HNRNPC haploinsufficiency affects alternative splicing of intellectual disability-associated genes and causes a neurodevelopmental disorder

Eva Niggl, Arjan Bouman*, Genomics England Research Consortium, Undiagnosed Diseases Network, Lauren C. Briere, Remco M. Hoogenboezem, Ilse Wallaard, Joohyun Park, Jakob Admard, Martina Wilke, Emilio D.R.O. Harris-Mostert, Minetta Elgersma, Jennifer Bain, Meena Balasubramanian, Siddharth Banka, Paul J. Benke, Miriam Bertrand, Alyssa E. Blesson, Jill Clayton-Smith, Jamie M. EllingfordMadelyn A. Gillentine, Dana H. Goodloe, Tobias B. Haack, Mahim Jain, Ian Krantz, Sharon M. Luu, Molly McPheron, Candace L. Muss, Sarah E. Raible, Nathaniel H. Robin, Michael Spiller, Susan Starling, David A. Sweetser, Isabelle Thiffault, Francesco Vetrini, Dennis Witt, Emily Woods, Dihong Zhou, Ype Elgersma*, Annelot C.M. van Esbroeck

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

2 Citations (Scopus)

Abstract

Heterogeneous nuclear ribonucleoprotein C (HNRNPC) is an essential, ubiquitously abundant protein involved in mRNA processing. Genetic variants in other members of the HNRNP family have been associated with neurodevelopmental disorders. Here, we describe 13 individuals with global developmental delay, intellectual disability, behavioral abnormalities, and subtle facial dysmorphology with heterozygous HNRNPC germline variants. Five of them bear an identical in-frame deletion of nine amino acids in the extreme C terminus. To study the effect of this recurrent variant as well as HNRNPC haploinsufficiency, we used induced pluripotent stem cells (iPSCs) and fibroblasts obtained from affected individuals. While protein localization and oligomerization were unaffected by the recurrent C-terminal deletion variant, total HNRNPC levels were decreased. Previously, reduced HNRNPC levels have been associated with changes in alternative splicing. Therefore, we performed a meta-analysis on published RNA-seq datasets of three different cell lines to identify a ubiquitous HNRNPC-dependent signature of alternative spliced exons. The identified signature was not only confirmed in fibroblasts obtained from an affected individual but also showed a significant enrichment for genes associated with intellectual disability. Hence, we assessed the effect of decreased and increased levels of HNRNPC on neuronal arborization and neuronal migration and found that either condition affects neuronal function. Taken together, our data indicate that HNRNPC haploinsufficiency affects alternative splicing of multiple intellectual disability-associated genes and that the developing brain is sensitive to aberrant levels of HNRNPC. Hence, our data strongly support the inclusion of HNRNPC to the family of HNRNP-related neurodevelopmental disorders.

Original languageEnglish
Pages (from-to)1414-1435
Number of pages22
JournalAmerican Journal of Human Genetics
Volume110
Issue number8
DOIs
Publication statusPublished - 3 Aug 2023

Bibliographical note

Funding Information:
The inclusion of individual 11 was made possible through access to the data and findings generated by the 100,000 Genomes Project. The 100,000 Genomes Project is managed by Genomics England Limited (a wholly owned company of the Department of Health and Social Care). The 100,000 Genomes Project is funded by the National Institute for Health Research and NHS England. The Wellcome Trust , Cancer Research UK , and the Medical Research Council have also funded research infrastructure. The 100,000 Genomes Project uses data provided by individuals and collected by the National Health Service as part of their care and support.

Funding Information:
First and foremost, we are grateful for all individuals and parents for their cooperation and permission to publish their clinical and genetic information in this manuscript. The inclusion of individual 11 was made possible through access to the data and findings generated by the 100,000 Genomes Project. The 100,000 Genomes Project is managed by Genomics England Limited (a wholly owned company of the Department of Health and Social Care). The 100,000 Genomes Project is funded by the National Institute for Health Research and NHS England. The Wellcome Trust, Cancer Research UK, and the Medical Research Council have also funded research infrastructure. The 100,000 Genomes Project uses data provided by individuals and collected by the National Health Service as part of their care and support. Further, we would like to thank the IPS core facility at the Erasmus MC for generating the IPS lines, registering them to hPSCreg, and providing help and support throughout the project. Also, we are appreciative for the RNA sequencing of the IPS lines by the Biomics facility at the Erasmus MC. Furthermore, we want to acknowledge the Erasmus MC Bioinformatics And Computational Network (BACON) for their instant help and support. Lastly, we would like to thank all funding bodies who made this work possible. A detailed description can be found in the supplemental acknowledgments. A.B. A.C.M.v.E. E.N. and Y.E. conceptualized, designed, and drafted the work. A.B. was responsible for the identification of individual 1, which initiated the study. A.B. was involved in gathering clinical data, as provided by A.E.B. C.L.M. D.H.G. D.A.S. D.Z. D.W. E.W. F.V. I.K. I.T. J.C.-S. J.B. J.M.E. J.P. L.C.B. M. Balasubramanian, M. Bertrand, M.A.G. M.J. M.M. M.S. N.H.R. P.J.B. S.B. S.M.L. S.E.R. S.S. and T.B.H. A.B. and M.W. were involved in the interpretation of the clinical data. The conception of the molecular and cellular studies was the responsibility of E.N. A.C.M.v.E. and Y.E. M.E. was responsible for cloning the HNRNPC-iso1 cDNAs and generating expression vectors for HNRNPC-iso1 and HNRNPC-iso1DEL (pYE1573, pYE1574). Other (tagged) HNRNPC constructs were generated by A.C.M.v.E. E.D.R.O.H.-M. contributed to the analysis and interpretation of the data. I.W. performed and analyzed in vitro and in vivo mouse experiments. E.N. J.P. J.A. L.C.B. and R.M.H. were involved in the gathering, analysis, and interpretation of RNA-seq data. A.B. A.C.M.v.E. E.N. and Y.E. were involved in drafting, writing, and editing the manuscript with significant contributions from L.C.B. M.W. M.A.G. and R.M.H. Scientific guidance on the molecular studies was provided by A.C.M.v.E. and Y.E. All authors revised the manuscript critically for intellectual content, approved the final manuscript for publication, and agreed to be accountable for their published work. The authors declare no competing interests.

Publisher Copyright:
© 2023 American Society of Human Genetics

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