[논문]Novel genes exhibiting DNA methylation alterations in Korean patients with chronic lymphocytic leukaemia: a methyl-CpG-binding domain sequencing study

Kim, Miyoung; Lee, Eunyup; Zang, Dae Young; Kim, Hyo Jung; Kim, Ho Young; Han, Boram; Kim, Han-Sung; Kang, Hee Jung; Hwang, Seungwoo; Lee, Young Kyung

doi:10.1038/s41598-020-57919-6

[해외논문] Novel genes exhibiting DNA methylation alterations in Korean patients with chronic lymphocytic leukaemia: a methyl-CpG-binding domain sequencing study 원문보기

Scientific reports, v.10, 2020년, pp.1085 -

Kim, Miyoung (Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Anyang, Republic of Korea) , Lee, Eunyup (Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Anyang, Republic of Korea) , Zang, Dae Young (Department of Internal Medicine, Hallym University Sacred Heart Hospital, Anyang, Republic of Korea) , Kim, Hyo Jung (Department of Internal Medicine, Hallym University Sacred Heart Hospital, Anyang, Republic of Korea) , Kim, Ho Young (Department of Internal Medicine, Hallym University Sacred Heart Hospital, Anyang, Republic of Korea) , Han, Boram (Department of Internal Medicine, Hallym University Sacred Heart Hospital, Anyang, Republic of Korea) , Kim, Han-Sung (Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Anyang, Republic of Korea) , Kang, Hee Jung (Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Anyang, Republic of Korea) , Hwang, Seungwoo (Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea) , Lee, Young Kyung (Department of Laboratory Medicine, Hallym University Sacred)

Abstract ▼ AI-Helper

Chronic lymphocytic leukaemia (CLL) exhibits differences between Asians and Caucasians in terms of incidence rate, age at onset, immunophenotype, and genetic profile. We performed genome-wide methylation profiling of CLL in an Asian cohort for the first time. Eight Korean patients without somatic immunoglobulin heavy chain gene hypermutations underwent methyl-CpG-binding domain sequencing (MBD-seq), as did five control subjects. Gene Ontology, pathway analysis, and network-based prioritization of differentially methylated genes were also performed. More regions were hypomethylated (2,062 windows) than were hypermethylated (777 windows). Promoters contained the highest proportion of differentially methylated regions (0.08%), while distal intergenic and intron regions contained the largest number of differentially methylated regions. Protein-coding genes were the most abundant, followed by long noncoding and short noncoding genes. The most significantly over-represented signalling pathways in the differentially methylated gene list included immune/cancer-related pathways and B-cell receptor signalling. Among the top 10 hub genes identified via network-based prioritization, four (UBC, GRB2, CREBBP, and GAB2) had no known relevance to CLL, while the other six (STAT3, PTPN6, SYK, STAT5B, XPO1, and ABL1) have previously been linked to CLL in Caucasians. As such, our analysis identified four novel candidate genes of potential significance to Asian patients with CLL.

참고문헌 (75)

1. Swerdlow, S. H. et al . Chronic lymphocytic leukaemia/small lymphocytic lymphoma. In WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues (eds. Campo, E. et al .) 216？219 (IARC, 2017).
2. Kim JA Genomic Profile of Chronic Lymphocytic Leukemia in Korea Identified by Targeted Sequencing PLoS One. 2016 11 e0167641 10.1371/journal.pone.0167641 27959900

상세보기
3. Jang MA Chronic lymphocytic leukemia in Korean patients: frequent atypical immunophenotype and relatively aggressive clinical behavior Int. J. Hematol. 2016 97 403 8 10.1007/s12185-013-1286-z

상세보기
4. Xia Y Frequencies of SF3B1, NOTCH1, MYD88, BIRC3 and IGHV mutations and TP53 disruptions in Chinese with chronic lymphocytic leukemia: disparities with Europeans Oncotarget. 2015 6 5426 34 25605254

상세보기
5. Chen SS Silencing of the inhibitor of DNA binding protein 4 (ID4) contributes to the pathogenesis of mouse and human CLL Blood. 2011 117 862 71 10.1182/blood-2010-05-284638 21098398

