Identifying candidate genes for 2p15p16.1 microdeletion syndrome using clinical, genomic, and functional analysis
Hani Bagheri, Chansonette Badduke, Ying Qiao, Rita Colnaghi, Iga Abramowicz, Diana Alcantara, Christopher Dunham, Jiadi Wen, Robert S. Wildin, Malgorzata J.M. Nowaczyk, Jennifer Eichmeyer, Anna Lehman, Bruno Maranda, Sally Martell, Xianghong Shan, Suzanne M.E. Lewis, Mark O’Driscoll, Cheryl Y. Gregory-Evans, Evica Rajcan-Separovic
Hani Bagheri, Chansonette Badduke, Ying Qiao, Rita Colnaghi, Iga Abramowicz, Diana Alcantara, Christopher Dunham, Jiadi Wen, Robert S. Wildin, Malgorzata J.M. Nowaczyk, Jennifer Eichmeyer, Anna Lehman, Bruno Maranda, Sally Martell, Xianghong Shan, Suzanne M.E. Lewis, Mark O’Driscoll, Cheryl Y. Gregory-Evans, Evica Rajcan-Separovic
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Research Article Genetics

Identifying candidate genes for 2p15p16.1 microdeletion syndrome using clinical, genomic, and functional analysis

Abstract

The 2p15p16.1 microdeletion syndrome has a core phenotype consisting of intellectual disability, microcephaly, hypotonia, delayed growth, common craniofacial features, and digital anomalies. So far, more than 20 cases of 2p15p16.1 microdeletion syndrome have been reported in the literature; however, the size of the deletions and their breakpoints vary, making it difficult to identify the candidate genes. Recent reports pointed to 4 genes (XPO1, USP34, BCL11A, and REL) that were included, alone or in combination, in the smallest deletions causing the syndrome. Here, we describe 8 new patients with the 2p15p16.1 deletion and review all published cases to date. We demonstrate functional deficits for the above 4 candidate genes using patients’ lymphoblast cell lines (LCLs) and knockdown of their orthologs in zebrafish. All genes were dosage sensitive on the basis of reduced protein expression in LCLs. In addition, deletion of XPO1, a nuclear exporter, cosegregated with nuclear accumulation of one of its cargo molecules (rpS5) in patients’ LCLs. Other pathways associated with these genes (e.g., NF-κB and Wnt signaling as well as the DNA damage response) were not impaired in patients’ LCLs. Knockdown of xpo1a, rel, bcl11aa, and bcl11ab resulted in abnormal zebrafish embryonic development including microcephaly, dysmorphic body, hindered growth, and small fins as well as structural brain abnormalities. Our multifaceted analysis strongly implicates XPO1, REL, and BCL11A as candidate genes for 2p15p16.1 microdeletion syndrome.

Authors

Hani Bagheri, Chansonette Badduke, Ying Qiao, Rita Colnaghi, Iga Abramowicz, Diana Alcantara, Christopher Dunham, Jiadi Wen, Robert S. Wildin, Malgorzata J.M. Nowaczyk, Jennifer Eichmeyer, Anna Lehman, Bruno Maranda, Sally Martell, Xianghong Shan, Suzanne M.E. Lewis, Mark O’Driscoll, Cheryl Y. Gregory-Evans, Evica Rajcan-Separovic

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Figure 2

Summary of CNVs involving the 2p15p16.1 region.

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Summary of CNVs involving the 2p15p16.1 region. The breakpoints of the m...
The breakpoints of the microdeletions are arranged on the basis of their start site. The black bars are published 2p15p16.1 microdeletion cases, and the red bars represent our 8 additional cases, presented here for the first time. The highlighted gray region is indicative of the 2p15p16.1 deletion region enriched in genes that are included in the smallest deletions and with the highest haploinsufficiency scores (approximately <10%). The 4 genes analyzed were XPO1, REL, USP34, and BCL11A and are highlighted in yellow. Enhancer elements that are located within and/or in the periphery of the CNVs are indicated with unique ID numbers and were extracted from the VISTA Enhancer Browser (http://enhancer.lbl.gov/). The numbers in parentheses following the reference citation in the left-hand column indicate the subject’s number.