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2. ARID1B-related disorder in 87 adults: Natural history and self-sustainability

Author

van der Sluijs, P.J., Gösgens, M., Dingemans, A.J.M., Striano, P., Riva, A., Mignot, C., Faudet, A., Vasileiou, G., Walther, M., Schrier Vergano, S.A., Alders, M., Alkuraya, F.S., Alorainy, I., Alsaif, H.S., Anderlid, B., Bache, I., van Beek, I., Blanluet, M., van Bon, B.W., Brunet, T., Brunner, H., Carriero, M.L., Charles, P., Chatron, N., Coccia, E., Dubourg, C., Earl, R.K., Eichler, E.E., Faivre, L., Foulds, N., Graziano, C., Guerrot, A.M., Hashem, M.O., Heide, S., Heron, D., Hickey, S.E., Hopman, S.M.J., Kattentidt-Mouravieva, A., Kerkhof, J., Klein Wassink-Ruiter, J.S., Kurtz-Nelson, E.C., Kušíková, K., Kvarnung, M., Lecoquierre, F., Leszinski, G.S., Loberti, L., Magoulas, P.L., Mari, F., Maystadt, I., Merla, G., Milunsky, J.M., Moortgat, S., Nicolas, G., Leary, M.O.’, Odent, S., Ozmore, J.R., Parbhoo, K., Pfundt, R., Piccione, M., Pinto, A.M., Popp, B., Putoux, A., Rehm, H.L., Reis, A., Renieri, A., Rosenfeld, J.A., Rossi, M., Salzano, E., Saugier-Veber, P., Seri, M., Severi, G., Sonmez, F.M., Strobl-Wildemann, G., Stuurman, K.E., Uctepe, E., Van Esch, H., Vitetta, G., de Vries, B.B.A., Wahl, D., Wang, T., Zacher, P., Heitink, K.R., Ropers, F.G., Steenbeek, D., Rybak, T., and Santen, G.W.E.

Published
2024
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4. Diagnostic utility of DNA methylation analysis in genetically unsolved pediatric epilepsies and CHD2 episignature refinement

Author

LaFlamme, CW, Rastin, C, Sengupta, S, Pennington, HE, Russ-Hall, SJ, Schneider, AL, Bonkowski, ES, Almanza Fuerte, EP, Allan, TJ, Zalusky, MP-G, Goffena, J, Gibson, SB, Nyaga, DM, Lieffering, N, Hebbar, M, Walker, EV, Darnell, D, Olsen, SR, Kolekar, P, Djekidel, MN, Rosikiewicz, W, McConkey, H, Kerkhof, J, Levy, MA, Relator, R, Lev, D, Lerman-Sagie, T, Park, KL, Alders, M, Cappuccio, G, Chatron, N, Demain, L, Genevieve, D, Lesca, G, Roscioli, T, Sanlaville, D, Tedder, ML, Gupta, S, Jones, EA, Weisz-Hubshman, M, Ketkar, S, Dai, H, Worley, KC, Rosenfeld, JA, Chao, H-T, Undiagnosed Diseases Network, Neale, G, Carvill, GL, University of Washington Center for Rare Disease Research, Wang, Z, Berkovic, SF, Sadleir, LG, Miller, DE, Scheffer, IE, Sadikovic, B, Mefford, HC, LaFlamme, CW, Rastin, C, Sengupta, S, Pennington, HE, Russ-Hall, SJ, Schneider, AL, Bonkowski, ES, Almanza Fuerte, EP, Allan, TJ, Zalusky, MP-G, Goffena, J, Gibson, SB, Nyaga, DM, Lieffering, N, Hebbar, M, Walker, EV, Darnell, D, Olsen, SR, Kolekar, P, Djekidel, MN, Rosikiewicz, W, McConkey, H, Kerkhof, J, Levy, MA, Relator, R, Lev, D, Lerman-Sagie, T, Park, KL, Alders, M, Cappuccio, G, Chatron, N, Demain, L, Genevieve, D, Lesca, G, Roscioli, T, Sanlaville, D, Tedder, ML, Gupta, S, Jones, EA, Weisz-Hubshman, M, Ketkar, S, Dai, H, Worley, KC, Rosenfeld, JA, Chao, H-T, Undiagnosed Diseases Network, Neale, G, Carvill, GL, University of Washington Center for Rare Disease Research, Wang, Z, Berkovic, SF, Sadleir, LG, Miller, DE, Scheffer, IE, Sadikovic, B, and Mefford, HC

Abstract

Sequence-based genetic testing identifies causative variants in ~ 50% of individuals with developmental and epileptic encephalopathies (DEEs). Aberrant changes in DNA methylation are implicated in various neurodevelopmental disorders but remain unstudied in DEEs. We interrogate the diagnostic utility of genome-wide DNA methylation array analysis on peripheral blood samples from 582 individuals with genetically unsolved DEEs. We identify rare differentially methylated regions (DMRs) and explanatory episignatures to uncover causative and candidate genetic etiologies in 12 individuals. Using long-read sequencing, we identify DNA variants underlying rare DMRs, including one balanced translocation, three CG-rich repeat expansions, and four copy number variants. We also identify pathogenic variants associated with episignatures. Finally, we refine the CHD2 episignature using an 850 K methylation array and bisulfite sequencing to investigate potential insights into CHD2 pathophysiology. Our study demonstrates the diagnostic yield of genome-wide DNA methylation analysis to identify causal and candidate variants as 2% (12/582) for unsolved DEE cases.

Published
2024

5. Prenatal microarray comparative genomic hybridization: Experience from the two first years of activity at the Lyon university-hospital

Author

Pons, L., Till, M., Alix, E., Abel, C., Boggio, D., Bordes, A., Caloone, J., Raskin, F.C., Chatron, N., Cordier, M.-P., Fichez, A., Labalme, A., Lajeunesse, C., Liaras, É., Massoud, M., Miribel, J., Ollagnon, E., Schluth-Bolard, C., Vichier-Cerf, A., Edery, P., Attia, J., Huissoud, C., Rudigoz, R.C., Massardier, J., Gaucherand, P., and Sanlaville, D.

Published
2017
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6. MED13L-related intellectual disability: involvement of missense variants and delineation of the phenotype

Author

Smol, T., Petit, F., Piton, A., Keren, B., Sanlaville, D., Afenjar, A., Baker, S., Bedoukian, E. C., Bhoj, E. J., Bonneau, D., Boudry-Labis, E., Bouquillon, S., Boute-Benejean, O., Caumes, R., Chatron, N., Colson, C., Coubes, C., Coutton, C., Devillard, F., Dieux-Coeslier, A., Doco-Fenzy, M., Ewans, L. J., Faivre, L., Fassi, E., Field, M., Fournier, C., Francannet, C., Genevieve, D., Giurgea, I., Goldenberg, A., Green, A. K., Guerrot, A. M., Heron, D., Isidor, B., Keena, B. A., Krock, B. L., Kuentz, P., Lapi, E., Le Meur, N., Lesca, G., Li, D., Marey, I., Mignot, C., Nava, C., Nesbitt, A., Nicolas, G., Roche-Lestienne, C., Roscioli, T., Satre, V., Santani, A., Stefanova, M., Steinwall Larsen, S., Saugier-Veber, P., Picker-Minh, S., Thuillier, C., Verloes, A., Vieville, G., Wenzel, M., Willems, M., Whalen, S., Zarate, Y. A., Ziegler, A., Manouvrier-Hanu, S., Kalscheuer, V. M., Gerard, B., and Ghoumid, Jamal

Published
2018
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7. Diagnostic Utility of Genome-wide DNA Methylation Analysis in Genetically Unsolved Developmental and Epileptic Encephalopathies and Refinement of a CHD2 Episignature.

Author

LaFlamme, CW, Rastin, C, Sengupta, S, Pennington, HE, Russ-Hall, SJ, Schneider, AL, Bonkowski, ES, Almanza Fuerte, EP, Galey, M, Goffena, J, Gibson, SB, Allan, TJ, Nyaga, DM, Lieffering, N, Hebbar, M, Walker, EV, Darnell, D, Olsen, SR, Kolekar, P, Djekidel, N, Rosikiewicz, W, McConkey, H, Kerkhof, J, Levy, MA, Relator, R, Lev, D, Lerman-Sagie, T, Park, KL, Alders, M, Cappuccio, G, Chatron, N, Demain, L, Genevieve, D, Lesca, G, Roscioli, T, Sanlaville, D, Tedder, ML, Hubshman, MW, Ketkar, S, Dai, H, Worley, KC, Rosenfeld, JA, Chao, H-T, Undiagnosed Diseases Network, Neale, G, Carvill, GL, University of Washington Center for Rare Disease Research, Wang, Z, Berkovic, SF, Sadleir, LG, Miller, DE, Scheffer, IE, Sadikovic, B, Mefford, HC, LaFlamme, CW, Rastin, C, Sengupta, S, Pennington, HE, Russ-Hall, SJ, Schneider, AL, Bonkowski, ES, Almanza Fuerte, EP, Galey, M, Goffena, J, Gibson, SB, Allan, TJ, Nyaga, DM, Lieffering, N, Hebbar, M, Walker, EV, Darnell, D, Olsen, SR, Kolekar, P, Djekidel, N, Rosikiewicz, W, McConkey, H, Kerkhof, J, Levy, MA, Relator, R, Lev, D, Lerman-Sagie, T, Park, KL, Alders, M, Cappuccio, G, Chatron, N, Demain, L, Genevieve, D, Lesca, G, Roscioli, T, Sanlaville, D, Tedder, ML, Hubshman, MW, Ketkar, S, Dai, H, Worley, KC, Rosenfeld, JA, Chao, H-T, Undiagnosed Diseases Network, Neale, G, Carvill, GL, University of Washington Center for Rare Disease Research, Wang, Z, Berkovic, SF, Sadleir, LG, Miller, DE, Scheffer, IE, Sadikovic, B, and Mefford, HC

Abstract

Sequence-based genetic testing currently identifies causative genetic variants in ∼50% of individuals with developmental and epileptic encephalopathies (DEEs). Aberrant changes in DNA methylation are implicated in various neurodevelopmental disorders but remain unstudied in DEEs. Rare epigenetic variations ("epivariants") can drive disease by modulating gene expression at single loci, whereas genome-wide DNA methylation changes can result in distinct "episignature" biomarkers for monogenic disorders in a growing number of rare diseases. Here, we interrogate the diagnostic utility of genome-wide DNA methylation array analysis on peripheral blood samples from 516 individuals with genetically unsolved DEEs who had previously undergone extensive genetic testing. We identified rare differentially methylated regions (DMRs) and explanatory episignatures to discover causative and candidate genetic etiologies in 10 individuals. We then used long-read sequencing to identify DNA variants underlying rare DMRs, including one balanced translocation, three CG-rich repeat expansions, and two copy number variants. We also identify pathogenic sequence variants associated with episignatures; some had been missed by previous exome sequencing. Although most DEE genes lack known episignatures, the increase in diagnostic yield for DNA methylation analysis in DEEs is comparable to the added yield of genome sequencing. Finally, we refine an episignature for CHD2 using an 850K methylation array which was further refined at higher CpG resolution using bisulfite sequencing to investigate potential insights into CHD2 pathophysiology. Our study demonstrates the diagnostic yield of genome-wide DNA methylation analysis to identify causal and candidate genetic causes as ∼2% (10/516) for unsolved DEE cases.

