Altered DNA methylation in leukocytes with trisomy 21.
The primary abnormality in Down syndrome (DS), trisomy 21, is well known; but how this chromosomal gain produces the complex DS phenotype, including immune system defects, is not well understood. We profiled DNA methylation in total peripheral blood leukocytes (PBL) and T-lymphocytes from adults with DS and normal controls and found gene-specific abnormalities of CpG methylation in DS, with many of the differentially methylated genes having known or predicted roles in lymphocyte development and function. Validation of the microarray data by bisulfite sequencing and methylation-sensitive Pyrosequencing (MS-Pyroseq) confirmed strong differences in methylation (p<0.0001) for each of 8 genes tested: TMEM131, TCF7, CD3Z/CD247, SH3BP2, EIF4E, PLD6, SUMO3, and CPT1B, in DS versus control PBL. In addition, we validated differential methylation of NOD2/CARD15 by bisulfite sequencing in DS versus control T-cells. The differentially methylated genes were found on various autosomes, with no enrichment on chromosome 21. Differences in methylation were generally stable in a given individual, remained significant after adjusting for age, and were not due to altered cell counts. Some but not all of the differentially methylated genes showed different mean mRNA expression in DS versus control PBL; and the altered expression of 5 of these genes, TMEM131, TCF7, CD3Z, NOD2, and NPDC1, was recapitulated by exposing normal lymphocytes to the demethylating drug 5-aza-2'deoxycytidine (5aza-dC) plus mitogens. We conclude that altered gene-specific DNA methylation is a recurrent and functionally relevant downstream response to trisomy 21 in human cells.
Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA.
Kristi
K
Kerkel
Nicole
N
Schupf
Kota
K
Hatta
Deborah
D
Pang
Martha
M
Salas
Alexander
A
Kratz
Mark
M
Minden
Vundavalli
V
Murty
Warren B
WB
Zigman
Richard P
RP
Mayeux
Edmund C
EC
Jenkins
Ali
A
Torkamani
Nicholas J
NJ
Schork
Wayne
W
Silverman
B Anne
BA
Croy
Benjamin
B
Tycko
D000328:Adult; D000375:Aging / Q000235:genetics; D001374:Azacitidine / Q000494:pharmacology; D002648:Child; D002675:Child, Preschool; D019175:DNA Methylation / Q000187:drug effects / Q000235:genetics*; D004314:Down Syndrome / Q000235:genetics*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000187:drug effects; D006801:Humans; D007223:Infant; D019169:Jurkat Cells; D007958:Leukocyte Count; D007962:Leukocytes / Q000187:drug effects / Q000378:metabolism*; D008214:Lymphocytes / Q000187:drug effects / Q000378:metabolism; D009419:Nerve Tissue Proteins / Q000235:genetics / Q000378:metabolism; D053473:Nod2 Signaling Adaptor Protein / Q000235:genetics / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D013447:Sulfites
C429018:NOD2 protein, human; C484270:NPDC1 protein, human; D009419:Nerve Tissue Proteins; D053473:Nod2 Signaling Adaptor Protein; D012333:RNA, Messenger; D013447:Sulfites; D001374:Azacitidine; C042345:hydrogen sulfite