131: 165–179.

14. HoffmanBG, ZavagliaB, WitzscheJ, Ruiz de AlgaraT, BeachM, et al. (2008) Identification of transcripts with enriched expression in the developing and adult pancreas. Genome biology 9: R99.

15. van ArensbergenJ, Garcia-HurtadoJ, MoranI, MaestroMA, XuX, et al. (2010) Derepression of Polycomb targets during pancreatic organogenesis allows insulin-producing beta-cells to adopt a neural gene activity program. Genome Res 20: 722–732.

16. SugiyamaT, RodriguezRT, McLeanGW, KimSK (2007) Conserved markers of fetal pancreatic epithelium permit prospective isolation of islet progenitor cells by FACS. Proceedings of the National Academy of Sciences of the United States of America 104: 175–180.

17. SugiyamaT, BenitezCM, GhodasaraA, LiuL, McLeanGW, et al. (2013) Reconstituting pancreas development from purified progenitor cells reveals genes essential for islet differentiation. Proceedings of the National Academy of Sciences of the United States of America 110: 12691–12696.

18. SeymourPA, SanderM (2011) Historical perspective: beginnings of the beta-cell: current perspectives in beta-cell development. Diabetes 60: 364–376.

19. SuAI, WiltshireT, BatalovS, LappH, ChingKA, et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proceedings of the National Academy of Sciences of the United States of America 101: 6062–6067.

20. SegalE, FriedmanN, KollerD, RegevA (2004) A module map showing conditional activity of expression modules in cancer. Nature genetics 36: 1090–1098.

21. BenitezCM, GoodyerWR, KimSK (2012) Deconstructing pancreas developmental biology. Cold Spring Harb Perspect Biol 4.

22. ZhouQ, BrownJ, KanarekA, RajagopalJ, MeltonDA (2008) In vivo reprogramming of adult pancreatic exocrine cells to beta-cells. Nature 455: 627–632.

23. LeeJ, SugiyamaT, LiuY, WangJ, GuX, et al. (2013) Expansion and conversion of human pancreatic ductal cells into insulin-secreting endocrine cells. Elife 2: e00940.

24. PagliucaFW, MeltonDA (2013) How to make a functional beta-cell. Development 140: 2472–2483.

25. MezzaT, KulkarniRN (2014) The regulation of pre- and post-maturational plasticity of mammalian islet cell mass. Diabetologia 57: 1291–1303.

26. ReinertRB, CaiQ, HongJY, PlankJL, AamodtK, et al. (2014) Vascular endothelial growth factor coordinates islet innervation via vascular scaffolding. Development 141: 1480–1491.

27. CleaverO, DorY (2012) Vascular instruction of pancreas development. Development 139: 2833–2843.

28. GeorgiaS, HinaultC, KawamoriD, HuJ, MeyerJ, et al. (2010) Cyclin D2 is essential for the compensatory beta-cell hyperplastic response to insulin resistance in rodents. Diabetes 59: 987–996.

29. TetaM, LongSY, WartschowLM, RankinMM, KushnerJA (2005) Very slow turnover of beta-cells in aged adult mice. Diabetes 54: 2557–2567.

30. GuC, SteinGH, PanN, GoebbelsS, HornbergH, et al. (2010) Pancreatic beta cells require NeuroD to achieve and maintain functional maturity. Cell Metab 11: 298–310.

31. GoodyerWR, GuX, LiuY, BottinoR, CrabtreeGR, et al. (2012) Neonatal beta cell development in mice and humans is regulated by calcineurin/NFAT. Developmental cell 23: 21–34.

32. McKnightKD, WangP, KimSK (2010) Deconstructing pancreas development to reconstruct human islets from pluripotent stem cells. Cell Stem Cell 6: 300–308.

33. De FrancoE, Shaw-SmithC, FlanaganSE, ShepherdMH, HattersleyAT, et al. (2013) GATA6 mutations cause a broad phenotypic spectrum of diabetes from pancreatic agenesis to adult-onset diabetes without exocrine insufficiency. Diabetes 62: 993–997.