상세보기
6. Corcoran M ZAP-70 methylation status is associated with ZAP-70 expression status in chronic lymphocytic leukemia Haematologica. 2005 90 1078 88 16079107

상세보기
7. Raval A Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia Cell. 2007 129 879 90 10.1016/j.cell.2007.03.043 17540169

상세보기
8. Seeliger B Wilop S Osieka R Galm O Jost E CpG island methylation patterns in chronic lymphocytic leukemia Leuk. Lymphoma. 2009 50 419 26 10.1080/10428190902756594 19347729

상세보기
9. Kanduri M Differential genome-wide array-based methylation profiles in prognostic subsets of chronic lymphocytic leukemia Blood. 2010 115 296 305 10.1182/blood-2009-07-232868 19897574

상세보기
10. Cahill N 450K-array analysis of chronic lymphocytic leukemia cells reveals global DNA methylation to be relatively stable over time and similar in resting and proliferative compartments Leukemia. 2013 27 150 8 10.1038/leu.2012.245 22922567

상세보기
11. Kulis M Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia Nat. Genet. 2012 44 1236 42 10.1038/ng.2443 23064414

상세보기
12. Landau DA Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia Cancer Cell. 2014 26 813 825 10.1016/j.ccell.2014.10.012 25490447

상세보기
13. Serre D Lee BH Ting AH MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome Nucleic Acids Res. 2010 38 391 9 10.1093/nar/gkp992 19906696

상세보기
14. Aberg KA MBD-seq as a cost-effective approach for methylome-wide association studies: demonstration in 1500 case？control samples Epigenomics. 2012 4 605 21 10.2217/epi.12.59 23244307

상세보기
15. Harris RA Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications Nat. Biotechnol. 2010 28 1097 105 10.1038/nbt.1682 20852635

상세보기
16. Subhash S Andersson PO Kosalai ST Kanduri C Kanduri M Global DNA methylation profiling reveals new insights into epigenetically deregulated protein coding and long noncoding RNAs in CLL Clin. Epigenetics. 2016 8 106 10.1186/s13148-016-0274-6 27777635

상세보기
17. Cahill N Rosenquist R Uncovering the DNA methylome in chronic lymphocytic leukemia Epigenetics. 2013 8 138 48 10.4161/epi.23439 23321535

상세보기
18. Pei L Genome-wide DNA methylation analysis reveals novel epigenetic changes in chronic lymphocytic leukemia Epigenetics. 2012 7 567 78 10.4161/epi.20237 22534504

상세보기
19. Kulis M Whole-genome fingerprint of the DNA methylome during human B cell differentiation Nat. Genet. 2015 47 746 56 10.1038/ng.3291 26053498

상세보기
20. Ehrlich M DNA methylation in cancer: too much, but also too little Oncogene. 2002 21 5400 5413 10.1038/sj.onc.1205651 12154403

상세보기
21. Ogishima T Increased heparanase expression is caused by promoter hypomethylation and upregulation of transcriptional factor early growth response-1 in human prostate cancer Clin. Cancer Res. 2005 11 1028 1036 15709168

상세보기
22. Gaudet F Induction of tumors in mice by genomic hypomethylation Science. 2003 300 489 492 10.1126/science.1083558 12702876

상세보기
23. Qu G Grundy PE Narayan A Ehrlich M Frequent hypomethylation in Wilms tumors of pericentromeric DNA in chromosomes 1 and 16 Cancer Genet. Cytogenet. 1999 109 34 39 10.1016/S0165-4608(98)00143-5 9973957

상세보기
24. Medvedeva YA Intergenic, gene terminal, and intragenic CpG islands in the human genome BMC Genomics. 2010 11 48 10.1186/1471-2164-11-48 20085634

상세보기
25. Baylin SB Herman JG DNA hypermethylation in tumorigenesis: epigenetics joins genetics Trends. Genet. 2000 16 168 74 10.1016/S0168-9525(99)01971-X 10729832

상세보기
26. Esteller M Epigenetic gene silencing in cancer: the DNA hypermethylome Hum. Mol. Genet. 2007 16 R50 9 10.1093/hmg/ddm018 17613547

상세보기
27. Weber B Stresemann C Brueckner B Lyko F Methylation of human microRNA genes in normal and neoplastic cells Cell Cycle. 2007 6 1001 5 10.4161/cc.6.9.4209 17457051

