دورية أكاديمية
أعرض في EDS

Integrative pan cancer analysis reveals epigenomic variation in cancer type and cell specific chromatin domains.

التفاصيل البيبلوغرافية
العنوان: Integrative pan cancer analysis reveals epigenomic variation in cancer type and cell specific chromatin domains.
المؤلفون: Gopi LK; Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.; Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA., Kidder BL; Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA. benjamin.kidder@wayne.edu.; Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA. benjamin.kidder@wayne.edu.
المصدر: Nature communications [Nat Commun] 2021 Mar 03; Vol. 12 (1), pp. 1419. Date of Electronic Publication: 2021 Mar 03.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [London] : Nature Pub. Group
مواضيع طبية MeSH: Epigenome* , Mutation*, Chromatin/*genetics , Histones/*metabolism , Neoplasms/*genetics, Cell Line, Tumor ; DNA Methylation ; Enhancer Elements, Genetic ; Genes, Tumor Suppressor ; Histone Code/genetics ; Histones/genetics ; Humans ; Long Interspersed Nucleotide Elements
مستخلص: Epigenetic mechanisms contribute to the initiation and development of cancer, and epigenetic variation promotes dynamic gene expression patterns that facilitate tumor evolution and adaptation. While the NCI-60 panel represents a diverse set of human cancer cell lines that has been used to screen chemical compounds, a comprehensive epigenomic atlas of these cells has been lacking. Here, we report an integrative analysis of 60 human cancer epigenomes, representing a catalog of activating and repressive histone modifications. We identify genome-wide maps of canonical sharp and broad H3K4me3 domains at promoter regions of tumor suppressors, H3K27ac-marked conventional enhancers and super enhancers, and widespread inter-cancer and intra-cancer specific variability in H3K9me3 and H4K20me3-marked heterochromatin domains. Furthermore, we identify features of chromatin states, including chromatin state switching along chromosomes, correlation of histone modification density with genetic mutations, DNA methylation, enrichment of DNA binding motifs in regulatory regions, and gene activity and inactivity. These findings underscore the importance of integrating epigenomic maps with gene expression and genetic variation data to understand the molecular basis of human cancer. Our findings provide a resource for mining epigenomic maps of human cancer cells and for identifying epigenetic therapeutic targets.
References: Am J Pathol. 2009 Oct;175(4):1353-61. (PMID: 19717641)
Nucleic Acids Res. 2019 Jan 8;47(D1):D941-D947. (PMID: 30371878)
Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10787-92. (PMID: 11553813)
Nat Rev Genet. 2002 Jun;3(6):415-28. (PMID: 12042769)
Mol Cell Biol. 2005 Apr;25(7):2525-38. (PMID: 15767660)
