Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage

被引：422

作者：

Amps, Katherine ^{[1
]}

Andrews, Peter W. ^{[1
]}

Anyfantis, George ^{[2
]}

Armstrong, Lyle ^{[2
]}

Avery, Stuart ^{[3
]}

Baharvand, Hossein ^{[4
]}

Baker, Julie ^{[5
]}

Baker, Duncan ^{[6
]}

Munoz, Maria B. ^{[7
]}

Beil, Stephen ^{[8
]}

Benvenisty, Nissim ^{[9
]}

Ben-Yosef, Dalit ^{[10
,11
]}

Biancotti, Juan-Carlos ^{[12
]}

Bosman, Alexis ^{[13
]}

Brena, Romulo Martin ^{[14
]}

Brison, Daniel ^{[15
]}

Caisander, Gunilla ^{[16
]}

Camarasa, Maria V. ^{[17
]}

Chen, Jieming ^{[18
]}

Chiao, Eric ^{[5
,19
]}

Choi, Young Min ^{[20
]}

Choo, Andre B. H. ^{[21
]}

Collins, Daniel ^{[22
]}

Colman, Alan ^{[3
,23
]}

Crook, Jeremy M. ^{[3
,23
,24
,25
,26
]}

Daley, George Q. ^{[27
,28
,29
,30
,31
]}

Dalton, Anne ^{[6
]}

De Sousa, Paul A. ^{[22
,32
]}

Denning, Chris ^{[7
]}

Downie, Janet ^{[22
]}

Dvorak, Petr ^{[33
]}

Montgomery, Karen D. ^{[34
]}

Feki, Anis ^{[35
]}

Ford, Angela ^{[1
]}

Fox, Victoria ^{[8
]}

Fraga, Ana M. ^{[36
]}

Frumkin, Tzvia ^{[10
]}

Ge, Lin ^{[37
]}

Gokhale, Paul J. ^{[1
]}

Golan-Lev, Tamar ^{[9
]}

Gourabi, Hamid ^{[4
]}

Gropp, Michal ^{[38
]}

Lu Guangxiu ^{[37
]}

Hampl, Ales ^{[39
,40
]}

Harron, Katie ^{[41
]}

Healy, Lyn ^{[42
]}

Herath, Wishva ^{[18
]}

Holm, Frida ^{[43
]}

Hovatta, Outi ^{[43
]}

Hyllner, Johan ^{[16
]}

机构：

[1] Univ Sheffield, Dept Biomed Sci, Ctr Stem Cell Biol, Sheffield S10 2TN, S Yorkshire, England

[2] Int Ctr Life, NE England Stem Cell Inst Life, Newcastle Upon Tyne, Tyne & Wear, England

[3] ASTAR, Inst Med Biol, Immunos, Singapore

[4] Royan Inst Reprod Biomed, Dept Genet, Tehran, Iran

[5] Stanford Univ, Stanford, CA 94305 USA

[6] Sheffield Childrens NHS Trust, Sheffield Diagnost Genet Serv, Sheffield, S Yorkshire, England

[7] Univ Nottingham, Ctr Biomol Sci, Wolfson Ctr Stem Cells Tissue Engn & Modelling ST, Nottingham NG7 2RD, England

[8] Univ So Calif, Keck Sch Med, USC Stem Cell Core Facil, Eli & Edythe Broad Ctr Regenerat Med & Stem Cell, Los Angeles, CA 90033 USA

[9] Hebrew Univ Jerusalem, Dept Genet, Alexander Silberman Inst Life Sci, Stem Cell Unit, IL-91904 Jerusalem, Israel

[10] Lis Matern Hosp, Tel Aviv Sourasky Med Ctr, Racine IVF Unit, Tel Aviv, Israel

[11] Tel Aviv Univ, Sackler Fac Med, Dept Cell Dev Biol, IL-69978 Tel Aviv, Israel

[12] Cedars Sinai Med Inst, Regenerat Med Inst, Los Angeles, CA USA

[13] Univ Geneva, Fac Med, Dept Pathol & Immunol, Geneva, Switzerland

[14] Univ So Calif, Keck Sch Med, USC Epigenome Ctr, Los Angeles, CA 90033 USA

[15] Cent Manchester NHS Fdn Trust, Manchester Acad Hlth Sci Ctr, St Maryss Hosp, Dept Reprod Med, Manchester, Lancs, England