Published
2023

9. Inhibition of G-protein signalling in cardiac dysfunction of intellectual developmental disorder with cardiac arrhythmia (IDDCA) syndrome

Author

De Nittis P., Efthymiou S., Sarre A., Guex N., Chrast J., Putoux A., Sultan T., Raza Alvi J., Ur Rahman Z., Zafar F., Rana N., Rahman F., Anwar N., Maqbool S., Zaki M. S., Gleeson J. G., Murphy D., Galehdari H., Shariati G., Mazaheri N., Sedaghat A., Lesca G., Chatron N., Salpietro V., Christoforou M., Houlden H., Simonds W. F., Pedrazzini T., Maroofian R., Reymond A., SYNAPS STUDY GROUP: SYNAPS Study Group: Stanislav Groppa, Blagovesta Marinova Karashova, Wolfgang Nachbauer, Sylvia Boesch, Larissa Arning, Dagmar Timmann, Bru Cormand, Belen Pérez-Dueñas, Jatinder S Goraya, Tipu Sultan, Jun Mine, Daniela Avdjieva, Hadil Kathom, Radka Tincheva, Selina Banu, Mercedes Pineda-Marfa, Pierangelo Veggiotti, Michel D. Ferrari, Arn M. J. M. van den Maagdenberg, Alberto Verrotti, Giangluigi Marseglia, Salvatore Savasta, Mayte García-Silva, Alfons Macaya Ruiz, Barbara Garavaglia, Eugenia Borgione, Simona Portaro, Benigno Monteagudo Sanchez, Richard Boles, Savvas Papacostas, Michail Vikelis, Eleni Zamba Papanicolaou, Efthymios Dardiotis, Shazia Maqbool, Shahnaz Ibrahim, Salman Kirmani, Nuzhat Noureen Rana, Osama Atawneh, George Koutsis, Salvatore Mangano, Carmela Scuderi, Giovanna Morello, Tanya Stojkovic, Massimo Zollo, Gali Heimer, Yves A. Dauvilliers, Pasquale Striano, Issam Al-Khawaja, Fuad Al-Mutairi, Hamed Sherifa., University of Lausanne (UNIL), University College of London [London] (UCL), Hôpital Femme Mère Enfant [CHU - HCL] (HFME), Hospices Civils de Lyon (HCL), Children's Hospital [Lahore], Institute of Child Health [Lahore], Children's Hospital [Multan], Institute of Child Health [Multan], National Research Centre - NRC (EGYPT), Howard Hughes Medical Institute (HHMI), Shahid Chamran University of Ahvaz (SCU), Ahvaz Jundishapur University of Medical Sciences (AJUMS), National Institutes of Health [Bethesda] (NIH), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Neuropsychiatrie : recherche épidémiologique et clinique (PSNREC), Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Université Montpellier 1 (UM1)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Lausanne = University of Lausanne (UNIL), Herrada, Anthony, P., De Nitti, S., Efthymiou, A., Sarre, N., Guex, J., Chrast, A., Putoux, T., Sultan, J., Raza Alvi, Z., Ur Rahman, F., Zafar, N., Rana, F., Rahman, N., Anwar, S., Maqbool, M. S., Zaki, J. G., Gleeson, D., Murphy, H., Galehdari, G., Shariati, N., Mazaheri, A., Sedaghat, G., Lesca, N., Chatron, V., Salpietro, M., Christoforou, H., Houlden, W. F., Simond, T., Pedrazzini, R., Maroofian, A., Reymond, STUDY GROUP: SYNAPS Study Group: Stanislav Groppa, Synap, Marinova Karashova, Blagovesta, Nachbauer, Wolfgang, Boesch, Sylvia, Arning, Larissa, Timmann, Dagmar, Cormand, Bru, Pérez-Dueñas, Belen, S Goraya, Jatinder, Sultan, Tipu, Mine, Jun, Avdjieva, Daniela, Kathom, Hadil, Tincheva, Radka, Banu, Selina, Pineda-Marfa, Mercede, Veggiotti, Pierangelo, Ferrari, Michel D., van den Maagdenberg, Arn M. J. M., Verrotti, Alberto, Marseglia, Giangluigi, Savasta, Salvatore, García-Silva, Mayte, Macaya Ruiz, Alfon, Garavaglia, Barbara, Borgione, Eugenia, Portaro, Simona, Monteagudo Sanchez, Benigno, Boles, Richard, Papacostas, Savva, Vikelis, Michail, Zamba Papanicolaou, Eleni, Dardiotis, Efthymio, Maqbool, Shazia, Ibrahim, Shahnaz, Kirmani, Salman, Noureen Rana, Nuzhat, Atawneh, Osama, Koutsis, George, Mangano, Salvatore, Scuderi, Carmela, Morello, Giovanna, Stojkovic, Tanya, Zollo, Massimo, Heimer, Gali, Dauvilliers, Yves A., Striano, Pasquale, Al-Khawaja, Issam, Al-Mutairi, Fuad, and Sherifa., Hamed

Subjects
Male, 0301 basic medicine, Developmental Disabilities, Batecs cardíacs, 0302 clinical medicine, Neurodevelopmental disorder, Heart Rate, Medicine, Child, Genetics (clinical), Mice, Knockout, Gnb5-null mouse models, GTP-Binding Protein beta Subunits, Cardiac muscle, Heart, Syndrome, IDDCA, Functional Genomics, Pedigree, [SDV.MHEP.CSC] Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, cardiac conduction anomalies, Gnb5 -null mouse models, GNB5 variants, medicine.anatomical_structure, Child, Preschool, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Female, medicine.symptom, Signal Transduction, Bradycardia, Cardiac function curve, Gnb5 -null mouse model, medicine.medical_specialty, Adolescent, [SDV.GEN.GH] Life Sciences [q-bio]/Genetics/Human genetics, Contractility, Young Adult, Brain damage, 03 medical and health sciences, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, GNB5variants, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Internal medicine, Exome Sequencing, Heart rate, Genetics, Animals, Humans, business.industry, Gene Expression Profiling, Heart beat, Proteins, Cardiac arrhythmia, Arrhythmias, Cardiac, GNB5 variant, medicine.disease, Mice, Inbred C57BL, Autonomic nervous system, 030104 developmental biology, Endocrinology, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Mutation, Lesions cerebrals, cardiac conduction anomalie, business, Proteïnes, 030217 neurology & neurosurgery
Abstract

BackgroundPathogenic variants of GNB5 encoding the β5 subunit of the guanine nucleotide-binding protein cause IDDCA syndrome, an autosomal recessive neurodevelopmental disorder associated with cognitive disability and cardiac arrhythmia, particularly severe bradycardia.MethodsWe used echocardiography and telemetric ECG recordings to investigate consequences of Gnb5 loss in mouse.ResultsWe delineated a key role of Gnb5 in heart sinus conduction and showed that Gnb5-inhibitory signalling is essential for parasympathetic control of heart rate (HR) and maintenance of the sympathovagal balance. Gnb5−/− mice were smaller and had a smaller heart than Gnb5+/+ and Gnb5+/−, but exhibited better cardiac function. Lower autonomic nervous system modulation through diminished parasympathetic control and greater sympathetic regulation resulted in a higher baseline HR in Gnb5−/− mice. In contrast, Gnb5−/− mice exhibited profound bradycardia on treatment with carbachol, while sympathetic modulation of the cardiac stimulation was not altered. Concordantly, transcriptome study pinpointed altered expression of genes involved in cardiac muscle contractility in atria and ventricles of knocked-out mice. Homozygous Gnb5 loss resulted in significantly higher frequencies of sinus arrhythmias. Moreover, we described 13 affected individuals, increasing the IDDCA cohort to 44 patients.ConclusionsOur data demonstrate that loss of negative regulation of the inhibitory G-protein signalling causes HR perturbations in Gnb5−/− mice, an effect mainly driven by impaired parasympathetic activity. We anticipate that unravelling the mechanism of Gnb5 signalling in the autonomic control of the heart will pave the way for future drug screening.

Published
2020
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10. Genomic and phenotypic characterization of 404 individuals with neurodevelopmental disorders caused by CTNNB1 variants

Author

Kayumi, S, Perez-Jurado, LA, Palomares, M, Rangu, S, Sheppard, SE, Chung, WK, Kruer, MC, Kharbanda, M, Amor, DJ, McGillivray, G, Cohen, JS, Garcia-Minaur, S, van Eyk, CL, Harper, K, Jolly, LA, Webber, DL, Barnett, CP, Santos-Simarro, F, Pacio-Miguez, M, del Pozo, A, Bakhtiari, S, Deardorff, M, Dubbs, HA, Izumi, K, Grand, K, Gray, C, Mark, PR, Bhoj, EJ, Li, D, Ortiz-Gonzalez, XR, Keena, B, Zackai, EH, Goldberg, EM, de Nanclares, GP, Pereda, A, Llano-Rivas, I, Arroyo, I, Fernandez-Cuesta, MA, Thauvin-Robinet, C, Faivre, L, Garde, A, Mazel, B, Bruel, A-L, Tress, ML, Brilstra, E, Fine, AS, Crompton, KE, Stegmann, APA, Sinnema, M, Stevens, SCJ, Nicolai, J, Lesca, G, Lion-Francois, L, Haye, D, Chatron, N, Piton, A, Nizon, M, Cogne, B, Srivastava, S, Bassetti, J, Muss, C, Gripp, KW, Procopio, RA, Millan, F, Morrow, MM, Assaf, M, Moreno-De-Luca, A, Joss, S, Hamilton, MJ, Bertoli, M, Foulds, N, McKee, S, MacLennan, AH, Gecz, J, Corbett, MA, Kayumi, S, Perez-Jurado, LA, Palomares, M, Rangu, S, Sheppard, SE, Chung, WK, Kruer, MC, Kharbanda, M, Amor, DJ, McGillivray, G, Cohen, JS, Garcia-Minaur, S, van Eyk, CL, Harper, K, Jolly, LA, Webber, DL, Barnett, CP, Santos-Simarro, F, Pacio-Miguez, M, del Pozo, A, Bakhtiari, S, Deardorff, M, Dubbs, HA, Izumi, K, Grand, K, Gray, C, Mark, PR, Bhoj, EJ, Li, D, Ortiz-Gonzalez, XR, Keena, B, Zackai, EH, Goldberg, EM, de Nanclares, GP, Pereda, A, Llano-Rivas, I, Arroyo, I, Fernandez-Cuesta, MA, Thauvin-Robinet, C, Faivre, L, Garde, A, Mazel, B, Bruel, A-L, Tress, ML, Brilstra, E, Fine, AS, Crompton, KE, Stegmann, APA, Sinnema, M, Stevens, SCJ, Nicolai, J, Lesca, G, Lion-Francois, L, Haye, D, Chatron, N, Piton, A, Nizon, M, Cogne, B, Srivastava, S, Bassetti, J, Muss, C, Gripp, KW, Procopio, RA, Millan, F, Morrow, MM, Assaf, M, Moreno-De-Luca, A, Joss, S, Hamilton, MJ, Bertoli, M, Foulds, N, McKee, S, MacLennan, AH, Gecz, J, and Corbett, MA

Abstract

PURPOSE: Germline loss-of-function variants in CTNNB1 cause neurodevelopmental disorder with spastic diplegia and visual defects (NEDSDV; OMIM 615075) and are the most frequent, recurrent monogenic cause of cerebral palsy (CP). We investigated the range of clinical phenotypes owing to disruptions of CTNNB1 to determine the association between NEDSDV and CP. METHODS: Genetic information from 404 individuals with collectively 392 pathogenic CTNNB1 variants were ascertained for the study. From these, detailed phenotypes for 52 previously unpublished individuals were collected and combined with 68 previously published individuals with comparable clinical information. The functional effects of selected CTNNB1 missense variants were assessed using TOPFlash assay. RESULTS: The phenotypes associated with pathogenic CTNNB1 variants were similar. A diagnosis of CP was not significantly associated with any set of traits that defined a specific phenotypic subgroup, indicating that CP is not additional to NEDSDV. Two CTNNB1 missense variants were dominant negative regulators of WNT signaling, highlighting the utility of the TOPFlash assay to functionally assess variants. CONCLUSION: NEDSDV is a clinically homogeneous disorder irrespective of initial clinical diagnoses, including CP, or entry points for genetic testing.

Published
2022

11. The enrichment of breakpoints in late-replicating chromatin provides novel insights into chromoanagenesis mechanisms

Author

Chatron, N., Giannuzzi, G., Rollat-Farnier, P., Diguet, F., Porcu, E., Yammine, T., Uguen, K., Bellil, Z., Zillhardt, J. Lauer, Sorlin, A., Ader, F., Afenjar, A., Andrieux, J., Bardel, Claire, Calpena, E., Chantot-Bastaraud, S., Callier, P., Chelloug, N., Chopin, E., Cordier, M., Dubourg, C., Faivre, L., Girard, F., Heide, S., Herenger, Y., Jaillard, S., Keren, B., Knight, S. J. L., Lespinasse, J., Lohmann, L., Marle, N., Maroofian, R., Masurel-Paulet, Alice, Mathieu-Dramard, M., Metay, C., Pagnamenta, A. T., Portnoi, M., Prieur, F., Rio, M., Siffroi, J., Valence, S., Taylor, J. C., Wilkie, A. O. M., Edery, P., Reymond, A., Sanlaville, D., Schluth-Bolard, C., Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon (HCL), Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Hospices Civils de Lyon, Departement de Neurologie (HCL), Université de Lausanne = University of Lausanne (UNIL), Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Laboratoire de Diagnostic Génétique [CHU Strasbourg], Université de Strasbourg (UNISTRA)-CHU Strasbourg, Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), Assistance publique-Hôpitaux de Paris - Espace éthique (AP-HP Espace éthique), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), CHU Trousseau [APHP], Service de neurophysiologie clinique (CHRU Lille), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), The Weatherall Institute of Molecular Medicine, University of Oxford, Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), CHU Pontchaillou [Rennes], Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), CHU Strasbourg, The Wellcome Trust Centre for Human Genetics [Oxford], Centre Hospitalier Métropole Savoie [Chambéry], Laboratoire CERBA [Saint Ouen l'Aumône], University College of London [London] (UCL), CHU Amiens-Picardie, CHU Henri Mondor [Créteil], Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E), CHU Necker - Enfants Malades [AP-HP], Université Paris 1 Panthéon-Sorbonne (UP1), Chard-Hutchinson, Xavier, Service de Génétique Cytogénétique et Embryologie [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Service d'Hépato-Gastro-Entérologie [CHU Pitié-Salpêtrière], CHU Henri Mondor, Centre Hospitalier Universitaire de Saint-Etienne (CHU de Saint-Etienne), Centre de recherche en neurosciences de Lyon (CRNL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Lausanne (UNIL), Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), University of Oxford [Oxford], Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre Hospitalier Régional Universitaire de Tours (CHRU TOURS), Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2020
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12. Bi-allelic GAD1 variants cause a neonatal onset syndromic developmental and epileptic encephalopathy