상세보기
28. Ling H Junk DNA and the long non-coding RNA twist in cancer genetics Oncogene. 2015 34 5003 5011 10.1038/onc.2014.456 25619839

상세보기
29. Yang G Lu X Yuan L LncRNA: a link between RNA and cancer Biochim. Biophys. Acta. 2014 1839 1097 1109 10.1016/j.bbagrm.2014.08.012 25159663

상세보기
30. Nobili L Ronchetti D Taiana E Neri A Long non-coding RNAs in B-cell malignancies: a comprehensive overview Oncotarget. 2017 8 60605 60623 10.18632/oncotarget.17303 28947998

상세보기
31. Sattari A Upregulation of long noncoding RNA MIAT in aggressive form of chronic lymphocytic leukemias Oncotarget. 2016 7 54174 54182 10.18632/oncotarget.11099 27527866

상세보기
32. Balatti V Acunzo M Pekarky Y Croce CM Novel mechanisms of regulation of miRNAs in CLL. Trends Cancer. 2016 2 134 143
33. Fabbri G Common nonmutational NOTCH1 activation in chronic lymphocytic leukemia Proc. Natl. Acad. Sci. USA 2017 114 E2911 E2919 10.1073/pnas.1702564114 28314854

상세보기
34. Gimenez N Mutations in the RAS-BRAF-MAPK-ERK pathway define a specific subgroup of patients with adverse clinical features and provide new therapeutic options in chronic lymphocytic leukemia Haematologica. 2019 104 576 586 10.3324/haematol.2018.196931 30262568

상세보기
35. Sharman J An open-label phase 2 trial of entospletinib (GS-9973), a selective spleen tyrosine kinase inhibitor, in chronic lymphocytic leukemia Blood. 2015 125 2336 43 10.1182/blood-2014-08-595934 25696919

상세보기
36. Wolf C NFATC1 activation by DNA hypomethylation in chronic lymphocytic leukemia correlates with clinical staging and can be inhibited by ibrutinib Int. J. Cancer. 2018 142 322 333 10.1002/ijc.31057 28921505

상세보기
37. Yepes S Torres MM Andrade RE Clustering of Expression Data in Chronic Lymphocytic Leukemia Reveals New Molecular Subdivisions PLoS One. 2015 10 e0137132 10.1371/journal.pone.0137132 26355846

상세보기
38. Bhalla S Gene expression-based biomarkers for discriminating early and late stage of clear cell renal cancer Sci. Rep. 2017 7 44997 10.1038/srep44997 28349958

상세보기
39. Tang Y Downregulation of ubiquitin inhibits the proliferation and radioresistance of non-small cell lung cancer cells in vitro and in vivo Sci. Rep. 2015 5 9476 10.1038/srep09476 25820571

상세보기
40. Ijaz M The Role of Grb2 in Cancer and Peptides as Grb2 Antagonists Protein. Pept. Lett. 2018 24 1084 1095 10.2174/0929866525666171123213148 29173143

상세보기
41. Dixon ZA CREBBP knockdown enhances RAS/RAF/MEK/ERK signaling in Ras pathway mutated acute lymphoblastic leukemia but does not modulate chemotherapeutic response Haematologica. 2017 102 736 745 10.3324/haematol.2016.145177 27979926

상세보기
42. Gao C Low CREBBP expression is associated with adverse long-term outcomes in paediatric acute lymphoblastic leukaemia Eur. J. Haematol. 2017 99 150 159 10.1111/ejh.12897 28452416

상세보기
43. Hashwah H Inactivation of CREBBP expands the germinal center B cell compartment, down-regulates MHCII expression and promotes DLBCL growth Proc. Natl. Acad. Sci. USA 2017 114 9701 9706 10.1073/pnas.1619555114 28831000

상세보기
44. Jia D Crebbp Loss Drives Small Cell Lung Cancer and Increases Sensitivity to HDAC Inhibition Cancer Discov. 2018 8 1422 1437 10.1158/2159-8290.CD-18-0385 30181244

상세보기
45. Mullighan CG CREBBP mutations in relapsed acute lymphoblastic leukaemia Nature. 2011 471 235 9 10.1038/nature09727 21390130

