A large genomic deletion leads to enhancer adoption by the lamin B1 gene: a second path to autosomal dominant adult-onset demyelinating leukodystrophy (ADLD).

Elisa Giorgio,Len A Pennacchio,Michel Guipponi,Cristiana Atzori,Daniel Robyr,Enza Ferrero,Giovanna Vaula,Eleonora Di Gregorio,Alfredo Brusco,Stylianos E Antonarakis,Daniele Imperiale,Denise Ferrera,Claudio Canale,Alessandro Brussino,Laura Gasparini,Malte Spielmann,Federico Santoni,Georgios Stamoulis

doi:10.1093/hmg/ddv065

Abstract

Chromosomal rearrangements with duplication of the lamin B1 (LMNB1) gene underlie autosomal dominant adult-onset demyelinating leukodystrophy (ADLD), a rare neurological disorder in which overexpression of LMNB1 causes progressive central nervous system demyelination. However, we previously reported an ADLD family (ADLD-1-TO) without evidence of duplication or other mutation in LMNB1 despite linkage to the LMNB1 locus and lamin B1 overexpression. By custom array-CGH, we further investigated this family and report here that patients carry a large (∼660 kb) heterozygous deletion that begins 66 kb upstream of the LMNB1 promoter. Lamin B1 overexpression was confirmed in further ADLD-1-TO tissues and in a postmortem brain sample, where lamin B1 was increased in the frontal lobe. Through parallel studies, we investigated both loss of genetic material and chromosomal rearrangement as possible causes of LMNB1 overexpression, and found that ADLD-1-TO plausibly results from an enhancer adoption mechanism. The deletion eliminates a genome topological domain boundary, allowing normally forbidden interactions between at least three forebrain-directed enhancers and the LMNB1 promoter, in line with the observed mainly cerebral localization of lamin B1 overexpression and myelin degeneration. This second route to LMNB1 overexpression and ADLD is a new example of the relevance of regulatory landscape modifications in determining Mendelian phenotypes.

Highlights

Autosomal dominant adult-onset demyelinating leukodystrophy (ADLD, OMIM #169 500) is a rare neurological disorder characterized by genetically determined, progressive loss of white matter (WM) within the central nervous system (CNS) [1]
Comparison between frontal lobe (FL) and cerebellar (C) LMNB1 protein levels by western blot demonstrated that in the patient, lamin B1 is about 3.6 times more abundant in FL compared to the control [FL/C ratio of 0.81 versus 0.22 in gray matter (GM), and 1.23 versus 0.36 in WM, Fig. 1B]
Lamin B1 overexpression was detected in proxy tissues from patients: by real-time polymerase chain reaction (PCR), lamin B1 transcripts were increased 2- to 3-fold in fibroblasts from patient VI-1 (Fig. 1C; mean ± standard error = 3.15 ± 0.73; P < 0.0001) and in PAXgene-stabilized whole blood obtained from patients VI-7 and VII-4 (Fig. 1C, mean ± standard error = 2.04 ± 0.31; P < 0.0001) with respect to healthy controls

Summary

Introduction

Autosomal dominant adult-onset demyelinating leukodystrophy (ADLD, OMIM #169 500) is a rare neurological disorder characterized by genetically determined, progressive loss of white matter (WM) within the central nervous system (CNS) [1]. The clinical onset of ADLD occurs in the fourth or fifth decade, usually with symptoms of autonomic dysfunction, followed by ataxia and cognitive impairment that signal pyramidal and cerebellar involvement. Genetic analyses led to the identification by Padiath et al of heterozygous duplications of the lamin B1 gene (LMNB1, chr5q23.2) as the disease-causing mutations in ADLD [9]. The disease is caused by increased levels of lamin B1 protein produced by the presence of a functional extra copy of the LMNB1 gene, making ADLD as part of a growing number of neurological disorders caused by gene copy number variation

Methods

Results

Conclusion