Author

Chatron, N, Becker, F, Morsy, H, Schmidts, M, Hardies, K, Tuysuz, B, Roselli, S, Najafi, M, Alkaya, DU, Ashrafzadeh, F, Nabil, A, Omar, T, Maroofian, R, Karimiani, EG, Hussien, H, Kok, F, Ramos, L, Gunes, N, Bilguvar, K, Labalme, A, Alix, E, Sanlaville, D, de Bellescize, J, Poulat, A-L, EuroEpinomics-RES consortium AR working group, Moslemi, A-R, Lerche, H, May, P, Lesca, G, Weckhuysen, S, Tajsharghi, H, Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], and University of Luxembourg: High Performance Computing - ULHPC [research center]

Subjects
cleft palate, Epilepsy, Hypsarrhythmia, omphalocele, GAD1, Suppression-burs, Developmental Syndrome, Genetics & genetic processes [F10] [Life sciences], Génétique & processus génétiques [F10] [Sciences du vivant], arthrogryposis
Abstract

Developmental and Epileptic Encephalopathies are a heterogeneous group of early-onset epilepsy syndromes dramatically impairing neurodevelopment. Modern genomic technologies have revealed a number of monogenic origins and opened the door to therapeutic hopes. Here we describe a new syndromic developmental and epileptic encephalopathies caused by bi-allelic loss of function variants in GAD1, as presented by eleven patients from 6 independent consanguineous families. Seizure onset occurred in the two first months of life in all patients. All 10 patients from whom early disease history was available, presented seizure onset in the first month of life, mainly consisting of epileptic spasms or myoclonic seizures. Early electroencephalography showed suppression-burst or pattern of burst attenuation or hypsarrhythmia if only recorded in the post-neonatal period. Eight patients had joint contractures and/or pes equinovarus. Seven patients presented a cleft palate and two also had an omphalocele, reproducing the phenotype of the knockout Gad1-/- mouse model. Four patients died before four years of age. GAD1 encodes the glutamate decarboxylase enzyme GAD67, a critical actor of the γ-aminobutyric acid (GABA) metabolism as it catalyzes the decarboxylation of glutamic acid to form GABA. Our findings evoke a novel syndrome related to GAD67 deficiency, characterized by the unique association of developmental and epileptic encephalopathies, cleft palate, joint contractures and/or omphalocele.

Published
2020

13. NEXMIF encephalopathy: an X-linked disorder with male and female phenotypic patterns

Author

Stamberger, H., Hammer, T.B., Gardella, E., Vlaskamp, D.R.M., Bertelsen, B., Mandelstam, S., Lange, I. de, Zhang, J., Myers, C.T., Fenger, C., Afawi, Z., Fuerte, E.P. Almanza, Andrade, D.M., Balcik, Y., Zeev, B. Ben, Bennett, M.F., Berkovic, S.F., Isidor, B., Bouman, A., Brilstra, E., Ø, L. Busk, Cairns, A., Caumes, R., Chatron, N., Dale, R.C., Geus, C. de, Edery, P., Gill, D., Granild-Jensen, J.B., Gunderson, L., Gunning, B., Heimer, G., Helle, J.R., Hildebrand, M.S., Hollingsworth, G., Kharytonov, V., Klee, E.W., Koeleman, B.P.C., Koolen, D.A., Korff, C., Küry, S., Lesca, G., Lev, D., Leventer, R.J., Mackay, M.T., Macke, E.L., McEntagart, M., Mohammad, S.S., Monin, P., Montomoli, M., Morava, E., Moutton, S., Muir, A.M., Parrini, E., Procopis, P., Ranza, E., Reed, L., Reif, P.S., Rosenow, F., Rossi, M., Sadleir, L.G., Sadoway, T., Schelhaas, H.J., Schneider, A.L., Shah, K., Shalev, R., Sisodiya, S.M., Smol, T., Stumpel, C., Stuurman, K., Symonds, J.D., Mau-Them, F.T., Verbeek, N., Verhoeven, J.S., Wallace, G., Yosovich, K., Zarate, Y.A., Zerem, A., Zuberi, S.M., Guerrini, R., Mefford, H.C., Patel, C., Zhang, Y.H., Møller, R.S., Scheffer, I.E., Stamberger, H., Hammer, T.B., Gardella, E., Vlaskamp, D.R.M., Bertelsen, B., Mandelstam, S., Lange, I. de, Zhang, J., Myers, C.T., Fenger, C., Afawi, Z., Fuerte, E.P. Almanza, Andrade, D.M., Balcik, Y., Zeev, B. Ben, Bennett, M.F., Berkovic, S.F., Isidor, B., Bouman, A., Brilstra, E., Ø, L. Busk, Cairns, A., Caumes, R., Chatron, N., Dale, R.C., Geus, C. de, Edery, P., Gill, D., Granild-Jensen, J.B., Gunderson, L., Gunning, B., Heimer, G., Helle, J.R., Hildebrand, M.S., Hollingsworth, G., Kharytonov, V., Klee, E.W., Koeleman, B.P.C., Koolen, D.A., Korff, C., Küry, S., Lesca, G., Lev, D., Leventer, R.J., Mackay, M.T., Macke, E.L., McEntagart, M., Mohammad, S.S., Monin, P., Montomoli, M., Morava, E., Moutton, S., Muir, A.M., Parrini, E., Procopis, P., Ranza, E., Reed, L., Reif, P.S., Rosenow, F., Rossi, M., Sadleir, L.G., Sadoway, T., Schelhaas, H.J., Schneider, A.L., Shah, K., Shalev, R., Sisodiya, S.M., Smol, T., Stumpel, C., Stuurman, K., Symonds, J.D., Mau-Them, F.T., Verbeek, N., Verhoeven, J.S., Wallace, G., Yosovich, K., Zarate, Y.A., Zerem, A., Zuberi, S.M., Guerrini, R., Mefford, H.C., Patel, C., Zhang, Y.H., Møller, R.S., and Scheffer, I.E.

Abstract

Contains fulltext : 231688.pdf (Publisher’s version ) (Closed access), PURPOSE: Pathogenic variants in the X-linked gene NEXMIF (previously KIAA2022) are associated with intellectual disability (ID), autism spectrum disorder, and epilepsy. We aimed to delineate the female and male phenotypic spectrum of NEXMIF encephalopathy. METHODS: Through an international collaboration, we analyzed the phenotypes and genotypes of 87 patients with NEXMIF encephalopathy. RESULTS: Sixty-three females and 24 males (46 new patients) with NEXMIF encephalopathy were studied, with 30 novel variants. Phenotypic features included developmental delay/ID in 86/87 (99%), seizures in 71/86 (83%) and multiple comorbidities. Generalized seizures predominated including myoclonic seizures and absence seizures (both 46/70, 66%), absence with eyelid myoclonia (17/70, 24%), and atonic seizures (30/70, 43%). Males had more severe developmental impairment; females had epilepsy more frequently, and varied from unaffected to severely affected. All NEXMIF pathogenic variants led to a premature stop codon or were deleterious structural variants. Most arose de novo, although X-linked segregation occurred for both sexes. Somatic mosaicism occurred in two males and a family with suspected parental mosaicism. CONCLUSION: NEXMIF encephalopathy is an X-linked, generalized developmental and epileptic encephalopathy characterized by myoclonic-atonic epilepsy overlapping with eyelid myoclonia with absence. Some patients have developmental encephalopathy without epilepsy. Males have more severe developmental impairment. NEXMIF encephalopathy arises due to loss-of-function variants.

Published
2021

14. Variants in USP48 encoding ubiquitin hydrolase are associated with autosomal dominant non-syndromic hereditary hearing loss

Author

Bassani, S., Beelen, E. van, Rossel, M., Voisin, N., Morgan, A., Arribat, Y., Chatron, N., Chrast, J., Cocca, M., Delprat, B., Faletra, F., Giannuzzi, G., Guex, N., Machavoine, R., Pradervand, S., Smits, J.J., Kamp, J.M. van de, Ziegler, A., Amati, F., Marlin, S., Kremer, H., Locher, H., Maurice, T., Gasparini, P., Girotto, G., Reymond, A., Bassani, S., Beelen, E. van, Rossel, M., Voisin, N., Morgan, A., Arribat, Y., Chatron, N., Chrast, J., Cocca, M., Delprat, B., Faletra, F., Giannuzzi, G., Guex, N., Machavoine, R., Pradervand, S., Smits, J.J., Kamp, J.M. van de, Ziegler, A., Amati, F., Marlin, S., Kremer, H., Locher, H., Maurice, T., Gasparini, P., Girotto, G., and Reymond, A.

Abstract

Item does not contain fulltext, Non-Syndromic Hereditary Hearing Loss (NSHHL) is a genetically heterogeneous sensory disorder with about 120 genes already associated. Through exome sequencing (ES) and data aggregation, we identified a family with six affected individuals and one unrelated NSHHL patient with predicted-to-be deleterious missense variants in USP48. We also uncovered an eighth patient presenting unilateral cochlear nerve aplasia and a de novo splice variant in the same gene. USP48 encodes a ubiquitin carboxyl-terminal hydrolase under evolutionary constraint. Pathogenicity of the variants is supported by in vitro assays that showed that the mutated proteins are unable to hydrolyze tetra-ubiquitin. Correspondingly, three-dimensional representation of the protein containing the familial missense variant is situated in a loop that might influence the binding to ubiquitin. Consistent with a contribution of USP48 to auditory function, immunohistology showed that the encoded protein is expressed in the developing human inner ear, specifically in the spiral ganglion neurons, outer sulcus, interdental cells of the spiral limbus, stria vascularis, Reissner's membrane and in the transient Kolliker's organ that is essential for auditory development. Engineered zebrafish knocked-down for usp48, the USP48 ortholog, presented with a delayed development of primary motor neurons, less developed statoacoustic neurons innervating the ears, decreased swimming velocity and circling swimming behavior indicative of vestibular dysfunction and hearing impairment. Corroboratingly, acoustic startle response assays revealed a significant decrease of auditory response of zebrafish lacking usp48 at 600 and 800 Hz wavelengths. In conclusion, we describe a novel autosomal dominant NSHHL gene through a multipronged approach combining ES, animal modeling, immunohistology and molecular assays.

Published
2021

15. Progressive Myoclonus Epilepsy Caused by a Homozygous Splicing Variant of SLC7A6OS

Author

Mazzola, L, Oliver, KL, Labalme, A, Baykan, B, Muona, M, Joensuu, TH, Courage, C, Chatron, N, Borsani, G, Alix, E, Ramond, F, Touraine, R, Bahlo, M, Bebek, N, Berkovic, SF, Lehesjoki, A-E, Lesca, G, Mazzola, L, Oliver, KL, Labalme, A, Baykan, B, Muona, M, Joensuu, TH, Courage, C, Chatron, N, Borsani, G, Alix, E, Ramond, F, Touraine, R, Bahlo, M, Bebek, N, Berkovic, SF, Lehesjoki, A-E, and Lesca, G

Abstract

Exome sequencing was performed in 2 unrelated families with progressive myoclonus epilepsy. Affected individuals from both families shared a rare, homozygous c.191A > G variant affecting a splice site in SLC7A6OS. Analysis of cDNA from lymphoblastoid cells demonstrated partial splice site abolition and the creation of an abnormal isoform. Quantitative reverse transcriptase polymerase chain reaction and Western blot showed a marked reduction of protein expression. Haplotype analysis identified a ~0.85cM shared genomic region on chromosome 16q encompassing the c.191A > G variant, consistent with a distant ancestor common to both families. Our results suggest that biallelic loss‐of‐function variants in SLC7A6OS are a novel genetic cause of progressive myoclonus epilepsy.

