PHARMACOGENOMICS

A high-content drug screening strategy to identify protein level modulators for genetic diseases: a proof-of-principle in Autosomal Dominant LeukoDystrophy (ADLD)

Giorgio E, Pesce E, Pozzi E, Sondo E, Ferrero M, Morerio C, Borrelli G, Della Sala E, Lorenzati M, Cortelli P, Buffo A, Pedemonte N, Brusco A

Hum Mutat. 2021 Jan;42(1):102-116.  doi: 10.1002/humu.24147. Epub 2020 Dec 8 

Abstract

In genetic diseases, the most prevalent mechanism of pathogenicity is an altered expression of dosage-sensitive genes. Drugs that restore physiological levels of these genes should be effective in treating the associated conditions. We developed a screening strategy, based on a bicistronic dual-reporter vector, for identifying compounds that modulate protein levels, and used it in a pharmacological screening approach. To provide a proof-of-principle, we chose autosomal dominant leukodystrophy (ADLD), an ultra-rare adult-onset neurodegenerative disorder caused by lamin B1 (LMNB1) overexpression. We used a stable Chinese hamster ovary (CHO) cell line that simultaneously expresses an AcGFP reporter fused to LMNB1 and a Ds-Red normalizer. Using high-content imaging analysis, we screened a library of 717 biologically active compounds and approved drugs, and identified alvespimycin, an HSP90 inhibitor, as a positive hit. We confirmed that alvespimycin can reduce LMNB1 levels by 30%-80% in five different cell lines (fibroblasts, NIH3T3, CHO, COS-7, and rat primary glial cells). In ADLD fibroblasts, alvespimycin reduced cytoplasmic LMNB1 by about 50%. We propose this approach for effectively identifying potential drugs for treating genetic diseases associated with deletions/duplications and paving the way toward Phase II clinical trials.

 

Haploinsufficiency of PRR12 causes a spectrum of neurodevelopmental, eye and multi-system abnormalities

Chowdhury F, Wang L, Al-Raqad M, Amor DJ, Baxová A, Bendová S, Biamino E, Brusco A, Caluseriu O, Cox NJ, Froukh T, Gunay-Aygun M, Hančárová M, Haynes D, Heide S, Hoganson G, Kaname T, Keren B, Kosaki K, Kubota K, Lemons JM, Magriña MA, Mark PR, McDonald MT, Montgomery S, Morley GM, Ohnishi H, Okamoto N, Rodriguez-Buritica D, Rump P, Sedláček Z, Schatz K, Streff H, Uehara T, Walia JS, Wheeler PG, Wiesener A, Zweier C, Kawakami C, Wentzensen IM, Lalani SR, Siu VM, Bi W, Balci TB

Genet Med. 2021 Apr 6.  doi: 10.1038/s41436-021-01129-6. Online ahead of print.

Abstract

Purpose: Proline Rich 12 (PRR12) is a gene of unknown function with suspected DNA-binding activity, expressed in developing mice and human brains. Predicted loss-of-function variants in this gene are extremely rare, indicating high intolerance of haploinsufficiency.

Methods: Three individuals with intellectual disability and iris anomalies and truncating de novo PRR12 variants were described previously. We add 21 individuals with similar PRR12 variants identified via matchmaking platforms, bringing the total number to 24.

Results: We observed 12 frameshift, 6 nonsense, 1 splice-site, and 2 missense variants and one patient with a gross deletion involving PRR12. Three individuals had additional genetic findings, possibly confounding the phenotype. All patients had developmental impairment. Variable structural eye defects were observed in 12/24 individuals (50%) including anophthalmia, microphthalmia, colobomas, optic nerve and iris abnormalities. Additional common features included hypotonia (61%), heart defects (52%), growth failure (54%), and kidney anomalies (35%). PrediXcan analysis showed that phecodes most strongly associated with reduced predicted PRR12 expression were enriched for eye- (7/30) and kidney- (4/30) phenotypes, such as wet macular degeneration and chronic kidney disease.

