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Parveen A, Tariq M, Khan SA, Kakar N, Arif A, Wasif N. A novel frameshift variant in UBA2 causing split-hand/foot malformations in a Pakistani family. Hum Genome Var 2023; 10:16. [PMID: 37221169 PMCID: PMC10206101 DOI: 10.1038/s41439-023-00242-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 05/25/2023] Open
Abstract
Split-hand/foot malformation (SHFM) shows diverse heterogeneity and manifests with reduced penetrance and variable expressivity. This study investigated the underlying genetic cause of a family segregating SHFM. Exome sequencing followed by Sanger sequencing identified a novel single nucleotide heterozygous variant (NC_000019.9 (NM_005499.3):c.1118del) in UBA2 cosegregating in the family in an autosomal dominant manner. Our findings conclude that reduced penetrance and variable expressivity are the two remarkable and unusual features of SHFM.
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Affiliation(s)
- Asia Parveen
- Faculty of Science and Technology, University of Central Punjab (UCP), Lahore, Pakistan
- Department of Biochemistry Faculty of Life Sciences, Gulab Devi Educational Complex, Lahore, Pakistan
| | - Muhammad Tariq
- Department of Medical Laboratory Technology, University College of Duba, University of Tabuk, Tabuk, Kingdom of Saudi Arabia
| | - Sher Alam Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, Pakistan
| | - Naseebullah Kakar
- Department of Biotechnology, BUITEMS, Quetta, Pakistan
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Luebeck, Germany
| | - Amina Arif
- Faculty of Science and Technology, University of Central Punjab (UCP), Lahore, Pakistan
| | - Naveed Wasif
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany.
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.
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Bang B, Eisfeldt J, Barbany G, Harila-Saari A, Heyman M, Zachariadis V, Taylan F, Nordgren A. A somatic UBA2 variant preceded ETV6-RUNX1 in the concordant BCP-ALL of monozygotic twins. Blood Adv 2022; 6:2275-2289. [PMID: 34982829 PMCID: PMC9006272 DOI: 10.1182/bloodadvances.2021005703] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 12/06/2021] [Indexed: 11/24/2022] Open
Abstract
Genetic analysis of leukemic clones in monozygotic twins with concordant acute lymphoblastic leukemia (ALL) has proved a unique opportunity to gain insight into the molecular phylogenetics of leukemogenesis. Using whole-genome sequencing, we characterized constitutional and somatic single nucleotide variants/insertion-deletions (indels) and structural variants in a monozygotic twin pair with concordant ETV6-RUNX1+ B-cell precursor ALL (BCP-ALL). In addition, digital PCR (dPCR) was applied to evaluate the presence of and quantify selected somatic variants at birth, diagnosis, and remission. A shared somatic complex rearrangement involving chromosomes 11, 12, and 21 with identical fusion sequences in leukemias of both twins offered direct proof of a common clonal origin. The ETV6-RUNX1 fusion detected at diagnosis was found to originate from this complex rearrangement. A shared somatic frameshift deletion in UBA2 was also identified in diagnostic samples. In addition, each leukemia independently acquired analogous deletions of 3 genes recurrently targeted in BCP-ALLs (ETV6, ATF7IP, and RAG1/RAG2), providing evidence of a convergent clonal evolution only explained by a strong concurrent selective pressure. Quantification of the UBA2 deletion by dPCR surprisingly indicated it persisted in remission. This, for the first time to our knowledge, provided evidence of a UBA2 variant preceding the well-established initiating event ETV6-RUNX1. Further, we suggest the UBA2 deletion exerted a leukemia predisposing effect and that its essential role in Small Ubiquitin-like Modifier (SUMO) attachment (SUMOylation), regulating nearly all physiological and pathological cellular processes such as DNA-repair by nonhomologous end joining, may hold a mechanistic explanation for the predisposition.
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Affiliation(s)
- Benedicte Bang
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Gisela Barbany
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Arja Harila-Saari
- Department of Women’s and Children’s Health, Uppsala University Hospital, Uppsala, Sweden
| | - Mats Heyman
- Department of Women’s and Children’s Health, Karolinska University Hospital Solna, Stockholm, Sweden; and
| | - Vasilios Zachariadis
- Department of Oncology-Pathology, Cancer Centre Karolinska (CCK), Karolinska Institutet, and Karolinska University Hospital, Stockholm, Sweden
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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3
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Sun L, Huang Y, Zhao S, Zhao J, Yan Z, Guo Y, Lin M, Zhong W, Yin Y, Chen Z, Zhang N, Zhang Y, Zhao Z, Li Q, Wang L, Dong X, Li Y, Li X, Qiu G, Zhang TJ, Wu Z, Tian W, Wu N. Deciphering the mutational signature of congenital limb malformations. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 24:961-970. [PMID: 34094714 PMCID: PMC8141661 DOI: 10.1016/j.omtn.2021.04.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/13/2021] [Indexed: 12/20/2022]
Abstract
Congenital limb malformations (CLMs) affect 1 in 500 live births. However, the value of exome sequencing (ES) for CLM is lacking. The purpose of this study was to decipher the mutational signature of CLM on an exome level. We enrolled a cohort of 66 unrelated probands (including 47 families) with CLM requiring surgical correction. ES was performed for all patients and available parental samples. A definite molecular diagnosis was achieved in 21 out of 66 (32%) patients. We identified 19 pathogenic or likely pathogenic single-nucleotide variants and three copy number variants, of which 11 variants were novel. We identified four variants of uncertain significance. Additionally, we identified RPL9 and UBA2 as novel candidate genes for CLM. By comparing the detailed phenotypic features, we expand the phenotypic spectrum of diastrophic dysplasia and chromosome 6q terminal deletion syndrome. We also found that the diagnostic rate was significantly higher in patients with a family history of CLM (p = 0.012) or more than one limb affected (p = 0.034). Our study expands our understanding of the mutational and phenotypic spectrum of CLM and provides novel insights into the genetic basis of these syndromes.
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Affiliation(s)
- Liying Sun
- Department of Hand Surgery, Beijing Jishuitan Hospital, Beijing 100035, China
| | - Yingzhao Huang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Junhui Zhao
- Department of Hand Surgery, Beijing Jishuitan Hospital, Beijing 100035, China
| | - Zihui Yan
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yang Guo
- Department of Hand Surgery, Beijing Jishuitan Hospital, Beijing 100035, China
| | - Mao Lin
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Wenyao Zhong
- Department of Hand Surgery, Beijing Jishuitan Hospital, Beijing 100035, China
| | - Yuehan Yin
- Department of Hand Surgery, Beijing Jishuitan Hospital, Beijing 100035, China
| | - Zefu Chen
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Nan Zhang
- Department of Hand Surgery, Beijing Jishuitan Hospital, Beijing 100035, China
| | - Yuanqiang Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Zongxuan Zhao
- Department of Hand Surgery, Beijing Jishuitan Hospital, Beijing 100035, China
| | - Qingyang Li
- Department of Hand Surgery, Beijing Jishuitan Hospital, Beijing 100035, China
| | - Lianlei Wang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xiying Dong
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yaqi Li
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Guixing Qiu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | | | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China.,Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Wen Tian
- Department of Hand Surgery, Beijing Jishuitan Hospital, Beijing 100035, China
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
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