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1. TREX tetramer disruption alters RNA processing necessary for corticogenesis in THOC6 Intellectual Disability Syndrome

Author

Werren, Elizabeth A., LaForce, Geneva R., Srivastava, Anshika, Perillo, Delia R., Li, Shaokun, Johnson, Katherine, Baris, Safa, Berger, Brandon, Regan, Samantha L., Pfennig, Christian D., de Munnik, Sonja, Pfundt, Rolph, Hebbar, Malavika, Jimenez-Heredia, Raúl, Karakoc-Aydiner, Elif, Ozen, Ahmet, Dmytrus, Jasmin, Krolo, Ana, Corning, Ken, Prijoles, E. J., Louie, Raymond J., Lebel, Robert Roger, Le, Thuy-Linh, Amiel, Jeanne, Gordon, Christopher T., Boztug, Kaan, Girisha, Katta M., Shukla, Anju, Bielas, Stephanie L., and Schaffer, Ashleigh E.

Published
2024
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2. Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals

Author

Bosch, E, Popp, B, Güse, E, Skinner, C, van der Sluijs, P, Maystadt, I, Pinto, A, Renieri, A, Bruno, L, Granata, S, Marcelis, C, Baysal, Ö, Hartwich, D, Holthöfer, L, Isidor, B, Cogne, B, Wieczorek, D, Capra, V, Scala, M, De Marco, P, Ognibene, M, Jamra, R, Platzer, K, Carter, L, Kuismin, O, van Haeringen, A, Maroofian, R, Valenzuela, I, Cuscó, I, Martinez-Agosto, J, Rabani, A, Mefford, H, Pereira, E, Close, C, Anyane-Yeboa, K, Wagner, M, Hannibal, M, Zacher, P, Thiffault, I, Beunders, G, Umair, M, Bhola, P, Mcginnis, E, Millichap, J, van de Kamp, J, Prijoles, E, Dobson, A, Shillington, A, Graham, B, Garcia, E, Galindo, M, Ropers, F, Nibbeling, E, Hubbard, G, Karimov, C, Goj, G, Bend, R, Rath, J, Morrow, M, Millan, F, Salpietro, V, Torella, A, Nigro, V, Kurki, M, Stevenson, R, Santen, G, Zweier, M, Campeau, P, Severino, M, Reis, A, Accogli, A, Vasileiou, G, Bosch E., Popp B., Güse E., Skinner C., van der Sluijs P. J., Maystadt I., Pinto A. M., Renieri A., Bruno L. P., Granata S., Marcelis C., Baysal Ö., Hartwich D., Holthöfer L., Isidor B., Cogne B., Wieczorek D., Capra V., Scala M., De Marco P., Ognibene M., Jamra R. A., Platzer K., Carter L. B., Kuismin O., van Haeringen A., Maroofian R., Valenzuela I., Cuscó I., Martinez-Agosto J. A., Rabani A. M., Mefford H. C., Pereira E. M., Close C., Anyane-Yeboa K., Wagner M., Hannibal M. C., Zacher P., Thiffault I., Beunders G., Umair M., Bhola P. T., McGinnis E., Millichap J., van de Kamp J. M., Prijoles E. J., Dobson A., Shillington A., Graham B. H., Garcia E. J., Galindo M. K., Ropers F. G., Nibbeling E. A. R., Hubbard G., Karimov C., Goj G., Bend R., Rath J., Morrow M. M., Millan F., Salpietro V., Torella A., Nigro V., Kurki M., Stevenson R. E., Santen G. W. E., Zweier M., Campeau P. M., Severino M., Reis A., Accogli A., Vasileiou G., Bosch, E, Popp, B, Güse, E, Skinner, C, van der Sluijs, P, Maystadt, I, Pinto, A, Renieri, A, Bruno, L, Granata, S, Marcelis, C, Baysal, Ö, Hartwich, D, Holthöfer, L, Isidor, B, Cogne, B, Wieczorek, D, Capra, V, Scala, M, De Marco, P, Ognibene, M, Jamra, R, Platzer, K, Carter, L, Kuismin, O, van Haeringen, A, Maroofian, R, Valenzuela, I, Cuscó, I, Martinez-Agosto, J, Rabani, A, Mefford, H, Pereira, E, Close, C, Anyane-Yeboa, K, Wagner, M, Hannibal, M, Zacher, P, Thiffault, I, Beunders, G, Umair, M, Bhola, P, Mcginnis, E, Millichap, J, van de Kamp, J, Prijoles, E, Dobson, A, Shillington, A, Graham, B, Garcia, E, Galindo, M, Ropers, F, Nibbeling, E, Hubbard, G, Karimov, C, Goj, G, Bend, R, Rath, J, Morrow, M, Millan, F, Salpietro, V, Torella, A, Nigro, V, Kurki, M, Stevenson, R, Santen, G, Zweier, M, Campeau, P, Severino, M, Reis, A, Accogli, A, Vasileiou, G, Bosch E., Popp B., Güse E., Skinner C., van der Sluijs P. J., Maystadt I., Pinto A. M., Renieri A., Bruno L. P., Granata S., Marcelis C., Baysal Ö., Hartwich D., Holthöfer L., Isidor B., Cogne B., Wieczorek D., Capra V., Scala M., De Marco P., Ognibene M., Jamra R. A., Platzer K., Carter L. B., Kuismin O., van Haeringen A., Maroofian R., Valenzuela I., Cuscó I., Martinez-Agosto J. A., Rabani A. M., Mefford H. C., Pereira E. M., Close C., Anyane-Yeboa K., Wagner M., Hannibal M. C., Zacher P., Thiffault I., Beunders G., Umair M., Bhola P. T., McGinnis E., Millichap J., van de Kamp J. M., Prijoles E. J., Dobson A., Shillington A., Graham B. H., Garcia E. J., Galindo M. K., Ropers F. G., Nibbeling E. A. R., Hubbard G., Karimov C., Goj G., Bend R., Rath J., Morrow M. M., Millan F., Salpietro V., Torella A., Nigro V., Kurki M., Stevenson R. E., Santen G. W. E., Zweier M., Campeau P. M., Severino M., Reis A., Accogli A., and Vasileiou G.

