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Challenges and Opportunities of Genomic Approaches in Therapeutics Development

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Translational Bioinformatics for Therapeutic Development

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2194))

Abstract

The magnitude of all therapeutic responses is significantly determined by genome structure, variation, and functional interactions. This determination occurs at many levels which are discussed in the current review. Well-established examples of structural variation between individuals are known to dictate an individual’s response to numerous drugs, as clearly illustrated by warfarin. The exponential rate of genomic-based interrogation is coupled with an expanding repertoire of genomic technologies and applications. This is leading to an ever more sophisticated appreciation of how structural variation, regulation of transcription and genomic structure, both individually and collectively, define cell therapeutic responses.

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References

  1. Fodor SP, Rava RP, Huang XC, Pease AC, Holmes CP, Adams CL (1993) Multiplexed biochemical assays with biological chips. Nature 364(6437):555–556

    Article  CAS  PubMed  Google Scholar 

  2. Gentalen E, Chee M (1999) A novel method for determining linkage between DNA sequences: hybridization to paired probe arrays. Nucleic Acids Res 27(6):1485–1491

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Eads CA, Danenberg KD, Kawakami K et al (2000) MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res 28(8):E32

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Smith LM, Sanders JZ, Kaiser RJ et al (1986) Fluorescence detection in automated DNA sequence analysis. Nature 321(6071):674–679

    Article  CAS  PubMed  Google Scholar 

  5. Sultan M, Schulz MH, Richard H et al (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321(5891):956–960

    Article  CAS  PubMed  Google Scholar 

  6. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18(9):1509–1517

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Adams DR, Eng CM (2018) Next-generation sequencing to diagnose suspected genetic disorders. N Engl J Med 379(14):1353–1362

    Article  CAS  PubMed  Google Scholar 

  8. Vora NL, Hui L (2018) Next-generation sequencing and prenatal 'omics: advanced diagnostics and new insights into human development. Genet Med 20(8):791–799

    Article  PubMed  PubMed Central  Google Scholar 

  9. Orlando V, Paro R (1993) Mapping Polycomb-repressed domains in the bithorax complex using in vivo formaldehyde cross-linked chromatin. Cell 75(6):1187–1198

    Article  CAS  PubMed  Google Scholar 

  10. Mockler TC, Chan S, Sundaresan A, Chen H, Jacobsen SE, Ecker JR (2005) Applications of DNA tiling arrays for whole-genome analysis. Genomics 85(1):1–15

    Article  CAS  PubMed  Google Scholar 

  11. Robertson G, Hirst M, Bainbridge M et al (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4(8):651–657

    Article  CAS  PubMed  Google Scholar 

  12. MacArthur J, Bowler E, Cerezo M et al (2017) The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog). Nucleic Acids Res 45(D1):D896–D901

    Article  CAS  PubMed  Google Scholar 

  13. Welter D, MacArthur J, Morales J et al (2014) The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res 42(Database issue):D1001–D1006

    Article  CAS  PubMed  Google Scholar 

  14. Maier W, Zobel A, Rietschel M (2003) Genetics of schizophrenia and affective disorders. Pharmacopsychiatry 36(Suppl 3):S195–S202

    CAS  PubMed  Google Scholar 

  15. Sadee W, Hoeg E, Lucas J, Wang D (2001) Genetic variations in human G protein-coupled receptors: implications for drug therapy. AAPS PharmSci 3(3):E22

    Article  CAS  PubMed  Google Scholar 

  16. Yang Q, Cui J, Chazaro I, Cupples LA, Demissie S (2005) Power and type I error rate of false discovery rate approaches in genome-wide association studies. BMC Genet 6(Suppl 1):S134

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  17. Saito A, Kamatani N (2002) Strategies for genome-wide association studies: optimization of study designs by the stepwise focusing method. J Hum Genet 47(7):360–365

    Article  CAS  PubMed  Google Scholar 

  18. Cooper GM, Johnson JA, Langaee TY et al (2008) A genome-wide scan for common genetic variants with a large influence on warfarin maintenance dose. Blood 112(4):1022–1027

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Strawn JR, Poweleit EA, Ramsey LB (2019) CYP2C19-guided escitalopram and sertraline dosing in pediatric patients: a pharmacokinetic modeling study. J Child Adolesc Psychopharmacol 29(5):340–347

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Scherr CL, Ramesh S, Marshall-Fricker C, Perera MA (2019) A review of African Americans' beliefs and attitudes about genomic studies: opportunities for message design. Front Genet 10:548

    Article  PubMed  PubMed Central  Google Scholar 

  21. Lauschke VM, Ingelman-Sundberg M (2019) Prediction of drug response and adverse drug reactions: from twin studies to next generation sequencing. Eur J Pharm Sci 130:65–77

    Article  CAS  PubMed  Google Scholar 

  22. Franks PW, Poveda A (2011) Gene-lifestyle and gene-pharmacotherapy interactions in obesity and its cardiovascular consequences. Curr Vasc Pharmacol 9(4):401–456

    Article  CAS  PubMed  Google Scholar 

  23. Mele M, Ferreira PG, Reverter F et al (2015) Human genomics. The human transcriptome across tissues and individuals. Science 348(6235):660–665

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Cancer Genome Atlas Research Network (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455(7216):1061–1068

    Article  CAS  Google Scholar 

  25. Cerami E, Gao J, Dogrusoz U et al (2012) The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov 2(5):401–404

    Article  PubMed  Google Scholar 

  26. Ecker JR, Geschwind DH, Kriegstein AR et al (2017) The BRAIN initiative cell census consortium: lessons learned toward generating a comprehensive BRAIN cell atlas. Neuron 96(3):542–557

