Systematic analysis of snRNA genes reveals frequent RNU2-2 variants in dominant and recessive developmental and epileptic encephalopathies
Leitão E, Santini A, Cogne B, Essid M, Athanasiadou M, LaFlamme CW, Marijon P, Bernard V, Jousselin K, Chatron N, Barcia G, Keren B, Mignot C, Charles P, Besnard T, Paluch R, de Sainte Agathe JM, Almanza Fuerte EP, Sengupta S, Milh M, Ramond F, Allan T, An I, Araujo C, Arpin S, Austin-Tse C, Auvin S, Baer S, Bahi-Buisson N, Bak M, Barth M, Baulac S, Bednarek-Weirauch N, Begemann M, Bennett MF, Bensabath U, Bézieau S, Bhouri R, Biehler M, Hammer TB, Bogoin J, Bonanno E, Boussion S, Bris C, Brosseau-Beauvir A, Bruel AL, Briand-Suleau A, Buratti J, Celse T, Chambon P, Chemaly N, Chesneau B, Colin E, Colmard M, Colson C, Conrad S, Courtin T, Creveaux I, Cullier AC, Dang LT, de Saint Martin A, de Vanssay de Blavous Legendre C, Demeer B, Denommé-Pichon AS, Diekhoff P, DiTroia S, Doco-Fenzy M, Dubourg C, Dubucs C, Ducreux S, Dufour L, Duquet R, Durand B, El Chehadeh S, Elbracht M, Faivre L, Faoucher M, Faudet A, Forlani S, Fradin M, Gaignard P, Ganne B, Garde A, Géraud J, Gill D, Goldenberg A, Grabli D, Grisel C, Gueden S, Gueguen P, Guerrot AM, Guichet A, Haack TB, Härting N, Häusler MG, Heide S, Herget T, Héron B, Héron D, Herwig J, Heulin M, Holling T, Houdayer C, Isidor B, Jacquette A, Januel L, Jean-Marçais N, Kaiser FJ, Kaya S, King C, Konyukh M, Kraft F, Krause J, Kirstetter R, Kuechler A, Kurth I, Kutsche K, Labalme A, Laloy JS, Laugel V, Le Bricquir F, Lèbre AS, Lebrun M, Leguern E, Levy J, Lieffering N, Lyonnet S, Lüthy K, Macdonald SMW, Mansour-Hendili L, Maraval J, Marquardt I, Mattausch C, Mercier S, Messaoud O, Morel G, Mortreux J, Munnich A, Nabbout R, Nambot S, Navarro V, Neale A, Nguyen L, Nizon M, Nowak F, O’Leary MC, Odent S, Ojeda NM, Olin V, Olivieri S, Õunap K, Pais LS, Panagiotakaki E, Patat O, Perrin-Sabourin L, Petit F, Philippe C, Piton A, Planes M, Poirsier C, Pouzet A, Prouteau C, Quéméner-Redon S, Renaud M, Richard AC, Rio M, Rivier C, Robin-Renaldo F, Rollier P, Rossi M, Roubertie A, Ruault V, Rupin-Mas M, Saugier-Veber P, Saunier A, Saneto R, Sarrazin E, Sarret C, Schaefer E, Schluth-Bolard C, Schneider A, Schumann I, Seplyarskiy VB, Spranger S, Smol T, Sturm M, Sunyaev SR, Sperelakis-Beedham B, Stenton SL, Stock F, Tharreau M, Torun D, Toulouse J, Thiyagarajah H, Valence S, Valleix S, Van-Gils J, Villard L, Ville D, Villeneuve N, Vitobello A, Waernessyckle A, Wagner J, Weber Y, Wieczorek D, Witkowski T, Yadavilli M, Yammine T, Zaafrane-Khachnaoui K, Zaki MS, Ziegler A, Bramswig NC, Lermine A, Nicolas G, Gleeson JG, Sadleir LG, Hildebrand MS, Scheffer IE, Whiffin N, O’Donnell-Luria A, Mefford HC, Blanc P, Thevenon J, Charbonnier C, Charenton C, Depienne C, Lesca G, Nava C.
