Nuclear Repositioning of the Non-Translocated <b><i>HLXB9</i></b> Allele in the Leukaemia Cell Line GDM-1 Harbouring a t(6;7)(q23;q36)

Abstract

Transcriptionally active and inactive topologically associated domains (TADs) occupy different areas in the cell nucleus, and chromosomal rearrangements relocating TADs could determine ectopic expression of the repositioned genes. In this study, we investigated the HLXB9 gene in a myeloid leukaemia cell line, GDM-1, known to harbour a rearrangement involving chromosome 7 with a breakpoint distal to HLXB9, highly expressed in these cells. We used FISH to target the regions involved in the translocation and to distinguish the translocated chromosome from the non-translocated one in interphase nuclei. Two-dimensional analysis of the interphase FISH data indicated that the 2 HLXB9 alleles had a different localisation in the cell nuclei, with the translocated allele consistently positioned in the nuclear periphery and the normal one in the more internal portion of the nucleus, known as the transcriptionally active compartment. Our data may indicate that HLXB9 transcripts in the GDM-1 cell line do not arise from the allele located in rearranged chromosome 7, suggesting that regulation of gene expression in cancer cells harbouring chromosomal translocations might be more complex than previously thought, paving the path to further investigations on mechanisms of gene expression.

Deletions of Chromosome 7q Affect Nuclear Organization and HLXB9Gene Expression in Hematological Disorders

“…This type of repositioning may influence the nuclear organization of the chromatin and the transcriptional activity of the repositioned genes. We show that HLXB9 becomes activated when relocated to the inner part of the nucleus, consistent with previously described observations [28,32,38]. We believe that our results will open new grounds for research in the field of cancer genome organization, sheding some light into the mechanisms leading to gene repositioning and gene regulation in tumor initiation and progression.…”

“…In this latter case, we can hypothesize that transcriptional activation could be due to anectopic activation of this allele, and may indicate a more complex mechanism leading to gene activation in leukemia. We described a similar scenario in the leukemia cell line GDM-1 where, in the presence of the translocation t(6;7)(q23;q36), the activation of HLXB9 seems to arise from the non-affected chromosome [32]. It is to be noted that it is still a topic of debate whether HLXB9 is active in non-pathological conditions and in certain differentiated cells, other than during embryonic development [39,51,52,53,54].…”

“…It was recently shown that evolutionarily successful chromosomal rearrangements do not alter the nuclear position of the regions involved. This is not the case in pathological situations, where the rearrangements typically alter the gene structure, and often also the gene nuclear position [32].…”

“…The localization of large number of hybridization signals relative to specific loci was determined according to well-established statistical methods that take into consideration the median value of all signals +/− confidence interval (CI) [10]. According to these methods, median values lower than 0.650 are indicative of loci positioned towards the nuclear interior [10,28,32,38].…”

“…Although gene density/GC content seem to be the underlying factors crucial forgenome organization, in proliferating cells individual chromosomes and genes can be non-randomly relocated to other nuclear compartments during development and differentiation to accomplish specific transcriptional needs [14,27,28]. In cancer, alterations to specific chromosomes and gene locations in nuclei are particularly noticeable [29,30,31,32]. These findings imply that genomic rearrangements occurring in cis could also affect the 3D genome organization due to different chromosomal regions being erroneously positioned in various nuclear compartments [33,34,35,36,37].…”