Jul 2026· American Journal of Human Genetics· Vol 113, pp. 1736-1753· 0 citations· 69 references
Medicine
TL;DR
This work provides mechanistic evidence that a position effect at the SOX3 locus can cause hereditary spastic paraplegia and identifies a 3D regulatory rewiring of SOX3 and transcriptional dysregulation of SOX3 targets in iPSC-derived neurons.
Abstract
Pathogenic rewiring of the three-dimensional (3D) genome architecture is increasingly being identified as the cause of genetic diseases, but recognizing the cis-regulatory effects of structural variation remains a challenge. The Xq27.1 region contains a quasi-palindrome identified as a pleiotropic hotspot for disease-causing interchromosomal insertions. In a large Danish family affected by X-linked recessive complex spastic paraplegia, we identified the segregation of a 149-kb interchromosomal insertion at Xq27.1 originating from 4q24. To understand the disease mechanism, we generated induced pluripotent stem cells (iPSCs) from affected individuals. Using CRISPR perturbation and neural differentiation experiments combined with high-throughput chromatin conformation capture (Hi-C) and transcriptomic analyses, we identify a 3D regulatory rewiring of SOX3 and transcriptional dysregulation of SOX3 targets in iPSC-derived neurons. Consistent with regulatory partitioning of the SOX3 topologically associating domain (TAD) in affected individuals, our experiments show that upstream cis-regulatory elements have a reduced ability to activate SOX3 expression and that the observed dysregulation depends on CTCF-binding sites within the insertion. This work provides mechanistic evidence that a position effect at the SOX3 locus can cause hereditary spastic paraplegia.
Functional modelling in zebrafish confirms a loss‑of-function mechanism and highlights species‑dependent differences specifically in the impact of the missense variant on protein function, and provides a cautionary tale about overreliance on animal models as a screening tool for variant classification.
H. Shamseldin, Dana Marafi, Mohammed A Al-Muhaizea et al.· Scientific Reports· 0 citations
Variants involving TBX4 are associated with ischiocoxopodopatellar syndrome with or without pulmonary arterial hypertension (ICPPS; also known as small patella syndrome), pulmonary arterial hypertension (PAH), and lethal lung developmental disorders. The variability of penetrance and expressivity of TBX4 variants remains a prominent challenge in understanding their genotype–phenotype correlations. We investigated a five‐generation family with 12 affected individuals presenting with isolated ICPPS, lung‐related manifestations with features of ICPPS, and other milder abnormalities. Whole‐genome sequencing was used to identify the causative and putative modifying variants. Wefound a complex genomic rearrangement (CGR) involving the TBX4 promoter and its 5 ′ untranslated region that segregated in the family. This CGR consists of an ~38 bp insertion, an ~24 bp deletion, an ~2.4 kb deletion, and an ~235 bp inversion. Computational analyses in the proband′s mother with pulmonary and skeletal manifestations revealed 27 candidate modifying noncoding SNVs in the TBX4 lung‐specific super‐enhancer and 45 SNVs within its topologically associating domain (TAD), including seven variants within the TBX4 promoter. To explain the variable expressivity of this CGR, we propose that one or more of the variants within the TBX4 lung‐specific super‐enhancer or TAD may act in trans with the pathogenic CGR, modulating TBX4 expression from the intact allele.
Shruti Pande, Hiuling Chan Joiner, P. Szafranski et al.· Human Mutation· 0 citations
ASXL3 patient truncations in neurodevelopmental condition Bainbridge-Ropers syndrome are shown to mediates gain-of-function (GOF) by escaping nonsense-mediated decay and Cullin 4-dependent degradation, resulting in aberrant protein accumulation, widespread transcriptional dysregulation, and altered chromatin accessibility.
Y. Nakamura, T. Nguyen, N. Mor et al.· medRxiv· 0 citations
The results support a dominant-negative mechanism for BRS causing truncating mutations, offering a compelling rationale for allele-specific ASO therapeutic strategy and new venues for treatment.
N. Mor, I. Shomer, S. Raviv et al.· medRxiv· 0 citations
A variety of genomic rearrangement mechanisms contribute to copy number variations at the 17p11.2 locus driven in part by its complex genomic architecture which is characterized by low copy repeats (LCRs) and other repetitive elements. These copy number variants are primarily mediated by nonallelic homologous recombination (NAHR) leading to recurrent tandem duplications and reciprocal deletions of the genomic interval mapping between the repeats. Two notable neurodevelopmental genomic disorders: Potocki-Lupski Syndrome (PTLS; MIM: 610883) and Smith-Magenis Syndrome (SMS; MIM: 182290) are driven by LCRs that undergo NAHR between the directly oriented repeats causing a duplication (PTLS) or deletion (SMS) encompassing the dosage-sensitive gene RAI1. We observed that other uncommon gains of varying sizes and extent at the 17p11.2 locus, which do not include the RAI1 gene, could be found in patients ascertained with a neurodevelopmental delay (NDD) phenotype. We ascertained 15 individuals from 11 families with copy number gains at the 17p11.2 locus not encompassing the driver gene-RAI1; such individuals manifested a broad spectrum of neurodevelopmental phenotypes. To validate our genomic findings, investigate DNA rearrangement mechanism(s), and refine our understanding at the breakpoint junctions, we performed a combination of high-resolution array CGH (n = 15), short-read whole-genome sequencing (sr-GS, n = 4), long-read GS (lr-GS; ONT; n = 4 and PacBio HiFi; n = 4), and breakpoint junctional analysis on this subset. Phenotypes in each individual were systematically studied. The phenotypes noted in these 15 individuals from 11 families primarily included developmental delay, intellectual disability, and behavioral problems. The genomic variations found in these 11 families included simple copy number gains (n = 7), higher order amplifications (n = 2), and complex genomic rearrangements (n = 2) at the 17p11.2 locus, surrounding the RAI1 gene and not encompassing it. Individuals from 4/11 families carried inherited variants. Identification of such rearrangement gains at the 17p11.2 locus that do not include the driver gene RAI1 and yet research subjects still exhibit neurodevelopmental phenotypes creates an opportunity to (i) dissect the gene(s) and genetic mechanisms that might contribute to phenotypic variability at the PTLS locus and (ii) uncover previously unrecognized genes or disease pathways and mechanisms.
Christopher M. Grochowski, Shruti A. Pande, Parneet Kaur et al.· American Journal of Medical...· 0 citations
Hirschsprung disease (HSCR) is a complex developmental disorder of the enteric nervous system, primarily driven by regulatory variants within enhancer elements of the RET gene. To investigate how these variants lead to aganglionosis, we developed a humanized mouse model by inserting an intact 77kb human RET genomic locus into the Rosa26 safe-harbor locus. Utilizing “big DNA” synthetic biology and Bxb1-mediated recombination, we integrated the complete human locus including all exons, introns, and upstream regulatory elements which we validated via nanopore and short-read sequencing. Functional analysis confirmed in vivo human RET expression; however, our initial HSCR-associated “sensitive” haplotype expressed at only 21% of wild-type levels. This significant reduction proved insufficient to rescue the viability when endogenous mouse Ret was deleted. We identified that this deficiency is partially driven by five risk SNPs within established enhancers. Specifically, using CRISPR/Cas9 to restore a conserved So×10 binding site (converting a sensitive SNP to a protective one) increased RET expression by 1.9-fold and restored transcription factor binding. This study provides a robust framework for modeling human-specific regulatory disorders and demonstrates the critical impact of non-coding variation on disease pathogenesis.
Ryan D. Fine, B. Low, Jarod A. Rollins et al.· bioRxiv· 0 citations