[16] Cellartis AB, Gothenburg, Sweden

[17] Univ Manchester, Fac Life Sci, Manchester, Lancs, England

[18] Genome Inst Singapore, Singapore, Singapore

[19] Hoffmann LaRoche, Nutley, NJ USA

[20] Seoul Natl Univ, Coll Med, Dept Obstet & Gynaecol, Seoul, South Korea

[21] Bioproc Technol Inst, Singapore, Singapore

[22] Roslin Cells Ltd, Roslin Bioctr, Roslin, Midlothian, Scotland

[23] ASTAR, Singapore Stem Cell Consortium, Singapore, Singapore

[24] Univ Melbourne, Ctr Neural Engn, Parkville, Vic 3052, Australia

[25] Univ Melbourne, Opt & Nanoelect Res Grp, NICTA Victorian Res Lab, Parkville, Vic 3052, Australia

[26] Univ Melbourne, St Vincents Hosp, Dept Surg, Fitzroy, Vic 3065, Australia

[27] Childrens Hosp, Howard Hughes Med Inst, Stem Cell Transplantat Program, Div Pediat Hematol Oncol,Manton Ctr Orphan Dis Re, Boston, MA 02115 USA

[28] Dana Farber Canc Inst, Boston, MA 02115 USA

[29] Brigham & Womens Hosp, Div Hematol, Boston, MA 02115 USA

[30] Harvard Univ, Sch Med, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA

[31] Harvard Stem Cell Inst, Boston, MA USA

[32] Univ Edinburgh, MRC, Ctr Regenerat Med, Edinburgh, Midlothian, Scotland

[33] Masaryk Univ, Dept Biol, Fac Med, Brno, Czech Republic

[34] WiCell Res Inst, Madison, WI USA

[35] Hop Cantonal Fribourgois, Dept Obstet & Gynecol, Freibourg, Switzerland

[36] Univ Sao Paulo, Dept Genet & Evolutionary Biol, Natl Lab Embryon Stem Cell Res LaNCE, Sao Paulo, Brazil

[37] Cent S Univ, Inst Reprod & Stem Cell Engn, Reprod & Genet Hosp CITIC XIANGYA, Changsha, Hunan, Peoples R China

[38] Hadassah Univ, Med Ctr, Goldyne Savad Inst Gene Therapy, Hadassah Human Embryon Stem Cell Res Ctr, Jerusalem, Israel

[39] Masaryk Univ, Fac Med, Dept Histol & Embryol, Brno, Czech Republic

[40] Inst Expt Med ASCR, Prague, Czech Republic

[41] UCL, Inst Child Hlth, MRC Ctr Epidemiol Child Hlth, London, England

[42] Natl Inst Biol Stand & Controls, Div Cell Biol & Imaging, UK Stem Cell Bank, S Mimms, Herts, England

[43] Karolinska Univ, Huddinge Hosp, Karolinska Inst, Dept Clin Sci Intervent & Technol, Stockholm, Sweden

[44] Indian Inst Sci, Jawaharlal Nehru Ctr Adv Sci Res, Bangalore 560012, Karnataka, India

[45] Kyoto Univ, Ctr iPS Cell Res & Applicat CiRA, Kyoto, Japan

[46] CAS Shanghai Jiao Tong Univ, Shanghai Inst Biol Sci, Key Lab Stem Cell Biol, Inst Hlth Sci,Sch Med, Shanghai, Peoples R China

[47] NRC Kurchatov Inst, Stem Cell Dept, Moscow, Russia

[48] Vavilov Inst Gen Genet, Moscow, Russia

[49] Illinois Masonic Med Ctr, Inst Reprod Genet, Chicago, IL 60657 USA

[50] CSIRO Mat Sci & Engn, Clayton, Vic, Australia

来源：

NATURE BIOTECHNOLOGY | 2011年 / 29卷 / 12期

基金：

英国生物技术与生命科学研究理事会; 英国医学研究理事会; 巴西圣保罗研究基金会; 日本学术振兴会; 芬兰科学院; 瑞士国家科学基金会;

关键词：

COMPARATIVE GENOMIC HYBRIDIZATION; COPY NUMBER VARIATION; HUMAN ES CELLS; DNA-SEQUENCE; CULTURE; GENES; LINES; PLURIPOTENCY; REVEALS; NANOG;

D O I：

10.1038/nbt.2051

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

The International Stem Cell Initiative analyzed 125 human embryonic stem (ES) cell lines and 11 induced pluripotent stem (iPS) cell lines, from 38 laboratories worldwide, for genetic changes occurring during culture. Most lines were analyzed at an early and late passage. Single-nucleotide polymorphism (SNP) analysis revealed that they included representatives of most major ethnic groups. Most lines remained karyotypically normal, but there was a progressive tendency to acquire changes on prolonged culture, commonly affecting chromosomes 1, 12, 17 and 20. DNA methylation patterns changed haphazardly with no link to time in culture. Structural variants, determined from the SNP arrays, also appeared sporadically. No common variants related to culture were observed on chromosomes 1, 12 and 17, but a minimal amplicon in chromosome 20q11.21, including three genes expressed in human ES cells, ID1, BCL2L1 and HM13, occurred in >20% of the lines. Of these genes, BCL2L1 is a strong candidate for driving culture adaptation of ES cells.