Conclusion: These findings support PRR12 haploinsufficiency as a cause for a novel disorder with a wide clinical spectrum marked chiefly by neurodevelopmental and eye abnormalities.

Clinical spectrum and follow-up in six individuals with Lamb–Shaffer syndrome (SOX5)

Innella G, Greco D, Carli D, Magini P, Giorgio E, Galesi O, Ferrero GB, Romano C, Brusco A, Graziano C.

Am J Med Genet A. 2021 Feb;185(2):608-613. doi: 10.1002/ajmg.a.62001. Epub 2020 Dec 9.

 

2021

Histone H3.3 beyond cancer: Germline mutations in Histone 3 Family 3A and 3B cause a previously unidentified neurodegenerative disorder in 46 patients

Laura Bryant 1, Dong Li 1, Samuel G Cox 2, Dylan Marchione 3, Evan F Joiner 4, Khadija Wilson 3, Kevin Janssen 3, Pearl Lee 5, Michael E March 1, Divya Nair 1, Elliott Sherr 6, Brieana Fregeau 6, Klaas J Wierenga 7, Alexandrea Wadley 7, Grazia M S Mancini 8, Nina Powell-Hamilton 9, Jiddeke van de Kamp 10, Theresa Grebe 11, John Dean 12, Alison Ross 12, Heather P Crawford 13, Zoe Powis 14, Megan T Cho 15, Marcia C Willing 16, Linda Manwaring 16, Rachel Schot 8, Caroline Nava 17 18, Alexandra Afenjar 19, Davor Lessel 20 21, Matias Wagner 22 23 24, Thomas Klopstock 25 26 27, Juliane Winkelmann 22 24 27 28, Claudia B Catarino 25, Kyle Retterer 15, Jane L Schuette 29, Jeffrey W Innis 29, Amy Pizzino 30 31, Sabine Lüttgen 32, Jonas Denecke 32, Tim M Strom 22 24, Kristin G Monaghan 15, DDD Study; Zuo-Fei Yuan 3, Holly Dubbs 30 31, Renee Bend 33, Jennifer A Lee 33, Michael J Lyons 33, Julia Hoefele 24, Roman Günthner 34 35, Heiko Reutter 36, Boris Keren 18, Kelly Radtke 37, Omar Sherbini 30 31, Cameron Mrokse 37, Katherine L Helbig 37, Sylvie Odent 38, Benjamin Cogne 39 40, Sandra Mercier 39 40, Stephane Bezieau 39 40, Thomas Besnard 39 40, Sebastien Kury 39 40, Richard Redon 40, Karit Reinson 41 42, Monica H Wojcik 43 44, Katrin Õunap 41 42, Pilvi Ilves 45, A Micheil Innes 46, Kristin D Kernohan 47 48, Care4Rare Canada Consortium; Gregory Costain 49, M Stephen Meyn 49 50, David Chitayat 49 51, Elaine Zackai 52, Anna Lehman 53, Hilary Kitson 54, CAUSES Study; Martin G Martin 55 56, Julian A Martinez-Agosto 57 58, Undiagnosed Diseases Network; Stan F Nelson 57 59, Christina G S Palmer 57 60, Jeanette C Papp 57, Neil H Parker 61, Janet S Sinsheimer 62, Eric Vilain 63, Jijun Wan 57, Amanda J Yoon 57, Allison Zheng 57, Elise Brimble 64, Giovanni Battista Ferrero 65, Francesca Clementina Radio 66, Diana Carli 65, Sabina Barresi 66, Alfredo Brusco 67, Marco Tartaglia 66, Jennifer Muncy Thomas 68, Luis Umana 69, Marjan M Weiss 10, Garrett Gotway 69, K E Stuurman 8, Michelle L Thompson 70, Kirsty McWalter 15, Constance T R M Stumpel 71, Servi J C Stevens 71, Alexander P A Stegmann 71, Kristian Tveten 72, Arve Vøllo 73, Trine Prescott 72, Christina Fagerberg 74, Lone Walentin Laulund 75, Martin J Larsen 74, Melissa Byler 76, Robert Roger Lebel 76, Anna C Hurst 77, Joy Dean 77, Samantha A Schrier Vergano 78, Jennifer Norman 79, Saadet Mercimek-Andrews 49, Juanita Neira 80, Margot I Van Allen 53 81, Nicola Longo 82, Elizabeth Sellars 83, Raymond J Louie 33, Sara S Cathey 33, Elly Brokamp 84, Delphine Heron 18, Molly Snyder 85, Adeline Vanderver 30 31, Celeste Simon 4, Xavier de la Cruz 86 87, Natália Padilla 86, J Gage Crump 2, Wendy Chung 88, Benjamin Garcia 2 3, Hakon H Hakonarson 1, Elizabeth J Bhoj 89