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Regev A, Teichmann SA, Lander ES et al (2017) The Human Cell Atlas. elife 6

    Google Scholar 

  28. Andersson C, Johnson AD, Benjamin EJ, Levy D, Vasan RS (2019) 70-year legacy of the Framingham Heart Study. Nat Rev Cardiol 16(11):687–698

    Article  PubMed  Google Scholar 

  29. Sudlow C, Gallacher J, Allen N et al (2015) UK biobank: an open access resource for identifying the causes of a wide range of complex diseases of middle and old age. PLoS Med 12(3):e1001779

    Article  PubMed  PubMed Central  Google Scholar 

  30. Spector-Bagdady K (2016) "The Google of Healthcare": enabling the privatization of genetic bio/databanking. Ann Epidemiol 26(7):515–519

    Article  PubMed  PubMed Central  Google Scholar 

  31. Krokosky A, Terry SF (2019) So what does that test result mean? Genetic counselors in the trenches. Genet Test Mol Biomarkers 23(8):507–508

    Article  PubMed  Google Scholar 

  32. Bamshad MJ, Magoulas PL, Dent KM (2018) Genetic counselors on the frontline of precision health. Am J Med Genet C Semin Med Genet 178(1):5–9

    Article  PubMed  PubMed Central  Google Scholar 

  33. Haidle JL, Sternen DL, Dickerson JA et al (2017) Genetic counselors save costs across the genetic testing spectrum. Am J Manag Care. 23(10 Spec No.):SP428-SP430

    Google Scholar 

  34. Tandy-Connor S, Guiltinan J, Krempely K et al (2018) False-positive results released by direct-to-consumer genetic tests highlight the importance of clinical confirmation testing for appropriate patient care. Genet Med 20(12):1515–1521

    Article  PubMed  PubMed Central  Google Scholar 

  35. Allyse MA, Robinson DH, Ferber MJ, Sharp RR (2018) Direct-to-consumer testing 2.0: emerging models of direct-to-consumer genetic testing. Mayo Clin Proc 93(1):113–120

    Article  PubMed  Google Scholar 

  36. Gill J, Obley AJ, Prasad V (2018) Direct-to-consumer genetic testing: the implications of the US FDA’s first marketing authorization for BRCA mutation testing. JAMA 319(23):2377–2378

    Article  PubMed  Google Scholar 

  37. Perou CM, Sorlie T, Eisen MB et al (2000) Molecular portraits of human breast tumours. Nature 406(6797):747–752

    Article  CAS  PubMed  Google Scholar 

  38. Perou CM, Jeffrey SS, van de Rijn M et al (1999) Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc Natl Acad Sci U S A 96(16):9212–9217

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Paul J (1981) Sir George Beatson and the Royal Beatson Memorial Hospital. Med Hist 25(2):200–201

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Kerr JF, Wyllie AH, Currie AR (1972) Apoptosis: a basic biological phenomenon with wide-ranging implications in tissue kinetics. Br J Cancer 26(4):239–257

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Barfeld SJ, Urbanucci A, Itkonen HM et al (2017) c-Myc antagonises the transcriptional activity of the androgen receptor in prostate cancer affecting key gene networks. EBioMedicine 18:83–93

    Article  PubMed  PubMed Central  Google Scholar 

  42. Toropainen S, Niskanen EA, Malinen M, Sutinen P, Kaikkonen MU, Palvimo JJ (2016) Global analysis of transcription in castration-resistant prostate cancer cells uncovers active enhancers and direct androgen receptor targets. Sci Rep 6:33510

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Bernard D, Pourtier-Manzanedo A, Gil J, Beach DH (2003) Myc confers androgen-independent prostate cancer cell growth. J Clin Invest 112(11):1724–1731

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Thurman RE, Rynes E, Humbert R et al (2012) The accessible chromatin landscape of the human genome. Nature 489(7414):75–82

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Wang Q, Li W, Zhang Y et al (2009) Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell 138(2):245–256

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Massie CE, Adryan B, Barbosa-Morais NL et al (2007) New androgen receptor genomic targets show an interaction with the ETS1 transcription factor. EMBO Rep 8(9):871–878

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Copeland BT, Pal SK, Bolton EC, Jones JO (2018) The androgen receptor malignancy shift in prostate cancer. Prostate 78(7):521–531

    Article  CAS  PubMed  Google Scholar 

  48. Chattopadhyay I, Wang J, Qin M et al (2017) Src promotes castration-recurrent prostate cancer through androgen receptor-dependent canonical and non-canonical transcriptional signatures. Oncotarget 8(6):10324–10347

    Article  PubMed  Google Scholar 

  49. Malinen M, Niskanen EA, Kaikkonen MU, Palvimo JJ (2017) Crosstalk between androgen and pro-inflammatory signaling remodels androgen receptor and NF-kappaB cistrome to reprogram the prostate cancer cell transcriptome. Nucleic Acids Res 45(2):619–630

    Article  CAS  PubMed  Google Scholar 

  50. Olsen JR, Azeem W, Hellem MR et al (2016) Context dependent regulatory patterns of the androgen receptor and androgen receptor target genes. BMC Cancer 16:377

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  51. Volante M, Tota D, Giorcelli J et al (2016) Androgen deprivation modulates gene expression profile along prostate cancer progression. Hum Pathol 56:81–88

