1
|
Hersch SJ, Chandrasekaran S, Lam J, Nafissi N, Slavcev RA. Manufacturing DNA in E. coli yields higher-fidelity DNA than in vitro enzymatic synthesis. Mol Ther Methods Clin Dev 2024; 32:101227. [PMID: 38516691 PMCID: PMC10951457 DOI: 10.1016/j.omtm.2024.101227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 02/26/2024] [Indexed: 03/23/2024]
Abstract
Biotechnologies such as gene therapy have brought DNA vectors to the forefront of pharmaceuticals. The quality of starting material plays a pivotal role in determining final product quality. Here, we examined the fidelity of DNA replication using enzymatic methods (in vitro) compared to plasmid DNA produced in vivo in E. coli. Next-generation sequencing approaches rely on in vitro polymerases, which have inherent limitations in sensitivity. To address this challenge, we introduce a novel assay based on loss-of-function (LOF) mutations in the conditionally toxic sacB gene. Our findings show that DNA production in E. coli results in significantly fewer LOF mutations (80- to 3,000-fold less) compared to enzymatic DNA replication methods such as polymerase chain reaction (PCR) and rolling circle amplification (RCA). These results suggest that using DNA produced by PCR or RCA may introduce a substantial number of mutation impurities, potentially affecting the quality and yield of final pharmaceutical products. Our study underscores that DNA synthesized in vitro has a significantly higher mutation rate than DNA produced traditionally in E. coli. Therefore, utilizing in vitro enzymatically produced DNA in biotechnology and biomanufacturing may entail considerable fidelity-related risks, while using DNA starting material derived from E. coli substantially mitigates this risk.
Collapse
Affiliation(s)
| | | | - Jamie Lam
- Mediphage Bioceuticals, Inc, Toronto, ON, Canada
| | - Nafiseh Nafissi
- Mediphage Bioceuticals, Inc, Toronto, ON, Canada
- School of Pharmacy, University of Waterloo, Waterloo, ON, Canada
| | - Roderick A. Slavcev
- Mediphage Bioceuticals, Inc, Toronto, ON, Canada
- School of Pharmacy, University of Waterloo, Waterloo, ON, Canada
- Centre for Eye and Vision Research, HKSTP, Ma Liu Shui, Hong Kong
| |
Collapse
|
2
|
Chemparathy A, Le Guen Y, Chen S, Lee EG, Leong L, Gorzynski JE, Jensen TD, Ferrasse A, Xu G, Xiang H, Belloy ME, Kasireddy N, Peña-Tauber A, Williams K, Stewart I, Talozzi L, Wingo TS, Lah JJ, Jayadev S, Hales CM, Peskind E, Child DD, Roeber S, Keene CD, Cong L, Ashley EA, Yu CE, Greicius MD. APOE loss-of-function variants: Compatible with longevity and associated with resistance to Alzheimer's disease pathology. Neuron 2024; 112:1110-1116.e5. [PMID: 38301647 PMCID: PMC10994769 DOI: 10.1016/j.neuron.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/31/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024]
Abstract
The ε4 allele of apolipoprotein E (APOE) is the strongest genetic risk factor for sporadic Alzheimer's disease (AD). Knockdown of ε4 may provide a therapeutic strategy for AD, but the effect of APOE loss of function (LoF) on AD pathogenesis is unknown. We searched for APOE LoF variants in a large cohort of controls and patients with AD and identified seven heterozygote carriers of APOE LoF variants. Five carriers were controls (aged 71-90 years), one carrier was affected by progressive supranuclear palsy, and one carrier was affected by AD with an unremarkable age at onset of 75 years. Two APOE ε3/ε4 controls carried a stop-gain affecting ε4: one was cognitively normal at 90 years and had no neuritic plaques at autopsy; the other was cognitively healthy at 79 years, and lumbar puncture at 76 years showed normal levels of amyloid. These results suggest that ε4 drives AD risk through the gain of abnormal function and support ε4 knockdown as a viable therapeutic option.
