CUX1 is a haploinsufficient tumor suppressor gene on chromosome 7 frequently inactivated in acute myeloid leukemia

Abstract

Key Points• CUX1 is a transcription factor encoded on a region of chromosome 7 that is frequently deleted in high-risk acute myeloid leukemia.• Haploinsufficiency of CUX1/ cut promotes hematopoietic overgrowth in both Drosophila melanogaster and human xenograft mouse models in vivo.Loss of chromosome 7 and del(7q) [؊7/del(7q)] are recurring cytogenetic abnormalities in hematologic malignancies, including acute myeloid leukemia and therapy-related myeloid neoplasms, and associated with an adverse prognosis. Despite intensive effort by many laboratories, the putative myeloid tumor suppressor(s) on chromosome 7 has not yet been identified. We performed transcriptome sequencing and SNP array analysis on de novo and therapy-related myeloid neoplasms, half with ؊7/del(7q). We identified a 2.17-Mb commonly deleted segment on chromosome band 7q22.1 containing CUX1, a gene encoding a homeodomain-containing transcription factor. In 1 case, CUX1 was disrupted by a translocation, resulting in a loss-of-function RNA fusion transcript. CUX1 was the most significantly differentially expressed gene within the commonly deleted segment and was expressed at haploinsufficient levels in ؊7/del(7q) leukemias. Haploinsufficiency of the highly conserved ortholog, cut, led to hemocyte overgrowth and tumor formation in Drosophila melanogaster. Similarly, haploinsufficiency of CUX1 gave human hematopoietic cells a significant engraftment advantage on transplantation into immunodeficient mice. Within the RNA-sequencing data, we identified a CUX1-associated cell cycle transcriptional gene signature, suggesting that CUX1 exerts tumor suppressor activity by regulating proliferative genes. These data identify CUX1 as a conserved, haploinsufficient tumor suppressor frequently deleted in myeloid neoplasms. (Blood. 2013;121(6):975-983) IntroductionLoss of chromosome 7 and del(7q) [Ϫ7/del(7q)] was first recognized as a frequent event in acute myeloid leukemia (AML) nearly 40 years ago. 1 Ϫ7/del(7q) occurs in 8% of de novo AML 2 and 50% of therapy-related myeloid neoplasms (t-MNs). 3 Ϫ7/del(7q) is also found in myelodysplastic syndromes, AMLs arising from myeloproliferative neoplasms, the blast phase of chronic myelogenous leukemia, Ph ϩ acute lymphoblastic leukemia, and AMLs associated with inherited syndromes. 4-10 Ϫ7/del(7q) is an adverserisk prognostic indicator in myeloid disorders, and the long-term outcome for patients is typically poor. The median overall survival for patients with de novo AML or t-MNs with Ϫ7/del(7q) is ϳ 6 months. 2,3 Loss of 1 or more tumor suppressor gene(s) (TSGs) is thought to contribute to leukemic growth in myeloid malignancies with Ϫ7/del(7q). Several groups have mapped a commonly deleted segment (CDS) of chromosome band 7q22 using polymorphic markers, conventional cytogenetic analysis, and FISH analysis. [11][12][13] In one study of 81 patients with malignant myeloid disorders characterized by chromosome 7 abnormalities, the CDS was mapped to a 2.52-Mb region of 7q22 by FISH using YAC clones. 11 However, deletion ...

CUX1, a haploinsufficient tumour suppressor gene overexpressed in advanced cancers

“…Two additional studies, using SNP array analysis on de novo and therapy-related myeloid neoplasms, identified CUX1 in the commonly deleted region of 7q22.1 (REFS 4,5). RNA sequencing and reverse transcription PCR analysis showed that CUX1 mRNA expression was reduced approximately twofold in leukaemic cells of affected patients 4,5 , and immunoblotting using a carboxy-terminal antibody showed that the fulllength CUX1 protein was reduced in AML cell lines with chromosome 7 and chromosome 7q loss karyotypes 5 . Reduced CUX1 mRNA expression was also documented in an AML sample that had a chimeric transcript containing CUX1 exon 1 upstream of claudin 7 (CLDN7) exons 2-4, probably resulting from a chromosomal translocation 5 .…”

“…In D. melanogaster, RNAi-mediated knockdown of ct in developing haemocytes led to the development of melanotic pseudotumours 5,11 , and ct knockdown in the proliferating eye disc increased the overproliferation phenotype caused by overexpression of the Notch-ligand Delta 11 . In human cord blood progenitors, partial knockdown of CUX1 led to a ~40% increase in engraftment on transplantation into immunodeficient mice 5 . CUX1 knockdown in KE37 T cell acute lymphoblastic leukaemia (T-ALL) cells increased tumour formation following subcutaneous injection into immuno deficient mice 11 .…”

“…In one study, the authors stated that the expression of nine of ten cell cycle genes was inversely correlated with CUX1 expression levels, suggesting that CUX1 inhibits cell cycle progression 5 . It is not possible to evaluate the experimental evidence, as the gene list was not provided.…”

“…Recent genetic mapping and expression analyses pointed to CUX1 as the tumour suppressor that is the target of loss-of-heterozygosity (LOH) on chromosome 7q22.1 . In cancers with CUX1 LOH, no mutations have been found in the remaining allele [7][8][9][10] and, in tested cases, CUX1 was expressed, albeit at a reduced level 4,5,11 . However, inactivating point mutations were shown in 1-5% of cancers in which the two CUX1 alleles are present 11 (FIG.…”

Newly emerged isolated Del(7q) in patients with prior cytotoxic therapies may not always be associated with therapy-related myeloid neoplasms

“…7 Del(7q)/ − 7 presents in~50% of patients with therapy-related myeloid neoplasms and are often associated with prior exposure to alkylating agents or ionizing radiation. 1,[8][9][10][11][12][13] Any newly emerged cytogenetic abnormalities in patients with a prior history of cytotoxic therapies often raises the concern of development of therapy-related myeloid neoplasms, especially when the abnormalities include del(7q)/ − 7.In our practice, we have observed that some patients develop isolated del(7q) in their bone marrow following cytotoxic therapies, yet never develop therapy-related myeloid neoplasms with close follow-up. In order to better understand the…”