    Article  CAS  PubMed  Google Scholar 

  52. Stuchbery R, Macintyre G, Cmero M et al (2016) Reduction in expression of the benign AR transcriptome is a hallmark of localised prostate cancer progression. Oncotarget 7(21):31384–31392

    Article  PubMed  PubMed Central  Google Scholar 

  53. Pomerantz MM, Li F, Takeda DY et al (2015) The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis. Nat Genet 47(11):1346–1351

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Lu J, Lonergan PE, Nacusi LP et al (2015) The cistrome and gene signature of androgen receptor splice variants in castration resistant prostate cancer cells. J Urol 193(2):690–698

    Article  CAS  PubMed  Google Scholar 

  55. Chen Y, Chi P, Rockowitz S et al (2013) ETS factors reprogram the androgen receptor cistrome and prime prostate tumorigenesis in response to PTEN loss. Nat Med 19(8):1023–1029

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Reid G, Metivier R, Lin CY et al (2005) Multiple mechanisms induce transcriptional silencing of a subset of genes, including oestrogen receptor alpha, in response to deacetylase inhibition by valproic acid and trichostatin A. Oncogene 24(31):4894–4907

    Article  CAS  PubMed  Google Scholar 

  57. Waghray A, Schober M, Feroze F, Yao F, Virgin J, Chen YQ (2001) Identification of differentially expressed genes by serial analysis of gene expression in human prostate cancer. Cancer Res 61(10):4283–4286

    CAS  PubMed  Google Scholar 

  58. Lopez SM, Agoulnik AI, Zhang M et al (2016) Nuclear receptor corepressor 1 expression and output declines with prostate cancer progression. Clin Cancer Res 22(15):3937–3949

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Doig CL, Singh PK, Dhiman VK et al (2013) Recruitment of NCOR1 to VDR target genes is enhanced in prostate cancer cells and associates with altered DNA methylation patterns. Carcinogenesis 34(2):248–256

    Article  CAS  PubMed  Google Scholar 

  60. Battaglia S, Maguire O, Thorne JL et al (2010) Elevated NCOR1 disrupts PPARalpha/gamma signaling in prostate cancer and forms a targetable epigenetic lesion. Carcinogenesis 31(9):1650–1660

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Hodgson MC, Shen HC, Hollenberg AN, Balk SP (2008) Structural basis for nuclear receptor corepressor recruitment by antagonist-liganded androgen receptor. Mol Cancer Ther 7(10):3187–3194

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Fereshteh MP, Tilli MT, Kim SE et al (2008) The nuclear receptor coactivator amplified in breast cancer-1 is required for Neu (ErbB2/HER2) activation, signaling, and mammary tumorigenesis in mice. Cancer Res 68(10):3697–3706

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Banwell CM, MacCartney DP, Guy M et al (2006) Altered nuclear receptor corepressor expression attenuates vitamin D receptor signaling in breast cancer cells. Clin Cancer Res 12(7 Pt 1):2004–2013

    Article  CAS  PubMed  Google Scholar 

  64. Cheng S, Brzostek S, Lee SR, Hollenberg AN, Balk SP (2002) Inhibition of the dihydrotestosterone-activated androgen receptor by nuclear receptor corepressor. Mol Endocrinol 16(7):1492–1501

    Article  CAS  PubMed  Google Scholar 

  65. Lavinsky RM, Jepsen K, Heinzel T et al (1998) Diverse signaling pathways modulate nuclear receptor recruitment of N-CoR and SMRT complexes. Proc Natl Acad Sci U S A 95(6):2920–2925

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Cancer Genome Atlas Research Network, Weinstein JN, Collisson EA et al (2013) The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet 45(10):1113–1120

    Article  CAS  PubMed Central  Google Scholar 

  67. Cancer Genome Atlas Research Network (2015) The molecular taxonomy of primary prostate cancer. Cell 163(4):1011–1025

    Article  CAS  Google Scholar 

  68. Sanda MG, Feng Z, Howard DH et al (2017) Association between combined TMPRSS2:ERG and PCA3 RNA urinary testing and detection of aggressive prostate cancer. JAMA Oncol 3(8):1085–1093

    Article  PubMed  PubMed Central  Google Scholar 

  69. Tomlins SA, Rhodes DR, Perner S et al (2005) Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 310(5748):644–648

    Article  CAS  PubMed  Google Scholar 

  70. Armenia J, Wankowicz SAM, Liu D et al (2018) The long tail of oncogenic drivers in prostate cancer. Nat Genet 50(5):645–651

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Jain P, Di Croce L (2016) Mutations and deletions of PRC2 in prostate cancer. BioEssays 38(5):446–454

    Article  CAS  PubMed  Google Scholar 

  72. Maki HE, Waltering KK, Wallen MJ et al (2006) Screening of genetic and expression alterations of SRC1 gene in prostate cancer. Prostate 66(13):1391–1398

    Article  CAS  PubMed  Google Scholar 

  73. Fraser M, Sabelnykova VY, Yamaguchi TN et al (2017) Genomic hallmarks of localized, non-indolent prostate cancer. Nature 541(7637):359–364

    Article  CAS  PubMed  Google Scholar 

  74. Volinia S, Calin GA, Liu CG et al (2006) A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci U S A 103(7):2257–2261

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Jackson BL, Grabowska A, Ratan HL (2014) MicroRNA in prostate cancer: functional importance and potential as circulating biomarkers. BMC Cancer 14:930

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  76. Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120(1):15–20