Published
2021

16. Defining and expanding the phenotype of QARS-associated developmental epileptic encephalopathy

Author

Johannesen, Km, Mitter, D, Janowski, R, Roth, C, Toulouse, J, Poulat, Al, Ville, Dm, Chatron, N, Brilstra, E, Geleijns, K, Born, Ap, McLean, S, Nugent, K, Baynam, G, Poulton, C, Dreyer, L, Gration, D, Schulz, S, Dieckmann, A, Helbig, Kl, Merkenschlager, A, Jamra, R, Finck, A, Gardella, E, Hjalgrim, H, Mirzaa, G, Brancati, F, Bierhals, T, Denecke, J, Hempel, M, Lemke, Jr, Rubboli, G, Muschke, P, Guerrini, R, Vetro, A, Niessing, D, Lesca, G, and Møller, Rs

Subjects
TRANSFER-RNA-SYNTHETASE, ILAE COMMISSION, POSITION PAPER, MUTATIONS, CLASSIFICATION, DEFICIENCY, FEATURES
Published
2020

17. Phenotypic spectrum and transcriptomic profile associated with germline variants in TRAF7

Author

Castilla-Vallmanya L, Selmer KK, Dimartino C, Raquel Rabionet Janssen, Blanco-Sánchez B, Yang S, Reijnders MRF, van Essen AJ, Oufadem M, Vigeland MD, Stadheim B, Houge G, Cox H, Kingston H, Clayton-Smith J, Innis JW, Iascone M, Cereda A, Gabbiadini S, Chung WK, Sanders V, Charrow J, Bryant E, Millichap J, Vitobello A, Thauvin C, Mau-Them FT, Faivre L, Lesca G, Labalme A, Rougeot C, Chatron N, Sanlaville D, Christensen KM, Kirby A, Lewandowski R, Gannaway R, Aly M, Lehman A, Clarke L, Graul-Neumann L, Zweier C, Lessel D, Lozic B, Aukrust I, Peretz R, Stratton R, Smol T, Dieux-Coëslier A, Meira J, Wohler E, Sobreira N, Beaver EM, Heeley J, Briere LC, High FA, Sweetser DA, Walker MA, Keegan CE, Jayakar P, Shinawi M, Kerstjens-Frederikse WS, Earl DL, Siu VM, Reesor E, Yao T, Hegele RA, Vaske OM, Rego S, Undiagnosed Diseases Network, Care4Rare Canada Consortium, Shapiro KA, Wong B, Gambello MJ, McDonald M, Karlowicz D, Colombo R, Serretti A, Pais L, O'Donnell-Luria A, Wray A, Sadedin S, Chong B, Tan TY, Christodoulou J, White SM, Slavotinek A, Barbouth D, Morel Swols D, Parisot M, Bole-Feysot C, Nitschké P, Pingault V, Munnich A, Cho MT, Cormier-Daire V, Balcells S, Lyonnet S, Grinberg-Vaisman DR, Amiel J, Urreizti R, and Gordon CT

Subjects
craniofacial development, patent ductus arteriosus, TRAF7, intellectual disability, blepharophimosis
Abstract

PURPOSE: Somatic variants in tumor necrosis factor receptor-associated factor 7 (TRAF7) cause meningioma, while germline variants have recently been identified in seven patients with developmental delay and cardiac, facial, and digital anomalies. We aimed to define the clinical and mutational spectrum associated with TRAF7 germline variants in a large series of patients, and to determine the molecular effects of the variants through transcriptomic analysis of patient fibroblasts. METHODS: We performed exome, targeted capture, and Sanger sequencing of patients with undiagnosed developmental disorders, in multiple independent diagnostic or research centers. Phenotypic and mutational comparisons were facilitated through data exchange platforms. Whole-transcriptome sequencing was performed on RNA from patient- and control-derived fibroblasts. RESULTS: We identified heterozygous missense variants in TRAF7 as the cause of a developmental delay-malformation syndrome in 45 patients. Major features include a recognizable facial gestalt (characterized in particular by blepharophimosis), short neck, pectus carinatum, digital deviations, and patent ductus arteriosus. Almost all variants occur in the WD40 repeats and most are recurrent. Several differentially expressed genes were identified in patient fibroblasts. CONCLUSION: We provide the first large-scale analysis of the clinical and mutational spectrum associated with the TRAF7 developmental syndrome, and we shed light on its molecular etiology through transcriptome studies.

Published
2020

18. Clinical spectrum of STX1B-related epileptic disorders

Author

Wolking, S, May, P, Mei, D, Møller, RS, Balestrini, S, Helbig, KL, Altuzarra, CD, Chatron, N, Kaiwar, C, Stöhr, K, Widdess-Walsh, P, Mendelsohn, BA, Numis, A, Cilio, MR, Van Paesschen, W, Svendsen, LL, Oates, S, Hughes, E, Goyal, S, Brown, K, Saenz, M, Dorn, T, Muhle, H, Pagnamenta, AT, Vavoulis, DV, Knight, SJL, Taylor, JC, Canevini, MP, Darra, F, Gavrilova, RH, Powis, Z, Tang, S, Marquetand, J, Armstrong, M, McHale, D, Klee, EW, Kluger, GJ, Lowenstein, DH, Weckhuysen, S, Pal, DK, Helbig, I, Guerrini, R, Thomas, RH, Rees, MI, Lesca, G, Sisodiya, SM, Weber, YG, Lal, D, Marini, C, Lerche, H, and Schubert, J

Subjects
Male, Drug Resistant Epilepsy, Adolescent, Developmental Disabilities, Mutation, Missense, Clinical Neurology, FEBRILE SEIZURES PLUS, GENERALIZED EPILEPSY, Syntaxin 1, PROTEIN, Article, Seizures, Febrile, Young Adult, Loss of Function Mutation, Humans, HETEROGENEITY, SCN1A, Child, Epilepstic disorders, Science & Technology, Learning Disabilities, Infant, Newborn, High-Throughput Nucleotide Sequencing, Infant, GENETIC-VARIATION, Electroencephalography, Sequence Analysis, DNA, SODIUM-CHANNEL, Epilepstic disorders, STX1B, Phenotype, DE-NOVO MUTATIONS, Child, Preschool, ONSET, STXBP1, STX1B, Anticonvulsants, Female, Human medicine, Epilepsies, Partial, Neurosciences & Neurology, Epileptic Syndromes, Life Sciences & Biomedicine
Abstract

OBJECTIVE: The aim of this study was to expand the spectrum of epilepsy syndromes related to STX1B, encoding the presynaptic protein syntaxin-1B, and establish genotype-phenotype correlations by identifying further disease-related variants. METHODS: We used next-generation sequencing in the framework of research projects and diagnostic testing. Clinical data and EEGs were reviewed, including already published cases. To estimate the pathogenicity of the variants, we used established and newly developed in silico prediction tools. RESULTS: We describe 17 new variants in STX1B, which are distributed across the whole gene. We discerned 4 different phenotypic groups across the newly identified and previously published patients (49 patients in 23 families): (1) 6 sporadic patients or families (31 affected individuals) with febrile and afebrile seizures with a benign course, generally good drug response, normal development, and without permanent neurologic deficits; (2) 2 patients with genetic generalized epilepsy without febrile seizures and cognitive deficits; (3) 13 patients or families with intractable seizures, developmental regression after seizure onset and additional neuropsychiatric symptoms; (4) 2 patients with focal epilepsy. More often, we found loss-of-function mutations in benign syndromes, whereas missense variants in the SNARE motif of syntaxin-1B were associated with more severe phenotypes. CONCLUSION: These data expand the genetic and phenotypic spectrum of STX1B-related epilepsies to a diverse range of epilepsies that span the International League Against Epilepsy classification. Variants in STX1B are protean and contribute to many different epilepsy phenotypes, similar to SCN1A, the most important gene associated with fever-associated epilepsies. ispartof: NEUROLOGY vol:92 issue:11 pages:E1238-E1249 ispartof: location:United States status: published

Published
2019
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19. Evaluation of DNA Methylation Episignatures for Diagnosis and Phenotype Correlations in 42 Mendelian Neurodevelopmental Disorders

Author

Aref-Eshghi, E., Kerkhof, J., Pedro, V.P., Barat-Houari, M., Ruiz-Pallares, N., Andrau, J.C., Lacombe, D., Van-Gils, J., Fergelot, P., Dubourg, C., Cormier-Daire, V., Rondeau, S., Lecoquierre, F., Saugier-Veber, P., Nicolas, G., Lesca, G., Chatron, N., Sanlaville, D., Vitobello, A., Faivre, L., Thauvin-Robinet, C., Laumonnier, F., Raynaud, M., Alders, M., Mannens, M., Henneman, P., Hennekam, R.C., Velasco, G., Francastel, C., Ulveling, D., Ciolfi, A., Pizzi, S., Tartaglia, M., Heide, S. van der, Heron, D., Mignot, C., Keren, B., Whalen, S., Afenjar, A., Bienvenu, T., Campeau, P.M., Rousseau, J., Levy, M.A., Brick, L., Kozenko, M., Balci, T.B., Siu, V.M., Stuart, A., Kadour, M., Masters, J., Takano, K., Kleefstra, T., Leeuw, N. de, Field, M., Shaw, M., Gecz, J., Ainsworth, P.J., Lin, H., Rodenhiser, D.I., Friez, M.J., Tedder, M., Lee, Jae Lyun, DuPont, B.R., Stevenson, R.E., Skinner, S.A., Schwartz, C.E., Genevieve, D., Sadikovic, B., Aref-Eshghi, E., Kerkhof, J., Pedro, V.P., Barat-Houari, M., Ruiz-Pallares, N., Andrau, J.C., Lacombe, D., Van-Gils, J., Fergelot, P., Dubourg, C., Cormier-Daire, V., Rondeau, S., Lecoquierre, F., Saugier-Veber, P., Nicolas, G., Lesca, G., Chatron, N., Sanlaville, D., Vitobello, A., Faivre, L., Thauvin-Robinet, C., Laumonnier, F., Raynaud, M., Alders, M., Mannens, M., Henneman, P., Hennekam, R.C., Velasco, G., Francastel, C., Ulveling, D., Ciolfi, A., Pizzi, S., Tartaglia, M., Heide, S. van der, Heron, D., Mignot, C., Keren, B., Whalen, S., Afenjar, A., Bienvenu, T., Campeau, P.M., Rousseau, J., Levy, M.A., Brick, L., Kozenko, M., Balci, T.B., Siu, V.M., Stuart, A., Kadour, M., Masters, J., Takano, K., Kleefstra, T., Leeuw, N. de, Field, M., Shaw, M., Gecz, J., Ainsworth, P.J., Lin, H., Rodenhiser, D.I., Friez, M.J., Tedder, M., Lee, Jae Lyun, DuPont, B.R., Stevenson, R.E., Skinner, S.A., Schwartz, C.E., Genevieve, D., and Sadikovic, B.

Abstract

Contains fulltext : 218274.pdf (Publisher’s version ) (Closed access), Genetic syndromes frequently present with overlapping clinical features and inconclusive or ambiguous genetic findings which can confound accurate diagnosis and clinical management. An expanding number of genetic syndromes have been shown to have unique genomic DNA methylation patterns (called "episignatures"). Peripheral blood episignatures can be used for diagnostic testing as well as for the interpretation of ambiguous genetic test results. We present here an approach to episignature mapping in 42 genetic syndromes, which has allowed the identification of 34 robust disease-specific episignatures. We examine emerging patterns of overlap, as well as similarities and hierarchical relationships across these episignatures, to highlight their key features as they are related to genetic heterogeneity, dosage effect, unaffected carrier status, and incomplete penetrance. We demonstrate the necessity of multiclass modeling for accurate genetic variant classification and show how disease classification using a single episignature at a time can sometimes lead to classification errors in closely related episignatures. We demonstrate the utility of this tool in resolving ambiguous clinical cases and identification of previously undiagnosed cases through mass screening of a large cohort of subjects with developmental delays and congenital anomalies. This study more than doubles the number of published syndromes with DNA methylation episignatures and, most significantly, opens new avenues for accurate diagnosis and clinical assessment in individuals affected by these disorders.

Published
2020

20. Whole Genome Sequencing of 9 patients allowed a better understanding of complex chromosomal rearrangements

Author

Girard, F., Jaillard, S., Keren, B., Lespinasse, J., Marle, N., Masurel, A., Mathieu, M., Metay, C., Portnoi, M., Prieur, F., Rio, M., Siffroi, J., Schluth-Bolard, C., Sanlaville, D., Chatron, N., Diguet, F., Rollat-Farnier, P., Uguen, K., Zillhardt, J. Lauer, Sorlin, A., Andrieux, J., Chantot-Bastaraud, S., Callier, P., Cordier, M., Dubourg, C., CHU Pontchaillou [Rennes], Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Laboratoire de cytogénétique (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), CHU Amiens-Picardie, Hôpital Henri Mondor, Centre Hospitalier Universitaire de Saint-Etienne (CHU de Saint-Etienne), Centre de recherche en neurosciences de Lyon (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Hospices Civils de Lyon (HCL), Hôpital de la Cavale Blanche - CHRU Brest (CHU - BREST ), Equipe GAD (LNC - U1231), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Génétique et Développement de Rennes (IGDR), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E), Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), and Jonchère, Laurent

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

24. Neurodevelopmental Disorder Caused by Deletion of CHASERR, a 1ncRNA Gene.

Author

Ganesh, V. S., Riquin, K., Chatron, N., Yoon, E., Lamar, K.-M., Aziz, M. I., Monin, P., O'Leary, M. C., Goodrich, J. K., Garimella, K. V., England, E., Weisburd, B., Aguet, F., Bacino, C. A., Murdock, D. R., Dai, H., Rosenfeld, J. A., Emrick, L. T., Ketkar, S., and Sarusi, Y.