Abstract

Purpose: Coffin-Siris and Nicolaides-Baraitser syndromes are recognizable neurodevelopmental disorders caused by germline variants in BAF complex subunits. The SMARCC2 BAFopathy was recently reported. Herein, we present clinical and molecular data on a large cohort.Methods: Clinical symptoms for 41 novel and 24 previously published affected individuals were analyzed using the Human Phenotype Ontology. For genotype-phenotype correlations, molecular data were standardized and grouped into non-truncating and likely gene-disrupting (LGD) variants. Missense variant protein expression and BAF-subunit interactions were examined using 3D protein modeling, co-immunoprecipitation, and proximity-ligation assays.Results: Neurodevelopmental delay with intellectual disability, muscular hypotonia, and behavioral disorders were the major manifestations. Clinical hallmarks of BAFopathies were rare. Clinical presentation differed significantly, with LGD variants being predominantly inherited and associated with mildly reduced or normal cognitive development, whereas non -truncating variants were mostly de novo and presented with severe developmental delay. These distinct manifestations and non-truncating variant clustering in functional domains suggest different pathomechanisms. In vitro testing showed decreased protein expression for N-terminal missense variants similar to LGD.Conclusion: This study improved SMARCC2 variant classification and identified discernible SMARCC2-associated phenotypes for LGD and non-truncating variants, which were distinct from other BAFopathies. The pathomechanism of most non-truncating variants has yet to be investigated.(c) 2023 The Authors. Published by Elsevier Inc. on behalf of American College of Medical Genetics and Genomics. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Published
2023