    Article  CAS  PubMed  Google Scholar 

  77. Lussier YA, Stadler WM, Chen JL (2012) Advantages of genomic complexity: bioinformatics opportunities in microRNA cancer signatures. J Am Med Inform Assoc 19(2):156–160

    Article  PubMed  Google Scholar 

  78. Loeb S, van den Heuvel S, Zhu X, Bangma CH, Schroder FH, Roobol MJ (2012) Infectious complications and hospital admissions after prostate biopsy in a European randomized trial. Eur Urol 61(6):1110–1114

    Article  PubMed  Google Scholar 

  79. Schwarzenbach H, Nishida N, Calin GA, Pantel K (2014) Clinical relevance of circulating cell-free microRNAs in cancer. Nat Rev Clin Oncol 11(3):145–156

    Article  CAS  PubMed  Google Scholar 

  80. Mihelich BL, Maranville JC, Nolley R, Peehl DM, Nonn L (2015) Elevated serum microRNA levels associate with absence of high-grade prostate cancer in a retrospective cohort. PLoS One 10(4):e0124245

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  81. Mitchell PS, Parkin RK, Kroh EM et al (2008) Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci U S A 105(30):10513–10518

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Loeb S, Chan DW, Sokoll L et al (2008) Prostate specific antigen assay standardization bias could affect clinical decision making. J Urol 180(5):1959–1962; discussion 1962-1953

    Article  CAS  PubMed  Google Scholar 

  83. Rupaimoole R, Calin GA, Lopez-Berestein G, Sood AK (2016) miRNA deregulation in cancer cells and the tumor microenvironment. Cancer Discov 6(3):235–246

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Frediani JN, Fabbri M (2016) Essential role of miRNAs in orchestrating the biology of the tumor microenvironment. Mol Cancer 15(1):42

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  85. Kohlhapp FJ, Mitra AK, Lengyel E, Peter ME (2015) MicroRNAs as mediators and communicators between cancer cells and the tumor microenvironment. Oncogene 34(48):5857–5868

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Hudson RS, Yi M, Esposito D et al (2013) MicroRNA-106b-25 cluster expression is associated with early disease recurrence and targets caspase-7 and focal adhesion in human prostate cancer. Oncogene 32(35):4139–4147

    Article  CAS  PubMed  Google Scholar 

  87. Goto Y, Kojima S, Nishikawa R et al (2014) The microRNA-23b/27b/24-1 cluster is a disease progression marker and tumor suppressor in prostate cancer. Oncotarget 5(17):7748–7759

    Article  PubMed  PubMed Central  Google Scholar 

  88. Singh PK, Preus L, Hu Q et al (2014) Serum microRNA expression patterns that predict early treatment failure in prostate cancer patients. Oncotarget 5(3):824–840

    Article  PubMed  PubMed Central  Google Scholar 

  89. Cagle P, Niture S, Srivastava A et al (2019) MicroRNA-214 targets PTK6 to inhibit tumorigenic potential and increase drug sensitivity of prostate cancer cells. Sci Rep 9(1):9776

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  90. Farran B, Dyson G, Craig D et al (2018) A study of circulating microRNAs identifies a new potential biomarker panel to distinguish aggressive prostate cancer. Carcinogenesis 39(4):556–561

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Yates C, Long MD, Campbell MJ, Sucheston-Campbell L (2017) miRNAs as drivers of TMPRSS2-ERG negative prostate tumors in African American men. Front Biosci (Landmark Ed) 22:212–229

    Article  CAS  Google Scholar 

  92. Alunni-Fabbroni M, Majunke L, Trapp EK et al (2018) Whole blood microRNAs as potential biomarkers in post-operative early breast cancer patients. BMC Cancer 18(1):141

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  93. Minemura H, Takagi K, Miki Y et al (2015) Abnormal expression of miR-1 in breast carcinoma as a potent prognostic factor. Cancer Sci 106(11):1642–1650

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Niu J, Xue A, Chi Y et al (2016) Induction of miRNA-181a by genotoxic treatments promotes chemotherapeutic resistance and metastasis in breast cancer. Oncogene 35(10):1302–1313

    Article  CAS  PubMed  Google Scholar 

  95. Gong Z, Wang J, Wang D et al (2019) Differences in microRNA expression in breast cancer between women of African and European ancestry. Carcinogenesis 40(1):61–69

    Article  CAS  PubMed  Google Scholar 

  96. Telonis AG, Rigoutsos I (2018) Race disparities in the contribution of miRNA isoforms and tRNA-derived fragments to triple-negative breast cancer. Cancer Res 78(5):1140–1154

    Article  CAS  PubMed  Google Scholar 

  97. Yao S, Graham K, Shen J et al (2013) Genetic variants in microRNAs and breast cancer risk in African American and European American women. Breast Cancer Res Treat 141(3):447–459

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Chakravarty D, Sboner A, Nair SS et al (2014) The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer. Nat Commun 5:5383

    Article  CAS  PubMed  Google Scholar 

  99. Zhang Y, Pitchiaya S, Cieslik M et al (2018) Analysis of the androgen receptor-regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression. Nat Genet 50(6):814–824

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Luo J, Wang K, Yeh S et al (2019) LncRNA-p21 alters the antiandrogen enzalutamide-induced prostate cancer neuroendocrine differentiation via modulating the EZH2/STAT3 signaling. Nat Commun 10(1):2571

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  101. Shang Z, Yu J, Sun L et al (2019) LncRNA PCAT1 activates AKT and NF-kappaB signaling in castration-resistant prostate cancer by regulating the PHLPP/FKBP51/IKKalpha complex. Nucleic Acids Res 47(8):4211–4225