Subjects
*NEURAL development, *CEREBRAL atrophy, *GENES, *PHENOTYPES, *GENETIC code, *BRAIN diseases
Abstract

CHASERR encodes a human long nor}coding RNA (IncRNA) adjacent to CHDZ, decoding gene in which de novo loss-of-function variants cause developmental and epileptic encephalopathy. Here, we report our findings in three unrelated children with a syndromic, early-onset neurodevelopmental disorder, each of whOm had de novo deletion in the CHASERR locus. The children had severe encephalopathy, shared facial dysmorphisms, cortical atrophy, and cerebral hypomyelination - phenotype that is distinct from the phenotypes of patients with CHD2 haploinsuf ficiency. We found that the CHASERR deletion results in increased CHD2 protein abundance in patient-derived celllines and increased expression of the CHD2 transcript in cis. These findings indicate that CHD2 has bidirectional dosage sensitivity in human disease, and we recommend that other IncRNA-encoding genes be evaluated, particularly those upstream of genes associated with mendelian disorders. [ABSTRACT FROM AUTHOR]

Published
2024
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25. The epilepsy phenotypic spectrum associated with a recurrent CUX2 variant

Author

Chatron, N, Moller, RS, Champaigne, NL, Schneider, AL, Kuechler, A, Labalme, A, Simonet, T, Baggett, L, Bardel, C, Kamsteeg, E-J, Pfundt, R, Romano, C, Aronsson, J, Alberti, A, Vinci, M, Miranda, MJ, Lacroix, A, Marjanovic, D, des Portes, V, Edery, P, Wieczorek, D, Gardella, E, Scheffer, IE, Mefford, H, Sanlaville, D, Carvill, GL, Lesca, G, Chatron, N, Moller, RS, Champaigne, NL, Schneider, AL, Kuechler, A, Labalme, A, Simonet, T, Baggett, L, Bardel, C, Kamsteeg, E-J, Pfundt, R, Romano, C, Aronsson, J, Alberti, A, Vinci, M, Miranda, MJ, Lacroix, A, Marjanovic, D, des Portes, V, Edery, P, Wieczorek, D, Gardella, E, Scheffer, IE, Mefford, H, Sanlaville, D, Carvill, GL, and Lesca, G

Abstract

OBJECTIVE: Cut homeodomain transcription factor CUX2 plays an important role in dendrite branching, spine development, and synapse formation in layer II to III neurons of the cerebral cortex. We identify a recurrent de novo CUX2 p.Glu590Lys as a novel genetic cause for developmental and epileptic encephalopathy (DEE). METHODS: The de novo p.Glu590Lys variant was identified by whole-exome sequencing (n = 5) or targeted gene panel (n = 4). We performed electroclinical and imaging phenotyping on all patients. RESULTS: The cohort comprised 7 males and 2 females. Mean age at study was 13 years (0.5-21.0). Median age at seizure onset was 6 months (2 months to 9 years). Seizure types at onset were myoclonic, atypical absence with myoclonic components, and focal seizures. Epileptiform activity on electroencephalogram was seen in 8 cases: generalized polyspike-wave (6) or multifocal discharges (2). Seizures were drug resistant in 7 or controlled with valproate (2). Six patients had a DEE: myoclonic DEE (3), Lennox-Gastaut syndrome (2), and West syndrome (1). Two had a static encephalopathy and genetic generalized epilepsy, including absence epilepsy in 1. One infant had multifocal epilepsy. Eight had severe cognitive impairment, with autistic features in 6. The p.Glu590Lys variant affects a highly conserved glutamine residue in the CUT domain predicted to interfere with CUX2 binding to DNA targets during neuronal development. INTERPRETATION: Patients with CUX2 p.Glu590Lys display a distinctive phenotypic spectrum, which is predominantly generalized epilepsy, with infantile-onset myoclonic DEE at the severe end and generalized epilepsy with severe static developmental encephalopathy at the milder end of the spectrum. Ann Neurol 2018;83:926-934.

Published
2018

26. Identification of the functional states of human vitamin K epoxide reductase from molecular dynamics simulations

Author

Chatron, N., Chalmond, B., Trouve, A., Benoit, Etienne, Caruel, H., Lattard, Virginie, Tchertanov, L., Liphatech, Centre de Mathématiques et de Leurs Applications (CMLA), École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Rongeurs Sauvages, Risques Sanitaires et Gestion des Populations - UR 1233 (RS2GP), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), GENCI-IDRIS 2016-077291, Rongeurs Sauvages – Risques Sanitaires et Gestion des Populations, INRA, VetAgro Sup ( USC1233/RS2GP ), Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Centre de Mathématiques et de Leurs Applications ( CMLA ), and École normale supérieure - Cachan ( ENS Cachan ) -Centre National de la Recherche Scientifique ( CNRS )

Subjects
vitamine k, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], [ SDV.BBM.BC ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], protéine, Chimie analytique, topologie membranaire, réticulum endoplasmique, Analytical chemistry, [ SDV.BBM.BS ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM]
Abstract

International audience; In mammalians, the enzymatic activity of vitamin K epoxide reductase (VKORC1) requires a protein conformational reorganisation that includes several transient enzymatic states involving a dynamic electron transfer. Regarding the structurally non-characterised human enzyme (hVKORC1), this process remains poorly explained and the different redox states of the enzyme generated by its biochemical transformation are unknown. Here, we report a 3D model of the fully reduced hVKORC1 at the atomistic level. By exploring this model through molecular dynamics (MD) simulations, we established the most probable intermediate states of the enzyme which were used for generation of the putative functionally-related enzymatic states. Enzymatic functionality of each state was assigned by probing their recognition properties with respect to vitamin K in its quinone and hydroxyquinone forms. Two states were identified as contributing to the two-step vitamin K transformation. The state highly selective for native vitamin K was further validated through analyses of its free energy of binding with vitamin K agonists (VKAs) that showed a high correlation with the experimental inhibiting constants.

Published
2017
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28. Severe cognitive impairment and early-onset epilepsy in six patients with the de novo p.Glu590Lys variant of CUX2

Author

Chatron, N., primary, Møller, R.S., additional, Champaigne, N.L., additional, Kuechler, A., additional, Labalme, A., additional, Baggett, L., additional, Wieczorek, D., additional, Portes, V. des, additional, Edery, P., additional, Gardella, E., additional, Scheffer, I.E., additional, Mefford, H., additional, Sanlaville, D., additional, Carvill, G.L., additional, and Lesca, G., additional

Published
2017
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29. Three new cases of asparagine synthetase deficiency: Confirmation of a poor neurological outcome and a new molecular mechanism

Author

Faoucher, M., primary, Putoux, A., additional, Francannet, C., additional, Poulat, A.L., additional, Chatron, N., additional, Aquaviva, C., additional, Labalme, A., additional, Schluth-Bolard, C., additional, Till, M., additional, Saban, C., additional, Desportes, V., additional, Sanlaville, D., additional, Edery, P., additional, and Lesca, G., additional

Published
2017
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31. Next-generation sequencing allows a diagnostic yield of 23.7% in monogenic epilepsies

Author

Lesca, G., primary, Labalme, A., additional, Mignot, C., additional, Chatron, N., additional, Van de Velde Boermans, L., additional, des Portes, V., additional, Bogoin, J., additional, Ville, D., additional, de Belescize, J., additional, Nougues, M.C., additional, Doummar, D., additional, Afenjar, A., additional, Poulat, A.L., additional, Panagiotakaki, E., additional, Valence, S., additional, Arzimanoglou, A., additional, Heron, D., additional, Leguern, E., additional, Sanlaville, D., additional, and Nava, C., additional

Published
2017
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35. Performance of semiconductor sequencing platform for non-invasive prenatal genetic screening for fetal aneuploidy: results from a multicenter prospective cohort study in a clinical setting.

Author

El Khattabi, L. Allach, Brun, S., Gueguen, P., Chatron, N., Guichoux, E., Schutz, S., Nectoux, J., Sorlin, A., Quere, M., Boudjarane, J., Tsatsaris, V., Mandelbrot, L., Schluth‐Bolard, C., Dupont, J. M., Rooryck, C., Cormier, Alexandre, Ferec, Claude, Da Foncesca Pipoli, Juliana, Letourneur, Franck, and Bonnet, Céline

Abstract

Objective: To validate and evaluate the performance metrics of the high-throughput semiconductor sequencing platform, Ion Proton®, in non-invasive prenatal genetic screening (NIPS) for common fetal aneuploidies in a clinical setting.Methods: This prospective cohort study included 2505 pregnant women from eight academic genetics laboratories (695 high risk for trisomy 21 (risk ≥ 1/250) pregnancies in a validation study, and 1810 such pregnancies, without ultrasound anomalies, in a real-life NIPS clinical setting). Outcome was available for all cases in the validation cohort and for 521 in the clinical cohort. Cell-free DNA from plasma samples was sequenced using the Ion Proton sequencer, and sequencing data were analyzed using the open-access software, WISECONDOR. Performance metrics for detection of trisomies 21, 18 and 13 were calculated based on either fetal karyotype result or clinical data collected at birth. We also evaluated the failure rate and compared three methods of fetal fraction quantification (RASSF1A assay, and DEFRAG and SANEFALCON software).Results: Results from both cohorts were consistent and their gestational age was not significantly different so their data were combined to increase the sample size for analysis. Sensitivities and specificities, respectively, were as follows: for trisomy 21, 98.3% (95% CI, 93.5-99.7%) and 99.9% (95% CI, 99.4-100%); for trisomy 18, 96.7% (95% CI, 80.9-99.8%) and 100% (95% CI, 99.6-100%); and for trisomy 13, 94.1% (95% CI, 69.2-99.7%) and 100% (95% CI, 99.6-100%). Our failure rate was 1.2% initially and as low as 0.6% after retesting some of the failed samples. Fetal fraction estimation by the RASSF1A assay was consistent with DEFRAG results, and both were adequate for routine diagnosis.Conclusions: We describe one of the largest studies evaluating Ion Proton-based NIPS and the first clinical study reporting pregnancy outcome in a large series of patients. This platform is highly efficient in detecting the three most common trisomies. Our protocol is robust and can be implemented easily in any medical genetics laboratory. Copyright © 2018 ISUOG. Published by John Wiley & Sons Ltd. [ABSTRACT FROM AUTHOR]

Published
2019
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37. Molecular cytogenetic characterization of five F8 complex rearrangements: utility for haemophilia A genetic counselling.

Author

Jourdy, Y., Chatron, N., Fretigny, M., Carage, M. L., Chambost, H., Claeyssens-Donadel, S., Roussel-Robert, V., Negrier, C., Sanlaville, D., and Vinciguerra, C.