34. SegalE, ShapiraM, RegevA, Pe'erD, BotsteinD, et al. (2003) Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nature genetics 34: 166–176.

35. NovershternN, RegevA, FriedmanN (2011) Physical Module Networks: an integrative approach for reconstructing transcription regulation. Bioinformatics 27: i177–185.

36. KanamoriM, KonnoH, OsatoN, KawaiJ, HayashizakiY, et al. (2004) A genome-wide and nonredundant mouse transcription factor database. Biochem Biophys Res Commun 322: 787–793.

37. RavasiT, SuzukiH, CannistraciCV, KatayamaS, BajicVB, et al. (2010) An atlas of combinatorial transcriptional regulation in mouse and man. Cell 140: 744–752.

38. ZhangHM, ChenH, LiuW, LiuH, GongJ, et al. (2012) AnimalTFDB: a comprehensive animal transcription factor database. Nucleic Acids Res 40: D144–149.

39. JoshiA, De SmetR, MarchalK, Van de PeerY, MichoelT (2009) Module networks revisited: computational assessment and prioritization of model predictions. Bioinformatics 25: 490–496.

40. SubramanianA, TamayoP, MoothaVK, MukherjeeS, EbertBL, et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America 102: 15545–15550.

41. ImamuraM, MaedaS (2011) Genetics of type 2 diabetes: the GWAS era and future perspectives [Review]. Endocr J 58: 723–739.

42. MorrisAP, VoightBF, TeslovichTM, FerreiraT, SegreAV, et al. (2012) Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes. Nat Genet 44: 981–990.

43. DimasAS, LagouV, BarkerA, KnowlesJW, MagiR, et al. (2014) Impact of type 2 diabetes susceptibility variants on quantitative glycemic traits reveals mechanistic heterogeneity. Diabetes 63: 2158–2171.

44. GradwohlG, DierichA, LeMeurM, GuillemotF (2000) neurogenin3 is required for the development of the four endocrine cell lineages of the pancreas. Proceedings of the National Academy of Sciences of the United States of America 97: 1607–1611.

45. LeeCS, PerreaultN, BrestelliJE, KaestnerKH (2002) Neurogenin 3 is essential for the proper specification of gastric enteroendocrine cells and the maintenance of gastric epithelial cell identity. Genes & development 16: 1488–1497.

46. WangS, JensenJN, SeymourPA, HsuW, DorY, et al. (2009) Sustained Neurog3 expression in hormone-expressing islet cells is required for endocrine maturation and function. Proceedings of the National Academy of Sciences of the United States of America 106: 9715–9720.

47. JuhlK, SarkarSA, WongR, JensenJ, HuttonJC (2008) Mouse pancreatic endocrine cell transcriptome defined in the embryonic Ngn3-null mouse. Diabetes 57: 2755–2761.

48. WhiteP, MayCL, LamounierRN, BrestelliJE, KaestnerKH (2008) Defining pancreatic endocrine precursors and their descendants. Diabetes 57: 654–668.

49. SoyerJ, FlasseL, RaffelsbergerW, BeucherA, OrvainC, et al. (2010) Rfx6 is an Ngn3-dependent winged helix transcription factor required for pancreatic islet cell development. Development 137: 203–212.

50. ArberS, LadleDR, LinJH, FrankE, JessellTM (2000) ETS gene Er81 controls the formation of functional connections between group Ia sensory afferents and motor neurons. Cell 101: 485–498.

51. CalabiF, PannellR, PavloskaG (2001) Gene targeting reveals a crucial role for MTG8 in the gut. Molecular and cellular biology 21: 5658–5666.

52. HerronBJ, LuW, RaoC, LiuS, PetersH, et al. (2002) Efficient generation and mapping of recessive developmental mutations using ENU mutagenesis. Nature genetics 30: 185–189.

53. SankaranVG, XuJ, RagoczyT, IppolitoGC, WalkleyCR, et al. (2009) Developmental and species-divergent globin switching are driven by BCL11A. Nature 460: 1093–1097.