Nat Genet. 2026 Mar 30. doi: 10.1038/s41588-026-02547-5. Online ahead of print.
ABSTRACT
Small nuclear RNAs (snRNAs) are essential components of the spliceosome. De novo variants in snRNA genes RNU4-2 (ReNU syndrome), RNU5B-1 and RNU2-2 have been linked to dominant neurodevelopmental disorders (NDDs), revealing a large unexpected contribution of noncoding RNA genes to genetic diseases. Here, through international collaborations, we analyze systematically 200 potentially functional snRNA genes in a French cohort of 34,329 people with rare disorders. We report RNU2-2 variants in 141 individuals, including 35 with recurrent dominant pathogenic variants and 91 affected members from 73 families with biallelic variants. Recessive RNU2-2 NDD is at least twice as frequent as the dominant form and often involves a de novo variant in trans with an inherited allele, consistent with the high mutability of snRNA genes. Dominant and recessive RNU2-2 NDDs share overlapping clinical features, with frequent epilepsy. Blood transcriptomics and DNA methylation analyses revealed subtle, variant-specific effects on splicing and episignatures. Our results support a gradient-of-impact model bridging dominant and recessive inheritance, and establish RNU2-2 variants as a principal contributor to NDDs, nearly as prevalent as ReNU syndrome.
PMID:
41912934 | DOI:
10.1038/s41588-026-02547-5
April 5, 2026
Gene DiscoveryGenetic Neurologic DiseaseNeurogenomics
Reconstructing the three-dimensional architecture of extrachromosomal DNA with ec3D
Chowdhury B, Zhu K, Li C, Alsing J, Luebeck J, Stefanova ME, Chapman OS, Kraft K, Zhang S, Lim JYS, Xie Y, Kim YJ, Wu S, Chavez L, Nir G, Henssen AG, Mischel PS, Chang HY, Bafna V.
Nat Commun. 2025 Dec 20. doi: 10.1038/s41467-025-67614-7. Online ahead of print.
ABSTRACT
Extrachromosomal DNAs (ecDNAs) are circular DNA molecules prevalent in human cancers that drive tumor evolution and drug resistance. Their circular topology, which disrupts topological domains and rewires regulatory circuits, has typically been studied via pairwise interactions. Here we develop ec3D, a computational method for reconstructing three-dimensional ecDNA structures from Hi-C data. Given a candidate ecDNA sequence and whole-genome Hi-C data, ec3D reconstructs spatial structures by maximizing the Poisson likelihood of observed interactions. We validate ec3D using simulated structures, previously characterized cancer cell lines, and microscopy imaging. Our reconstructions reveal that ecDNAs occupy spherical configurations and mediate unique long-range regulatory interactions involved in gene regulation. Through algorithmic innovations, ec3D can resolve complex structures with duplicated segments, identify multi-way interactions, and identify potential intermolecular (trans) interactions. Our findings provide insights into how ecDNA’s spatial organization bypasses normal chromosomal constraints and contributes to increased oncogene expression.
PMID:
41422275 | DOI:
10.1038/s41467-025-67614-7
December 20, 2025
Gene Discovery
Clinical Variants in C. elegans Expressing Human STXBP1 Reveals a Novel Class of Pathogenic Variants and Classifies Variants of Uncertain Significance
Hopkins CE, McCormick K, Brock T, Wood M, Helbig I, Mcbride K, Kim C, Lawson JA, Bainbridge MN
Genetics in Medicine Open (2023), doi: https://doi.org/10.1016/j.gimo.2023.100823.
Abstract
Purpose: Modeling disease variants in animals is useful for drug discovery, understanding disease pathology, as well as classifying variants of uncertain significance (VUS) as pathogenic or benign.
Methods
Using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), we performed a Whole-gene Humanized Animal Model (WHAM) procedure to replace the coding sequence of the animal model’s unc-18 ortholog with the coding sequence for the human STXBP1 gene. Next, we used CRISPR to introduce precise point variants in the WHAM-humanized STXBP1 locus from three clinical categories (benign, pathogenic, and VUS). 26 phenotypic features extracted from video recordings were used to train machine learning classifiers on 25 pathogenic and 32 benign variants.