PMID: 33268356 PMCID: PMC7821880 DOI: 10.1126/sciadv.abc9207

 

2020

Abstract

Although somatic mutations in Histone 3.3 (H3.3) are well-studied drivers of oncogenesis, the role of germline mutations remains unreported. We analyze 46 patients bearing de novo germline mutations in histone 3 family 3A (H3F3A) or H3F3B with progressive neurologic dysfunction and congenital anomalies without malignancies. Molecular modeling of all 37 variants demonstrated clear disruptions in interactions with DNA, other histones, and histone chaperone proteins. Patient histone posttranslational modifications (PTMs) analysis revealed notably aberrant local PTM patterns distinct from the somatic lysine mutations that cause global PTM dysregulation. RNA sequencing on patient cells demonstrated up-regulated gene expression related to mitosis and cell division, and cellular assays confirmed an increased proliferative capacity. A zebrafish model showed craniofacial anomalies and a defect in Foxd3-derived glia. These data suggest that the mechanism of germline mutations are distinct from cancer-associated somatic histone mutations but may converge on control of cell proliferation.

Missense variant contribution to USP9X female syndrome

 

Lachlan A Jolly 1, Euan Parnell 2, Alison E Gardner 3, Mark A Corbett 3, Luis A Pérez-Jurado 3 4 5 6, Marie Shaw 3, Gaetan Lesca 7 8, Catherine Keegan 9, Michael C Schneider 10, Emily Griffin 11, Felicitas Maier 12, Courtney Kiss 13, Andrea Guerin 14, Kathleen Crosby 15, Kenneth Rosenbaum 15, Pranoot Tanpaiboon 15, Sandra Whalen 16, Boris Keren 17, Julie McCarrier 18, Donald Basel 18, Simon Sadedin 19 20 21, Susan M White 19 20 21, Martin B Delatycki 19 20 21, Tjitske Kleefstra 22, Sébastien Küry 23 24, Alfredo Brusco 25 26, Elena Sukarova-Angelovska 27, Slavica Trajkova 25, Sehoun Yoon 2, Stephen A Wood 28, Michael Piper 29 30, Peter Penzes 2, Jozef Gecz 31 32

 

Affiliations

1University of Adelaide and Robinson Research Institute, Adelaide, SA, 5005, Australia. Lachlan.Jolly@adelaide.edu.au.

2Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, Il, USA.

3University of Adelaide and Robinson Research Institute, Adelaide, SA, 5005, Australia.

4Women's and Children's Hospital, Adelaide, SA, 5006, Australia.

5South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia.

6Hospital del Mar Research Institute (IMIM), Network Research Centre for Rare Diseases (CIBERER) and Universitat Pompeu Fabra, Barcelona, 08003, Spain.

7Institut Neuromyogène, métabolisme énergétique et développement durable, CNRS UMR 5310, INSERM U1217, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France.