Subjects
*HEMOPHILIA, *CYTOGENETICS, *HEMOPHILIACS, *GENETIC counseling, *GENOMES, *GENETICS
Abstract

Background Genomic inversions are usually balanced, but unusual patterns have been described in haemophilia A ( HA) patients for intron 22 (Inv22) and intron 1 (Inv1) inversions leading to the hypothesis of more complex rearrangements involving deletions or duplications. Aim To characterize five abnormal patterns either in Southern blot and long-range PCR for Inv22 or in PCR for Inv1. Materials and methods All patients were studied using cytogenetic microarray analysis ( CMA). Results In all cases, CMA analysis found that each inversion was associated with complex Xq28 rearrangement. In three patients, CMA analysis showed large duplication ranging from 230 to 1302 kb and encompassing a various number of contiguous genes among which RAB39B. RAB39B duplication is a strong candidate gene for X-linked intellectual disability ( XLID). Surprisingly, none of the severe HA patients with RAB39B duplication reported in this study or in the literature exhibited XLID. We hypothesise that F8 complex rearrangement down regulated RAB39B expression. In the two remaining patients, CMA analysis found Xq28 large deletion (from 285 to 522 kb). Moyamoya syndrome was strongly suspected in one of them who carried BRCC3 deletion. Conclusion Because several F8 neighbouring genes are associated with other pathologies such as XLID and cardiovascular disease, all HA patients where complex Xq28 rearrangement was suspected should be referred to a geneticist for possible utility of a pangenomic study. Such investigation should be carefully considered in genetic counselling in female carriers to assess the risk of transmitting severe HA with a 'contiguous gene syndrome'. [ABSTRACT FROM AUTHOR]

Published
2017
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39. Phenotypic spectrum and transcriptomic profile associated with germline variants in TRAF7

Author

Robert A. Hegele, Maria Iascone, Kevin A. Shapiro, Nicolas Chatron, Marwan Shinawi, Joel Charrow, Jeffrey W. Innis, Luitgard Graul-Neumann, Joanna Goes Castro Meira, Anna Lehman, Dawn L. Earl, Victoria R. Sanders, Shannon Rego, David A. Sweetser, Clémantine Dimartino, Wilhelmina S. Kerstjens-Frederikse, Antonio Vitobello, Davor Lessel, Daniel Grinberg, Laurence Faivre, Ryan Peretz, Katherine M. Christensen, Emma Reesor, Erin Beaver, Elizabeth Wohler, Margot R.F. Reijnders, Deborah Barbouth, Anna Cereda, Kaja Kristine Selmer, Melissa A. Walker, Barbro Stadheim, Alessandro Serretti, Helen Kingston, Jill Clayton-Smith, Raymond Lewandowski, Bernarda Lozić, Robert Stratton, Amelia Kirby, Anne H. O’Donnell-Luria, Sara Gabbiadini, Susanna Balcells, Myriam Oufadem, Christel Thauvin, Maha Aly, Wendy K. Chung, Susan M. White, Lauren C. Briere, Thomas Smol, Stanislas Lyonnet, Roberto Colombo, Catherine E. Keegan, Marie T. McDonald, Melanie Parisot, Tiong Yang Tan, Brian Wong, Christopher T. Gordon, Magnus Dehli Vigeland, Frances A. High, Emily Bryant, Audrey Labalme, Nara Sobreira, Arnold Munnich, Jeanne Amiel, Dayna Morel Swols, Raquel Rabionet, Laura Castilla-Vallmanya, Jennifer Heeley, Gunnar Houge, Michael J. Gambello, Bernardo Blanco-Sánchez, Lynn Pais, Olena M. Vaske, Roser Urreizti, Alison Wray, Veronique Pingault, Damien Sanlaville, John Christodoulou, John Millichap, Valérie Cormier-Daire, Parul Jayakar, Helen Cox, Frédéric Tran Mau-Them, Belinda Chong, Victoria Mok Siu, Anne Slavotinek, Antonie J. van Essen, Ingvild Aukrust, Lorne A. Clarke, Rachel Gannaway, Anne Dieux-Coeslier, Patrick Nitschké, Tony Yao, Simon Sadedin, Danielle Karlowicz, Christelle Rougeot, Christine Bole-Feysot, Sandra Yang, Megan T. Cho, Gaetan Lesca, Christiane Zweier, Castilla-Vallmanya L., Selmer K.K., Dimartino C., Rabionet R., Blanco-Sanchez B., Yang S., Reijnders M.R.F., van Essen A.J., Oufadem M., Vigeland M.D., Stadheim B., Houge G., Cox H., Kingston H., Clayton-Smith J., Innis J.W., Iascone M., Cereda A., Gabbiadini S., Chung W.K., Sanders V., Charrow J., Bryant E., Millichap J., Vitobello A., Thauvin C., Mau-Them F.T., Faivre L., Lesca G., Labalme A., Rougeot C., Chatron N., Sanlaville D., Christensen K.M., Kirby A., Lewandowski R., Gannaway R., Aly M., Lehman A., Clarke L., Graul-Neumann L., Zweier C., Lessel D., Lozic B., Aukrust I., Peretz R., Stratton R., Smol T., Dieux-Coeslier A., Meira J., Wohler E., Sobreira N., Beaver E.M., Heeley J., Briere L.C., High F.A., Sweetser D.A., Walker M.A., Keegan C.E., Jayakar P., Shinawi M., Kerstjens-Frederikse W.S., Earl D.L., Siu V.M., Reesor E., Yao T., Hegele R.A., Vaske O.M., Rego S., Shapiro K.A., Wong B., Gambello M.J., McDonald M., Karlowicz D., Colombo R., Serretti A., Pais L., O'Donnell-Luria A., Wray A., Sadedin S., Chong B., Tan T.Y., Christodoulou J., White S.M., Slavotinek A., Barbouth D., Morel Swols D., Parisot M., Bole-Feysot C., Nitschke P., Pingault V., Munnich A., Cho M.T., Cormier-Daire V., Balcells S., Lyonnet S., Grinberg D., Amiel J., Urreizti R., Gordon C.T., MUMC+: DA KG Polikliniek (9), and RS: FHML non-thematic output

Subjects
0301 basic medicine, NF-KAPPA-B, PROTEIN, 030105 genetics & heredity, medicine.disease_cause, Germline, Transcriptome, ACTIVATION, POLYUBIQUITINATION, Missense mutation, Exome, Genetics (clinical), Genetics, Sanger sequencing, Mutation, leads, Necrosi, craniofacial development, Phenotype, Tumor Necrosis Factor Receptor-Associated Peptides and Proteins, intellectual disability, patent ductus arteriosu, symbols, Mutation, Missense, Biology, traf7, Article, akt1, target, 03 medical and health sciences, symbols.namesake, Necrosis, patent ductus arteriosus, medicine, Humans, blepharophimosi, Tumors, MUTATIONS, Fibroblasts, medicine.disease, Blepharophimosis, TRAF7, blepharophimosis, GENOMIC ANALYSIS, Germ Cells, 030104 developmental biology, MENINGIOMAS
Abstract

PURPOSE: Somatic variants in tumor necrosis factor receptor-associated factor 7 (TRAF7) cause meningioma, while germline variants have recently been identified in seven patients with developmental delay and cardiac, facial, and digital anomalies. We aimed to define the clinical and mutational spectrum associated with TRAF7 germline variants in a large series of patients, and to determine the molecular effects of the variants through transcriptomic analysis of patient fibroblasts.METHODS: We performed exome, targeted capture, and Sanger sequencing of patients with undiagnosed developmental disorders, in multiple independent diagnostic or research centers. Phenotypic and mutational comparisons were facilitated through data exchange platforms. Whole-transcriptome sequencing was performed on RNA from patient- and control-derived fibroblasts.RESULTS: We identified heterozygous missense variants in TRAF7 as the cause of a developmental delay-malformation syndrome in 45 patients. Major features include a recognizable facial gestalt (characterized in particular by blepharophimosis), short neck, pectus carinatum, digital deviations, and patent ductus arteriosus. Almost all variants occur in the WD40 repeats and most are recurrent. Several differentially expressed genes were identified in patient fibroblasts.CONCLUSION: We provide the first large-scale analysis of the clinical and mutational spectrum associated with the TRAF7 developmental syndrome, and we shed light on its molecular etiology through transcriptome studies.

Published
2020

40. Variants in the degron of AFF3 are associated with intellectual disability, mesomelic dysplasia, horseshoe kidney, and epileptic encephalopathy

Author

Rhonda E. Schnur, Fabio Sirchia, Olga Levchenko, Caroline Nava, Jane Juusola, Sarah Verheyen, Marketa Vlckova, Lindsay Rhodes, Gregory M. Cooper, Darina Prchalova, Thomas Courtin, Øystein L. Holla, David Kronn, Akemi J. Tanaka, E. Martina Bebin, Tara Funari, Miroslava Hancarova, Ennio Del Giudice, Nicolas Guex, Astrid Eisenkölbl, Dawn L. Earl, Toshiki Takenouchi, Ursula Gruber-Sedlmayr, Sedlácek Z, Sofia Douzgou, Heidelis A. Seebacher, Gerarda Cappuccio, Jasmin Blatterer, Anna Mikhaleva, Dian Donnai, Wendy K. Chung, Else Merckoll, Natasha J Brown, Elizabeth A. Sellars, Stefan Mundlos, Susan M. Hiatt, Giuliana Giannuzzi, Sinje Geuer, Giuseppina Vitiello, Séverine Lorrain, Alexandre Reymond, David J. Amor, Nicolas Chatron, Julien Delafontaine, Martine Doco, Kristian Tveten, Cecilie F. Rustad, Sylvain Pradervand, Delphine Héron, Alfredo Brusco, Elena L. Dadali, Nicola Brunetti-Pierri, Boris Keren, Yuri A. Zarate, Crystle Lee, Joel Charrow, Binnaz Yalcin, Heidi Taska-Tench, Elin Tønne, Tomoko Uehara, Alexander Lavrov, Jennifer Norman, Norine Voisin, Anna C.E. Hurst, Victoria R. Sanders, Ganka Douglas, Diana Johnson, Kenjiro Kosaki, Université de Lausanne = University of Lausanne (UNIL), Cooper Medical School of Rowan University [Camden] (CMSRU), Manchester University NHS Foundation Trust (MFT), University of Manchester [Manchester], HudsonAlpha Institute for Biotechnology [Huntsville, AL], Oslo University Hospital [Oslo], Victorian Clinical Genetics Services [Melbourne, VIC, Australia] (VCGS), Murdoch Children's Research Institute (MCRI), University of Melbourne, Seattle Children’s Hospital, Groupe de Recherche Clinique : Déficience Intellectuelle et Autisme [ CHU Pitié-Salpêtrière AP-HP] (GRC : DIA), Université Pierre et Marie Curie - Paris 6 (UPMC)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Research Centre for Medical Genetics [Moscow, Russia] (RCMG), Max Planck Institute for Molecular Genetics (MPIMG), Max-Planck-Gesellschaft, Medical University of Graz, Sheffield Children's NHS Foundation Trust, University of Arkansas at Little Rock, Charles University [Prague] (CU), University Hospital Motol [Prague], University of Alabama at Birmingham [ Birmingham] (UAB), Università degli studi di Torino = University of Turin (UNITO), Azienda Ospedalerio - Universitaria Città della Salute e della Scienza di Torino = University Hospital Città della Salute e della Scienza di Torino, University of Naples Federico II = Università degli studi di Napoli Federico II, Ann & Robert H. Lurie Children's Hospital of Chicago, Swiss Institute of Bioinformatics [Lausanne] (SIB), Hémostase et Remodelage Vasculaire Post-Ischémie (HERVI - EA 3801), Université de Reims Champagne-Ardenne (URCA), GeneDx [Gaithersburg, MD, USA], Johannes Kepler University Linz [Linz] (JKU), Telemark Hospital Trust [Skien, Norway], New York Medical College (NYMC), Integris Pediatric Neurology [Oklahoma City, OK, USA] (IPN), Institute for Maternal and Child Health - IRCCS 'Burlo Garofolo' [Trieste], Keio University School of Medicine [Tokyo, Japan], Columbia University [New York], Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Manchester Centre for Genomic Medicine [Manchester, UK] (MCGM), St Mary's Hospital Manchester-Manchester Academic Health Science Centre (MAHSC), University of Manchester [Manchester]-University of Manchester [Manchester]-Manchester University NHS Foundation Trust (MFT)-Faculty of Biology, Medicine and Health [Manchester, UK], Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Dupuis, Christine, Voisin, N., Schnur, R. E., Douzgou, S., Hiatt, S. M., Rustad, C. F., Brown, N. J., Earl, D. L., Keren, B., Levchenko, O., Geuer, S., Verheyen, S., Johnson, D., Zarate, Y. A., Hancarova, M., Amor, D. J., Bebin, E. M., Blatterer, J., Brusco, A., Cappuccio, G., Charrow, J., Chatron, N., Cooper, G. M., Courtin, T., Dadali, E., Delafontaine, J., Del Giudice, E., Doco, M., Douglas, G., Eisenkolbl, A., Funari, T., Giannuzzi, G., Gruber-Sedlmayr, U., Guex, N., Heron, D., Holla, O. L., Hurst, A. C. E., Juusola, J., Kronn, D., Lavrov, A., Lee, C., Lorrain, S., Merckoll, E., Mikhaleva, A., Norman, J., Pradervand, S., Prchalova, D., Rhodes, L., Sanders, V. R., Sedlacek, Z., Seebacher, H. A., Sellars, E. A., Sirchia, F., Takenouchi, T., Tanaka, A. J., Taska-Tench, H., Tonne, E., Tveten, K., Vitiello, G., Vlckova, M., Uehara, T., Nava, C., Yalcin, B., Kosaki, K., Donnai, D., Mundlos, S., Brunetti Pierri, N., Chung, W. K., and Reymond, A.