Collapse
Affiliation(s)
- Augustine Chemparathy
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Yann Le Guen
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA; Quantitative Sciences Unit, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Sunny Chen
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA
| | - Eun-Gyung Lee
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA
| | - Lesley Leong
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA
| | - John E Gorzynski
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Tanner D Jensen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Alexis Ferrasse
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Guangxue Xu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Hong Xiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael E Belloy
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Nandita Kasireddy
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Andrés Peña-Tauber
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Kennedy Williams
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Ilaria Stewart
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Lia Talozzi
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Thomas S Wingo
- Emory University School of Medicine, Atlanta, GA, USA; Goizueta Alzheimer's Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - James J Lah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Suman Jayadev
- Department of Neurology, University of Washington, Seattle, WA, USA
| | - Chadwick M Hales
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA; Department of Neurology, University of Washington, Seattle, WA, USA
| | - Elaine Peskind
- Veterans Affairs Northwest Network Mental Illness Research, Education, and Clinical Center, Veteran Affairs Puget Sound Health Care System, Seattle, WA, USA; Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Daniel D Child
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Sigrun Roeber
- Center for Neuropathology and Prion Research, Faculty of Medicine, LMU Munich, Munich, Germany
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Le Cong
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Euan A Ashley
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Center for Inherited Cardiovascular Disease, Stanford University, Stanford, CA, USA; Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Chang-En Yu
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA; Department of Medicine, University of Washington, Seattle, WA, USA
| | - Michael D Greicius
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.
| |
Collapse
|
3
|
Tian Y, Zhai QX, Li XJ, Shi Z, Cheng CF, Fan CX, Tang B, Zhang Y, He YY, Li WB, Luo S, Hou C, Chen WX, Liao WP, Wang J. Corrigendum: ATP6V0C is associated with febrile seizures and epilepsy with febrile seizures plus. Front Mol Neurosci 2024; 17:1385915. [PMID: 38495552 PMCID: PMC10940531 DOI: 10.3389/fnmol.2024.1385915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/19/2024] Open
Abstract
[This corrects the article DOI: 10.3389/fnmol.2022.889534.].
Collapse
Affiliation(s)
- Yang Tian
- Department of Neurology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Qiong-Xiang Zhai
- Department of Pediatrics, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xiao-Jing Li
- Department of Neurology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Zhen Shi
- Department of Neurology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Chuan-Fang Cheng
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, Ministry of Education of China, Guangzhou, China
| | - Cui-Xia Fan
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, Ministry of Education of China, Guangzhou, China
| | - Bin Tang
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, Ministry of Education of China, Guangzhou, China
| | - Ying Zhang
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yun-Yan He
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, Ministry of Education of China, Guangzhou, China
| | - Wen-Bin Li
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, Ministry of Education of China, Guangzhou, China
| | - Sheng Luo
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, Ministry of Education of China, Guangzhou, China
| | - Chi Hou
- Department of Neurology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Wen-Xiong Chen
- Department of Neurology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Wei-Ping Liao
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, Ministry of Education of China, Guangzhou, China
| | - Jie Wang
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, Ministry of Education of China, Guangzhou, China
| |
Collapse
|
4
|
Mehawej C, Ibrahim M, Khalife L, Chouery E, El Hachem S, Sayad A, El Traboulsi A, Inati A, Megarbane A. A homozygous frameshift variant expands the clinical spectrum of SAMD9 gene defects. Clin Genet 2024; 105:202-208. [PMID: 37830462 DOI: 10.1111/cge.14439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/14/2023]
Abstract
SAMD9, a ubiquitously expressed protein, is involved in several mechanisms, including endosome fusion, growth suppression and modulation of innate immune responses to stress and viral infections. While biallelic mutations in SAMD9 are linked to normophosphatemic familial tumoral calcinosis, heterozygous gain-of-function mutations in the same gene are responsible for MIRAGE, a multisystemic syndrome characterized by myelodysplasia, infection, restriction of growth, adrenal hypoplasia, genital phenotypes, and enteropathy. A two-and-a-half-year-old girl, from a consanguineous Lebanese family, was included in this study. She presents with pre- and post-natal growth retardation, recurrent fevers, persistent diarrhea, elevated CRP and intermittent hypoglycemia. Whole genome sequencing revealed a homozygous frameshift variant in SAMD9 (NM_017654.4: c.480_481del; p.Val162Ilefs*5) in the proband. Sanger sequencing confirms its segregation with the disease in the family, and immunoblotting showed that the detected variant abolishes SAMD9 expression in the patient. Our findings expand the clinical spectrum linked to SAMD9 and highlight the importance of investigating further cases with mutations in this gene, as this will pave the way towards the understanding of the pathways driving these diseases.