8Service de Génétique, Hospices Civils de Lyon, Lyon, France.

9Division of Genetics, Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA.

10Section of Neurology, Department of Pediatrics, St. Christopher's Hospital for Children, Drexel University College of Medicine, Philadelphia, PA, USA.

11Division of Clinical Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.

12Dr. von Hauner Children's Hospital, LMU - Ludwig-Maximilians-Universität Munich, University of Munich Medical Center, Munich, Germany.

13Kingston Health Sciences Centre, Kingston, ON, K7L 2V7, Canada.

14Division of Medical Genetics, Department of Pediatrics, Kingston General Hospital, Kingston, ON, Canada.

15Division of Genetics and Metabolism, Children's National Hospital, Washington, DC, USA.

16Unité Fonctionnelle de génétique clinique, Hôpital Armand Trousseau, Assistance publique-Hôpitaux de Paris, Centre de Référence Maladies Rares des anomalies du développement et syndromes malformatifs, Paris, France.

17Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France.

18Division of Genetics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA.

19Victorian Clinical Genetics Service, Melbourne, VIC, Australia.

20Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.

21Murdoch Children's Research Institute, Melbourne, VIC, Australia.

22Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6500, HB, the Netherlands.

23Service de Génétique Médicale, CHU Nantes, 44093, Nantes, France.

24l'Institut du Thorax, INSERM, CNRS, UNIV Nantes, 44007, Nantes, France.

25Department of Medical Sciences, University of Turin, Torino, Italy.

26Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Torino, Italy.

27Department of Endocronology and Genetics, University Clinic for Children's Diseases, Medical Faculty, University Sv. Kiril i Metodij, Skopje, Republic of Macedonia.

28Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD, Australia.

29School of Biomedical Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.

30Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.

31University of Adelaide and Robinson Research Institute, Adelaide, SA, 5005, Australia. Jozef.Gecz@adelaide.edu.au.

32South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia. Jozef.Gecz@adelaide.edu.au.

 

NPJ Genom Med . 2020 Dec 9;5(1):53.  doi: 10.1038/s41525-020-00162-9.

2020

Abstract

USP9X is an X-chromosome gene that escapes X-inactivation. Loss or compromised function of USP9X leads to neurodevelopmental disorders in males and females. While males are impacted primarily by hemizygous partial loss-of-function missense variants, in females de novo heterozygous complete loss-of-function mutations predominate, and give rise to the clinically recognisable USP9X-female syndrome. Here we provide evidence of the contribution of USP9X missense and small in-frame deletion variants in USP9X-female syndrome also. We scrutinise the pathogenicity of eleven such variants, ten of which were novel. Combined application of variant prediction algorithms, protein structure modelling, and assessment under clinically relevant guidelines universally support their pathogenicity. The core phenotype of this cohort overlapped with previous descriptions of USP9X-female syndrome, but exposed heightened variability. Aggregate phenotypic information of 35 currently known females with predicted pathogenic variation in USP9X reaffirms the clinically recognisable USP9X-female syndrome, and highlights major differences when compared to USP9X-male associated neurodevelopmental disorders.

 

A Novel CCT5 Missense Variant Associated with Early Onset Motor Neuropathy

Vincenzo Antona,1,† Federica Scalia,2,3,† Elisa Giorgio,4 Francesca C. Radio,5 Alfredo Brusco,4 Massimiliano Oliveri,6 Giovanni Corsello,1 Fabrizio Lo Celso,7,8 Maria Vadalà,2,3 Everly Conway de Macario,9 Alberto J. L. Macario,3,9 Francesco Cappello,2,3,* and Mario Giuffrè1

Int J Mol Sci. 2020 Oct; 21(20): 7631.

