Rare deleterious mutations of HNRNP genes result in shared neurodevelopmental disorders

Abstract

Background With the increasing number of genomic sequencing studies, hundreds of genes have been implicated in neurodevelopmental disorders (NDDs). The rate of gene discovery far outpaces our understanding of genotype–phenotype correlations, with clinical characterization remaining a bottleneck for understanding NDDs. Most disease-associated Mendelian genes are members of gene families, and we hypothesize that those with related molecular function share clinical presentations. Methods We tested our hypothesis by considering gene families that have multiple members with an enrichment of de novo variants among NDDs, as determined by previous meta-analyses. One of these gene families is the heterogeneous nuclear ribonucleoproteins (hnRNPs), which has 33 members, five of which have been recently identified as NDD genes (HNRNPK, HNRNPU, HNRNPH1, HNRNPH2, and HNRNPR) and two of which have significant enrichment in our previous meta-analysis of probands with NDDs (HNRNPU and SYNCRIP). Utilizing protein homology, mutation analyses, gene expression analyses, and phenotypic characterization, we provide evidence for variation in 12 HNRNP genes as candidates for NDDs. Seven are potentially novel while the remaining genes in the family likely do not significantly contribute to NDD risk. Results We report 119 new NDD cases (64 de novo variants) through sequencing and international collaborations and combined with published clinical case reports. We consider 235 cases with gene-disruptive single-nucleotide variants or indels and 15 cases with small copy number variants. Three hnRNP-encoding genes reach nominal or exome-wide significance for de novo variant enrichment, while nine are candidates for pathogenic mutations. Comparison of HNRNP gene expression shows a pattern consistent with a role in cerebral cortical development with enriched expression among radial glial progenitors. Clinical assessment of probands (n = 188–221) expands the phenotypes associated with HNRNP rare variants, and phenotypes associated with variation in the HNRNP genes distinguishes them as a subgroup of NDDs. Conclusions Overall, our novel approach of exploiting gene families in NDDs identifies new HNRNP-related disorders, expands the phenotypes of known HNRNP-related disorders, strongly implicates disruption of the hnRNPs as a whole in NDDs, and supports that NDD subtypes likely have shared molecular pathogenesis. To date, this is the first study to identify novel genetic disorders based on the presence of disorders in related genes. We also perform the first phenotypic analyses focusing on related genes. Finally, we show that radial glial expression of these genes is likely critical during neurodevelopment. This is important for diagnostics, as well as developing strategies to best study these genes for the development of therapeutics.

Rett Syndrome Spectrum in Monogenic Developmental-Epileptic Encephalopathies and Epilepsies: A Review

“…Unsurprisingly, the majority of genes included in this review have multiple known, experimentally determined interactions (and these mainly include the DE-EE genes encoding for ion channels and receptors), while a second group of tightly connected genes involves transcription factors and chromatin modulators. Not unexpectedly, the two members of the heterogeneous nuclear ribonucleoproteins family HNRNPU and HNRNP2 appear functionally related to each other [97] but not with the main network, and additional genes with single RSS case descriptions lack evidence of functional connection or co-expression with the main network (Figure 3). Major alterations affecting several neurological processes, such as the regulation of synaptic transmission, inflammatory and stress-related processes, DNA binding and mRNA stability were confirmed in RTT with a transcriptomic approach [98].…”

Interconnected Gene Networks Underpin the Clinical Overlap of HNRNPH1-Related and Rubinstein–Taybi Intellectual Disability Syndromes

“…To identify differentially expressed genes [DRGs as well as URGs (upregulated genes)], a paired differential gene expression (DGE) analysis (using patients/controls as covariate) was conducted by using DESeq2 package (Love et al, 2014) Bain-type ID (Bain et al, 2016(Bain et al, , 2021. Both NDDs result from monoallelic pathogenic variants preferentially affecting the nuclear localization domain, indispensable to nuclear transport of the hnRNPH1/H2proteins, though HNRNPH1 variant types, different from HNRNPH2 ones, span the entirety of hnRNPH1 (Gillentine et al, 2021). The main function of hnRNPH1/H2 is to control microexon inclusion and inhibition of cryptic polyadenylation sites during neurogenesis, safeguarding the integrity of the transcriptome.…”

“…RNASeq of iNeurons from individuals with Rubinstein–Taybi syndrome (RSTS, MIM# 180849, and #613684), an intellectual disability (ID) disorder caused by monoallelic pathogenic variants in the genes encoding CBP/p300 lysine acetyltransferases (Hennekam, 2006 ), revealed that RSTS-univocal downregulated genes (DRGs) encoding a coherent network of RNA-binding proteins (RBPs) are implicated in RNA processing and ribosome complex biogenesis (Calzari et al, 2020 ). Variation or misregulation of several genes for heterogeneous nuclear ribonuclear proteins (hnRNP), a well-characterized family of RBPs implicated in RNA splicing and processing (Geuens et al, 2016 ), has been linked to neurological and neurodevelopmental disorders supporting a variably shared molecular pathogenesis of disease subtypes that enhances the identification of new family-related NDD genes (Gillentine et al, 2021 ). Interestingly, like hnRNPs, lysine acetyltransferases have been identified as a gene family involved in RNA processing reaching the FDR significance from meta-analyses of >10.000 NDD exomes (Coe et al, 2019 ; Gillentine et al, 2021 ).…”

“…Variation or misregulation of several genes for heterogeneous nuclear ribonuclear proteins (hnRNP), a well-characterized family of RBPs implicated in RNA splicing and processing (Geuens et al, 2016 ), has been linked to neurological and neurodevelopmental disorders supporting a variably shared molecular pathogenesis of disease subtypes that enhances the identification of new family-related NDD genes (Gillentine et al, 2021 ). Interestingly, like hnRNPs, lysine acetyltransferases have been identified as a gene family involved in RNA processing reaching the FDR significance from meta-analyses of >10.000 NDD exomes (Coe et al, 2019 ; Gillentine et al, 2021 ). We discuss herein RSTS and HNRNPH1 -related syndromic ID based on their interconnected gene networks and shared phenotypic spectra.…”

“…The HNRNPH1 gene has been recently implicated in a syndromic form of intellectual disability (Pilch et al, 2018 ; Reichert et al, 2020 ), which presents some phenotypic overlap with H2 -caused or Bain-type ID (Bain et al, 2016 , 2021 ). Both NDDs result from monoallelic pathogenic variants preferentially affecting the nuclear localization domain, indispensable to nuclear transport of the hnRNPH1/H2proteins, though HNRNPH1 variant types, different from HNRNPH2 ones, span the entirety of hnRNPH1 (Gillentine et al, 2021 ). The main function of hnRNPH1/H2 is to control microexon inclusion and inhibition of cryptic polyadenylation sites during neurogenesis, safeguarding the integrity of the transcriptome.…”