54. KarsunkyH, ZengH, SchmidtT, ZevnikB, KlugeR, et al. (2002) Inflammatory reactions and severe neutropenia in mice lacking the transcriptional repressor Gfi1. Nature genetics 30: 295–300.

55. HockH, HamblenMJ, RookeHM, TraverD, BronsonRT, et al. (2003) Intrinsic requirement for zinc finger transcription factor Gfi-1 in neutrophil differentiation. Immunity 18: 109–120.

56. PinheiroI, MargueronR, ShukeirN, EisoldM, FritzschC, et al. (2012) Prdm3 and Prdm16 are H3K9me1 methyltransferases required for mammalian heterochromatin integrity. Cell 150: 948–960.

57. CollombatP, Hecksher-SorensenJ, KrullJ, BergerJ, RiedelD, et al. (2007) Embryonic endocrine pancreas and mature beta cells acquire alpha and PP cell phenotypes upon Arx misexpression. J Clin Invest 117: 961–970.

58. MiyoshiH, KozuT, ShimizuK, EnomotoK, MasekiN, et al. (1993) The t(8;21) translocation in acute myeloid leukemia results in production of an AML1-MTG8 fusion transcript. The EMBO journal 12: 2715–2721.

59. KimYR, KimMS, LeeSH, YooNJ (2011) Mutational analysis of RUNX1T1 gene in acute leukemias, breast and lung carcinomas. Leukemia research 35: e157–158.

60. ChiangC, AyyanathanK (2013) Snail/Gfi-1 (SNAG) family zinc finger proteins in transcription regulation, chromatin dynamics, cell signaling, development, and disease. Cytokine Growth Factor Rev 24: 123–131.

61. BramswigNC, EverettLJ, SchugJ, DorrellC, LiuC, et al. (2013) Epigenomic plasticity enables human pancreatic alpha to beta cell reprogramming. The Journal of clinical investigation 123: 1275–1284.

62. ThorelF, NepoteV, AvrilI, KohnoK, DesgrazR, et al. (2010) Conversion of adult pancreatic alpha-cells to beta-cells after extreme beta-cell loss. Nature 464: 1149–1154.

63. CourtneyM, GjernesE, DruelleN, RavaudC, VieiraA, et al. (2013) The inactivation of Arx in pancreatic alpha-cells triggers their neogenesis and conversion into functional beta-like cells. PLoS Genet 9: e1003934.

64. DhawanS, GeorgiaS, TschenSI, FanG, BhushanA (2011) Pancreatic beta cell identity is maintained by DNA methylation-mediated repression of Arx. Developmental cell 20: 419–429.

65. HebrokM (2012) Generating beta cells from stem cells-the story so far. Cold Spring Harbor perspectives in medicine 2: a007674.

66. PeirisH, RaghupathiR, JessupCF, ZaninMP, MohanasundaramD, et al. (2012) Increased expression of the glucose-responsive gene, RCAN1, causes hypoinsulinemia, beta-cell dysfunction, and diabetes. Endocrinology 153: 5212–5221.

67. Al-HasaniK, PfeiferA, CourtneyM, Ben-OthmanN, GjernesE, et al. (2013) Adult Duct-Lining Cells Can Reprogram into beta-like Cells Able to Counter Repeated Cycles of Toxin-Induced Diabetes. Developmental cell 26: 86–100.

68. EllardS, Lango AllenH, De FrancoE, FlanaganSE, HysenajG, et al. (2013) Improved genetic testing for monogenic diabetes using targeted next-generation sequencing. Diabetologia 56: 1958–1963.

69. LiuP, KellerJR, OrtizM, TessarolloL, RachelRA, et al. (2003) Bcl11a is essential for normal lymphoid development. Nature immunology 4: 525–532.

70. SatterwhiteE, SonokiT, WillisTG, HarderL, NowakR, et al. (2001) The BCL11 gene family: involvement of BCL11A in lymphoid malignancies. Blood 98: 3413–3420.

71. XuJ, PengC, SankaranVG, ShaoZ, EsrickEB, et al. (2011) Correction of sickle cell disease in adult mice by interference with fetal hemoglobin silencing. Science 334: 993–996.