3. Delineation of a KDM2B-related neurodevelopmental disorder and its associated DNA methylation signature.

Author

Jaarsveld, R.H. van, Reilly, J., Cornips, M.C., Hadders, M.A., Agolini, E., Ahimaz, P., Anyane-Yeboa, K., Bellanger, S.A., Binsbergen, E. van, Boogaard, M.J. van den, Brischoux-Boucher, E., Caylor, R.C., Ciolfi, A., Essen, T.A. van, Fontana, P., Hopman, S., Iascone, M., Javier, M.M., Kamsteeg, E.J., Kerkhof, J., Kido, J., Kim, H.G., Kleefstra, T., Lonardo, F., Lai, A., Lev, D., Levy, M.A., Lewis, M.E.S., Lichty, A., Mannens, M.M., Matsumoto, N., Maya, I., McConkey, H., Megarbane, A., Michaud, V., Miele, E., Niceta, M., Novelli, A., Onesimo, R., Pfundt, R.P., Popp, B., Prijoles, E., Relator, R., Redon, S., Rots, D., Rouault, K., Saida, K., Schieving, J.H., Tartaglia, M., Tenconi, R., Uguen, K., Verbeek, N., Walsh, C.A., Yosovich, K., Yuskaitis, C.J., Zampino, G., Sadikovic, B., Alders, M., Oegema, R., Jaarsveld, R.H. van, Reilly, J., Cornips, M.C., Hadders, M.A., Agolini, E., Ahimaz, P., Anyane-Yeboa, K., Bellanger, S.A., Binsbergen, E. van, Boogaard, M.J. van den, Brischoux-Boucher, E., Caylor, R.C., Ciolfi, A., Essen, T.A. van, Fontana, P., Hopman, S., Iascone, M., Javier, M.M., Kamsteeg, E.J., Kerkhof, J., Kido, J., Kim, H.G., Kleefstra, T., Lonardo, F., Lai, A., Lev, D., Levy, M.A., Lewis, M.E.S., Lichty, A., Mannens, M.M., Matsumoto, N., Maya, I., McConkey, H., Megarbane, A., Michaud, V., Miele, E., Niceta, M., Novelli, A., Onesimo, R., Pfundt, R.P., Popp, B., Prijoles, E., Relator, R., Redon, S., Rots, D., Rouault, K., Saida, K., Schieving, J.H., Tartaglia, M., Tenconi, R., Uguen, K., Verbeek, N., Walsh, C.A., Yosovich, K., Yuskaitis, C.J., Zampino, G., Sadikovic, B., Alders, M., and Oegema, R.

Abstract

01 januari 2023, Item does not contain fulltext, PURPOSE: Pathogenic variants in genes involved in the epigenetic machinery are an emerging cause of neurodevelopment disorders (NDDs). Lysine-demethylase 2B (KDM2B) encodes an epigenetic regulator and mouse models suggest an important role during development. We set out to determine whether KDM2B variants are associated with NDD. METHODS: Through international collaborations, we collected data on individuals with heterozygous KDM2B variants. We applied methylation arrays on peripheral blood DNA samples to determine a KDM2B associated epigenetic signature. RESULTS: We recruited a total of 27 individuals with heterozygous variants in KDM2B. We present evidence, including a shared epigenetic signature, to support a pathogenic classification of 15 KDM2B variants and identify the CxxC domain as a mutational hotspot. Both loss-of-function and CxxC-domain missense variants present with a specific subepisignature. Moreover, the KDM2B episignature was identified in the context of a dual molecular diagnosis in multiple individuals. Our efforts resulted in a cohort of 21 individuals with heterozygous (likely) pathogenic variants. Individuals in this cohort present with developmental delay and/or intellectual disability; autism; attention deficit disorder/attention deficit hyperactivity disorder; congenital organ anomalies mainly of the heart, eyes, and urogenital system; and subtle facial dysmorphism. CONCLUSION: Pathogenic heterozygous variants in KDM2B are associated with NDD and a specific epigenetic signature detectable in peripheral blood.

