SNP Chip Analysis of Myelodysplastic Syndromes Disclosed High Frequency of Uniparental Disomy and a Novel Dominant Mutation as the Target of 11q UPD.
Authors: Sanada Masashi , Shih Lee-Yung , Suzuki Takahiro , Yamamoto Go , Nannya Yasuhito , Sakata Mamiko Y. , Kato Motohiro , Kumano Keiki , Kawamata Norihiko , Mori Hiraku , Kurokawa Mineo , Chiba Shigeru , Omine Mitsuhiro , Koeffler Phillip H. , Ogawa Seishi 
Published: October 2019

Abstract
Myelodysplastic syndromes (MDS) are clonal disorders of hematopoietic progenitors characterized by ineffective hematopoiesis and high propensity to leukemias. One of the prominent features of MDS is the high frequency of copy number changes that result in genetic imbalances. Loss of heterozygosity (LOH) may be also closely related to the pathogenesis of MDS, but genome-wide LOH mapping of MDS is still unexplored. We developed a robust program, CNAG/AsCNAR, to explore genetic alterations of the cancer genome, using Affymetrix® GeneChip® SNP arrays. Implementing a series of data compensation algorithms, it enables accurate copy number estimation in cancer genomes. In addition, by sensing subtle distortions in allele-specific signals caused by allelic imbalance using anonymous controls, sensitive detection of LOH is enabled with accurate determination of allele-specific copy numbers even in the face of up to 70% normal cell contamination. Using GeneChip with CNAG/AsCNAR analysis, we analyzed a total of 172 MDS and MDS/MPD specimens in order to identify relevant potential target genes for development of MDS. Nnumerous copy number alterations were sensitively detected in MDS genomes, however more interesting finding was the high frequency of copy number neutral LOH (Uniparental disomy, UPD) observed in 51 of 172 (∼30%) MDS cases. They preferentially involved 1p, 1q, 4q, 7q, 11q, 17p and other chromosomal segments, which were associated with homozygous mutations of tumor suppressor genes and oncogenes, including TP53 (17p UPD), AML1/RUNX1 (in 21q UPD), Nras and cMPL (1p UPD), JAK-2 (9p UPD), and FLT3 (13q UPD). In addition we identified the target of 11q UPD, internally called mds11, which showed homozygous mutations in 8 of 9 MDS cases with 11q UPD (CMML=5, RAEB=3, overt leukemia=1). Mutations of mds11 were rare in non-11q UPD cases (1/163), demonstrating the mutation is tightly linked to 11q UPD. NIH-3T3 cells transduced with these mutatnts showed increased colony formation in soft agar and were tumorigenic in nude mice. To investigate the functions of these mutants in hematopoietic cells, we introduced this mutant gene into c-kit(+)Sca1(+)Lin(−) murine bone marrow cells, and examined their replating capacities in methylcellurose culture, where all the mutants showed enhanced capacities. These observations also present a novel examples that duplication of a dominant mutation (11qUPD) with exclusioin of the wild-type allele is an important mechanism of tumorigenesis. In conclusion, UPD is an important mechanism of development of MDS, in which both gain-of-function and loss-of-function mutations are duplicated with exclusion of wild-type allele. Analysis of 11q UPD disclosed novel gain-of-function mutations. Identification of the targets of UPDs in 1q, 4q and 7q should also be important to gain a novel insight into the pathogenesis of MDS.