Results
Using multiple models, we were able to obtain a diagnostic sensitivity near 0.9. Twenty-three VUS were also interrogated and 8 of 23 (34.8%) were observed to be functionally abnormal. Interestingly, unsupervised clustering identified two distinct subsets of known pathogenic variants with distinct phenotypic features; Both p.Tyr75Cys and p.Arg406Cys cluster away from other variants and show an increase in swim speed compared to hSTXBP1 worms. This leads to the hypothesis that the mechanism of disease for these two variants may differ from most STXBP1-mutated patients and may account for some of the clinical heterogeneity observed in the patient population
DOI:10.1016/j.gimo.2023.100823
July 25, 2023
Gene Discovery
The Genomic landscape of short tandem repeats across multiple ancestries
Vijayaraghavan P, Batalov S, Ding Y, Sanford E, Kingsmore SF, Dimmock D, Hobbs C, Bainbridge M.
PLoS One. 2023 Jan 26;18(1):e0279430. doi: 10.1371/journal.pone.0279430. eCollection 2023.
ABSTRACT
Short Tandem Repeats (STRs) have been found to play a role in a myriad of complex traits and genetic diseases. We examined the variability in the lengths of over 850,000 STR loci in 996 children with suspected genetic disorders and 1,178 parents across six separate ancestral groups: Africans, Europeans, East Asians, Admixed Americans, Non-admixed Americans, and Pacific Islanders. For each STR locus we compared allele length between and within each ancestry group. In relation to Europeans, admixed Americans had the most similar STR lengths with only 623 positions either significantly expanded or contracted, while the divergence was highest in Africans, with 4,933 chromosomal positions contracted or expanded. We also examined probands to identify STR expansions at known pathogenic loci. The genes TCF4, AR, and DMPK showed significant expansions with lengths 250% greater than their various average allele lengths in 49, 162, and 11 individuals respectively. All 49 individuals containing an expansion in TCF4 and six individuals containing an expansion in DMPK presented with allele lengths longer than the known pathogenic length for these genes. Next, we identified individuals with significant expansions in highly conserved loci across all ancestries. Eighty loci in conserved regions met criteria for divergence. Two of these individuals were found to have exonic STR expansions: one in ZBTB4 and the other in SLC9A7, which is associated with X-linked mental retardation. Finally, we used parent-child trios to detect and analyze de novo mutations. In total, we observed 3,219 de novo expansions, where proband allele lengths are greater than twice the longest parental allele length. This work helps lay the foundation for understanding STR lengths genome-wide across ancestries and may help identify new disease genes and novel mechanisms of pathogenicity in known disease genes.
PMID:
36701310 DOI:
10.1371/journal.pone.0279430
January 26, 2023
Gene DiscoveryRare Disease
NGLY1 deficiency: estimated incidence, clinical features, and genotypic spectrum from the NGLY1 Registry
Stanclift CR, Dwight SS, Lee K, Eijkenboom QL, Wilsey M, Wilsey K, Kobayashi ES, Tong S, Bainbridge MN.
December 17, 2022
Gene Discovery
Variants in CLDN5 cause a syndrome characterized by seizures, microcephaly and brain calcifications
Deshwar AR, Cytrynbaum C, Murthy H, Zon J, Chitayat D, Volpatti J, Newbury-Ecob R, Ellard S, Lango Allen H, Yu EP, Noche R, Walker S, Scherer SW, Mahida S, Elitt CM, Nicolas G, Goldenberg A, Saugier-Veber P, Lecoquierre F, Dabaj I, Meddaugh H, Marble M, Keppler-Noreuil KM, Drayson L, Barañano KW, Chassevent A, Agre K, Létard P, Bilan F, Le Guyader G, Laquerrière A, Ramsey K, Henderson L, Brady L, Tarnopolsky M, Bainbridge M, Friedman J, Capri Y, Athayde L, Kok F, Gurgel-Giannetti J, Ramos LLP, Blaser S, Dowling JJ, Weksberg R.