Collapse
Affiliation(s)
- Cybel Mehawej
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - Maroun Ibrahim
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - Lynn Khalife
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - Eliane Chouery
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - Setrida El Hachem
- Department of Natural Sciences, Lebanese American University, Byblos, Lebanon
| | - Alain Sayad
- Department of Pediatrics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - Aya El Traboulsi
- Department of Pediatric Hematology, Rafic Hariri University Hospital, Beirut and North Specialty Clinics, Tripoli, Lebanon
| | - Adlette Inati
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
- Division of Pediatric Hematology Oncology, Nini Hospital, Tripoli, Lebanon
| | - Andre Megarbane
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
- Institut Jérôme Lejeune, Paris, France
| |
Collapse
|
5
|
González-Garrido A, López-Ramírez O, Cerda-Mireles A, Navarrete-Miranda T, Flores-Arenas AI, Rojo-Domínguez A, Arregui L, Iturralde P, Antúnez-Argüelles E, Domínguez-Pérez M, Jacobo-Albavera L, Carnevale A, Villarreal-Molina T. KCNQ1 p.D446E Variant as a Risk Allele for Arrhythmogenic Phenotypes: Electrophysiological Characterization Reveals a Complex Phenotype Affecting the Slow Delayed Rectifier Potassium Current (IKs) Voltage Dependence by Causing a Hyperpolarizing Shift and a Lack of Response to Protein Kinase A Activation. Int J Mol Sci 2024; 25:953. [PMID: 38256028 PMCID: PMC10816087 DOI: 10.3390/ijms25020953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/05/2024] [Accepted: 01/07/2024] [Indexed: 01/24/2024] Open
Abstract
Genetic testing is crucial in inherited arrhythmogenic channelopathies; however, the clinical interpretation of genetic variants remains challenging. Incomplete penetrance, oligogenic, polygenic or multifactorial forms of channelopathies further complicate variant interpretation. We identified the KCNQ1/p.D446E variant in 2/63 patients with long QT syndrome, 30-fold more frequent than in public databases. We thus characterized the biophysical phenotypes of wildtype and mutant IKs co-expressing these alleles with the β-subunit minK in HEK293 cells. KCNQ1 p.446E homozygosity significantly shifted IKs voltage dependence to hyperpolarizing potentials in basal conditions (gain of function) but failed to shift voltage dependence to hyperpolarizing potentials (loss of function) in the presence of 8Br-cAMP, a protein kinase A activator. Basal IKs activation kinetics did not differ among genotypes, but in response to 8Br-cAMP, IKs 446 E/E (homozygous) activation kinetics were slower at the most positive potentials. Protein modeling predicted a slower transition of the 446E Kv7.1 tetrameric channel to the stabilized open state. In conclusion, biophysical and modelling evidence shows that the KCNQ1 p.D446E variant has complex functional consequences including both gain and loss of function, suggesting a contribution to the pathogenesis of arrhythmogenic phenotypes as a functional risk allele.
Collapse
Affiliation(s)
- Antonia González-Garrido
- Laboratorio de Enfermedades Mendelianas, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (A.G.-G.); (A.C.-M.); (T.N.-M.); (A.I.F.-A.); (A.C.)
| | - Omar López-Ramírez
- Instituto de Oftalmología Fundación de Asistencia Privada Conde de la Valenciana, I.A.P., Mexico City 06800, Mexico;
| | - Abel Cerda-Mireles
- Laboratorio de Enfermedades Mendelianas, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (A.G.-G.); (A.C.-M.); (T.N.-M.); (A.I.F.-A.); (A.C.)