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Huang P, Li F, Li L et al (2018) lncRNA profile study reveals the mRNAs and lncRNAs associated with docetaxel resistance in breast cancer cells. Sci Rep 8(1):17970

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Ma Y, Bu D, Long J, Chai W, Dong J (2019) LncRNA DSCAM-AS1 acts as a sponge of miR-137 to enhance Tamoxifen resistance in breast cancer. J Cell Physiol 234(3):2880–2894

    Article  CAS  PubMed  Google Scholar 

  104. Olgun G, Sahin O, Tastan O (2018) Discovering lncRNA mediated sponge interactions in breast cancer molecular subtypes. BMC Genomics 19(1):650

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  105. Wu X, Xiao Y, Zhou Y, Zhou Z, Yan W (2019) LncRNA FOXP4-AS1 is activated by PAX5 and promotes the growth of prostate cancer by sequestering miR-3184-5p to upregulate FOXP4. Cell Death Dis 10(7):472

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  106. Long MD, Singh PK, Russell JR et al (2019) The miR-96 and RARgamma signaling axis governs androgen signaling and prostate cancer progression. Oncogene 38(3):421–444

    Article  CAS  PubMed  Google Scholar 

  107. Jiang L, Yu X, Ma X et al (2019) Identification of transcription factor-miRNA-lncRNA feed-forward loops in breast cancer subtypes. Comput Biol Chem 78:1–7

    Article  PubMed  CAS  Google Scholar 

  108. Wu Q, Qin H, Zhao Q, He XX (2015) Emerging role of transcription factor-microRNA-target gene feed-forward loops in cancer. Biomed Rep 3(5):611–616

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Zhao M, Sun J, Zhao Z (2013) Synergetic regulatory networks mediated by oncogene-driven microRNAs and transcription factors in serous ovarian cancer. Mol BioSyst 9(12):3187–3198

    Article  CAS  PubMed  Google Scholar 

  110. Yan Z, Shah PK, Amin SB et al (2012) Integrative analysis of gene and miRNA expression profiles with transcription factor-miRNA feed-forward loops identifies regulators in human cancers. Nucleic Acids Res 40(17):e135

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. El Baroudi M, Cora D, Bosia C, Osella M, Caselle M (2011) A curated database of miRNA mediated feed-forward loops involving MYC as master regulator. PLoS One 6(3):e14742

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  112. Thorne JL, Maguire O, Doig CL et al (2011) Epigenetic control of a VDR-governed feed-forward loop that regulates p21(waf1/cip1) expression and function in non-malignant prostate cells. Nucleic Acids Res 39(6):2045–2056

    Article  CAS  PubMed  Google Scholar 

  113. Koido M, Tani Y, Tsukahara S, Okamoto Y, Tomida A (2018) InDePTH: detection of hub genes for developing gene expression networks under anticancer drug treatment. Oncotarget 9(49):29097–29111

    Article  PubMed  PubMed Central  Google Scholar 

  114. Zhang XQ, Wang ZL, Poon MW, Yang JH (2017) Spatial-temporal transcriptional dynamics of long non-coding RNAs in human brain. Hum Mol Genet 26(16):3202–3211

    CAS  PubMed  Google Scholar 

  115. Chou SJ, Wang C, Sintupisut N et al (2016) Analysis of spatial-temporal gene expression patterns reveals dynamics and regionalization in developing mouse brain. Sci Rep 6:19274

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Berglund E, Maaskola J, Schultz N et al (2018) Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity. Nat Commun 9(1):2419

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  117. Labbe DP, Brown M (2018) Transcriptional regulation in prostate cancer. Cold Spring Harb Perspect Med 8(11)

    Google Scholar 

  118. McNair C, Xu K, Mandigo AC et al (2018) Differential impact of RB status on E2F1 reprogramming in human cancer. J Clin Invest 128(1):341–358

    Article  PubMed  Google Scholar 

  119. Kron KJ, Murison A, Zhou S et al (2017) TMPRSS2-ERG fusion co-opts master transcription factors and activates NOTCH signaling in primary prostate cancer. Nat Genet 49(9):1336–1345

    Article  CAS  PubMed  Google Scholar 

  120. Jung SH, Shin S, Kim MS et al (2016) Genetic progression of high grade prostatic intraepithelial neoplasia to prostate cancer. Eur Urol 69(5):823–830

    Article  CAS  PubMed  Google Scholar 

  121. Castro E, Jugurnauth-Little S, Karlsson Q et al (2015) High burden of copy number alterations and c-MYC amplification in prostate cancer from BRCA2 germline mutation carriers. Ann Oncol 26(11):2293–2300

    Article  CAS  PubMed  Google Scholar 

  122. Nora EP, Lajoie BR, Schulz EG et al (2012) Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485(7398):381–385

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Dixon JR, Selvaraj S, Yue F et al (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485(7398):376–380

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Taberlay PC, Achinger-Kawecka J, Lun AT et al (2016) Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations. Genome Res 26(6):719–731

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Fabre PJ, Leleu M, Mormann BH et al (2017) Large scale genomic reorganization of topological domains at the HoxD locus. Genome Biol 18(1):149

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  126. Koch L (2016) Chromatin: going a TAD out on a limb. Nat Rev Genet 17(12):717

    Article  CAS  PubMed  Google Scholar 

  127. Lupianez DG, Kraft K, Heinrich V et al (2015) Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell 161(5):1012–1025

