Large-scale CpG methylation analysis identifies novel candidate genes and reveals methylation hotspots in acute lymphoblastic leukemia

Kristen H. Taylor, Keila E. Pena-Hernandez, J. Wade Davis, Gerald L. Arthur, Deiter J. Duff, Huidong Shi, Farah B. Rahmatpanah, Ozy Sjahputera, Charles W. Caldwell

Research output: Contribution to journalArticle

103 Citations (Scopus)

Abstract

This study examined DNA methylation associated with acute lymphoblastic leukemia (ALL) and showed that selected molecular targets can be pharmacologically modulated to reverse gene silencing. A CpG island (CGI) microarray containing more than 3,400 unique clones that span all human chromosomes was used for large-scale discovery experiments and led to 262 unique CGI loci being statistically identified as methylated in ALL lymphoblasts. The methylation status of 10 clones encompassing 11 genes (DCC, DLC-1, DDX51, KCNK2, LRP1B, NKX6-1, NOPE, PCDHGA12, RPIB9, ABCB1, and SLC2A14) identified as differentially methylated between ALL patients and controls was independently verified. Consequently, the methylation status of DDX51 was found to differentiate patients with B- and T-ALL subtypes (P = 0.011, Fisher's exact test). Next, the relationship between methylation and expression of these genes was examined in ALL cell lines (NALM-6 and Jurkat) before and after treatments with 5-aza-2-deoxycytidine and trichostatin A. More than a 10-fold increase in mRNA expression was observed for two previously identified tumor suppressor genes (DLC-1 and DCC) and also for RPLB9 and PCDHGA12. Although the mechanisms that lead to the CGI methylation of these genes are unknown, bisulfite sequencing of the promoter of RPIB9 suggests that expression is inhibited by methylation within SP1 and AP2 transcription factor binding motifs. Finally, specific chromosomal methylation hotspots were found to be associated with ALL. This study sets the stage for acquiring a better biological understanding of ALL and for the identification of epigenetic biomarkers useful for differential diagnosis, therapeutic monitoring, and the detection of leukemic relapse.

Original languageEnglish (US)
Pages (from-to)2617-2625
Number of pages9
JournalCancer Research
Volume67
Issue number6
DOIs
StatePublished - Mar 15 2007
Externally publishedYes

Fingerprint

Precursor Cell Lymphoblastic Leukemia-Lymphoma
Methylation
CpG Islands
Genes
decitabine
DCC Genes
trichostatin A
Transcription Factor AP-2
Clone Cells
Human Chromosomes
Gene Silencing
DNA Methylation
Tumor Suppressor Genes
Epigenomics
Differential Diagnosis
Biomarkers
Gene Expression
Recurrence
Cell Line
Messenger RNA

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

Cite this

Large-scale CpG methylation analysis identifies novel candidate genes and reveals methylation hotspots in acute lymphoblastic leukemia. / Taylor, Kristen H.; Pena-Hernandez, Keila E.; Davis, J. Wade; Arthur, Gerald L.; Duff, Deiter J.; Shi, Huidong; Rahmatpanah, Farah B.; Sjahputera, Ozy; Caldwell, Charles W.

In: Cancer Research, Vol. 67, No. 6, 15.03.2007, p. 2617-2625.

Research output: Contribution to journalArticle

Taylor, KH, Pena-Hernandez, KE, Davis, JW, Arthur, GL, Duff, DJ, Shi, H, Rahmatpanah, FB, Sjahputera, O & Caldwell, CW 2007, 'Large-scale CpG methylation analysis identifies novel candidate genes and reveals methylation hotspots in acute lymphoblastic leukemia', Cancer Research, vol. 67, no. 6, pp. 2617-2625. https://doi.org/10.1158/0008-5472.CAN-06-3993
Taylor, Kristen H. ; Pena-Hernandez, Keila E. ; Davis, J. Wade ; Arthur, Gerald L. ; Duff, Deiter J. ; Shi, Huidong ; Rahmatpanah, Farah B. ; Sjahputera, Ozy ; Caldwell, Charles W. / Large-scale CpG methylation analysis identifies novel candidate genes and reveals methylation hotspots in acute lymphoblastic leukemia. In: Cancer Research. 2007 ; Vol. 67, No. 6. pp. 2617-2625.
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AU - Duff, Deiter J.

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AU - Rahmatpanah, Farah B.

AU - Sjahputera, Ozy

AU - Caldwell, Charles W.

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N2 - This study examined DNA methylation associated with acute lymphoblastic leukemia (ALL) and showed that selected molecular targets can be pharmacologically modulated to reverse gene silencing. A CpG island (CGI) microarray containing more than 3,400 unique clones that span all human chromosomes was used for large-scale discovery experiments and led to 262 unique CGI loci being statistically identified as methylated in ALL lymphoblasts. The methylation status of 10 clones encompassing 11 genes (DCC, DLC-1, DDX51, KCNK2, LRP1B, NKX6-1, NOPE, PCDHGA12, RPIB9, ABCB1, and SLC2A14) identified as differentially methylated between ALL patients and controls was independently verified. Consequently, the methylation status of DDX51 was found to differentiate patients with B- and T-ALL subtypes (P = 0.011, Fisher's exact test). Next, the relationship between methylation and expression of these genes was examined in ALL cell lines (NALM-6 and Jurkat) before and after treatments with 5-aza-2-deoxycytidine and trichostatin A. More than a 10-fold increase in mRNA expression was observed for two previously identified tumor suppressor genes (DLC-1 and DCC) and also for RPLB9 and PCDHGA12. Although the mechanisms that lead to the CGI methylation of these genes are unknown, bisulfite sequencing of the promoter of RPIB9 suggests that expression is inhibited by methylation within SP1 and AP2 transcription factor binding motifs. Finally, specific chromosomal methylation hotspots were found to be associated with ALL. This study sets the stage for acquiring a better biological understanding of ALL and for the identification of epigenetic biomarkers useful for differential diagnosis, therapeutic monitoring, and the detection of leukemic relapse.

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