| | - Thania Navarrete-Miranda
- Laboratorio de Enfermedades Mendelianas, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (A.G.-G.); (A.C.-M.); (T.N.-M.); (A.I.F.-A.); (A.C.)
| | - Aranza Iztanami Flores-Arenas
- Laboratorio de Enfermedades Mendelianas, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (A.G.-G.); (A.C.-M.); (T.N.-M.); (A.I.F.-A.); (A.C.)
| | - Arturo Rojo-Domínguez
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Mexico City 05348, Mexico; (A.R.-D.); (L.A.)
| | - Leticia Arregui
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Mexico City 05348, Mexico; (A.R.-D.); (L.A.)
| | - Pedro Iturralde
- Departamento de Electrofisiología, Instituto Nacional de Cardiología “Ignacio Chávez”, Mexico City 14080, Mexico;
| | | | - Mayra Domínguez-Pérez
- Laboratorio de Genómica de Enfermedades Cardiovasculares, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (M.D.-P.); (L.J.-A.)
| | - Leonor Jacobo-Albavera
- Laboratorio de Genómica de Enfermedades Cardiovasculares, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (M.D.-P.); (L.J.-A.)
| | - Alessandra Carnevale
- Laboratorio de Enfermedades Mendelianas, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (A.G.-G.); (A.C.-M.); (T.N.-M.); (A.I.F.-A.); (A.C.)
| | - Teresa Villarreal-Molina
- Laboratorio de Genómica de Enfermedades Cardiovasculares, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (M.D.-P.); (L.J.-A.)
| |
Collapse
|
6
|
Arunkumar R, Zhou SO, Day JP, Bakare S, Pitton S, Zhang Y, Hsing CY, O’Boyle S, Pascual-Gil J, Clark B, Chandler RJ, Leitão AB, Jiggins FM. Natural selection has driven the recurrent loss of an immunity gene that protects Drosophila against a major natural parasite. Proc Natl Acad Sci U S A 2023; 120:e2211019120. [PMID: 37552757 PMCID: PMC10438844 DOI: 10.1073/pnas.2211019120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 06/26/2023] [Indexed: 08/10/2023] Open
Abstract
Polymorphisms in immunity genes can have large effects on susceptibility to infection. To understand the origins of this variation, we have investigated the genetic basis of resistance to the parasitoid wasp Leptopilina boulardi in Drosophila melanogaster. We found that increased expression of the gene lectin-24A after infection by parasitic wasps was associated with a faster cellular immune response and greatly increased rates of killing the parasite. lectin-24A encodes a protein that is strongly up-regulated in the fat body after infection and localizes to the surface of the parasite egg. In certain susceptible lines, a deletion upstream of the lectin-24A has largely abolished expression. Other mutations predicted to abolish the function of this gene have arisen recurrently in this gene, with multiple loss-of-expression alleles and premature stop codons segregating in natural populations. The frequency of these alleles varies greatly geographically, and in some southern African populations, natural selection has driven them near to fixation. We conclude that natural selection has favored the repeated loss of an important component of the immune system, suggesting that in some populations, a pleiotropic cost to lectin-24A expression outweighs the benefits of resistance.