December 8, 2022
Gene Discovery
Improved attention linked to sustained phenylalanine reduction in adults with early-treated phenylketonuria
Bilder DA, Arnold GL, Dimmock D, Grant ML, Janzen D, Longo N, Nguyen-Driver M, Jurecki E, Merilainen M, Amato G, Waisbren S
Am J Med Genet A. 2021 Nov 26. doi: 10.1002/ajmg.a.62574. Online ahead of print.
ABSTRACT
Pegvaliase is approved to reduce phenylalanine (Phe) levels for people with phenylketonuria (PKU). PRISM-1 (NCT01819727) and PRISM-2 (NCT01889862) data were analyzed to evaluate the relationship between Phe and inattention in adult participants with PKU. In the modified-intent-to-treat population (N = 156), baseline mean (SE) plasma Phe was 1263 (29) μmol/L and the Attention Deficit Hyperactivity Disorder Rating Scale-IV Inattentive (IA) symptoms score was 9.8 (0.5). Mean (SE) IA scores fell 9.0 (1.1) in Quartile 1 (Phe reduction between 1166 and 2229 μmol/L) versus 4.3 (0.7) in Quartile 4 (Phe reduction of 139 μmol/L to increase of 934 μmol/L), p = 0.004. Least squares mean (SE) change from baseline IA score was -7.9 (0.7) for participants with final Phe ≤ 360 μmol/L and -4.5 (0.7) for final Phe > 360 μmol/L, p < 0.001. In the inattention subgroup, IA scores fell 13.3 (1.5) in Quartile 1 (Phe reduction between 1288 and 2229 μmol/L) versus 6.2 (1.3) in Quartile 4 (Phe reduction of 247 to increase of 934 μmol/L), p = 0.009. Inattention symptoms improved among those whose Phe levels decreased, particularly those with high baseline IA scores. IA improvements were larger among participants with the greatest plasma Phe reductions, supporting this value as a therapeutic goal.
PMID:
34826353 | DOI:
10.1002/ajmg.a.62574
December 2, 2021
Gene Discovery
Expanding the phenotypic spectrum of BCS1L-related mitochondrial disease
Hikmat O, Isohanni P, Keshavan N, Ferla MP, Fassone E, Abbott MA, Bellusci M, Darin N, Dimmock D, Ghezzi D, Houlden H, Invernizzi F, Kamarus Jaman NB, Kurian MA, Morava E, Naess K, Ortigoza-Escobar JD, Parikh S, Pennisi A, Barcia G, Tylleskär KB, Brackman D, Wortmann SB, Taylor JC, Bindoff LA, Fellman V, Rahman S.
Ann Clin Transl Neurol. 2021 Oct 18. doi: 10.1002/acn3.51470. Online ahead of print.
ABSTRACT
OBJECTIVE: To delineate the full phenotypic spectrum of BCS1L-related disease, provide better understanding of the genotype-phenotype correlations and identify reliable prognostic disease markers.
METHODS: We performed a retrospective multinational cohort study of previously unpublished patients followed in 15 centres from 10 countries. Patients with confirmed biallelic pathogenic BCS1L variants were considered eligible. Clinical, laboratory, neuroimaging and genetic data were analysed. Patients were stratified into different groups based on the age of disease onset, whether homozygous or compound heterozygous for the c.232A>G (p.Ser78Gly) variant, and those with other pathogenic BCS1L variants.
RESULTS: Thirty-three patients were included. We found that growth failure, lactic acidosis, tubulopathy, hepatopathy and early death were more frequent in those with disease onset within the first month of life. In those with onset after 1 month, neurological features including movement disorders and seizures were more frequent. Novel phenotypes, particularly involving movement disorder, were identified in this group. The presence of the c.232A>G (p.Ser78Gly) variant was associated with significantly worse survival and exclusively found in those with disease onset within the first month of life, whilst other pathogenic BCS1L variants were more frequent in those with later symptom onset.
INTERPRETATION: The phenotypic spectrum of BCS1L-related disease comprises a continuum of clinical features rather than a set of separate syndromic clinical identities. Age of onset defines BCS1L-related disease clinically and early presentation is associated with poor prognosis. Genotype correlates with phenotype in the presence of the c.232A>G (p.Ser78Gly) variant.
PMID:
34662929 | DOI:
10.1002/acn3.51470
October 19, 2021
Gene Discovery