Published
2023

4. SEMA6B variants cause intellectual disability and alter dendritic spine density and axon guidance

Author

Cordovado, A., Schaettin, M., Jeanne, M., Panasenkava, V., Denomme-Pichon, A. -S., Keren, B., Mignot, C., Doco-Fenzy, M., Rodan, L., Ramsey, K., Narayanan, V., Jones, J. R., Prijoles, E. J., Mitchell, W. G., Ozmore, J. R., Juliette, K., Torti, E., Normand, E. A., Granger, L., Petersen, A. K., Au, M. G., Matheny, J. P., Phornphutkul, C., Chambers, M. -K., Fernandez-Ramos, J. -A., Lopez-Laso, E., Kruer, M. C., Bakhtiari, S., Zollino, Marcella, Morleo, M., Marangi, Giuseppe, Mei, D., Pisano, T., Guerrini, R., Louie, R. J., Childers, A., Everman, D. B., Isidor, B., Audebert-Bellanger, S., Odent, S., Bonneau, D., Gilbert-Dussardier, B., Redon, R., Bezieau, S., Laumonnier, F., Stoeckli, E. T., Toutain, A., Vuillaume, M. -L., Zollino M. (ORCID:0000-0003-4871-9519), Marangi G. (ORCID:0000-0002-6898-8882), Cordovado, A., Schaettin, M., Jeanne, M., Panasenkava, V., Denomme-Pichon, A. -S., Keren, B., Mignot, C., Doco-Fenzy, M., Rodan, L., Ramsey, K., Narayanan, V., Jones, J. R., Prijoles, E. J., Mitchell, W. G., Ozmore, J. R., Juliette, K., Torti, E., Normand, E. A., Granger, L., Petersen, A. K., Au, M. G., Matheny, J. P., Phornphutkul, C., Chambers, M. -K., Fernandez-Ramos, J. -A., Lopez-Laso, E., Kruer, M. C., Bakhtiari, S., Zollino, Marcella, Morleo, M., Marangi, Giuseppe, Mei, D., Pisano, T., Guerrini, R., Louie, R. J., Childers, A., Everman, D. B., Isidor, B., Audebert-Bellanger, S., Odent, S., Bonneau, D., Gilbert-Dussardier, B., Redon, R., Bezieau, S., Laumonnier, F., Stoeckli, E. T., Toutain, A., Vuillaume, M. -L., Zollino M. (ORCID:0000-0003-4871-9519), and Marangi G. (ORCID:0000-0002-6898-8882)

Abstract

Intellectual disability (ID) is a neurodevelopmental disorder frequently caused by monogenic defects. In this study, we collected 14 SEMA6B heterozygous variants in 16 unrelated patients referred for ID to different centers. Whereas, until now, SEMA6B variants have mainly been reported in patients with progressive myoclonic epilepsy, our study indicates that the clinical spectrum is wider and also includes non-syndromic ID without epilepsy or myoclonus. To assess the pathogenicity of these variants, selected mutated forms of Sema6b were overexpressed in Human Embryonic Kidney 293T (HEK293T) cells and in primary neuronal cultures. shRNAs targeting Sema6b were also used in neuronal cultures to measure the impact of the decreased Sema6b expression on morphogenesis and synaptogenesis. The overexpression of some variants leads to a subcellular mislocalization of SEMA6B protein in HEK293T cells and to a reduced spine density owing to loss of mature spines in neuronal cultures. Sema6b knockdown also impairs spine density and spine maturation. In addition, we conducted in vivo rescue experiments in chicken embryos with the selected mutated forms of Sema6b expressed in commissural neurons after knockdown of endogenous SEMA6B. We observed that expression of these variants in commissural neurons fails to rescue the normal axon pathway. In conclusion, identification of SEMA6B variants in patients presenting with an overlapping phenotype with ID and functional studies highlight the important role of SEMA6B in neuronal development, notably in spine formation and maturation and in axon guidance. This study adds SEMA6B to the list of ID-related genes.

Published
2022

9. Development and evaluation of an educational resource for parents of children with 22q11.2 deletion syndrome about the psychiatric manifestations of the condition.