Abstract

Diseases associated with acquired or genetic defects in members of the chaperoning system (CS) are increasingly found and have been collectively termed chaperonopathies. Illustrative instances of genetic chaperonopathies involve the genes for chaperonins of Groups I (e.g., Heat shock protein 60, Hsp60) and II (e.g., Chaperonin Containing T-Complex polypeptide 1, CCT). Examples of the former are hypomyelinating leukodystrophy 4 (HLD4 or MitCHAP60) and hereditary spastic paraplegia (SPG13). A distal sensory mutilating neuropathy has been linked to a mutation [p.(His147Arg)] in subunit 5 of the CCT5 gene. Here, we describe a new possibly pathogenic variant [p.(Leu224Val)] of the same subunit but with a different phenotype. This yet undescribed disease affects a girl with early onset demyelinating neuropathy and a severe motor disability. By whole exome sequencing (WES), we identified a homozygous CCT5 c.670C>G p.(Leu224Val) variant in the CCT5 gene. In silico 3D-structure analysis and bioinformatics indicated that this variant could undergo abnormal conformation and could be pathogenic. We compared the patient’s clinical, neurophysiological and laboratory data with those from patients carrying p.(His147Arg) in the equatorial domain. Our patient presented signs and symptoms absent in the p.(His147Arg) cases. Molecular dynamics simulation and modelling showed that the Leu224Val mutation that occurs in the CCT5 intermediate domain near the apical domain induces a conformational change in the latter. Noteworthy is the striking difference between the phenotypes putatively linked to mutations in the same CCT subunit but located in different structural domains, offering a unique opportunity for elucidating their distinctive roles in health and disease

 

Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism

Branko Aleksic, Richard Anney, Mafalda Barbosa, Somer Bishop, Alfredo Brusco, Jonas Bybjerg-Grauholm, Angel Carracedo, Marcus C Y Chan, Andreas G Chiocchetti, Brian H Y Chung, Hilary Coon, Michael L Cuccaro, Aurora Curró, Bernardo Dalla Bernardina, Ryan Doan, Enrico Domenici, Shan Dong, Chiara Fallerini, Montserrat Fernández-Prieto, Giovanni Battista Ferrero, Christine M Freitag, Menachem Fromer, J Jay Gargus, Daniel Geschwind, Elisa Giorgio, Javier González-Peñas, Stephen Guter, Danielle Halpern, Emily Hansen-Kiss, Xin He, Gail E Herman, Irva Hertz-Picciotto, David M Hougaard, Christina M Hultman, Iuliana Ionita-Laza, Suma Jacob, Jesslyn Jamison, Astanand Jugessur, Miia Kaartinen, Gun Peggy Knudsen, Alexander Kolevzon, Itaru Kushima, So Lun Lee, Terho Lehtimäki, Elaine T Lim, Carla Lintas, W Ian Lipkin, Diego Lopergolo, Fátima Lopes, Yunin Ludena, Patricia Maciel, Per Magnus, Behrang Mahjani, Nell Maltman, Dara S Manoach, Gal Meiri, Idan Menashe, Judith Miller, Nancy Minshew, Eduarda M S Montenegro, Danielle Moreira, Eric M Morrow, Ole Mors, Preben Bo Mortensen, Matthew Mosconi, Pierandrea Muglia, Benjamin M Neale, Merete Nordentoft, Norio Ozaki, Aarno Palotie, Mara Parellada, Maria Rita Passos-Bueno, Margaret Pericak-Vance, Antonio M Persico, Isaac Pessah, Kaija Puura, Abraham Reichenberg, Alessandra Renieri, Evelise Riberi, Elise B Robinson, Kaitlin E Samocha, Sven Sandin, Susan L Santangelo, Gerry Schellenberg, Stephen W Scherer, Sabine Schlitt, Rebecca Schmidt, Lauren Schmitt, Isabela M W Silva, Tarjinder Singh, Paige M Siper, Moyra Smith, Gabriela Soares, Camilla Stoltenberg, Pål Suren, Ezra Susser, John Sweeney, Peter Szatmari, Lara Tang, Flora Tassone, Karoline Teufel, Elisabetta Trabetti, Maria Del Pilar Trelles, Christopher A Walsh, Lauren A Weiss, Thomas Werge, Donna M Werling, Emilie M Wigdor, Emma Wilkinson, A Jeremy Willsey, Timothy W Yu, Mullin H C Yu, Ryan Yuen, Elaine Zachi, Esben Agerbo, Thomas Damm Als, Vivek Appadurai, Marie Bækvad-Hansen, Rich Belliveau, Alfonso Buil, Caitlin E Carey, Felecia Cerrato, Kimberly Chambert, Claire Churchhouse, Søren Dalsgaard, Ditte Demontis, Ashley Dumont, Jacqueline Goldstein, Christine S Hansen, Mads Engel Hauberg, Mads V Hollegaard, Daniel P Howrigan, Hailiang Huang, Julian Maller, Alicia R Martin, Joanna Martin, Manuel Mattheisen, Jennifer Moran, Jonatan Pallesen, Duncan S Palmer, Carsten Bøcker Pedersen, Marianne Giørtz Pedersen, Timothy Poterba, Jesper Buchhave Poulsen, Stephan Ripke, Andrew J Schork, Wesley K Thompson, Patrick Turley, Raymond K Walters

