Biology subjects

Semina, E. V.

Publications and source records attributed to Semina, E. V..

3 recordsLinked to original sources

bioRxiv2025

Copy number variants (CNV) interfere with human Accelerated Regions (HARs) to cause neurodevelopmental disorders: a large-scale cohort study

Neurodevelopmental disorders (NDDs) represent a heterogeneous group of conditions affecting the central nervous system, the etiology of which involves a wide range of factors, including genetic contributors. A proportion of this genetic component is mediated by copy number variations (CNVs) - deletions and duplications of genomic segments that are associated with a broad spectrum of neurodevelopmental and neuropsychiatric phenotypes. In recent years, there has also been growing interest in studying Human Accelerated Regions (HARs) in relation to these disorders. HARs are highly conserved genomic elements across mammals that have accumulated human-specific sequence changes. These regions are thought to contribute both to the evolution of higher cognitive functions in humans and, paradoxically, to an increased susceptibility to NDDs. Thus, both HARs and CNVs are expected to play key roles in the genetic architecture and pathogenesis of NDDs. However, despite active research on HARs and CNVs separately, integrative studies examining copy-number-driven disruptions specifically within HARs in patients with neurodevelopmental disorders have been extremely limited. This is the first study to assess the contribution of CNVs affecting HARs in 821 children with NDDs. Our bioinformatic evaluation of CNV profiles in this clinical cohort demonstrated that HARs are indeed susceptible to structural alterations in the form of deletions and duplications, supporting the notion that CNVs have shaped the evolution of these regions. Our findings further indicate that HARs, overall, are less frequently affected by duplications compared to other genomic regions. We identified three recurrent HAR loci most strongly associated with neurodevelopmental impairment: HAR_Merge50-02702, HAR_Merge50-02080, and HAR_Merge50-02689. Additionally, we found that HARs disrupted by CNVs form coordinated functional clusters corresponding to genomic regions that harbor extremely rare or entirely absent CNVs in the general population (e.g., HARs associated with RBFOX1, DOC2B, ZMYND11, AFF2, OPHN1). These same genes exhibit a high haploinsufficiency index (HI = 3) according to ClinGen, highlighting their dosage sensitivity. Analysis of the most frequently affected HARs confirmed that their associated genes are significantly enriched for core NDD phenotypes. The absence of a direct correlation with genomic instability suggests that HARs represent functionally vulnerable elements and that compensatory mechanisms may restrict the accumulation of additional structural damage in these regions. Taken together, our study reinforces the importance of HARs in the evolution and functioning of the human central nervous system and provides new evidence supporting the functional relevance of HAR-associated disruptions in neurodevelopmental disorders. We anticipate that future research will further elucidate the complex regulatory processes within the genome and help identify specific HAR regions that may be informative for diagnostic purposes and the development of targeted therapeutic approaches.

genomics↗

bioRxiv2024

Investigating a possible role of R3HCC1L in embryonic development and ocular disease

Peters anomaly (PA) is an anterior segment ocular disorder with wide phenotypic variability and genetic heterogeneity. Here we report a family consisting of a male with a diagnosis of syndromic PA and his unaffected parents, with no causative variants identified in known developmental ocular genes. Exome sequencing analysis identified compound heterozygous missense variants, c. 1022A>T p.(Asp341Val) and c.1457T>A p.(Phe486Tyr), in R3HCC1L. Both variants are ultra-rare in control populations and have CADD scores of 21.9 and 23.3, respectively, suggesting possible deleterious effects. The R3HCC1L transcript variants encode three different protein isoforms all sharing two conserved C-terminal domains, an RNA recognition motif (RRM) and a coiled-coil domain (CCD), and likely represent an RNA-binding protein involved in post-transcriptional gene regulation; the identified patient variants are located within the N-terminal part of the protein shared by two of the three protein isoforms, upstream of the RRM and CCD domains. To investigate the possible role of R3HCC1L in embryonic development, the single zebrafish ortholog of R3HCC1L, r3hcc1l, was examined for its expression and function. In situ expression studies showed that zebrafish r3hcc1l is expressed in the developing lens, cornea, retina and hyaloid vasculature, supporting its possible role in ocular development in vertebrates. CRISPR-Cas9 gene editing was used to generate a zebrafish line with a 4-bp deletion in r3hcc1l, c.623-626del, that is predicted to result in a nonsense-mediated decay and, if expressed, a nonfunctional truncated protein (p.Thr208fs*39) lacking 80% of the RRM and the entire CCD. The resultant r3hcc1lc.623-626del heterozygous and homozygous animals did not show any visible structural abnormalities in the eye or any other systems, with normal survival of all genotypes to adulthood, providing no support for its possible role in the congenital phenotype of interest. However, the function of r3hcc1l may not be completely conserved with human R3HCC1L, and/or zebrafish may have compensatory mechanisms that are not present in humans. In addition, the engineered zebrafish variant disrupts the most conserved C-terminal region of R3HCC1L/r3hcc1l shared by all protein isoforms and likely leads to a complete loss-of-function of this gene, which may be different from the disease mechanism associated with the specific missense alleles identified in the patient. Finally, while it is important to consider the possible limitations of animal models, it is also necessary to highlight that the identified R3HCC1L variants may not have any role in the phenotype observed in this single patient. Identification of new R3HCC1L variants of interest in families affected with PA or other congenital phenotypes, if successful, will provide further support for the possible developmental function of this gene.

genetics↗

bioRxiv2019

notum1, acting downstream of pitx2, is essential for proper eye and craniofacial development.

Axenfeld-Rieger syndrome (ARS) is a rare autosomal dominant developmental disorder characterized by ocular anterior chamber anomalies with an increased risk of glaucoma and systemic defects. Mutations in the transcription factor PITX2 were the first identified genetic cause of ARS. Despite the developmental importance of PITX2 and its role in ARS, the pathways downstream of PITX2 have yet to be fully characterized. Comparative transcriptome analyses involving pitx2-enriched cell populations isolated via fluorescence activated cell sorting of tissues expressing (Tg(-2.6pitx2-CE4:GFP)) reporter in wild-type and pitx2M64* mutant zebrafish embryos identified the highly down-regulated target notum1b, an ortholog of human NOTUM encoding a secreted carboxylesterase that cleaves a necessary palmitoleate moiety from WNT proteins. Further experiments confirmed a decrease in notum1b and identified down-regulation of another NOTUM ortholog, notum1a, in the developing mutant eye. CRISPR-generated permanent double knockout zebrafish lines of notum1b and notum1a, notum1-/-, displayed defects in craniofacial and ocular development, including corneal defects, small lenses, increased sizes of the anterior and posterior chambers, and anomalies in teeth development. Analysis of head transcriptome of notum1-/- zebrafish in comparison to wild-type predicted an up-regulation of the WNT pathway. We present NOTUM/notum1 as an important factor in ocular and craniofacial development and a novel downstream member of the PITX2/pitx2 pathway.

genetics↗