Disrupting integrator complex subunit INTS6 causes neurodevelopmental disorders and impairs neurogenesis and synapse development
Xiaoxia Peng, et al.
Xiaoxia Peng, et al.
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Research Article Genetics Neuroscience

Disrupting integrator complex subunit INTS6 causes neurodevelopmental disorders and impairs neurogenesis and synapse development

Abstract

The Integrator complex plays essential roles in RNA polymerase II (RNAPII) transcription termination and RNA processing. Here, we identify INTS6, a subunit of the Integrator complex, as a novel gene associated with neurodevelopmental disorders (NDDs). Through analysis of large NDD cohorts and international collaborations, we identified 23 families harboring monoallelic likely gene-disruptive or de novo missense variants in INTS6. Phenotypic characterization revealed shared features, including language and motor delays, autism, intellectual disability, and sleep disturbances. Using a nervous-system conditional KO (cKO) mouse model, we show that Ints6 deficiency disrupts early neurogenesis, cortical lamination, and synaptic development. Ints6 cKO mice had a thickened ventricular zone/subventricular zone, thinning of the cortical plate, reduced neuronal differentiation, and increased apoptosis in cortical layer 6. Behavioral assessments of heterozygous mice revealed deficits in social novelty preference, spatial memory, and hyperactivity, mirroring phenotypes observed in individuals with INTS6 variants. Molecular analyses further revealed that INTS6 deficiency alters RNAPII dynamics, disrupts transcriptional regulation, and impairs synaptic gene expression. Treatment with a CDK9 inhibitor (CDK9i) reduced RNAPII phosphorylation, thereby limiting its binding to target genes. Notably, CDK9i reversed neurosphere overproliferation and rescued the abnormal dendritic spine phenotype caused by Ints6 deficiency. This work advances understanding of INTS-related NDD pathogenesis and highlights potential therapeutic targets for intervention.

Authors

Xiaoxia Peng, Xiangbin Jia, Hanying Wang, Jingjing Chen, Xiaolei Zhang, Senwei Tan, Xinyu Duan, Can Qiu, Mengyuan Hu, Haiyan Hou, Ilaria Parenti, Alma Kuechler, Frank J. Kaiser, Alicia Renck, Raymond Caylor, Cindy Skinner, Joseph Peeden, Benjamin Cogne, Bertrand Isidor, Sandra Mercier, Gael Nicolas, Anne-Marie Guerrot, Flavio Faletra, Luciana Musante, Lior Cohen, Gaber Bergant, Goran Čuturilo, Borut Peterlin, Andrea Seeley, Kristine Bachman, Julian A. Martinez-Agosto, Conny van Ravenswaaij-Arts, Dennis Bos, Katherine H. Kim, Tobias Bartolomaeus, Zelia Schmederer, Rami Abou Jamra, Erfan Aref-Eshghi, Wenjing Zhao, Yongyi Zou, Zhengmao Hu, Qian Pan, Faxiang Li, Guodong Chen, Jiada Li, Zhangxue Hu, Kun Xia, Jieqiong Tan, Hui Guo

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Figure 7

Ints6 deficiency interferes synapse development.

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Ints6 deficiency interferes synapse development. (A) Dendritic spine fr...
(A) Dendritic spine from 5-week-old mice harboring the Thy1-GFP transgene. Density of dendritic spine and the 3 different morphological spine types expressed as the number of spines normalized to 10 μm of dendritic length. Scale bar: 5 μm. (B) Golgi staining of dendritic spines in the cortex layer 2/3 neurons. Density of dendritic spine and the 3 different morphological spine types expressed as the number of spines normalized to 10 pixel of dendritic length. Scale bar: 100 pixels. P values were determined from a 2-tailed unpaired Mann-Whitney and t test. (C) Brain tissue slices from 7-week-old mice were imaged using electron microscopy to visualize synaptic structures. The red arrow indicates the dense postsynaptic region. ImageJ software was used to measure the length of the synapse contact and count synapses. Scale bar: 0.5 μm. (D) PSD-95 (red) and synaptophysin (green) antibodies were used to stain synapses in the cortical in 2-month-old mice. Graphs depict relative integrated density of PSD-95 and synaptophysin. Scale bar: 2 μm. (E) Analysis of SynGO cell components shows overlapping genes represented in a sector diagram. The central sector corresponds to the highest-level term, “synapse,” with subsequent outward sectors depicting its subclasses. (F) Representative images showing spine density in neurons transfected with WT or variant constructs. The graphs display statistical analyses of total, immature, mushroom, and stubby spine densities. Scale bar: 5 μm. P values were determined from 1-way ANOVA with Dunnett’s multiple comparisons test. (A, C, and D). P values were determined from a 2-tailed unpaired t test. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. Each biological replicate (mouse) is color-coded; gray dots show individual data points, and colored dots indicate the mean per mouse. Data are reported as mean ± SEM.