Science. 2009 Oct 9;326(5950):289-93. (PMID: 19815776)
Nature. 2012 Mar 28;483(7391):603-7. (PMID: 22460905)
Nature. 2011 Jan 20;469(7330):314-22. (PMID: 21248838)
Nat Genet. 2005 Apr;37(4):391-400. (PMID: 15765097)
Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21931-6. (PMID: 21106759)
Mol Cell. 2017 Sep 21;67(6):1049-1058.e6. (PMID: 28938092)
Curr Opin Struct Biol. 2008 Apr;18(2):236-42. (PMID: 18206362)
J Cell Sci. 2004 May 15;117(Pt 12):2491-501. (PMID: 15128874)
Genes Dev. 2015 Feb 1;29(3):238-49. (PMID: 25644600)
Carcinogenesis. 2010 Jun;31(6):974-83. (PMID: 20053926)
Science. 2012 May 25;336(6084):1040-4. (PMID: 22628656)
Front Pharmacol. 2019 Apr 11;10:361. (PMID: 31105558)
Methods Mol Biol. 2014;1150:175-87. (PMID: 24743998)
Development. 2012 Mar;139(6):1045-57. (PMID: 22354838)
Science. 2001 Apr 6;292(5514):110-3. (PMID: 11283354)
Nucleic Acids Res. 2019 Jan 8;47(D1):D235-D243. (PMID: 30371817)
Genes Dev. 2005 Feb 15;19(4):431-5. (PMID: 15681608)
BMC Bioinformatics. 2017 May 31;18(1):287. (PMID: 28569135)
Genome Biol. 2014 Feb 04;15(2):R32. (PMID: 24495580)
Cell. 2018 Apr 5;173(2):386-399.e12. (PMID: 29625054)
Epigenetics Chromatin. 2017 Feb 23;10:8. (PMID: 28250819)
Nat Immunol. 2011 Sep 20;12(10):918-22. (PMID: 21934668)
Cell. 2013 Nov 7;155(4):948-62. (PMID: 24183448)
Front Oncol. 2018 Nov 20;8:529. (PMID: 30524960)
Annu Rev Cell Dev Biol. 2018 Oct 6;34:265-288. (PMID: 30044650)
Cold Spring Harb Symp Quant Biol. 2004;69:209-18. (PMID: 16117651)
Proc Natl Acad Sci U S A. 2008 Dec 16;105(50):19809-14. (PMID: 19060200)
Nat Clin Pract Oncol. 2005 Dec;2 Suppl 1:S4-11. (PMID: 16341240)
EMBO Rep. 2014 Mar;15(3):244-53. (PMID: 24531722)
Cancer Res. 2007 Dec 1;67(23):11335-43. (PMID: 18056460)
Cell. 2013 Nov 7;155(4):934-47. (PMID: 24119843)
Cell. 2014 Jul 31;158(3):673-88. (PMID: 25083876)
Cancer Res. 2013 Jul 15;73(14):4372-82. (PMID: 23856246)
Genome Biol. 2003;4(5):P3. (PMID: 12734009)
Carcinogenesis. 2010 Jan;31(1):27-36. (PMID: 19752007)
Cell. 2006 Apr 21;125(2):315-26. (PMID: 16630819)
Genes Dev. 2007 May 1;21(9):1050-63. (PMID: 17437993)
Science. 2013 Mar 29;339(6127):1567-70. (PMID: 23539597)
Oncogene. 2010 Jan 28;29(4):576-88. (PMID: 19881540)
Trends Genet. 2013 Oct;29(10):569-74. (PMID: 23810203)
Cell. 2013 Apr 11;153(2):320-34. (PMID: 23582323)
Nature. 2015 Feb 19;518(7539):317-30. (PMID: 25693563)
Cell. 2012 Nov 21;151(5):994-1004. (PMID: 23159369)
Cancer Res. 2019 Jul 1;79(13):3514-3524. (PMID: 31113817)
Cancer Res. 2003 Dec 15;63(24):8634-47. (PMID: 14695175)
Trends Cancer. 2019 Mar;5(3):183-194. (PMID: 30898265)
Epigenetics Chromatin. 2015 Jan 15;8:3. (PMID: 25788984)
Bioinformatics. 2010 Apr 1;26(7):976-8. (PMID: 20179076)
Nat Genet. 2015 Oct;47(10):1149-57. (PMID: 26301496)
Trends Genet. 2003 Nov;19(11):629-39. (PMID: 14585615)
Cold Spring Harb Perspect Biol. 2010 Aug;2(8):a000794. (PMID: 20591991)