Subjects
Male, Models, Molecular, Hypertrichosis, [SDV]Life Sciences [q-bio], Mesomelic Dysplasia, Transcriptome, Mice, Gene Frequency, Missense mutation, Child, Zebrafish, Genetics (clinical), Genetics, Brain Diseases, 0303 health sciences, biology, Protein Stability, 030305 genetics & heredity, AFF3, AFF4, horseshoe kidney, intellectual disability, mesomelic dysplasia, Nuclear Proteins, Syndrome, Phenotype, Ubiquitin ligase, [SDV] Life Sciences [q-bio], Child, Preschool, Female, Transcriptional Elongation Factors, Adolescent, Mutation, Missense, Osteochondrodysplasias, Article, Evolution, Molecular, Young Adult, 03 medical and health sciences, medicine, Animals, Humans, Amino Acid Sequence, Fused Kidney, 030304 developmental biology, Epilepsy, Infant, Horseshoe kidney, biology.organism_classification, medicine.disease, biology.protein
Abstract

International audience; The ALF transcription factor paralogs, AFF1, AFF2, AFF3, and AFF4, are components of the transcriptional super elongation complex that regulates expression of genes involved in neurogenesis and development. We describe an autosomal dominant disorder associated with de novo missense variants in the degron of AFF3, a nine amino acid sequence important for its binding to ubiquitin ligase, or with de novo deletions of this region. The sixteen affected individuals we identified, along with two previously reported individuals, present with a recognizable pattern of anomalies, which we named KINSSHIP syndrome (KI for horseshoe kidney, NS for Nievergelt/Savarirayan type of mesomelic dysplasia, S for seizures, H for hypertrichosis, I for intellectual disability, and P for pulmonary involvement), partially overlapping the AFF4-associated CHOPS syndrome. Whereas homozygous Aff3 knockout mice display skeletal anomalies, kidney defects, brain malformations, and neurological anomalies, knockin animals modeling one of the microdeletions and the most common of the missense variants identified in affected individuals presented with lower mesomelic limb deformities like KINSSHIP-affected individuals and early lethality, respectively. Overexpression of AFF3 in zebrafish resulted in body axis anomalies, providing some support for the pathological effect of increased amount of AFF3. The only partial phenotypic overlap of AFF3-and AFF4-associated syndromes and the previously published transcriptome analyses of ALF transcription factors suggest that these factors are not redundant and each contributes uniquely to proper development.

Published
2021
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41. Novel Digital Anomalies, Hippocampal Atrophy, and Mutations Expand the Genotypic and Phenotypic Spectra of CNKSR2 in the Houge Type of X-Linked Syndromic Intellectual Development Disorder (MRXSHG).

Author

Ghasemi MR, Fateh ST, Ben-Mahmoud A, Gupta V, Stühn LG, Lesca G, Chatron N, Platzer K, Edery P, Sadeghi H, Isidor B, Cogné B, Schulz HL, Krauspe-Stübecke I, Periyasamy R, Nampoothiri S, Mirfakhraie R, Alijanpour S, Syrbe S, Pfeifer U, Spranger S, Grundmann-Hauser K, Haack TB, Papadopoulou MT, da Silva Gonçalves T, Panagiotakaki E, Arzimanoglou A, Tonekaboni SH, Rossi M, Korenke GC, Lacassie Y, Jang MH, Layman LC, Miryounesi M, and Kim HG

Abstract

The Houge type of X-linked syndromic intellectual developmental disorder (MRXSHG) encompasses a spectrum of neurodevelopmental disorders characterized by intellectual disability (ID), language/speech delay, attention issues, and epilepsy. These conditions arise from hemizygous or heterozygous deletions, along with point mutations, affecting CNKSR2, a gene located at Xp22.12. CNKSR2, also known as CNK2 or MAGUIN, functions as a synaptic scaffolding molecule within the neuronal postsynaptic density (PSD) of the central nervous system. It acts as a link connecting postsynaptic structural proteins, such as PSD95 and S-SCAM, by employing multiple functional domains crucial for synaptic signaling and protein-protein interactions. Predominantly expressed in dendrites, CNKSR2 is vital for dendritic spine morphogenesis in hippocampal neurons. Its loss-of-function variants result in reduced PSD size and impaired hippocampal development, affecting processes including neuronal proliferation, migration, and synaptogenesis. We present 15 patients including three from the MENA (Middle East and North Africa), a region with no documented mutations in CNKSR2. Each individual displays unique clinical presentations that encompass developmental delay, ID, language/speech delay, epilepsy, and autism. Genetic analyses revealed 14 distinct variants in CNKSR2, comprising five nonsense, three frameshift, two splice, and four missense variants, of which 13 are novel. The ACMG guidelines unanimously interpreted these 14 variants in 15 individuals as pathogenic, highlighting the detrimental impact of these CNKSR2 genetic alterations and confirming the molecular diagnosis of MRXSHG. Importantly, variants Ser767Phe and Ala827Pro may lead to proteasomal degradation or reduced PSD size, contributing to the neurodevelopmental phenotype. Furthermore, these two amino acids, along with another two affected by four missense variants, exhibit complete conservation in nine vertebrate species, illuminating their crucial role in the gene's functionality. Our study revealed unique new digital and brain phenotype, including pointed fingertips (fetal pads of fingertips), syndactyly, tapering fingers, and hippocampal atrophy. These novel clinical features in MRXSHG, combined with 13 novel variants, expand the phenotypic and genotypic spectra of MRXSHG associated with CNKSR2 mutations., (© 2024 The Author(s). American Journal of Medical Genetics Part A published by Wiley Periodicals LLC.)

Published
2024
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42. Clinical and genetic characterization of a progressive RBL2-associated neurodevelopmental disorder.

Author

Aughey GN, Cali E, Maroofian R, Zaki MS, Pagnamenta AT, Ali Z, Abdulllah U, Rahman F, Menzies L, Shafique A, Suri M, Roze E, Aguennouz M, Ghizlane Z, Saadi SM, Fatima A, Cheema HA, Anjum MN, Morel G, Robin S, McFarland R, Altunoglu U, Kraus V, Shoukier M, Murphy D, Flemming K, Yttervik H, Rhouda H, Lesca G, Chatron N, Rossi M, Murtaza BN, Ur Rehman M, Lord J, Giacopuzzi E, Hayat A, Siraj M, Badv RS, Seo GH, Beetz C, Kayserili H, Krioulie Y, Chung WK, Naz S, Maqbool S, Chandler K, Kershaw C, Wright T, Banka S, Gleeson JG, Taylor JC, Efthymiou S, Baig SM, Severino M, Jepson JEC, and Houlden H

Abstract

Retinoblastoma (RB) proteins are highly conserved transcriptional regulators that play important roles during development by regulating cell-cycle gene expression. RBL2 dysfunction has been linked to a severe neurodevelopmental disorder. However, to date, clinical features have only been described in six individuals carrying five biallelic predicted loss of function (pLOF) variants. To define the phenotypic effects of RBL2 mutations in detail, we identified and clinically characterized a cohort of 35 patients from 20 families carrying pLOF variants in RBL2, including fifteen new variants that substantially broaden the molecular spectrum. The clinical presentation of affected individuals is characterized by a range of neurological and developmental abnormalities. Global developmental delay and intellectual disability were uniformly observed, ranging from moderate to profound and involving lack of acquisition of key motor and speech milestones in most patients. Disrupted sleep was also evident in some patients. Frequent features included postnatal microcephaly, infantile hypotonia, aggressive behaviour, stereotypic movements, seizures, and non-specific dysmorphic features. Neuroimaging features included cerebral atrophy, white matter volume loss, corpus callosum hypoplasia and cerebellar atrophy. In parallel, we used the fruit fly, Drosophila melanogaster, to investigate how disruption of the conserved RBL2 orthologue Rbf impacts nervous system function and development. We found that Drosophila Rbf LOF mutants recapitulate several features of patients harbouring RBL2 variants, including developmental delay, alterations in head and brain morphology, locomotor defects, and perturbed sleep. Surprisingly, in addition to its known role in controlling tissue growth during development, we found that continued Rbf expression is also required in fully differentiated post-mitotic neurons for normal locomotion in Drosophila, and that adult-stage neuronal re-expression of Rbf is sufficient to rescue Rbf mutant locomotor defects. Taken together, our study provides a clinical and experimental basis to understand genotype-phenotype correlations in an RBL2-linked neurodevelopmental disorder, and suggests that restoring RBL2 expression through gene therapy approaches may ameliorate some symptoms caused by RBL2 pLOF., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Guarantors of Brain.)

Published
2024
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43. RORA-neurodevelopmental disorder: a unique triad of developmental disability, cerebellar anomalies, and myoclonic seizures.

Author

Talarico M, de Bellescize J, De Wachter M, Le Guillou X, Le Meur G, Egloff M, Isidor B, Cogné B, Beysen D, Rollier P, Fradin M, Pasquier L, Guella I, Hickey SE, Benke PJ, Shillington A, Kumps C, Vanakker O, Gerkes EH, Lakhani S, Romanova I, Kanivets I, Brugger M, Vill K, Caylor RC, Skinner C, Tinker RJ, Stödberg T, Nümann A, Haack TB, Deininger N, Hengel H, Jury J, Conrad S, Mercier S, Yoon G, Tsuboyama M, Barcia G, Gitiaux C, Rio M, Bevot A, Redon S, Uguen K, Wonneberger A, Schulz A, Timmann D, Karlowicz DH, Chatron N, Carnevale A, Mahida S, Õunap K, Kury S, Cabet S, and Lesca G

Abstract

Purpose: RORA encodes the RAR-related orphan receptor-α (RORα), playing a pivotal role in cerebellar maturation and function. Here, we report the largest series of individuals with RORA-related-neurodevelopmental disorder (RORA-NDD)., Methods: Forty individuals (30 unrelated; 10 siblings from 4 families) carrying RORA pathogenic/likely pathogenic variants were collected through an international collaboration., Results: The 33 variants (29 de novo, 4 inherited, one shared), identified by genome/exome sequencing (n=21), chromosomal-microarray-analysis (n=7) or gene panels (n=4), included frameshift (n=18/33), missense (n=9/33) and stop-codon (n=6/33). Developmental disability (n=32/37), intellectual disability (n=22/32), and cerebellar signs (n=25/34) were the most striking clinical features. Cerebellar symptoms were divided into early-onset, late-onset and progressive subgroups. Cerebellar hypoplasia, atrophy, or both (n=16/25) were more frequent in individuals with missense variants in the DNA-binding-domain (DBD). Epilepsy (n=18/38), with prominent myoclonic seizure types (n=11/18), was classified in: i) genetic generalized epilepsy (n=10/18) with a syndromic diagnosis identifiable for six: epilepsy with eyelid myoclonia (n=5/6), epilepsy with myoclonic absence (n=1/6); ii) developmental and epileptic encephalopathy (n=5/18); and iii) unclassified (n=3/18). A participant with rapid deterioration of visual acuity and cone/rod dystrophy was reported., Conclusion: Missense variants in DBD correlate to a more severe cerebellar phenotype. The RORA-NDD triad comprises developmental disability, cerebellar features and a spectrum of myoclonic epilepsy., (Copyright © 2024. Published by Elsevier Inc.)

Published
2024
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44. Mobile Element Insertion in the APOB Exon 3 Coding Sequence: A New Challenge in Hypobetalipoproteinemia Diagnosis.

Author

Surles L, Janin A, Molitor C, Chatron N, Moret M, Nony S, Dumont S, Marmontel O, Simonet T, Sassolas A, Moulin P, and Di Filippo M

Abstract

Mobile elements (ME) can transpose by copy-and-paste mechanisms. A heterozygous insertion in APOB exon 3 coding sequence was suspected in a patient with hypobetalipoproteinemia (HBL), by gel electrophoresis of the PCR products. An insertion of a 85 bp fragment flanked by a polyA stretch and a target replication site duplication was identified as a ME insertion (MEI) from the AluYa5 subfamily, NM_000384.3(APOB):c.135_136ins(160). Then, the DNA was reanalyzed using our NGS custom panel. Routine analysis did not reveal any causative variant, but manual inspection of the alignments and MELT enabled us to detect this MEI from NGS data. A functional study revealed that this MEI introduces a stop codon p.(Phe46Alafs*2) and additionally leads to p.(Lys41Serfs*2) due to an exon skipping. This is the first report of a MEI into APOB, as a cause of HBL. Furthermore, our study highlights the value of including MEI-callers in routine pipelines to improve primary dyslipidemia diagnosis., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

Published
2024
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45. Exposure and resistance to anticoagulant rodenticides in invasive and endemic Chadian urban rodent species to develop a rational management strategy.