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Cutrupi AN, Brewer MH, Nicholson GA, Kennerson ML (2018) Structural variations causing inherited peripheral neuropathies: a paradigm for understanding genomic organization, chromatin interactions, and gene dysregulation. Mol Genet Genomic Med 6(3):422–433

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Wu P, Li T, Li R et al (2017) 3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations. Nat Commun 8(1):1937

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  130. daSilva LF, Beckedorff FC, Ayupe AC et al (2018) Chromatin landscape distinguishes the genomic loci of hundreds of androgen-receptor-associated LincRNAs from the loci of non-associated LincRNAs. Front Genet 9:132

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  131. Roe JS, Hwang CI, Somerville TDD et al (2017) Enhancer reprogramming promotes pancreatic cancer metastasis. Cell 170(5):875–888.e20

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Nguyen VT, Barozzi I, Faronato M et al (2015) Differential epigenetic reprogramming in response to specific endocrine therapies promotes cholesterol biosynthesis and cellular invasion. Nat Commun 6:10044

    Article  CAS  PubMed  Google Scholar 

  133. Krum SA, Miranda-Carboni GA, Lupien M, Eeckhoute J, Carroll JS, Brown M (2008) Unique ERalpha cistromes control cell type-specific gene regulation. Mol Endocrinol 22(11):2393–2406

    Article  CAS  PubMed  Google Scholar 

  134. Jozwik KM, Chernukhin I, Serandour AA, Nagarajan S, Carroll JS (2016) FOXA1 directs H3K4 monomethylation at enhancers via recruitment of the methyltransferase MLL3. Cell Rep 17(10):2715–2723

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. Theodorou V, Stark R, Menon S, Carroll JS (2013) GATA3 acts upstream of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility. Genome Res 23(1):12–22

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  136. Haller F, Bieg M, Will R et al (2019) Enhancer hijacking activates oncogenic transcription factor NR4A3 in acinic cell carcinomas of the salivary glands. Nat Commun 10(1):368

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  137. Martin-Garcia D, Navarro A, Valdes-Mas R et al (2019) CCND2 and CCND3 hijack immunoglobulin light-chain enhancers in cyclin D1(−) mantle cell lymphoma. Blood 133(9):940–951

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Cuartero S, Merkenschlager M (2018) Three-dimensional genome organization in normal and malignant haematopoiesis. Curr Opin Hematol 25(4):323–328

    Article  CAS  PubMed  Google Scholar 

  139. Zimmerman MW, Liu Y, He S et al (2018) MYC drives a subset of high-risk pediatric neuroblastomas and is activated through mechanisms including enhancer hijacking and focal enhancer amplification. Cancer Discov 8(3):320–335

    Article  CAS  PubMed  Google Scholar 

  140. Ryan RJ, Drier Y, Whitton H et al (2015) Detection of enhancer-associated rearrangements reveals mechanisms of oncogene dysregulation in B-cell lymphoma. Cancer Discov 5(10):1058–1071

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  141. Northcott PA, Lee C, Zichner T et al (2014) Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma. Nature 511(7510):428–434

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  142. Luo H, Wang F, Zha J et al (2018) CTCF boundary remodels chromatin domain and drives aberrant HOX gene transcription in acute myeloid leukemia. Blood 132(8):837–848

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Petrovic J, Zhou Y, Fasolino M et al (2019) Oncogenic Notch promotes long-range regulatory interactions within hyperconnected 3D cliques. Mol Cell 73(6):1174–1190.e12

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  144. Negi S, Bolt CC, Zhang H, Stubbs L (2019) An extended regulatory landscape drives Tbx18 activity in a variety of prostate-associated cell lineages. Dev Biol 446(2):180–192

    Article  CAS  PubMed  Google Scholar 

  145. Rickman DS, Soong TD, Moss B et al (2012) Oncogene-mediated alterations in chromatin conformation. Proc Natl Acad Sci U S A 109(23):9083–9088

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  146. Rickman DS, Chen YB, Banerjee S et al (2010) ERG cooperates with androgen receptor in regulating trefoil factor 3 in prostate cancer disease progression. Neoplasia 12(12):1031–1040

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  147. Taberlay PC, Statham AL, Kelly TK, Clark SJ, Jones PA (2014) Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer. Genome Res 24(9):1421–1432

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  148. Long MD, Smiraglia DJ, Campbell MJ (2017) The genomic impact of DNA CpG methylation on gene expression; relationships in prostate cancer. Biomol Ther 7(1)

    Google Scholar 

  149. Campbell MJ, Turner BM (2013) Altered histone modifications in cancer. Adv Exp Med Biol 754:81–107

    Article  CAS  PubMed  Google Scholar 

  150. Battaglia S, Maguire O, Campbell MJ (2010) Transcription factor co-repressors in cancer biology: roles and targeting. Int J Cancer 126(11):2511–2519

    CAS  PubMed  PubMed Central  Google Scholar 

  151. Ambatipudi S, Horvath S, Perrier F et al (2017) DNA methylome analysis identifies accelerated epigenetic ageing associated with postmenopausal breast cancer susceptibility. Eur J Cancer 75:299–307

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  152. Horvath S, Raj K (2018) DNA methylation-based biomarkers and the epigenetic clock theory of ageing. Nat Rev Genet 19(6):371–384

    Article  CAS  PubMed  Google Scholar 

  153. Levine ME, Hosgood HD, Chen B, Absher D, Assimes T, Horvath S (2015) DNA methylation age of blood predicts future onset of lung cancer in the women’s health initiative. Aging (Albany NY) 7(9):690–700

