Loss of Chromosome 7q

Abstract It has been well known that cytogenetics study plays an important role in cancer patient care, in particular in the diagnosis, treatment and prognosis of hematological malignancies. The MCIM test system, a combination of studies of cell morphology (M), cytogenetics (C), immunophenotype (I) and molecular genetics (M), has become a useful test system in hematologic disease diagnosis. It provides physicians more comprehensive and accurate diagnostic laboratory information. Deletions in the long arm of chromosome 7 are among the most common abnormalities observed in hematologic disorders. These changes were usually viewed as markers for myeloid malignancies, in particular myelodysplastic syndrome and acute myeloid leukemia. Recently, interstitial 7q deletions, a subset of the 7q deletions, have been found to be associated with B-cell lymphoproliferative disorders (LPDs). The correlation of narrow 7q deletions with specific subsets of B-cell LPDs has been extensively studied. However, the frequency of interstitial 7q deletions associated with B-cell LPDs has not been well investigated. We recently studied 7q deletions collected from our clinical cases done by the MCIM system at US Labs over the past two years. Deletions of chromosome 7q were observed in 85 of 19,483 cases. Interstitial 7q deletions were detected in 46 of the 85 cases with 7q deletions. In combination with the findings of flow cytometry, interstitial 7q deletions were found to be associated with B-cell LPDs in 10 out of the 46 cases, accounting for 21.7% of all the observed interstitial 7q deletions and 11.8% of all the 7q deletions. The B-cell LPDs associated with 7q interstitial deletion are diverse, including hairy cell leukemia, atypical chronic lymphocytic leukemia, splenic marginal zone lymphoma, and large B-cell lymphoma. Interestingly, the deleted region in the 10 cases with B-cell LPDs in this study was solely confined to 7q22-32. This is so far, to our knowledge, the largest series reported in the literature. Our investigation showed that the frequency of 7q interstitial deletions associated with B-cell LPDs is substantially high. We conclude that (1) association of B-cell LPDs must be taken into account when an interstitial 7q deletion is observed, in particular when the deleted region is confined to 7q22-32; (2) together with the flow cytometry analysis in the MCIM system within a clinical laboratory diagnostic facility, cytogenetics study can provide clinicians more accurate diagnostic information, thus strengthening patient care by improving the management of hematological malignancies. (The authors are grateful to Deanna Collins for her cooperation to collect the data in this study.)

Download Full-text

Molecular Characterization of Distinct Hot Spot Regions on Chromosome 7q in Myeloid Leukemias.

Blood ◽

10.1182/blood.v108.11.2349.2349 ◽

2006 ◽

Vol 108 (11) ◽

pp. 2349-2349 ◽

Cited By ~ 4

Author(s):

Konstanze Dohner ◽

Marianne Habdank ◽

Frank G. Rucker ◽

Simone Miller ◽

Stefan Frohling ◽

...

Keyword(s):

Human Genome ◽

Molecular Characterization ◽

Array Cgh ◽

Hot Spot ◽

Chromosome 7 ◽

Myeloid Leukemias ◽

Translocation Breakpoints ◽

Chromosome 7Q ◽

Chromosomal Bands

Abstract In recent years several groups initiated the molecular characterization of deletion and translocation breakpoints affecting the long arm of chromosome 7 (7q−) to identify genes that are involved in the pathogenesis of myeloid leukemias. Based on these studies a commonly deleted segment (CDS) of approximately 2 Mb in size was identified in chromosomal band 7q22 flanked by the microsatellite markers D7S1503 and D7S1841. Recently, the MLL5 gene (mixed lineage leukemia 5) has been cloned and mapped to the CDS as an interesting candidate gene for chromosome 7q associated leukemias. However, the pathogenic role of MLL5 in myeloid leukemias has not been demonstrated yet. In addition, for the less frequent deletion/translocation breakpoints affecting the distal part of chromosome 7q a 4 to 5 Mb sized CDS was defined encompassing chromosomal bands 7q35 to q36. The heterogeneity of deletion/translocation breakpoints on 7q suggests the existence of more than one disease-related gene. We aimed to identify and characterize translocation and deletion breakpoints in a large series of myeloid leukemias with chromosome 7q aberrations using fluorescence in situ hybridisation (FISH) and array-based comparative genomic hybridization (array CGH). Once, novel hot spot regions were identified, transcriptional map(s) were constructed allowing the identification of candidate genes, expressed sequences or miR-sites. FISH with a physical map of well defined YAC/BAC/PAC clones covering the long arm of chromosome 7 was performed on a series of 105 myeloid leukemias [acute myeloid leukaemia, (AML); myelodysplastic syndrome (MDS); myeloproliferative disorders, (MPD)] exhibiting chromosome 7q aberrations on banding analysis. Selected patients were analysed by array CGH and results were confirmed by hybridisation of the corresponding DNA clones. Transcriptional map(s) were constructed using public databases. While most of the deletions were large encompassing the previously published CDS, we identified a distinct 2 Mb sized CDS in the proximal part of 7q22 that was defined by five patients all exhibiting small deletions. This segment contains several candidate genes including the putative tumor-suppressor genes CUTL1, RASA4, EPO and FBXL13. Interestingly, this CDS is located close to multiple miR-sites, which usually indicate common fragile sites in the human genome. In chromosomal bands 7q35–q36 we localized the breakpoint of an unbalanced translocation from a patient with secondary AML between the markers D7S1925 and D7S1395. This region was recently characterized as a common fragile site in the human genome, named FRA7I. Furthermore, the translocation breakpoint t(3;7)(p13;q35) of a second patient with therapy-related AML was cloned into a 100 kb sized genomic segment located centromeric the CNTNAP2-gene close to the proximal border of the CDS. Our data further indicate the remarkable heterogeneity of deletion and translocation breakpoints on 7q supporting the hypothesis of multiple genes involved in 7q-associated myeloid leukemias. Using techniques such as FISH and array CGH known CDS as well as novel hot spot regions were identified. Transcriptional maps from those regions may serve as important starting points for the identification of pathogenetically relevant genes.