Author

Blankenship K, Chieffo S, Morris E, Slomp C, Batallones R, Prijoles E, Hill-Chapman C, and Austin J

Subjects
Humans, Male, Child, Female, Mental Disorders genetics, Mental Disorders psychology, Adult, Parents psychology, DiGeorge Syndrome psychology, DiGeorge Syndrome genetics
Abstract

Parents of children with 22q11.2 deletion syndrome (22q11DS) report concern about the psychiatric manifestations of the condition, but typically receive little information about this in clinical encounters and instead find information about it elsewhere. We developed an educational booklet about the psychiatric manifestations of 22q11DS and assessed its utility among parents of children with the condition. First, six parents of individuals with 22q11DS completed cognitive interviews to review an established generic booklet about the genetics of psychiatric conditions-and to suggest 22q11DS-specific adaptations. We used these suggestions to develop a novel booklet specific to psychiatric conditions and 22q1DS. Then, before and 1-month after reading the novel 22q11DS-specific online booklet, 73 parents of children with 22q11DS (with/without psychiatric conditions) completed validated scales (measuring empowerment, stigma, intolerance of uncertainty), an adapted version of a scale measuring worry about their child developing psychiatric illness, and purpose-designed items assessing perceptions of understanding of 22q11DS and mental illness, confidence in recognizing early signs, etc. After reading the 22q11DS online booklet, participants' feelings of empowerment increased (p = 0.002), while feelings of worry about their child developing psychiatric illness decreased (p = 0.05), and they reported better understanding 22q11DS and mental illness, and increased confidence in recognizing early warning signs. There is potential benefit in broadly distributing this educational booklet to parents of children with 22q11DS., (© 2023 The Authors. Journal of Genetic Counseling published by Wiley Periodicals LLC on behalf of National Society of Genetic Counselors.)

Published
2024
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10. Mechanisms of mRNA processing defects in inherited THOC6 intellectual disability syndrome.

Author

Werren E, LaForce G, Srivastava A, Perillo D, Johnson K, Berger B, Regan S, Pfennig C, Baris S, de Munnik S, Pfundt R, Hebbar M, Jimenez Heredia R, Karakoc-Aydiner E, Ozen A, Dmytrus J, Krolo A, Corning K, Prijoles E, Louie R, Lebel R, Le TL, Amiel J, Gordon C, Boztug K, Girisha K, Shukla A, Bielas S, and Schaffer A

Abstract

THOC6 is the genetic basis of autosomal recessive THOC6 Intellectual Disability Syndrome (TIDS). THOC6 facilitates the formation of the Transcription Export complex (TREX) tetramer, composed of four THO monomers. The TREX tetramer supports mammalian mRNA processing that is distinct from yeast TREX dimer functions. Human and mouse TIDS model systems allow novel THOC6-dependent TREX tetramer functions to be investigated. Biallelic loss-of-functon(LOF) THOC6 variants do not influence the expression and localization of TREX members in human cells, but our data suggests reduced binding affinity of ALYREF. Impairment of TREX nuclear export functions were not detected in cells with biallelic THOC6 LOF. Instead, mRNA mis-splicing was observed in human and mouse neural tissue, revealing novel insights into THOC6-mediated TREX coordination of mRNA processing. We demonstrate that THOC6 is required for regulation of key signaling pathways in human corticogenesis that dictate the transition from proliferative to neurogenic divisions that may inform TIDS neuropathology., Competing Interests: COMPETING INTERESTS The authors declare no competing interests.

Published
2023
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11. Delineation of a KDM2B-related neurodevelopmental disorder and its associated DNA methylation signature.

Author

van Jaarsveld RH, Reilly J, Cornips MC, Hadders MA, Agolini E, Ahimaz P, Anyane-Yeboa K, Bellanger SA, van Binsbergen E, van den Boogaard MJ, Brischoux-Boucher E, Caylor RC, Ciolfi A, van Essen TAJ, Fontana P, Hopman S, Iascone M, Javier MM, Kamsteeg EJ, Kerkhof J, Kido J, Kim HG, Kleefstra T, Lonardo F, Lai A, Lev D, Levy MA, Lewis MES, Lichty A, Mannens MMAM, Matsumoto N, Maya I, McConkey H, Megarbane A, Michaud V, Miele E, Niceta M, Novelli A, Onesimo R, Pfundt R, Popp B, Prijoles E, Relator R, Redon S, Rots D, Rouault K, Saida K, Schieving J, Tartaglia M, Tenconi R, Uguen K, Verbeek N, Walsh CA, Yosovich K, Yuskaitis CJ, Zampino G, Sadikovic B, Alders M, and Oegema R

