CUX1 is a transcription factor encoded on a region of chromosome 7 that is frequently deleted in high-risk acute myeloid leukemia. 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, gave human hematopoietic cells a significant engraftment advantage on transplantation into immunodeficient mice. Within the RNA-sequencing data, we identified a exerts tumor suppressor activity by regulating proliferative genes. These data identify as a conserved, haploinsufficient tumor suppressor frequently deleted in myeloid neoplasms. Introduction Loss of chromosome 7 and del(7q) [?7/del(7q)] was first recognized as a frequent event in acute myeloid leukemia (AML) nearly 40 years ago.1 ?7/del(7q) occurs in 8% of de novo AML2 and 50% of therapy-related myeloid neoplasms (t-MNs).3 ?7/del(7q) is also found in myelodysplastic syndromes, AMLs arising from myeloproliferative neoplasms, the blast MLN9708 supplier phase of chronic myelogenous leukemia, Ph+ acute lymphoblastic leukemia, and AMLs associated with inherited syndromes.4C10 ?7/del(7q) is an adverse-risk prognostic indicator in myeloid disorders, and the long-term outcome for patients is typically poor. The median overall survival for patients Efnb1 with de novo AML or t-MNs with ?7/del(7q) is 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 ?7/del(7q). Several groups have mapped a commonly deleted segment (CDS) of chromosome band 7q22 using polymorphic markers, conventional cytogenetic analysis, and FISH analysis.11C13 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 of a 2-Mb syntenic region in mice did not result in overt myeloid disease.14 Other studies have mapped rearrangements involving 7q22 and identified similar15 or slightly more centromeric intervals (Physique 1).12,13,16 Determine 1 is within the 2.17-Mb MLN9708 supplier CDS of 7q22.1. Copy number analysis of 7q derived from SNP arrays of 35 samples of de novo AML or t-MNs. Thirty-four samples are from primary leukemia samples, and UoCM1 is usually a cell line derived from the leukemia cells of a patient … In this study, we used single nucleotide polymorphism (SNP) arrays to map the 7q22 CDS with resolution of 1 kb. Overlaying transcriptome-sequencing with copy number aberrations, we identified the gene encoding the transcription factor, ortholog, hemocytes led to hemocyte overproliferation and melanotic tumor formation in vivo. Similarly, MLN9708 supplier decreased manifestation of led to an engraftment advantage for human hematopoietic progenitors transplanted into immunodeficient mice. Thus, from invertebrates to humans, is usually a conserved, haploinsufficient hematopoietic TSG. Methods Patient samples This research was approved by the University of Chicago Institutional Review Board. Leukemia samples were obtained from the University of Chicago Hematopathology and Cancer Cytogenetics Laboratories (supplemental Table 1, available on the Web site; see the Supplemental Materials link at the top of the online article) with informed consent per the Declaration of Helsinki. SNP array DNA was analyzed on Infinium HumanOmni2.5-Quad Version 1.0 DNA Analysis BeadChips (Illumina). Log R ratio and W allele frequencies generated using GenomeStudio (Illumina) were used to identify copy number aberrations by GenoCN.17 GEO accession number is “type”:”entrez-geo”,”attrs”:”text”:”GSE42482″,”term_id”:”42482″,”extlink”:”1″GSE42482. RNA sequencing library preparation Paired-end libraries were prepared following the standard protocol recommended by Illumina. MLN9708 supplier In brief, purified mRNA (MicroPoly(A) Purist kit, Ambion) was fragmented for 7 minutes at 85C, and first-strand cDNA generated (Superscript II Reverse Transcriptase, Invitrogen) with random hexamers (Invitrogen), followed by second-strand synthesis with RNaseH and DNA Polymerase I (New England Biolabs). cDNA was repaired and polished with T4 DNA polymerase, Klenow, and T4 PolyNucleotide Kinase (New England Biolabs), followed by adenosine addition with Klenow Fragment 3 5 exo? (New England Biolabs). Paired-end adaptors (Illumina) were ligated with DNA T4 MLN9708 supplier ligase, and libraries were amplified with p5 and p7 primers (Illumina) and Platinum Pfx taq polymerase (Invitrogen) for 18 PCR cycles; 450-bp fragments were gel-extracted using QIAquick Solution Extraction kit (QIAGEN). Sequence analysis Paired-end reads of lengths 36-100 bp were generated on the Illumina Genome Analyzer II. Reads were individually trimmed from the 3 end, such that the trimmed 3 bases had an average Phred-scaled quality score < 15. Reads were aligned to the human research genome hg18 using TopHat (Version 1.3.1)18 and output in the BAM format.19 Further alignment manipulation was performed with SAMTools (Version 0.1.18),19 Picard (Version 1.52, http://picard.sourceforge.net), and custom perl scripts. Read alignments with mapping qualities < 10 were removed. Alignments were refined with the Genome Analysis Toolkit (Version 1.0.5) RealignerTargetCreator and IndelRealigner tools.20 Cufflinks (Version 1.3.0) was used to.