    Article  CAS  Google Scholar 

  154. Zheng Y, Joyce BT, Colicino E et al (2016) Blood epigenetic age may predict cancer incidence and mortality. EBioMedicine 5:68–73

    Article  PubMed  PubMed Central  Google Scholar 

  155. Levine ME, Lu AT, Quach A et al (2018) An epigenetic biomarker of aging for lifespan and healthspan. Aging (Albany NY) 10(4):573–591

    Article  Google Scholar 

  156. Marioni RE, Shah S, McRae AF et al (2015) DNA methylation age of blood predicts all-cause mortality in later life. Genome Biol 16:25

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  157. Keegan THM, Kushi LH, Li Q et al (2018) Cardiovascular disease incidence in adolescent and young adult cancer survivors: a retrospective cohort study. J Cancer Surviv 12(3):388–397

    Article  PubMed  Google Scholar 

  158. Perna L, Zhang Y, Mons U, Holleczek B, Saum KU, Brenner H (2016) Epigenetic age acceleration predicts cancer, cardiovascular, and all-cause mortality in a German case cohort. Clin Epigenetics 8:64

    Article  PubMed  PubMed Central  Google Scholar 

  159. Chen BH, Marioni RE, Colicino E et al (2016) DNA methylation-based measures of biological age: meta-analysis predicting time to death. Aging (Albany NY) 8(9):1844–1865

    Article  CAS  Google Scholar 

  160. Ilich JZ, Kelly OJ, Inglis JE (2016) Osteosarcopenic obesity syndrome: what is it and how can it be identified and diagnosed? Curr Gerontol Geriatr Res 2016:7325973

    Article  PubMed  PubMed Central  Google Scholar 

  161. Gonnelli S, Caffarelli C, Nuti R (2014) Obesity and fracture risk. Clin Cases Miner Bone Metab 11(1):9–14

    PubMed  PubMed Central  Google Scholar 

  162. Wilson D, Jackson T, Sapey E, Lord JM (2017) Frailty and sarcopenia: the potential role of an aged immune system. Ageing Res Rev 36:1–10

    Article  PubMed  Google Scholar 

  163. Franceschi C, Garagnani P, Morsiani C et al (2018) The continuum of aging and age-related diseases: common mechanisms but different rates. Front Med (Lausanne) 5:61

    Article  Google Scholar 

  164. Pistore C, Giannoni E, Colangelo T et al (2017) DNA methylation variations are required for epithelial-to-mesenchymal transition induced by cancer-associated fibroblasts in prostate cancer cells. Oncogene 36(40):5551–5566

    Article  CAS  PubMed  Google Scholar 

  165. Camoriano M, Kinney SR, Moser MT et al (2008) Phenotype-specific CpG island methylation events in a murine model of prostate cancer. Cancer Res 68(11):4173–4182

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  166. Sinha KM, Bagheri-Yarmand R, Lahiri S et al (2019) Oncogenic and osteolytic functions of histone demethylase NO66 in castration-resistant prostate cancer. Oncogene 38(25):5038–5049

    Article  CAS  PubMed  Google Scholar 

  167. Beltran H, Prandi D, Mosquera JM et al (2016) Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer. Nat Med 22(3):298–305

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  168. Braadland PR, Urbanucci A (2019) Chromatin reprogramming as an adaptation mechanism in advanced prostate cancer. Endocr Relat Cancer 26(4):R211–R235

    Article  CAS  PubMed  Google Scholar 

  169. Labbe DP, Sweeney CJ, Brown M et al (2017) TOP2A and EZH2 provide early detection of an aggressive prostate cancer subgroup. Clin Cancer Res 23(22):7072–7083

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  170. Panja S, Hayati S, Epsi NJ, Parrott JS, Mitrofanova A (2018) Integrative (epi) genomic analysis to predict response to androgen-deprivation therapy in prostate cancer. EBioMedicine 31:110–121

    Article  PubMed  PubMed Central  Google Scholar 

  171. Zou M, Toivanen R, Mitrofanova A et al (2017) Transdifferentiation as a mechanism of treatment resistance in a mouse model of castration-resistant prostate cancer. Cancer Discov 7(7):736–749

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  172. Baylin SB, Herman JG, Graff JR, Vertino PM, Issa JP (1998) Alterations in DNA methylation: a fundamental aspect of neoplasia. Adv Cancer Res 72:141–196

    Article  CAS  PubMed  Google Scholar 

  173. Jones PA (1996) DNA methylation errors and cancer. Cancer Res 56(11):2463–2467

    CAS  PubMed  Google Scholar 

  174. Jones PA, Gonzalgo ML (1997) Altered DNA methylation and genome instability: a new pathway to cancer? Proc Natl Acad Sci U S A 94(6):2103–2105

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  175. Gama-Sosa MA, Slagel VA, Trewyn RW et al (1983) The 5-methylcytosine content of DNA from human tumors. Nucleic Acids Res 11(19):6883–6894

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  176. Costello JF, Fruhwald MC, Smiraglia DJ et al (2000) Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat Genet 24(2):132–138

    Article  CAS  PubMed  Google Scholar 

  177. Massie CE, Mills IG, Lynch AG (2016) The importance of DNA methylation in prostate cancer development. J Steroid Biochem Mol Biol 166:1–15