Subjects
Mice, Animals, Humans, DNA Methylation genetics, DNA, Mutation, Neurodevelopmental Disorders genetics, Intellectual Disability genetics
Abstract

Purpose: Pathogenic variants in genes involved in the epigenetic machinery are an emerging cause of neurodevelopment disorders (NDDs). Lysine-demethylase 2B (KDM2B) encodes an epigenetic regulator and mouse models suggest an important role during development. We set out to determine whether KDM2B variants are associated with NDD., Methods: Through international collaborations, we collected data on individuals with heterozygous KDM2B variants. We applied methylation arrays on peripheral blood DNA samples to determine a KDM2B associated epigenetic signature., Results: We recruited a total of 27 individuals with heterozygous variants in KDM2B. We present evidence, including a shared epigenetic signature, to support a pathogenic classification of 15 KDM2B variants and identify the CxxC domain as a mutational hotspot. Both loss-of-function and CxxC-domain missense variants present with a specific subepisignature. Moreover, the KDM2B episignature was identified in the context of a dual molecular diagnosis in multiple individuals. Our efforts resulted in a cohort of 21 individuals with heterozygous (likely) pathogenic variants. Individuals in this cohort present with developmental delay and/or intellectual disability; autism; attention deficit disorder/attention deficit hyperactivity disorder; congenital organ anomalies mainly of the heart, eyes, and urogenital system; and subtle facial dysmorphism., Conclusion: Pathogenic heterozygous variants in KDM2B are associated with NDD and a specific epigenetic signature detectable in peripheral blood., Competing Interests: Conflict of Interest The authors declare no conflicts of interest., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

Published
2023
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12. A novel mutation in GLUD1 causing hyperinsulinism-hyperammonemia in a patient with high density of homozygosity on microarray: a case report.

Author

Odom J, Gieron-Korthals M, Shulman D, Newkirk P, Prijoles E, and Sanchez-Valle A

Subjects
Child, Preschool, Female, Fetal Growth Retardation, Homozygote, Humans, Hyperinsulinism drug therapy, Hypoglycemia drug therapy, Mutation, Oligonucleotide Array Sequence Analysis, Abnormalities, Multiple genetics, Developmental Disabilities genetics, Glutamate Dehydrogenase genetics, Hyperinsulinism genetics, Hypoglycemia genetics
Abstract

Background: Hyperinsulinism-hyperammonemia syndrome is the second most common cause of congenital hyperinsulinism and is easily treated with diazoxide; however, the symptoms in our patient were very difficult to control with typical medical therapy. To the best of our knowledge, neither our patient's mutation, nor a case of hyperinsulinism-hyperammonemia presenting with dysmorphic features and intrauterine growth restriction has previously been reported., Case Presentation: We describe a 2-year-old Hispanic girl with an unusual presentation of dysmorphic features and intrauterine growth restriction who was later found to have hyperinsulinism-hyperammonemia syndrome. Chromosomal microarray analysis revealed no copy number variants but demonstrated a high density of noncontiguous regions of homozygosity consistent with limited outbreeding. Sequencing of her GLUD1 gene revealed a previously undescribed mutation of cytosine to thymine at position 1519 resulting in an amino acid change of histidine to tyrosine at position 507. Although no functional studies were performed, function prediction tools in combination with our patient's phenotype support the hypothesis that the mutation is deleterious. Despite treatment with a maximum dose of diazoxide (15 mg/kg/day), phenobarbital (8.5 mg/kg/day divided twice daily) and a protein-restricted diet, she has global developmental delay, and continues to have seizures and recurrent episodes of hypoglycemia., Conclusions: It remains unclear if her clinical presentation can be solely explained by hyperinsulinism-hyperammonemia syndrome or is the result of an undiagnosed recessive disorder related to her homozygosity. It is our hope that clinicians may learn from our patient when formulating treatment plans for refractory cases of hyperinsulinism-hyperammonemia and avoid the morbidities associated with delayed diagnosis and treatment.

Published
2016
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