상세보기
46. Gu H Neel BG The “Gab” in signal transduction Trends Cell Biol. 2003 13 122 30 10.1016/S0962-8924(03)00002-3 12628344

상세보기
47. Huang E Gene expression predictors of breast cancer outcomes Lancet. 2003 361 1590 1596 10.1016/S0140-6736(03)13308-9 12747878

상세보기
48. Chen Y GAB2 promotes cell proliferation by activating the ERK signaling pathway in hepatocellular carcinoma Tumour Biol. 2016 37 11763 11773 10.1007/s13277-016-5019-9 27026230

상세보기
49. Coutts AS La Thangue NB The p53 response: emerging levels of co-factor complexity Biochem. Biophys. Res. Commun. 2005 331 778 85 10.1016/j.bbrc.2005.03.150 15865933

상세보기
50. Lev Maor G Yearim A Ast G The alternative role of DNA methylation in splicing regulation Trends Genet. 2015 31 274 80 10.1016/j.tig.2015.03.002 25837375

상세보기
51. Oakes CC DNA methylation dynamics during B cell maturation underlie a continuum of disease phenotypes in chronic lymphocytic leukemia Nat. Genet. 2016 48 253 64 10.1038/ng.3488 26780610

상세보기
52. Beekman R The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia Nat. Med. 2018 24 868 880 10.1038/s41591-018-0028-4 29785028

상세보기
53. Kanduri M Distinct transcriptional control in major immunogenetic subsets of chronic lymphocytic leukemia exhibiting subset-biased global DNA methylation profiles Epigenetics. 2012 7 1435 42 10.4161/epi.22901 23154584

상세보기
54. Ronchetti D Distinct patterns of global promoter methylation in early stage chronic lymphocytic leukemia Genes Chromosomes Cancer. 2014 53 264 73 10.1002/gcc.22139 24347044

상세보기
55. Hovestadt V Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing Nature. 2014 510 537 41 10.1038/nature13268 24847876

상세보기
56. Aran D Sabato S Hellman A DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes Genome Biol. 2013 14 R21 10.1186/gb-2013-14-3-r21 23497655

상세보기
57. Yamasaki S Docking protein Gab2 is phosphorylated by ZAP-70 and negatively regulates T cell receptor signaling by recruitment of inhibitory molecules J. Biol. Chem. 2001 276 45175 83 10.1074/jbc.M105384200 11572860

상세보기
58. Wilson AS Power BE Molloy PL DNA hypomethylation and human diseases Biochim. Biophys. Acta. 2007 1775 138 62 17045745
59. Jaffe, E. S., Harris, N. L., Stein, H. & Vardiman, J. W. Chronic lymphocytic leukaemia/small lymphocytic lymphoma. In WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues (eds. Muller-Hermelink, H. K., Montserrat, E., Catovsky, D. & Harris, N. L.) 127？130 (IARC, 2001).
60. Swerdlow, S. H. et al . Chronic lymphocytic leukaemia/small lymphocytic lymphoma. In WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues (eds. Muller-Hermelink, H.K. et al .) 180？182 (IARC, 2008).
61. Hallek M Guidelines for the diagnosis and treatment of chronic lymphocytic leukemia: a report from the International Workshop on Chronic Lymphocytic Leukemia updating the National Cancer Institute-Working Group 1996 guidelines Blood. 2008 111 5446 56 10.1182/blood-2007-06-093906 18216293

상세보기
62. Bolger AM Lohse M Usadel B Trimmomatic: a flexible trimmer for Illumina sequence data Bioinformatics. 2014 30 2114 20 10.1093/bioinformatics/btu170 24695404

상세보기
63. Langmead B Trapnell C Pop M Salzberg SL Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biol. 2009 10 R25 10.1186/gb-2009-10-3-r25 19261174

상세보기
64. Lienhard M Grimm C Morkel M Herwig R Chavez L MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments Bioinformatics. 2014 30 284 6 10.1093/bioinformatics/btt650 24227674

상세보기
65. Robinson MD McCarthy DJ Smyth GK edgeR: a Bioconductor package for differential expression analysis of digital gene expression data Bioinformatics. 2010 26 139 40 10.1093/bioinformatics/btp616 19910308

