Cloning of genes involved in chromosomal translocations by high-resolution single nucleotide polymorphism genomic microarray.
High-resolution single nucleotide polymorphism genomic microarray (SNP-chip) is a useful tool to define gene dosage levels over the whole genome, allowing precise detection of deletions and duplications/amplifications of chromosomes in cancer cells. We found that this new technology can also identify breakpoints of chromosomes involved in unbalanced translocations, leading to identification of fusion genes. Using this technique, we found that the PAX5 gene was rearranged to a variety of partner genes including ETV6, FOXP1, AUTS2, and C20orf112 in pediatric acute lymphoblastic leukemia (ALL). The 3' end of the PAX5 gene was replaced by the partner gene. The PAX5 fusion products bound to PAX5 recognition sequences as strongly as wild-type PAX5 and suppressed its transcriptional activity in a dominant-negative fashion. In human B cell leukemia cells, binding of wild-type PAX5 to a regulatory region of BLK, one of the direct downstream target genes of PAX5, was diminished by expression of the PAX5-fusion protein, leading to repression of BLK. Expression of PAX5-fusion genes in murine bone marrow cells blocked development of mature B cells. PAX5-fusion proteins may contribute to leukemogenesis by blocking differentiation of hematopoietic cells into mature B cells. SNP-chip is a powerful tool to identify fusion genes in human cancers.
Kawamata
Norihiko
N
Hematology/Oncology, Cedars-Sinai Medical Center/UCLA School of Medicine, Los Angeles, CA 90048, USA. kawamatan@cshs.org
Ogawa
Seishi
S
Zimmermann
Martin
M
Niebuhr
Birte
B
Stocking
Carol
C
Sanada
Masashi
M
Hemminki
Kari
K
Yamatomo
Go
G
Nannya
Yasuhito
Y
Koehler
Rolf
R
Flohr
Thomas
T
Miller
Carl W
CW
Harbott
Jochen
J
Ludwig
Wolf-Dieter
WD
Stanulla
Martin
M
Schrappe
Martin
M
Bartram
Claus R
CR
Koeffler
H Phillip
HP
D000818:Animals; D001483:Base Sequence; D002460:Cell Line; D003001:Cloning, Molecular; D004247:DNA / Q000235:genetics; D016678:Genome / Q000235:genetics*; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D051757:PAX5 Transcription Factor / Q000235:genetics / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D014158:Transcription, Genetic / Q000235:genetics; D014178:Translocation, Genetic / Q000235:genetics*
D051757:PAX5 Transcription Factor; C497281:PAX5 protein, human; D004247:DNA