72. SealeP, BjorkB, YangW, KajimuraS, ChinS, et al. (2008) PRDM16 controls a brown fat/skeletal muscle switch. Nature 454: 961–967.

73. BjorkBC, Turbe-DoanA, PrysakM, HerronBJ, BeierDR (2010) Prdm16 is required for normal palatogenesis in mice. Human molecular genetics 19: 774–789.

74. MorishitaK (2007) Leukemogenesis of the EVI1/MEL1 gene family. International journal of hematology 85: 279–286.

75. ChuikovS, LeviBP, SmithML, MorrisonSJ (2010) Prdm16 promotes stem cell maintenance in multiple tissues, partly by regulating oxidative stress. Nature cell biology 12: 999–1006.

76. OhS, ShinS, JanknechtR (2012) ETV1, 4 and 5: an oncogenic subfamily of ETS transcription factors. Biochimica et biophysica acta 1826: 1–12.

77. AmannJM, ChylaBJ, EllisTC, MartinezA, MooreAC, et al. (2005) Mtgr1 is a transcriptional corepressor that is required for maintenance of the secretory cell lineage in the small intestine. Molecular and cellular biology 25: 9576–9585.

78. BjerknesM, ChengH (2010) Cell Lineage metastability in Gfi1-deficient mouse intestinal epithelium. Dev Biol 345: 49–63.

79. DorrellC, SchugJ, LinCF, CanadayPS, FoxAJ, et al. (2011) Transcriptomes of the major human pancreatic cell types. Diabetologia 54: 2832–2844.

80. Munoz-BravoJL, Hidalgo-FigueroaM, PascualA, Lopez-BarneoJ, Leal-CerroA, et al. (2013) GDNF is required for neural colonization of the pancreas. Development 140: 3669–3679.

81. BuenrostroJD, GiresiPG, ZabaLC, ChangHY, GreenleafWJ (2013) Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10: 1213–1218.

82. SeymourPA, FreudeKK, DuboisCL, ShihHP, PatelNA, et al. (2008) A dosage-dependent requirement for Sox9 in pancreatic endocrine cell formation. Dev Biol 323: 19–30.

83. HaraM, WangX, KawamuraT, BindokasVP, DizonRF, et al. (2003) Transgenic mice with green fluorescent protein-labeled pancreatic beta -cells. American journal of physiology Endocrinology and metabolism 284: E177–183.

84. ReimannF, HabibAM, TolhurstG, ParkerHE, RogersGJ, et al. (2008) Glucose sensing in L cells: a primary cell study. Cell metabolism 8: 532–539.

85. BlumB, HrvatinSS, SchuetzC, BonalC, RezaniaA, et al. (2012) Functional beta-cell maturation is marked by an increased glucose threshold and by expression of urocortin 3. Nature biotechnology 30: 261–264.

86. de HoonMJ, ImotoS, NolanJ, MiyanoS (2004) Open source clustering software. Bioinformatics 20: 1453–1454.

87. EdgarR, DomrachevM, LashAE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207–210.

88. MurphyR, EllardS, HattersleyAT (2008) Clinical implications of a molecular genetic classification of monogenic beta-cell diabetes. Nat Clin Pract Endocrinol Metab 4: 200–213.

89. Oliveros JC (2007) VENNY: An interactive tool for comparing lists with Venn Diagrams. BioinfoGP, CNB-CSIC.

Štítky
Genetika Reprodukčná medicína

Článok vyšiel v časopise

PLOS Genetics


2014 Číslo 10
Najčítanejšie tento týždeň
Najčítanejšie v tomto čísle
Kurzy

Zvýšte si kvalifikáciu online z pohodlia domova

Získaná hemofilie - Povědomí o nemoci a její diagnostika
nový kurz

Eozinofilní granulomatóza s polyangiitidou
Autori: doc. MUDr. Martina Doubková, Ph.D.

Všetky kurzy
Prihlásenie
Zabudnuté heslo

Zadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.

Prihlásenie

Nemáte účet?  Registrujte sa

#ADS_BOTTOM_SCRIPTS#