상세보기
66. Servant N EMA - A R package for Easy Microarray data analysis BMC Res. Notes. 2010 3 277 10.1186/1756-0500-3-277 21047405

상세보기
67. Yu G Wang LG He QY ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization Bioinformatics. 2015 31 2382 3 10.1093/bioinformatics/btv145 25765347

상세보기
68. Yu G Wang LG Han Y He QY clusterProfiler: an R package for comparing biological themes among gene clusters OMICS. 2012 16 284 7 10.1089/omi.2011.0118 22455463

상세보기
69. Kanehisa M Sato Y Furumichi M Morishima K Tanabe M New approach for understanding genome variations in KEGG Nucleic Acids Res. 2019 47 D590 D595 10.1093/nar/gky962 30321428

상세보기
70. Luo W Pant G Bhavnasi YK Blanchard SG Jr. Brouwer C Pathview Web: user friendly pathway visualization and data integration Nucleic Acids Res. 2017 45 W501 W508 10.1093/nar/gkx372 28482075

상세보기
71. Pinero J DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants Nucleic Acids Res. 2017 45 D833 D839 10.1093/nar/gkw943 27924018

상세보기
72. Shannon P Cytoscape: a software environment for integrated models of biomolecular interaction networks Genome Res. 2003 13 2498 504 10.1101/gr.1239303 14597658

상세보기
73. Martin A BisoGenet: a new tool for gene network building, visualization and analysis BMC Bioinformatics. 2010 11 91 10.1186/1471-2105-11-91 20163717

상세보기
74. Wu, G., Dawson, E., Duong, A., Haw, R. & Stein, L. ReactomeFIViz: a Cytoscape app for pathway and network-based data analysis. Version 2 , F1000Res (2014).
75. Doncheva NT Assenov Y Domingues FS Albrecht M Topological analysis and interactive visualization of biological networks and protein structures Nat. Protoc. 2012 7 670 85 10.1038/nprot.2012.004 22422314

상세보기

LOADING...

활용도 분석정보

상세보기

다운로드

내보내기

활용도 Top5 논문

해당 논문의 주제분야에서 활용도가 높은 상위 5개 콘텐츠를 보여줍니다.
더보기 버튼을 클릭하시면 더 많은 관련자료를 살펴볼 수 있습니다.

표제어: PCR

동의어: Packet Collision Rate

용어 설명 출처 목록 (6)

용어 설명: PCR은 세균 특이성이 있는 primer를 이용하여 적은 수의 세균이 있을지라도 쉽게 검출할 수 있는 유용한 방법이며, 이를 이용하여 구강 내 치면세균막이나 타액에서 직접 세균을 검출할 수 있게 되었다[8].

내보내기 구분	파일저장 인쇄 메일전송
구성항목	기본정보 상세정보 관리번호, 논문명, 저널/프로시딩명, 저자 , 발행년, 권, 호, 시작페이지, 끝페이지, 발행기관 관리번호, 논문명, 대등논문명, 저자 , 저널/프로시딩명, 발행기관, 발행년, 발행언어, 권, 호, 시작페이지, 끝페이지, ISBN, ISSN, 주제분야, 키워드, 초록(한글), 초록(영문), 저자(소속기관)
저장형식	Text(ASCII format) Excel format RefWorks Direct Export RIS format (for Reference Manager, ProCite, EndNote), Scholar's Aids, Mendeley
메일정보	받는사람 (필수) @ 보내는사람 (선택) @ 제목 내용 KISTI 검색결과 이메일 서비스
안내	총 건의 자료가 검색되었습니다. 다운받으실 자료의 인덱스를 입력하세요. (1-10,000) 검색결과의 순서대로 최대 10,000건 까지 다운로드가 가능합니다. 데이타가 많을 경우 속도가 느려질 수 있습니다.(최대 2~3분 소요) 다운로드 파일은 UTF-8 형태로 저장됩니다. 파일의 내용이 제대로 보이지 않을실 때는 웹브라우저 상단의 보기 -> 인코딩 -> 자동선택 여부를 확인하십시오. ~ Text(ASCII format) Excel format

연합인증