Hs.500667 and DNTT (TdT): ‘Partners in crime’ in a novel t(5;10) translocation in ALL

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Molecular dissection of chromosome translocations has identified many genes important to the cause or progression of leukemia. Aside from their diagnostic and prognostic value, the identification of these genes is critical to our understanding of the molecular pathways of leukemogenesis and a necessary precedent to the design of targeted, less toxic treatments. However, the genetic basis of up to 40% of acute lymphoblastic leukemia (ALL) cases remains unknown. We hypothesize that novel chromosome translocations may mark the location of genes potentially rearranged more frequently by cryptic submicroscopic mechanisms in leukemia patients. We have targeted the breakpoints of a novel t(5;10)(q22;q24) translocation found as the sole abnormality in the leukemic cells of a 59 year old male with ALL. Our positional cloning efforts using a combination of fluorescent in situ hybridization, large-insert bacterial-, yeast- and P1-artificial chromosome (BAC, YAC, PAC) clones, end-sequencing, in silico analyses, leukemic t(5;10) metaphase studies, custom PCR analyses and Southern hybridization studies of patient DNA, have mapped the 10q24 breakpoint to a 700 bp genomic region, physically disrupting UniGene Hs.500667 which encodes a novel RNA transcript. Using RACE and Northern blot analyses we have confirmed the unique transcriptional activity of Hs.500667, a novel gene now newly implicated in this case of ALL. Chromosome 5 sequences abnormally fused to Hs.500667, disrupt its normal transcription and unknown function, and potentially links it to the etiology of this ALL. In addition, Hs.500667 overlaps the promoter of the deoxynucleotidyltransferase terminal (DNTT) gene and transcribes in the opposite direction of, and from within, DNTT intron 1, suggesting a possible coordinated regulation or shared promoter between Hs.500667 and DNTT. The breakpoint site within Hs.500667 is less than 5 kb centromeric of DNTT and only 27 kb telomeric of the B-cell linker protein (BLNK) gene, in a tightly regulated genomic region directly involved in lymphocyte development that has not previously been associated with leukemia. This translocation likely causes or contributes to the genetic basis of this ALL and may still prove to generate a fusion gene and/or deregulate the transcription of DNTT. Suspicions have previously focused on DNTT which exhibits abnormal activity in many leukemias, but this remains to be explained and the genomic evidence has so far been absent. Any deregulation of DNTT is likely to have major downstream effects, as this gene is expressed stage-specifically in lymphoid cells and encodes terminal deoxynucleotidyltransferase (TdT), the enzymatic component of a recombinase complex essential for N-region antibody diversity in V(D)J recombination and which is active in double strand break repair.