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 4

XPO1 dysfunction in patients’ cells as determined by abnormal distribution of rpS5.

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XPO1 dysfunction in patients’ cells as determined by abnormal distribut...
(A) Normal physiological XPO1-mediated export of 40S rpS5 and approximately 200 different proteins, mRNAs, and miRs from the nucleus to the cytoplasm. Suppression of XPO1 leads to blocked XPO1-mediated cargo and retention of proteins, mRNAs, and miRs in the nucleus. (B) Immunofluorescence images (original magnification, ×40) of patients’ LCLs showing that haploinsufficiency of XPO1 was associated with impaired nuclear export of a known cargo protein, rpS5. LCLs were either untreated (Unt) or treated with leptomycin B (LeptB), which inhibits XPO1-mediated nuclear export of cargo. Untreated control LCLs (C) showed a preponderance of cytoplasmic rpS5 staining, consistent with its role at the ribosome. Upon leptomycin B treatment, nuclear accumulation of rpS5 was evident, consistent with XPO1 inhibition. A similar response was evident in LCLs from the patient in case 4, who possessed 2 copies (+/+) of XPO1. In stark contrast, LCLs from individuals with a deletion of XPO1 (+/–) (cases 3 and 8) each exhibited significant nuclear accumulation of rpS5 when untreated, and this distribution was unaffected by treatment with leptomycin B. (C) Western blotting of WCEs from LCLs untreated (–) or treated (+) with leptomycin B showed equal rpS5 expression. LCLs, lymphoblast cell lines; WCEs, whole-cell extracts.