Author

Mahamat AB, Groud K, Djibrine SI, Soro SD, Fourel I, Rached A, Chatron N, Benoit E, and Lattard V

Subjects
Animals, Chad, Introduced Species, Murinae genetics, Cities, Rodentia genetics, Rodenticides pharmacology, Rodent Control, Anticoagulants, Drug Resistance genetics, Vitamin K Epoxide Reductases genetics
Abstract

Rodent management involves the use of anticoagulant rodenticides (ARs). This use has resulted in the selection of numerous resistance alleles in the Vkorc1 gene, encoding the target enzyme of ARs. In Africa, although rodents are a major problem as a consequence of their transport and transmission of zoonotic pathogens, and damage to crops, the use of ARs and the spread of resistance alleles are poorly documented. We attempted to address both issues in Chad which is one of the largest countries in Africa. Owing to its location at the crossroads of central and northern Africa, Chad is representative of many African countries., Methods: Using a sampling of nearly 300 rodents composed of invasive and endemic rodents collected in six of Chad's largest cities, exposure to ARs was analyzed by their quantification in the liver; the spread of AR resistance alleles was analyzed by Vkorc1 sequencing., Results: We demonstrate the use of both ARs generations in Chadian cities and report the total sequencing of the Vkorc1 for 44 Mastomys natalensis with detection of two different haplotypes, the sequencing of the Vkorc1 for two other endemic rodent species, M. kollmannspergeri and Arvicanthis niloticus, and finally the detection of three new missense mutations - V29E, V69E and D127V - in R. rattus, potentially associated with resistance to ARs., Discussion: These results should argue for the implementation of a reasoned management of rodent populations in Africa to avoid the spread of ARs resistance alleles. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry., (© 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.)

Published
2024
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46. Familial severe skeletal Class II malocclusion with gingival hyperplasia caused by a complex structural rearrangement at the KCNJ2-KCNJ16 locus.

Author

Maroofian R, Pagnamenta AT, Navabazam A, Schwessinger R, Roberts HE, Lopopolo M, Dehghani M, Vahidi Mehrjardi MY, Haerian A, Soltanianzadeh M, Noori Kooshki MH, Knight SJL, Miller KA, McGowan SJ, Chatron N, Timberlake AT, Melo US, Mundlos S, Buck D, Twigg SRF, Taylor JC, Wilkie AOM, and Calpena E

Subjects
Humans, Female, Male, Phenotype, Genetic Loci, Polymorphism, Single Nucleotide, SOX9 Transcription Factor genetics, Malocclusion, Angle Class II genetics, Pedigree, Gingival Hyperplasia genetics, Gingival Hyperplasia pathology, Potassium Channels, Inwardly Rectifying genetics
Abstract

The aim of this work was to identify the underlying genetic cause in a four-generation family segregating an unusual phenotype comprising a severe form of skeletal Class II malocclusion with gingival hyperplasia. SNP array identified a copy number gain on chromosome 1 (chr1); however, this chromosomal region did not segregate correctly in the extended family. Exome sequencing also failed to identify a candidate causative variant but highlighted co-segregating genetic markers on chr17 and chr19. Short- and long-read genome sequencing allowed us to pinpoint and characterize at nucleotide-level resolution a chromothripsis-like complex rearrangement (CR) inserted into the chr17 co-segregating region at the KCNJ2-SOX9 locus. The CR involved the gain of five different regions from chr1 that are shuffled, chained, and inserted as a single block (∼828 kb) at chr17q24.3. The inserted sequences contain craniofacial enhancers that are predicted to interact with KCNJ2/KCNJ16 through neo-topologically associating domain (TAD) formation to induce ectopic activation. Our findings suggest that the CR inserted at chr17q24.3 is the cause of the severe skeletal Class II malocclusion with gingival hyperplasia in this family and expands the panoply of phenotypes linked to variation at the KCNJ2-SOX9 locus. In addition, we highlight a previously overlooked potential role for misregulation of the KCNJ2/KCNJ16 genes in the pathomechanism of gingival hyperplasia associated with deletions and other rearrangements of the 17q24.2-q24.3 region (MIM 135400)., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Published
2024
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48. Germline mutations in a G protein identify signaling cross-talk in T cells.

Author

Ham H, Jing H, Lamborn IT, Kober MM, Koval A, Berchiche YA, Anderson DE, Druey KM, Mandl JN, Isidor B, Ferreira CR, Freeman AF, Ganesan S, Karsak M, Mustillo PJ, Teo J, Zolkipli-Cunningham Z, Chatron N, Lecoquierre F, Oler AJ, Schmid JP, Kuhns DB, Xu X, Hauck F, Al-Herz W, Wagner M, Terhal PA, Muurinen M, Barlogis V, Cruz P, Danielson J, Stewart H, Loid P, Rading S, Keren B, Pfundt R, Zarember KA, Vill K, Potocki L, Olivier KN, Lesca G, Faivre L, Wong M, Puel A, Chou J, Tusseau M, Moutsopoulos NM, Matthews HF, Simons C, Taft RJ, Soldatos A, Masle-Farquhar E, Pittaluga S, Brink R, Fink DL, Kong HH, Kabat J, Kim WS, Bierhals T, Meguro K, Hsu AP, Gu J, Stoddard J, Banos-Pinero B, Slack M, Trivellin G, Mazel B, Soomann M, Li S, Watts VJ, Stratakis CA, Rodriguez-Quevedo MF, Bruel AL, Lipsanen-Nyman M, Saultier P, Jain R, Lehalle D, Torres D, Sullivan KE, Barbarot S, Neu A, Duffourd Y, Similuk M, McWalter K, Blanc P, Bézieau S, Jin T, Geha RS, Casanova JL, Makitie OM, Kubisch C, Edery P, Christodoulou J, Germain RN, Goodnow CC, Sakmar TP, Billadeau DD, Küry S, Katanaev VL, Zhang Y, Lenardo MJ, and Su HC

Subjects
Humans, Cell Movement genetics, Cell Proliferation, Immunity genetics, MAP Kinase Signaling System, Phosphatidylinositol 3-Kinases metabolism, Phosphatidylinositol 3-Kinases genetics, Proto-Oncogene Proteins c-akt metabolism, ras Proteins metabolism, ras Proteins genetics, Signal Transduction, Pedigree, Germ-Line Mutation, GTP-Binding Protein alpha Subunit, Gi2 genetics, ras GTPase-Activating Proteins genetics, Receptors, Antigen, T-Cell metabolism, T-Lymphocytes immunology, T-Lymphocytes metabolism
Abstract

Humans with monogenic inborn errors responsible for extreme disease phenotypes can reveal essential physiological pathways. We investigated germline mutations in GNAI2 , which encodes G αi2 , a key component in heterotrimeric G protein signal transduction usually thought to regulate adenylyl cyclase-mediated cyclic adenosine monophosphate (cAMP) production. Patients with activating G αi2 mutations had clinical presentations that included impaired immunity. Mutant G αi2 impaired cell migration and augmented responses to T cell receptor (TCR) stimulation. We found that mutant G αi2 influenced TCR signaling by sequestering the guanosine triphosphatase (GTPase)-activating protein RASA2, thereby promoting RAS activation and increasing downstream extracellular signal-regulated kinase (ERK)/mitogen-activated protein kinase (MAPK) and phosphatidylinositol 3-kinase (PI3K)-AKT S6 signaling to drive cellular growth and proliferation.

Published
2024
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49. Clinical and genetic delineation of autosomal recessive and dominant ACTL6B-related developmental brain disorders.

Author

Cali E, Quirin T, Rocca C, Efthymiou S, Riva A, Marafi D, Zaki MS, Suri M, Dominguez R, Elbendary HM, Alavi S, Abdel-Hamid MS, Morsy H, Mau-Them FT, Nizon M, Tesner P, Ryba L, Zafar F, Rana N, Saadi NW, Firoozfar Z, Gencpinar P, Unay B, Ustun C, Bruel AL, Coubes C, Stefanich J, Sezer O, Agolini E, Novelli A, Vasco G, Lettori D, Milh M, Villard L, Zeidler S, Opperman H, Strehlow V, Issa MY, El Khassab H, Chand P, Ibrahim S, Nejad-Rashidi A, Miryounesi M, Larki P, Morrison J, Cristian I, Thiffault I, Bertsch NL, Noh GJ, Pappas J, Moran E, Marinakis NM, Traeger-Synodinos J, Hosseini S, Abbaszadegan MR, Caumes R, Vissers LELM, Neshatdoust M, Montazer MZ, El Fahime E, Canavati C, Kamal L, Kanaan M, Askander O, Voinova V, Levchenko O, Haider S, Halbach SS, Maia ER, Mansoor S, Vivek J, Tawde S, Santhosh R Challa V, Gowda VK, Srinivasan VM, Victor LA, Pinero-Banos B, Hague J, Ei-Awady HA, Maria de Miranda Henriques-Souza A, Cheema HA, Anjum MN, Idkaidak S, Alqarajeh F, Atawneh O, Mor-Shaked H, Harel T, Zifarelli G, Bauer P, Kok F, Kitajima JP, Monteiro F, Josahkian J, Lesca G, Chatron N, Ville D, Murphy D, Neul JL, Mullegama SV, Begtrup A, Herman I, Mitani T, Posey JE, Tay CG, Javed I, Carr L, Kanani F, Beecroft F, Hane L, Abdelkreem E, Macek M, Bispo L, Elmaksoud MA, Hashemi-Gorji F, Pehlivan D, Amor DJ, Jamra RA, Chung WK, Ghayoor EK, Campeau P, Alkuraya FS, Pagnamenta AT, Gleeson J, Lupski JR, Striano P, Moreno-De-Luca A, Lafontaine DLJ, Houlden H, and Maroofian R

Abstract

Purpose: This study aims to comprehensively delineate the phenotypic spectrum of ACTL6B-related disorders, previously associated with both autosomal recessive and autosomal dominant neurodevelopmental disorders. Molecularly, the role of the nucleolar protein ACTL6B in contributing to the disease has remained unclear., Methods: We identified 105 affected individuals, including 39 previously reported cases, and systematically analysed detailed clinical and genetic data for all individuals. Additionally, we conducted knockdown experiments in neuronal cells to investigate the role of ACTL6B in ribosome biogenesis., Results: Biallelic variants in ACTL6B are associated with severe-to-profound global developmental delay/intellectual disability (GDD/ID), infantile intractable seizures, absent speech, autistic features, dystonia, and increased lethality. De novo monoallelic variants result in moderate-to-severe GDD/ID, absent speech, and autistic features, while seizures and dystonia were less frequently observed. Dysmorphic facial features and brain abnormalities, including hypoplastic corpus callosum, parenchymal volume loss/atrophy, are common findings in both groups. We reveal that in the nucleolus, ACTL6B plays a crucial role in ribosome biogenesis, in particular in pre-rRNA processing., Conclusion: This study provides a comprehensive characterization of the clinical spectrum of both autosomal recessive and dominant forms of ACTL6B-associated disorders. It offers a comparative analysis of their respective phenotypes provides a plausible molecular explanation and suggests their inclusion within the expanding category of 'ribosomopathies'., (Copyright © 2024. Published by Elsevier Inc.)

Published
2024
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50. Possible incomplete penetrance of Xq28 int22h-1/int22h-2 duplication.

Author

Billes A, Pujalte M, Jedraszak G, Amsallem D, Boudry-Labis E, Boute O, Bouquillon S, Brischoux-Boucher E, Callier P, Coutton C, Denizet AA, Dieterich K, Kuentz P, Lespinasse J, Mazel B, Morin G, Amram F, Pennamen P, Rio M, Piard J, Putoux A, Rama M, Roze-Guillaumey V, Schluth-Bolard C, Till M, Trouvé C, Vieville G, Rooryck C, Sanlaville D, and Chatron N

Subjects
Humans, Male, Female, Child, Adult, Adolescent, Child, Preschool, Phenotype, Chromosome Duplication genetics, Gene Duplication, Pedigree, Young Adult, Penetrance, Chromosomes, Human, X genetics, Intellectual Disability genetics
Abstract

Xq28 int22h-1/int22h-2 duplication is the result of non-allelic homologous recombination between int22h-1/int22h-2 repeats separated by 0.5 Mb. It is responsible for a syndromic form of intellectual disability (ID), with recurrent infections and atopic diseases. Minor defects, nonspecific facial dysmorphic features, and overweight have also been described. Half of female carriers have been reported with ID, whereas all reported evaluated born males present mild to moderate ID, suggesting complete penetrance. We collected data on 15 families from eight university hospitals. Among them, 40 patients, 21 females (one fetus), and 19 males (two fetuses), were carriers of typical or atypical Xq28 int22h-1/int22h-2 duplication. Twenty-one individuals were considered asymptomatic (16 females and 5 males), without significantly higher rate of recurrent infections, atopia, overweight, or facial dysmorphism. Approximately 67% live-born males and 23% live-born female carriers of the typical duplication did not have obvious signs of intellectual disability, suggesting previously undescribed incomplete penetrance or low expression in certain carriers. The possibility of a second-hit or modifying factors to this possible susceptibility locus is yet to be studied but a possible observational bias should be considered in assessing such challenging X-chromosome copy number gains. Additional segregation studies should help to quantify this newly described incomplete penetrance., (© 2024 The Authors. Clinical Genetics published by John Wiley & Sons Ltd.)

Published
2024
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