Affiliations

1Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.

2Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.

3Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA.

4Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

5Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, Republic of Korea.

6Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA.

7The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Center for Genomics and Personalized Medicine, Aarhus, Denmark; Department of Biomedicine - Human Genetics, Aarhus University, Aarhus, Denmark.

8Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.

9Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.

10Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

11Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.

12Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.

13Computer Engineering Department, Bilkent University, Ankara, Turkey.

14Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.

15Center for Autism Research and Translation, University of California, Irvine, Irvine, CA, USA.

16MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California, Davis, Davis, CA, USA.

17Division of Genetics, Boston Children's Hospital, Boston, MA, USA; Division of Developmental Medicine, Boston Children's Hospital, Boston, MA, USA.

18Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine, Institut de Biologie Paris Seine, Paris, France.

19Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA.

20Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland.

21Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Molecular Physiology and Biophysics and Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, USA.

22National Institute of Mental Health, NIH, Bethesda, MD, USA.

23Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.

24The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Center for Genomics and Personalized Medicine, Aarhus, Denmark; Department of Biomedicine - Human Genetics, Aarhus University, Aarhus, Denmark; Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark.

25Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA; Computer Engineering Department, Bilkent University, Ankara, Turkey.

26Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA. Electronic address: stephan.sanders@ucsf.edu.

27Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA; Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA. Electronic address: roeder@andrew.cmu.edu.

28Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland. Electronic address: mjdaly@broadinstitute.org.

29Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Electronic address: joseph.buxbaum@mssm.edu.

PMID: 31981491 PMCID: PMC7250485 DOI: 10.1016/j.cell.2019.12.036

 

2020

Abstract

We present the largest exome sequencing study of autism spectrum disorder (ASD) to date (n = 35,584 total samples, 11,986 with ASD). Using an enhanced analytical framework to integrate de novo and case-control rare variation, we identify 102 risk genes at a false discovery rate of 0.1 or less. Of these genes, 49 show higher frequencies of disruptive de novo variants in individuals ascertained to have severe neurodevelopmental delay, whereas 53 show higher frequencies in individuals ascertained to have ASD; comparing ASD cases with mutations in these groups reveals phenotypic differences. Expressed early in brain development, most risk genes have roles in regulation of gene expression or neuronal communication (i.e., mutations effect neurodevelopmental and neurophysiological changes), and 13 fall within loci recurrently hit by copy number variants. In cells from the human cortex, expression of risk genes is enriched in excitatory and inhibitory neuronal lineages, consistent with multiple paths to an excitatory-inhibitory imbalance underlying ASD.

