Molecular delineation of the smallest commonly deleted region of chromosome 5 in malignant myeloid diseases to 1–1.5 Mb and preparation of a PAC-based physical map

Abstract

Loss of a whole chromosome 5 or a deletion of the long arm, del(5q), is a recurring abnormality in malignant myeloid diseases. In previous studies, we delineated a commonly deleted segment of Ϸ4 Mb within band 5q31 that was f lanked by IL9 on the proximal side and D5S166 on the distal side. We have generated a physical map of P1 (PAC), bacterial (BAC), and yeast artificial chromosome (YAC) clones of this interval. The contig consists of 108 clones (78 PACs, 2 BACs, and 28 YACs) to which 125 markers (5 genes, 11 expressed sequence tags, 12 polymorphisms, and 97 sequence-tagged sites) have been mapped. Using PAC clones for f luorescence in situ hybridization analysis of leukemia cells with a del(5q), we have narrowed the commonly deleted segment to 1-1.5 Mb between D5S479 and D5S500. To search for allele loss, we used 7 microsatellite markers within and f lanking the commonly deleted segment to examine leukemia cells from 28 patients with loss of 5q, and 14 patients without cytogenetically detectable loss of 5q. In the first group of patients, we detected hemizygous deletions, consistent with the cytogenetically visible loss; no homozygous deletions were detected. No allele loss was detected in patients without abnormalities of chromosome 5, suggesting that allele loss on 5q is the result of visible chromosomal abnormalities. The development of a stable PAC contig and the identification of the smallest commonly deleted segment will facilitate the molecular cloning of a myeloid leukemia suppressor gene on 5q.

Deletions of PURA, at 5q31, and PURB, at 7p13, in myelodysplastic syndrome and progression to acute myelogenous leukemia

“…The data presented indicate that PURA and EGR-1 are approximately 1.1 Mb apart with PURA telomeric (Figure 4). The high frequency of deletion of PURA in patients with 5q abnormalities and the strict correlation of deletions of PURA and EGR-1 indicate that the minimally deleted regions reported to be between polymorphic markers D5S479 and D5S500 5 and between D5S500 and D5S594 11 most likely extend telomeric to the PURA locus. The borders of these regions are approximations based on LOH of loci that are spaced in most cases Ͼ50 kb apart on small groups of specimens.…”

“…Nearly 71% of patients with t-MDS/t-AML have abnormalities of chromosomes 5 and/or 7, and approximately 22% have abnormalities of both 5 and 7 simultaneously. 4,5 In MDS and AML the deletions of the long arms of chromosome 5 are frequently interstitial and the breakpoints are variable. 6,7 The most commonly deleted segment of 5q in MDS, within band region 5q31, is a subject of considerable investigation.…”

“…6,7 The most commonly deleted segment of 5q in MDS, within band region 5q31, is a subject of considerable investigation. 5,[8][9][10][11] Many genes involved in myeloid cell growth and differentiation have been mapped to band region 5q31, including IRF1, 12 IL-9, EGR-1, CDC25C, 5 CD14, 13 and Smad5. 14 It has frequently been speculated that the deletion of this chromosomal region leads to inactivation of one or more tumor suppressor genes.…”

Deletion 5q in myelodysplastic syndrome: a paradigm for the study of hemizygous deletions in cancer

“…24,25 A distinct CDR has been defined at 5q31 in patients with MDS or AML with 5q deletions who do not have the 5qÀ syndrome. [26][27][28] This deletion is also seen in patients with therapy-related MDS or AML, and is often associated with additional cytogenetic abnormalities. Multiple candidate tumor suppressor genes are contained within this locus, including EGR1, CDC25C and CTNNA1.…”

“…Multiple candidate tumor suppressor genes are contained within this locus, including EGR1, CDC25C and CTNNA1. [26][27][28] In addition to the two CDRs, the long arm of chromosome 5 contains a fascinating array of genes that are relevant to hematopoiesis and malignancy. Numerous cytokine genes are located on 5q, including a cluster at 5q31 encoding interleukins 3, 4, 5, 9, 13 and 17b, and granulocyte-monocyte colonystimulating factor.…”