    Article  PubMed  CAS  Google Scholar 

  178. Bird AP, Wolffe AP (1999) Methylation-induced repression—belts, braces, and chromatin. Cell 99(5):451–454

    Article  CAS  PubMed  Google Scholar 

  179. Singh PK, Doig CL, Dhiman VK, Turner BM, Smiraglia DJ, Campbell MJ (2013) Epigenetic distortion to VDR transcriptional regulation in prostate cancer cells. J Steroid Biochem Mol Biol 136:258–263

    Article  CAS  PubMed  Google Scholar 

  180. Campbell MJ, Park S, Uskokovic MR, Dawson MI, Koeffler HP (1998) Expression of retinoic acid receptor-beta sensitizes prostate cancer cells to growth inhibition mediated by combinations of retinoids and a 19-nor hexafluoride vitamin D3 analog. Endocrinology 139(4):1972–1980

    Article  CAS  PubMed  Google Scholar 

  181. Litovkin K, Van Eynde A, Joniau S et al (2015) DNA methylation-guided prediction of clinical failure in high-risk prostate cancer. PLoS One 10(6):e0130651

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  182. Haldrup C, Mundbjerg K, Vestergaard EM et al (2013) DNA methylation signatures for prediction of biochemical recurrence after radical prostatectomy of clinically localized prostate cancer. J Clin Oncol 31(26):3250–3258

    Article  CAS  PubMed  Google Scholar 

  183. Bogdanovic O, Smits AH, de la Calle Mustienes E et al (2016) Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nat Genet 48(4):417–426

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  184. Charlet J, Duymich CE, Lay FD et al (2016) Bivalent regions of cytosine methylation and H3K27 acetylation suggest an active role for DNA methylation at enhancers. Mol Cell 62(3):422–431

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  185. Irizarry RA, Ladd-Acosta C, Wen B et al (2009) The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 41(2):178–186

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  186. Stadler MB, Murr R, Burger L et al (2011) DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480(7378):490–495

    Article  CAS  PubMed  Google Scholar 

  187. Aran D, Sabato S, Hellman A (2013) DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes. Genome Biol 14(3):R21

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  188. Aran D, Hellman A (2013) Unmasking risk loci: DNA methylation illuminates the biology of cancer predisposition: analyzing DNA methylation of transcriptional enhancers reveals missed regulatory links between cancer risk loci and genes. BioEssays 36(2):184–190

    Article  PubMed  CAS  Google Scholar 

  189. Aran D, Hellman A (2013) DNA methylation of transcriptional enhancers and cancer predisposition. Cell 154(1):11–13

    Article  CAS  PubMed  Google Scholar 

  190. Fleischer T, Tekpli X, Mathelier A et al (2017) DNA methylation at enhancers identifies distinct breast cancer lineages. Nat Commun 8(1):1379

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  191. Yin Y, Morgunova E, Jolma A et al (2017) Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science 356(6337)

    Google Scholar 

  192. Guo H, Ci X, Ahmed M et al (2019) ONECUT2 is a driver of neuroendocrine prostate cancer. Nat Commun 10(1):278

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  193. Rotinen M, You S, Yang J et al (2018) ONECUT2 is a targetable master regulator of lethal prostate cancer that suppresses the androgen axis. Nat Med 24(12):1887–1898

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  194. Patten DK, Corleone G, Gyorffy B et al (2018) Enhancer mapping uncovers phenotypic heterogeneity and evolution in patients with luminal breast cancer. Nat Med 24(9):1469–1480

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  195. Taslim C, Chen Z, Huang K, Huang TH, Wang Q, Lin S (2012) Integrated analysis identifies a class of androgen-responsive genes regulated by short combinatorial long-range mechanism facilitated by CTCF. Nucleic Acids Res 40(11):4754–4764

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  196. Hogeweg P (2011) The roots of bioinformatics in theoretical biology. PLoS Comput Biol 7(3):e1002021

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  197. Weaver W (1970) Molecular biology: origin of the term. Science 170(3958):581–582

    Article  CAS  PubMed  Google Scholar 

  198. Danna K, Nathans D (1971) Specific cleavage of simian virus 40 DNA by restriction endonuclease of Hemophilus influenzae. Proc Natl Acad Sci U S A 68(12):2913–2917

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  199. Saiki RK, Gelfand DH, Stoffel S et al (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239(4839):487–491

    Article  CAS  PubMed  Google Scholar 

  200. Hunkapiller T, Kaiser RJ, Koop BF, Hood L (1991) Large-scale and automated DNA sequence determination. Science 254(5028):59–67

    Article  CAS  PubMed  Google Scholar 

  201. Roberts L, Davenport RJ, Pennisi E, Marshall E (2001) A history of the human genome project. Science 291(5507):1195

    Article  CAS  PubMed  Google Scholar 

  202. Birney E (2012) The making of ENCODE: lessons for big-data projects. Nature 489(7414):49–51

    Article  CAS  PubMed  Google Scholar 

  203. ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA et al (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447(7146):799–816

    Article  CAS  Google Scholar 

  204. Soller M, Fray R (2019) RNA modifications in gene expression control. Biochim Biophys Acta Gene Regul Mech 1862(3):219–221

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

Funding: This work was funded by the National Cancer Institute (NCI) grant awarded to the OSUCCC The James, CCSG P30CA016058.

Declaration of Interest: We declare that there is no conflict of interest that could be perceived as prejudicing the impartiality of the research reported.

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Gray, J.S., Campbell, M.J. (2021). Challenges and Opportunities of Genomic Approaches in Therapeutics Development. In: Markowitz, J. (eds) Translational Bioinformatics for Therapeutic Development. Methods in Molecular Biology, vol 2194. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0849-4_7

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