An oligodendrocyte silencer element underlies the pathogenic impact of lamin B1 structural variants

Autosomal Dominant Leukodystrophy (ADLD) is a fatal, adult-onset neurological disorder characterized by extensive CNS demyelination. Most cases of ADLD are caused by tandem genomic duplications involving the lamin B1 gene (LMNB1), while a small subset result from genomic deletions upstream of the gene. However, recently identified families carrying the LMNB1 gene duplication, but lacking demyelination, have been found, suggesting the involvement of a non-coding regulatory element. To investigate this, a LMNB1-specific aCGH was conducted using DNA from these newly discovered families and canonical ADLD cases. This approach identified a genomic region, belonging to a silencer element, that is absent in ADLD cases with a LMNB1 duplication or deletion. Genomic DNA was isolated from whole blood from individuals with LMNB1 duplications or deletions. The DNA was analyzed using a custom 8×15K HD-CGH microarray designed to detect copy number variations specifically within the LMNB1 gene (Design# 035726_20110728). DNA isolation (Gentra Puregene kit (Qiagen)) and preparation (Agilent SureTag DNA Labeling Kit) were performed according to the manufacturer’s protocols. Test DNA was labeled with Cy5-dUTP, and control DNA with Cy3-dUTP. The samples were hybridized and scanned at 5 µm resolution using the Agilent G2565CA microarray scanner. Image data was extracted using Agilent’s Feature Extraction program, then normalized and analyzed with Agilent CytoGenomics v. 4.0.3.12. All genome coordinates were based on the human genome assembly GRCh37/hg19. Please note that the raw data file for GSM8703288 has been updated on Jan 3, 2024.