Differential DNA methylation patterns of small B-cell lymphoma subclasses with different clinical behavior.
Non-Hodgkin's lymphoma (NHL) is a group of malignancies of the immune system with variable clinical behaviors and diverse molecular features. Despite the progress made in classification of NHLs based on classical methods, molecular classifications are a work in progress. Toward this goal, we used an array-based technique called differential methylation hybridization (DMH) to study small B-cell lymphoma (SBCL) subtypes. A total of 43 genomic DMH experiments were performed. From these results, several statistical methods were used to generate a set of differentially methylated genes for further validation. Methylation of LHX2, POU3F3, HOXC10, NRP2, PRKCE, RAMP, MLLT2, NKX6.1, LRP1B and ARF4 was validated in cell lines and patient samples and demonstrated subtype-related preferential methylation patterns. For LHX2 and LRP1B, bisulfite sequencing, real-time reverse transcriptase-polymerase chain reaction and induction of gene expression following treatment with the demethylating agent, 5'-aza-2'-deoxycytidine, were confirmed. This new epigenetic information is helping to define molecular portraits of distinct subtypes of SBCL that are not recognized by current classification systems and provides valuable potential insights into the biology of these tumors.
Rahmatpanah
F B
FB
Department of Pathology and Anatomical Sciences, Ellis Fischel Cancer Center, University of Missouri School of Medicine, Columbia, MO 65203, USA.
Carstens
S
S
Guo
J
J
Sjahputera
O
O
Taylor
K H
KH
Duff
D
D
Shi
H
H
Davis
J W
JW
Hooshmand
S I
SI
Chitma-Matsiga
R
R
Caldwell
C W
CW
D000328:Adult; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D018899:CpG Islands / Q000502:physiology; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D023281:Genomics / Q000379:methods; D018398:Homeodomain Proteins / Q000235:genetics; D006801:Humans; D060850:LIM-Homeodomain Proteins; D015451:Leukemia, Lymphocytic, Chronic, B-Cell / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D016393:Lymphoma, B-Cell / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D008297:Male; D009693:Nucleic Acid Hybridization / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000032:analysis; D011973:Receptors, LDL / Q000235:genetics; D013447:Sulfites; D014157:Transcription Factors / Q000235:genetics
D018398:Homeodomain Proteins; C489783:LHX2 protein, human; D060850:LIM-Homeodomain Proteins; C434476:LRP1B protein, human; D012333:RNA, Messenger; D011973:Receptors, LDL; D013447:Sulfites; D014157:Transcription Factors; C042345:hydrogen sulfite