Transcriptional Consequences of 16p11.2 Deletion and Duplication in Mouse Cortex and Multiplex Autism Families

Abstract

Reciprocal copy-number variation (CNV) of a 593 kb region of 16p11.2 is a common genetic cause of autism spectrum disorder (ASD), yet it is not completely penetrant and can manifest in a wide array of phenotypes. To explore its molecular consequences, we performed RNA sequencing of cerebral cortex from mouse models with CNV of the syntenic 7qF3 region and lymphoblast lines from 34 members of 7 multiplex ASD-affected families harboring the 16p11.2 CNV. Expression of all genes in the CNV region correlated well with their DNA copy number, with no evidence of dosage compensation. We observed effects on gene expression outside the CNV region, including apparent positional effects in cis and in trans at genomic segments with evidence of physical interaction in Hi-C chromosome conformation data. One of the most significant positional effects was telomeric to the 16p11.2 CNV and includes the previously described "distal" 16p11.2 microdeletion. Overall, 16p11.2 CNV was associated with altered expression of genes and networks that converge on multiple hypotheses of ASD pathogenesis, including synaptic function (e.g., NRXN1, NRXN3), chromatin modification (e.g., CHD8, EHMT1, MECP2), transcriptional regulation (e.g., TCF4, SATB2), and intellectual disability (e.g., FMR1, CEP290). However, there were differences between tissues and species, with the strongest effects being consistently within the CNV region itself. Our analyses suggest that through a combination of indirect regulatory effects and direct effects on nuclear architecture, alteration of 16p11.2 genes disrupts expression networks that involve other genes and pathways known to contribute to ASD, suggesting an overlap in mechanisms of pathogenesis.

The Immune Signaling Adaptor LAT Contributes to the Neuroanatomical Phenotype of 16p11.2 BP2-BP3 CNVs

“…60 In support of the possible interplay between LAT and the BP4-BP5 mapping loci, copy number variants of the BP4-BP5 interval was associated with LAT differential expression in human lymphoblastoid cell lines. 45 Our findings suggest that LAT, like CD247 and ZAP70, [41][42][43][44] plays a role in neurogenesis and that perturbation of this pathway may lead to neurodevelopmental phenotypes. They also provide an interesting example of the non-random organization of the genome 61 as gene dosage modification of (at least) one and five of the 9 and 28 genes mapping within the 220 kb BP2-BP3 and 600 kb BP4-BP5 intervals can influence the PTEN-antagonized (phosphatase and tensin homolog) PI3K/AKT and Ras/MAPK pathways: LAT, TAOK2, that encodes a PTEN-binding MAP kinase kinase kinase essential for dendrite morphogenesis, 62,63 MVP, the product of which interacts with PTEN and regulates its intracellular localization, 59,64,65 MAPK3, KCTD13, 37 and CDIPT (MIM: 605893) encoding an enzyme of the phosphatidylinositol synthesis pathway.…”

“…2,4,6,7,9,15,17 As shown by 4C-seq, FISH, and Hi-C, the two 16p11.2 CNV-prone regions are reciprocally engaged in evolutionary-conserved complex chromatin looping, as well as coordinated expression of encompassed genes. 17,45 Here we assessed whether these findings were paralleled by genetic interactions between the 28 and 9 single-copy genes within the 16p11.2 600 kb BP4-BP5 and 220 kb BP2-BP3 intervals, respectively. Our zebrafish and mouse data indicate that LAT (linker for activation of T cells) is a major driver of the 16p11.2 220 kb BP2-BP3 CNV head size phenotype, a pathology seen consistently in CNV carriers, where the duplication is associated with microcephaly and the deletion is associated with macrocephaly.…”

“…[2][3][4][5]9,10 The two CNVs have also been shown to interact at the chromatin level, by 4C, FISH, Hi-C, and concomitant expression changes. 17,45 To investigate whether the two regions are also conducive to genetic interactions, we co-injected LAT, the driver of the HC phenotype of the BP2-BP3 CNVs, with mRNAs encoding KCTD13, the driver of the HC phenotype of the BP4-BP5 CNVs, and MAPK3 or MVP, modifiers of the same BP4-BP5 HC phenotype, and we evaluated the number of proliferating cells. Single injections of LAT and KCTD13 led to a decreased number of proliferating cells in the brain ranging from 10% to 18%, respectively.…”

CHD8 regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors

“…We performed RNA-seq on all lines using our previously published customization of the strand-specific dUTP method ( Fig. 1 B and C) (16) and also carried out Western blotting using three independent commercially available antibodies (Fig. 1D).…”

Discovery of Rare Mutations in Autism: Elucidating Neurodevelopmental Mechanisms

“…Head circumference was also highly correlated with expression of TAOK2, CORO1A, KCTD13, and QPRT. Another transcriptome analysis of 16p11.2 deletions and duplications in 1) cortical mouse tissue and 2) human lymphoblasts from multiplex autism families found dysregulated gene expression in synaptic functioning (e.g., NRXN1, NRXN3), chromatin modification (e.g., CHD8, EHMT1, MECP2), transcriptional regulation (e.g., TCF4, SATB2), and ID (e.g., FMR1) [137].…”