Cell. 2013 Apr 11;153(2):307-19. (PMID: 23582322)
BMC Genomics. 2018 Jul 3;19(1):514. (PMID: 29969988)
Cell. 2007 May 18;129(4):823-37. (PMID: 17512414)
EMBO J. 2005 Feb 23;24(4):800-12. (PMID: 15678104)
Nature. 2012 Aug 2;488(7409):116-20. (PMID: 22763441)
Nat Rev Cancer. 2006 Oct;6(10):813-23. (PMID: 16990858)
Nat Rev Genet. 2012 Sep;13(9):613-26. (PMID: 22868264)
Nat Methods. 2012 Mar 04;9(4):357-9. (PMID: 22388286)
Science. 2017 Jul 21;357(6348):. (PMID: 28729483)
Mol Cell. 2010 May 28;38(4):576-89. (PMID: 20513432)
Nat Methods. 2012 Feb 28;9(3):215-6. (PMID: 22373907)
Cell. 2017 Feb 9;168(4):629-643. (PMID: 28187285)
Annu Rev Cell Dev Biol. 2010;26:471-501. (PMID: 19575672)
Science. 2003 Aug 8;301(5634):798-802. (PMID: 12907790)
Nature. 2009 May 7;459(7243):108-12. (PMID: 19295514)
Bioinformatics. 2009 Aug 1;25(15):1952-8. (PMID: 19505939)
Genes Dev. 2008 Aug 1;22(15):2048-61. (PMID: 18676810)
PLoS Genet. 2008 Aug 15;4(8):e1000155. (PMID: 18704159)
Nat Rev Cancer. 2015 Sep;15(9):515-27. (PMID: 26289315)
Nat Biotechnol. 2010 May;28(5):495-501. (PMID: 20436461)
Science. 2012 Sep 7;337(6099):1190-5. (PMID: 22955828)
Nucleic Acids Res. 2014 Mar;42(5):2976-87. (PMID: 24335146)
Cancer Res. 2017 Feb 1;77(3):601-612. (PMID: 27923837)
Nat Struct Mol Biol. 2017 Nov;24(11):1000-1006. (PMID: 28967881)
Cell. 1993 Jan 29;72(2):233-45. (PMID: 8425220)
Methods Mol Biol. 2014;1150:3-20. (PMID: 24743988)
Genes Dev. 2003 Aug 1;17(15):1870-81. (PMID: 12897054)
Nat Genet. 2007 Apr;39(4):457-66. (PMID: 17334365)
Nat Cell Biol. 2004 Jan;6(1):73-7. (PMID: 14661024)
Cell Rep. 2013 Aug 15;4(3):609-20. (PMID: 23933261)
Cell. 2012 Jun 8;149(6):1381-92. (PMID: 22682255)
Cancer Res. 2012 Jul 15;72(14):3499-511. (PMID: 22802077)
Cell Stem Cell. 2008 Feb 7;2(2):160-9. (PMID: 18371437)
Cancer J. 2007 Jan-Feb;13(1):3-8. (PMID: 17464240)
Nat Genet. 2011 Jun 26;43(8):768-75. (PMID: 21706001)
Cell. 2015 Mar 12;160(6):1049-59. (PMID: 25768903)
Nat Rev Cancer. 2013 Jul;13(7):497-510. (PMID: 23760024)
Genome Med. 2011 Nov 29;3(11):75. (PMID: 22126538)
PLoS One. 2014 Mar 26;9(3):e92047. (PMID: 24670534)
Nature. 2002 Sep 26;419(6905):407-11. (PMID: 12353038)
Anticancer Res. 1992 Jul-Aug;12(4):1035-53. (PMID: 1503399)
Nat Protoc. 2017 Dec;12(12):2478-2492. (PMID: 29120462)
Mob DNA. 2016 Oct 31;7:20. (PMID: 27807467)
Genes Dev. 2004 Jun 1;18(11):1251-62. (PMID: 15145825)
Nature. 2013 Sep 19;501(7467):328-37. (PMID: 24048065)
Cell. 2013 Jan 31;152(3):642-54. (PMID: 23333102)
المشرفين على المادة: 0 (Chromatin)
0 (Histones)
0 (histone H3 trimethyl Lys4)
تواريخ الأحداث: Date Created: 20210304 Date Completed: 20210318 Latest Revision: 20210322
رمز التحديث: 20240628
مُعرف محوري في PubMed: PMC7930052
DOI: 10.1038/s41467-021-21707-1
PMID: 33658503
قاعدة البيانات: MEDLINE
الوصف
تدمد:2041-1723
DOI:10.1038/s41467-021-21707-1