Download Full-text

Chromosome 7q Hemizygosity Recapitulates MDS-Related Cellular Phenotypes In Genetically Engineered Human Pluripotent Stem Cells

Blood ◽

10.1182/blood.v122.21.862.862 ◽

2013 ◽

Vol 122 (21) ◽

pp. 862-862

Author(s):

Andriana Kotini ◽

Ibrahim Boussaad ◽

Eirini P Papapetrou

Keyword(s):

Genetic Material ◽

Response To Therapy ◽

Phenotypic Characterization ◽

Hesc Line ◽

Telomeric Region ◽

Hematopoietic Differentiation ◽

Differentiation Potential ◽

Chromosome 7Q ◽

Cellular Phenotypes ◽

The Impact

Abstract Loss of the entire or part of one copy of chromosome 7 [del(7/7q)] is a recurrent cytogenetic abnormality in MDS. Its strong association with previous exposure to alkylating agents, consistently poor response to therapy and discrete gene expression profile strongly suggest that del(7/7q)-MDS is a distinct disease in the MDS spectrum whose pathogenesis is intimately linked to loss of chr7q genetic material. Understanding the role of chr7q loss in cell biology can provide key insights into the pathogenesis of MDS and leukemogenesis. Narrowing down the responsible region on chr7q presents a challenge that has proved intractable with existing approaches. Chr7q deletions physically mapped in large cohorts of patients are typically very large and dispersed along most of the length of chr7q. Modeling in the mouse is problematic for reasons of synteny. Deletion of the syntenic region of one commonly deleted region (7q22 CDR) failed to demonstrate a phenotype. Several lines of evidence point to haploinsufficiency of chr7q genetic material – rather than a 2-hit model – as the underlying mechanism in del(7q)-MDS. No inactivating mutations of candidate 7q genes have been detected by resequencing the remaining allele and haploinsufficiency of coding and miRNA genes has been strongly linked to the pathogenesis of del(5q)-MDS. Haploinsufficiency can only be assessed through functional studies (and not genomic technologies), but these are currently hindered by the lack of a clearly described del(7q)-associated phenotype. With recent advances in human pluripotent stem cell (hPSC) research and genetic engineering technologies, reverse human genetics in an isogenic setting by disruption of genomic elements into their cognate genomic and cellular context - hitherto unthinkable for the human genome – are now a realistic prospect. To determine the impact of hemizygous chr7q loss on the cellular phenotype, we have generated isogenic del(7q)- and normal hPSCs by engineering deletions spanning variable overlapping regions encompassing the entire length of chr7q using adeno-associated virus (AAV)-mediated gene targeting combined with Cre-lox technology. Specifically, we targeted two inverted loxP sites together with a positive (puro) and a negative (HSVtk) selection marker in a near-telomeric region of chromosome 7q (7q36.3) into the H1 hESC line, as well as a karyotypically normal iPSC line (line 2-12) derived from BMMCs of a patient with del(7q)-MDS. Following transient expression of Cre recombinase and ganciclovir selection, clones were screened by qPCR probing different regions along the length of chr7. Four H1-derived and four 2-12-derived clones were selected following screening of 24 and 34 clones, respectively, and after excluding clones with additional chromosomal abnormalities by karyotyping and the exact extent of their chr7q deletions was mapped by aCGH. We focused our phenotypic characterization on two cellular phenotypes that we recently reported in del(7q)-iPSCs derived from MDS BMMCs: cell proliferation and in vitro hematopoietic differentiation potential. 7 of the 8 clones harboring deletions spanning variable lengths along the entire chr7q had a lower (by ½ log) proliferation rate than their corresponding isogenic parental lines. All these clones also exhibited a markedly reduced differentiation potential along all hematopoietic lineages and almost absent clonogenic capacity in methylcellulose. These cellular phenotypes are highly similar to those we find in our del(7q)-MDS-iPSCs. Notably, one of the eight clones (2-12.Cre-44), harboring a smaller deletion spanning 7q11.21-7q.31.1 retained comparable proliferation and differentiation capacity to that of normal isogenic and non-isogenic hPSCs. In conclusion, our results demonstrate that hemizygous loss of chr7q material recapitulates the cellular phenotypes of impaired proliferation and hematopoietic differentiation that we find in del(7q)-MDS-iPSCs, supporting a haploinsufficiency pathogenesis of del(7q)-MDS. Correlation of the phenotypes with the boundaries of chr7q deletions in our collection of hESC and iPSC clones points to a region spanning 7q31.1-7q36.1 as the critical region in del(7q)-MDS. Further studies in additional clones harboring smaller chr7q deletions will further narrow down the responsible region and guide prioritization of candidate genes. Disclosures: No relevant conflicts of interest to declare.

Download Full-text