Rare deleterious mutations of HNRNP genes result in shared neurodevelopmental disorders
Authors: Gillentine Madelyn A. , Wang Tianyun , Hoekzema Kendra , Rosenfeld Jill , Liu Pengfei , Guo Hui , Kim Chang N. , De Vries Bert B. A. , Vissers Lisenka E. L. M. , Nordenskjold Magnus , Kvarnung Malin , Lindstrand Anna , Nordgren Ann , Gecz Jozef , Iascone Maria , Cereda Anna , Scatigno Agnese , Maitz Silvia , Zanni Ginevra , Bertini Enrico , Zweier Christiane , Schuhmann Sarah , Wiesener Antje , Pepper Micah , Panjwani Heena , Torti Erin , Abid Farida , Anselm Irina , Srivastava Siddharth , Atwal Paldeep , Bacino Carlos A. , Bhat Gifty , Cobian Katherine , Bird Lynne M. , Friedman Jennifer , Wright Meredith S. , Callewaert Bert , Petit Florence , Mathieu Sophie , Afenjar Alexandra , Christensen Celenie K. , White Kerry M. , Elpeleg Orly , Berger Itai , Espineli Edward J. , Fagerberg Christina , Brasch-Andersen Charlotte , Hansen Lars Kjærsgaard , Feyma Timothy , Hughes Susan , Thiffault Isabelle , Sullivan Bonnie , Yan Shuang , Keller Kory , Keren Boris , Mignot Cyril , Kooy Frank , Meuwissen Marije , Basinger Alice , Kukolich Mary , Philips Meredith , Ortega Lucia , Drummond-Borg Margaret , Lauridsen Mathilde , Sorensen Kristina , Lehman Anna ,   CAUSES Study, Lopez-Rangel Elena , Levy Paul , Lessel Davor , Lotze Timothy , Madan-Khetarpal Suneeta , Sebastian Jessica , Vento Jodie , Vats Divya , Benman L. Manace , Mckee Shane , Mirzaa Ghayda M. , Muss Candace , Pappas John , Peeters Hilde , Romano Corrado , Elia Maurizio , Galesi Ornella , Simon Marleen E. H. , van Gassen Koen L. I. , Simpson Kara , Stratton Robert , Syed Sabeen , Thevenon Julien , Palafoll Irene Valenzuela , Vitobello Antonio , Bournez Marie , Faivre Laurence , Xia Kun ,   SPARK Consortium, Acampado John , Ace Andrea J. , Amatya Alpha , Astrovskaya Irina , Bashar Asif , Brooks Elizabeth , Butler Martin E. , Cartner Lindsey A. , Chin Wubin , Chung Wendy K. , Daniels Amy M. , Feliciano Pamela , Fleisch Chris , Ganesan Swami , Jensen William , Lash Alex E. , Marini Richard , Myers Vincent J. , O’Connor Eirene , Rigby Chris , Robertson Beverly E. , Shah Neelay , Shah Swapnil , Singer Emily , Snyder Lee Anne G. , Stephens Alexandra N. , Tjernagel Jennifer , Vernoia Brianna M. , Volfovsky Natalia , White Loran Casey , Hsieh Alexander , Shen Yufeng , Zhou Xueya , Turner Tychele N. , Bahl Ethan , Thomas Taylor R. , Brueggeman Leo , Koomar Tanner , Michaelson Jacob J. , O’Roak Brian J. , Barnard Rebecca A. , Gibbs Richard A. , Muzny Donna , Sabo Aniko , Baalman Ahmed Kelli L. , Eichler Evan E. , Siegel Matthew , Abbeduto Leonard , Amaral David G. , Hilscher Brittani A. , Li Deana , Smith Kaitlin , Thompson Samantha , Albright Charles , Butter Eric M. , Eldred Sara , Hanna Nathan , Jones Mark , Coury Daniel Lee , Scherr Jessica , Pifher Taylor , Roby Erin , Dennis Brandy , Higgins Lorrin , Brown Melissa , Alessandri Michael , Gutierrez Anibal , Hale Melissa N. , Herbert Lynette M. , Schneider Hoa Lam , David Giancarla , Annett Robert D. , Sarver Dustin E. , Arriaga Ivette , Camba Alexies , Gulsrud Amanda C. , Haley Monica , McCracken James T. , Sandhu Sophia , Tafolla Maira , Yang Wha S. , Carpenter Laura A. , Bradley Catherine C. , Gwynette Frampton , Manning Patricia , Shaffer Rebecca , Thomas Carrie , Bernier Raphael A. , Fox Emily A. , Gerdts Jennifer A. , Pepper Micah , Ho Theodore , Cho Daniel , Piven Joseph , Lechniak Holly , Soorya Latha V. , Gordon Rachel , Wainer Allison , Yeh Lisa , Ochoa-Lubinoff Cesar , Russo Nicole , Berry-Kravis Elizabeth , Booker Stephanie , Erickson Craig A. , Prock Lisa M. , Pawlowski Katherine G. , Matthews Emily T. , Brewster Stephanie J. , Hojlo Margaret A. , Abada Evi , Lamarche Elena , Wang Tianyun , Murali Shwetha C. , Harvey William T. , Kaplan Hannah E. , Pierce Karen L. , DeMarco Lindsey , Horner Susannah , Pandey Juhi , Plate Samantha , Sahin Mustafa , Riley Katherine D. , Carmody Erin , Constantini Julia , Esler Amy , Fatemi Ali , Hutter Hanna , Landa Rebecca J. , McKenzie Alexander P. , Neely Jason , Singh Vini , Van Metre Bonnie , Wodka Ericka L. , Fombonne Eric J. , Huang-Storms Lark Y. , Pacheco Lillian D. , Mastel Sarah A. , Coppola Leigh A. , Francis Sunday , Jarrett Andrea , Jacob Suma , Lillie Natasha , Gunderson Jaclyn , Istephanous Dalia , Simon Laura , Wasserberg Ori , Rachubinski Angela L. , Rosenberg Cordelia R. , Kanne Stephen M. , Shocklee Amanda D. , Takahashi Nicole , Bridwell Shelby L. , Klimczac Rebecca L. , Mahurin Melissa A. , Cotrell Hannah E. , Grant Cortaiga A. , Hunter Samantha G. , Martin Christa Lese , Taylor Cora M. , Walsh Lauren K. , Dent Katherine A. , Mason Andrew , Sziklay Anthony , Smith Christopher J. , Earl Rachel K. , Nowakowski Tomasz , Bernier Raphael A. , Eichler Evan E. 
Published: April 2021

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.