引用

页码：1132 / U113

页数：15

共 70 条

[61] Genetic analysis of childhood germ cell tumors with comparative genomic hybridization [J].

Schneider, DT ;

Schuster, AE ;

Fritsch, MK ;

Calaminus, G ;

Harms, D ;

Göbel, U ;

Perlman, EJ .

KLINISCHE PADIATRIE, 2001, 213 (04) :204-211

[62] Implications of human genome architecture for rearrangement-based disorders: the genomic basis of disease [J].

Shaw, CJ ;

Lupski, JR .

HUMAN MOLECULAR GENETICS, 2004, 13 :R57-R64

[63]

Skotheim RI, 2002, CANCER RES, V62, P2359

[64] Recurrent chromosomal abnormalities in human embryonic stem cells [J].

Spits, Claudia ;

Mateizel, Ileana ;

Geens, Mieke ;

Mertzanidou, Afroditi ;

Staessen, Catherine ;

Vandeskelde, Yves ;

Van der Elst, Josiane ;

Liebaers, Inge ;

Sermon, Karen .

NATURE BIOTECHNOLOGY, 2008, 26 (12) :1361-1363

[65] PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data [J].

Wang, Kai ;

Li, Mingyao ;

Hadley, Dexter ;

Liu, Rui ;

Glessner, Joseph ;

Grant, Struan F. A. ;

Hakonarson, Hakon ;

Bucan, Maja .

GENOME RESEARCH, 2007, 17 (11) :1665-1674

[66]

WANG N, 1980, CANCER RES, V40, P796

[67] Characterization of human embryonic stem cells with features of neoplastic progression [J].

Werbowetski-Ogilvie, Tamra E. ;

Bosse, Marc ;

Stewart, Morag ;

Schnerch, Angelique ;

Ramos-Mejia, Veronica ;

Rouleau, Anne ;

Wynder, Tracy ;

Smith, Mary-Jo ;

Dingwall, Steve ;

Carter, Tim ;

Williams, Christopher ;

Harris, Charles ;

Dolling, Joanna ;

Wynder, Christopher ;

Boreham, Doug ;

Bhatia, Mickie .

NATURE BIOTECHNOLOGY, 2009, 27 (01) :91-97

[68] Epigenetic stem cell signature in cancer [J].

Widschwendter, Martin ;

Fiegl, Heidi ;

Egle, Daniel ;

Mueller-Holzner, Elisabeth ;

Spizzo, Gilbert ;

Marth, Christian ;

Weisenberger, Daniel J. ;

Campan, Mihaela ;

Young, Joanne ;

Jacobs, Ian ;

Laird, Peter W. .

NATURE GENETICS, 2007, 39 (02) :157-158

[69] Copy number variant analysis of human embryonic stem cells [J].

Wu, Hao ;

Kim, Kevin J. ;

Mehta, Kshama ;

Paxia, Salvatore ;

Sundstrom, Andrew ;

Anantharaman, Thomas ;

Kuraishy, Ali I. ;

Doan, Tri ;

Ghosh, Jayati ;

Pyle, April D. ;

Clark, Amander ;

Lowry, William ;

Fan, Guoping ;

Baxter, Tim ;

Mishra, Bud ;

Sun, Yi ;

Teitell, Michael A. .

STEM CELLS, 2008, 26 (06) :1484-1489

[70] DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage [J].

Zody, MC ;

Garber, M ;

Adams, DJ ;

Sharpe, T ;

Harrow, J ;

Lupski, JR ;

Nicholson, C ;

Searle, SM ;

Wilming, L ;

Young, SK ;

Abouelleil, A ;

Allen, NR ;

Bi, WM ;

Bloom, T ;

Borowsky, ML ;

Bugalter, BE ;

Butler, J ;

Chang, JL ;

Chen, CK ;

Cook, A ;

Corum, B ;

Cuomo, CA ;

de Jong, PJ ;

DeCaprio, D ;

Dewar, K ;

FitzGerald, M ;

Gilbert, J ;

Gibson, R ;

Gnerre, S ;

Goldstein, S ;

Grafham, DV ;

Grocock, R ;

Hafez, N ;

Hagopian, DS ;

Hart, E ;

Norman, CH ;

Humphray, S ;

Jaffe, DB ;

Jones, M ;

Kamal, M ;

Khodiyar, VK ;

LaButti, K ;

Laird, G ;

Lehoczky, J ;

Liu, XH ;

Lokyitsang, T ;

Loveland, J ;

Lui, A ;

Macdonald, P ;

Major, JE .

NATURE, 2006, 440 (7087) :1045-1049

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