 

Novel LRPPRC compound heterozygous mutation in a child with early-onset Leigh syndrome French-Canadian type: case report of an Italian patient

Ettore Piro, Gregorio Serra, Vincenzo Antona, Mario Giuffrè, Elisa Giorgio, Fabio Sirchia, Ingrid Anne Mandy Schierz, Alfredo Brusco & Giovanni Corsello
 
Italian Journal of Pediatrics volume 46, Article number: 140 (2020) 
2020

Abstract

Background

Mitochondrial diseases, also known as oxidative phosphorylation (OXPHOS) disorders, with a prevalence rate of 1:5000, are the most frequent inherited metabolic diseases. Leigh Syndrome French Canadian type (LSFC), is caused by mutations in the nuclear gene (2p16) leucine-rich pentatricopeptide repeat-containing (LRPPRC). It is an autosomal recessive neurogenetic OXPHOS disorder, phenotypically distinct from other types of Leigh syndrome, with a carrier frequency up to 1:23 and an incidence of 1:2063 in the Saguenay-Lac-St Jean region of Quebec. Recently, LSFC has also been reported outside the French-Canadian population.

Patient presentation

We report a male Italian (Sicilian) child, born preterm at 28 + 6/7 weeks gestation, carrying a novel LRPPRC compound heterozygous mutation, with facial dysmorphisms, neonatal hypotonia, non-epileptic paroxysmal motor phenomena, and absent sucking-swallowing-breathing coordination requiring, at 4.5 months, a percutaneous endoscopic gastrostomy tube placement. At 5 months brain Magnetic Resonance Imaging showed diffuse cortical atrophy, hypoplasia of corpus callosum, cerebellar vermis hypoplasia, and unfolded hippocampi. Both auditory and visual evoked potentials were pathological. In the following months Video EEG confirmed the persistence of sporadic non epileptic motor phenomena. No episode of metabolic decompensation, acidosis or ketosis, frequently observed in LSFC has been reported. Actually, aged 14 months corrected age for prematurity, the child shows a severe global developmental delay. Metabolic investigations and array Comparative Genomic Hybridization (aCGH) results were normal. Whole-genome sequencing (WGS) found a compound heterozygous mutation in the LRPPRC gene, c.1921–7A > G and c.2056A > G (p.Ile686Val), splicing-site and missense variants, inherited from the mother and the father, respectively.

Conclusions

We first characterized the clinical and molecular features of a novel LRPPRC variant in a male Sicilian child with early onset encephalopathy and psychomotor impairment. Our patient showed a phenotype characterized by a severe neurodevelopmental delay and absence of metabolic decompensation attributable to a probable residual enzymatic activity. LRPPRC is a rare cause of metabolic encephalopathy outside of Québec. Our patient adds to and broaden the spectrum of LSFC phenotypes. WGS analysis is a pivotal genetic test and should be performed in infants and children with hypotonia and developmental delay in whom metabolic investigations and aCGH are normal.
 

 

Design of a multiplex ligation-dependent probe amplification assay for SLC20A2: identification of two novel deletions in primary familial brain calcification

Giorgio E, Garelli E, Carando A, Bellora S, Rubino E, Quarello P, Sirchia F, Marrama F, Gallone S, Grosso E, Pasini B, Massa R, Brussino A, Brusco A.
 
