Haider, Shozeb

Primary enlargement of the cerebrospinal fluid (CSF)–filled brain ventricles, known as congenital cerebral ventriculomegaly (CCV), is a hallmark of congenital hydrocephalus. CCV is also enigmatically but frequently associated with autism and other neurodevelopmental disorders. To gain insight into the developmental genetic regulation of the human CSF-ventricular system, we conducted an integrated, multiomic study of about 2700 trio-based exomes from patients with primary CCV. We found that about 25% of cases were associated with rare, damaging de novo variants in mutation-intolerant genes, many of which are linked to other dominant Mendelian disorders. Thirty-five exome-wide significant CCV genes and dozens of other high-confidence CCV genes converged on pathways involved in ATP-dependent Brahma-related gene 1/Brahma-associated factor chromatin remodeling, histone H3 lysine 4 methylation, and phosphoinositide 3-kinase signaling. Knockout of selected CCV genes in mouse models supported that de novo variants in CCV genes caused ventriculomegaly by impairing both CSF dynamics and cortical cytoarchitecture through dysregulation of neuroprogenitor cell growth and maturation in the ventricular and subventricular zones. These findings indicated that genetic and epigenetic programs coordinate the “hand-in-glove” development of the CSF-ventricular system with that of the cerebral cortex and establish a genetic connection between CCV and neurodevelopmental disorders, potentially explaining why some patients with hydrocephalus continue to exhibit CCV and neurodevelopmental disorders despite CSF shunting. We suggest that combined brain imaging and whole-exome sequencing could enable early detection of, and intervention for, autism and other neurodevelopmental disorders.

Abstract BACKGROUND IDH-mutant gliomas are diffusely infiltrating, slow-growing brain tumors that inevitably undergo malignant progression to grade IV astrocytoma - a highly aggressive and uniformly fatal disease with dismal prognosis. Despite extensive research, the molecular mechanisms underlying this transformation remain poorly understood. While alterations in canonical driver genes such as CDKN2A, PTEN, and PDGFRA have been implicated, the broader landscape of genetic drivers involved in IDH-mutant glioma progression is largely uncharacterized. In contrast to many other malignancies, IDH-mutant gliomas acquire relatively few somatic point mutations during progression - typically in the range of 30 to 40 - suggesting that alternative mechanisms may be driving tumor evolution. Notably, these tumors exhibit widespread chromosomal instability, resulting in a heterogeneous and highly prevalent pattern of copy number alterations (CNAs). This observation raises the possibility that gene dosage changes due to CNAs play a critical role in tumor progression. MATERIAL AND METHODS To investigate this hypothesis, we performed integrative analysis of IDH-mutant glioma cohorts from the Mayo Clinic and TCGA datasets (~1,500 patients), identifying twelve highly recurrent CNAs significantly associated with patient outcomes. We refer to these as malignant IDH-associated CNAs (mIDH CNAs). We hypothesized that these recurrent CNAs harbor driver genes that confer selective growth advantages, thereby contributing to their recurrence and prognostic relevance. To systematically assess the functional impact of genes within these regions, we developed a novel in vivo CRISPR-based screening platform, termed CRISPR-Knock Out and Activation Linked Assay (CRISPR-KOALA). This approach utilizes stereotaxic delivery of lentiviral gRNA libraries - targeting mouse orthologs of ~1,800 genes within recurrently deleted regions and ~1,200 genes within amplified regions - into the brains of a genetically engineered mouse model of IDH-mutant glioma (rs557mut;IDHmut;P53KO;AtrxKO;Cas9GFP: Yanchus et. al Science 2022). RESULTS Mice injected with mIDH CNA-targeting libraries developed tumors significantly more rapidly than control cohorts. Deconvolution of the CRISPR-KOALA screen identified several putative driver genes, including regulators of the NOTCH signaling pathway, lipid metabolism modulators such as THEM6, and the NMDA receptor modulator GRINA - implicating dysregulation of metabolism, immune response, and glutamatergic signaling in the malignant transformation of IDH-mutant gliomas. CONCLUSION Together, these findings provide critical insights into the genetic mechanisms driving the progression of IDH-mutant gliomas and identify new candidate genes and pathways for potential therapeutic targeting.

Abstract Moyamoya disease, a cerebrovascular disease leading to strokes in children and young adults, is characterized by progressive occlusion of the distal internal carotid arteries and the formation of collateral vessels. Altered genes play a prominent role in the aetiology of moyamoya disease, but a causative gene is not identified in the majority of cases. Exome sequencing data from 151 individuals from 84 unsolved families were analysed to identify further genes for moyamoya disease, then candidate genes assessed in additional cases (150 probands). Two families had the same rare variant in ANO1, which encodes a calcium-activated chloride channel, anoctamin-1. Haplotype analyses found the families were related, and ANO1 p.Met658Val segregated with moyamoya disease in the family with an LOD score of 3.3. Six additional ANO1 rare variants were identified in moyamoya disease families. The ANO1 rare variants were assessed using patch-clamp recordings, and the majority of variants, including ANO1 p.Met658Val, displayed increased sensitivity to intracellular Ca2+. Patients harbouring these gain-of-function ANO1 variants had classic features of moyamoya disease, but also had aneurysm, stenosis and/or occlusion in the posterior circulation. Our studies support that ANO1 gain-of-function pathogenic variants predispose to moyamoya disease and are associated with unique involvement of the posterior circulation.