Journal of Human Genetics volume 64, pages1083–1090(2019)
    2019

    Abstract

    AbstractPrimary familial brain calcification (PFBC) is a rare disease characterized by brain calcifications that mainly affect the basal ganglia, thalamus, and cerebellum. Among the four autosomal-dominant genes known to be associated with the disease, SLC20A2 pathogenic variants are the most common, accounting for up to 40% of PFBC dominant cases; variants include both point mutations, small insertions/deletions and intragenic deletions. Over the last 7 years, we have collected a group of 50 clinically diagnosed PFBC patients, who were screened for single nucleotide changes and small insertions/deletions in SLC20A2 by Sanger sequencing. We found seven pathogenic/likely pathogenic variants: four were previously described by our group, and three are reported here (c.303delG, c.21delG, and c.1795-1G>A). We developed and validated a synthetic Multiplex Ligation-dependent Probe Amplification (MLPA) assay for SLC20A2 deletions, covering all ten coding exons and the 5′ UTR (SLC20A2-MLPA). Using this method, we screened a group of 43 PFBC-patients negative for point mutations and small insertions/deletions, and identified two novel intragenic deletions encompassing exon 6 NC_000008.10:g.(42297172_42302163)_(423022281_42317413)del, and exons 7–11 including the 3′UTR NC_000008.10:g.(?_42275320)_(42297172_42302163)del. Overall, SLC20A2 deletions may be highly underestimated PFBC cases, and we suggest MLPA should be included in the routine molecular test for PFBC diagnosis.

     

    Therapeutic application of allele-specific silencing by siRNA for gene duplication disorders: a proof-of-principle in Autosomal Dominant LeukoDystrophy (ADLD)

     2019 Jul 1;142(7):1905-1920. doi: 10.1093/brain/awz139.
     
    1
    University of Torino, Department of Medical Sciences, Torino, Italy.
    2
    University of Torino, Department of Neuroscience Rita Levi Montalcini and Neuroscience Institute Cavalieri Ottolenghi (NICO), Orbassano, Torino, Italy.
    3
    University of Milan, Department of Biosciences, Laboratory of Stem Cell Biology and Pharmacology of Neurodegenerative Diseases, Milan, Italy.
    4
    IRCCS Istituto delle Scienze Neurologiche di Bologna, Bellaria Hospital, Bologna, Italy.
    5
    Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Universiteitsweg 99, CG, Utrecht, The Netherlands.
    6
    Department of Molecular Medicine and Medical Biotechnology, University of Naples 'Federico II', Naples, Italy.
    7
    University of Bologna, Department of Biomedical and Neuromotor Sciences, Bologna, Italy.
    8
    University of Trento, Centre for Integrative Biology (CIBIO), Laboratory of Computational Oncology, Trento, Italy.
    9
    National Institute of Molecular Genetics (INGM) Romeo and Enrica Invernizzi, Milano, Italy.
    10
    Città della Salute e della Scienza University Hospital, Medical Genetics Unit, Torino, Italy.

     

    2019

    Abstract

    Allele-specific silencing by RNA interference (ASP-siRNA) holds promise as a therapeutic strategy for downregulating a single mutant allele with minimal suppression of the corresponding wild-type allele. This approach has been effectively used to target autosomal dominant mutations and single nucleotide polymorphisms linked with aberrantly expanded trinucleotide repeats. Here, we propose ASP-siRNA as a preferable choice to target duplicated disease genes, avoiding potentially harmful excessive downregulation. As a proof-of-concept, we studied autosomal dominant adult-onset demyelinating leukodystrophy (ADLD) due to lamin B1 (LMNB1) duplication, a hereditary, progressive and fatal disorder affecting myelin in the CNS. Using a reporter system, we screened the most efficient ASP-siRNAs preferentially targeting one of the alleles at rs1051644 (average minor allele frequency: 0.45) located in the 3' untranslated region of the gene. We identified four siRNAs with a high efficacy and allele-specificity, which were tested in ADLD patient-derived fibroblasts. Three of the small interfering RNAs were highly selective for the target allele and restored both LMNB1 mRNA and protein levels close to control levels. Furthermore, small interfering RNA treatment abrogates the ADLD-specific phenotypes in fibroblasts and in two disease-relevant cellular models: murine oligodendrocytes overexpressing human LMNB1, and neurons directly reprogrammed from patients' fibroblasts. In conclusion, we demonstrated that ASP-silencing by RNA interference is a suitable and promising therapeutic option for ADLD. Moreover, our results have a broad translational value extending to several pathological conditions linked to gene-gain in copy number variations.

     

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