Collapse
Affiliation(s)
- Ramesh Arunkumar
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Shuyu Olivia Zhou
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Jonathan P. Day
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Sherifat Bakare
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
- Department of Biochemical Sciences, School of Biosciences, University of Surrey, 388 Stag Hill, Guildford,GU2 7XH, United Kingdom
| | - Simone Pitton
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
- Biosciences Department, Università degli Studi di Milano, Via Celoria 26, Milano, MI20133, Italy
| | - Yexin Zhang
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Chi-Yun Hsing
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Sinead O’Boyle
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
- School of Biomolecular and Biomedical Science, University College Dublin, DublinD04 V1W8, Ireland
| | - Juan Pascual-Gil
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
- Facultad de Ciencias, Universidad Autónoma de Madrid, C. Francisco Tomás y Valiente 7, 28049Madrid, Spain
| | - Belinda Clark
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Rachael J. Chandler
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
- Department of Biochemical Sciences, School of Biosciences, University of Surrey, 388 Stag Hill, Guildford,GU2 7XH, United Kingdom
| | - Alexandre B. Leitão
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Francis M. Jiggins
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| |
Collapse
|
7
|
Delpire E, Koumangoye R. NKCC1 in human diseases: is the SLC12A2 gene haploinsufficient? Am J Physiol Cell Physiol 2023; 325:C385-C390. [PMID: 37399495 PMCID: PMC10393318 DOI: 10.1152/ajpcell.00238.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/17/2023] [Accepted: 06/17/2023] [Indexed: 07/05/2023]
Abstract
Mutations in the SLC12A2 gene, which encodes the Na-K-2Cl cotransporter-1 (NKCC1), are linked to various conditions such as neurodevelopmental deficits, deafness, and fluid secretion in different epithelia. Cases of complete NKCC1 deficiency in young patients are straightforward, leading to clinical presentations that overlap with the phenotypes observed in NKCC1 knockout mouse models. However, cases involving deleterious variants in one allele are more difficult, as the clinical presentation is variable, and the cause-effect relationship is not always clear. For instance, we worked on a single patient's case from multiple angles and published six related papers to convince ourselves of the cause-and-effect relationship between her NKCC1 mutation and her clinical presentations. The cluster of mutations in a small portion of the carboxyl terminus and its association with deafness point to a cause-and-effect relationship, even if the molecular mechanism is unknown. Overall, the preponderance of evidence suggests that the SLC12A2 gene is a human disease-causing and likely haploinsufficient gene that requires further investigation.
Collapse
Affiliation(s)
- Eric Delpire
- Department of Anesthesiology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States
| | - Rainelli Koumangoye
- Department of Anesthesiology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States
| |
Collapse
|
8
|
Asano T, Utsumi T, Kagawa R, Karakawa S, Okada S. Inborn errors of immunity with loss- and gain-of-function germline mutations in STAT1. Clin Exp Immunol 2023; 212:96-106. [PMID: 36420581 PMCID: PMC10128167 DOI: 10.1093/cei/uxac106] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/01/2022] [Accepted: 11/19/2022] [Indexed: 11/25/2022] Open
Abstract
STAT1 dysfunction causes a wide range of immune dysregulation phenotypes, which have been classified into four disease types, namely, (i) autosomal recessive (AR) complete STAT1 deficiency, (ii) AR partial STAT1 deficiency, (iii) autosomal dominant (AD) STAT1 deficiency, and (iv) AD STAT1 gain of function (GOF), based on their mode of inheritance and function. Disease types (i, ii, and iii) are caused by STAT1 loss-of-function (LOF) mutations, whereas disease type (iv) is caused by STAT1 GOF mutations. Therefore, the functional analysis of mutations is necessary for the precise diagnosis.
Collapse
Affiliation(s)
- Takaki Asano
- Department of Pediatrics, Hiroshima University, Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Takanori Utsumi
- Department of Pediatrics, Hiroshima University, Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Reiko Kagawa
- Department of Pediatrics, Hiroshima University, Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Shuhei Karakawa
- Department of Pediatrics, Hiroshima University, Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Satoshi Okada
- Department of Pediatrics, Hiroshima University, Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| |
Collapse
|
9
|
Arteche-López A, Avila-Fernandez A, Damian A, Soengas-Gonda E, de la Fuente RP, Gómez PR, Merlo JG, Burgos LH, Fernández CC, Rosales JML, Martínez JFG, Quesada-Espinosa JF, Corton M, Guerrero-Molina MP. New Cerebellar Ataxia, Neuropathy, Vestibular Areflexia Syndrome cases are caused by the presence of a nonsense variant in compound heterozygosity with the pathogenic repeat expansion in the RFC1 gene. Clin Genet 2023; 103:236-241. [PMID: 36250766 DOI: 10.1111/cge.14249] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/28/2022] [Accepted: 10/07/2022] [Indexed: 01/20/2023]
Abstract
The biallelic pathogenic repeat (AAGGG)400-2000 intronic expansion in the RFC1 gene has been recently described as the cause of cerebellar ataxia, neuropathy, vestibular areflexia syndrome (CANVAS) and as a major cause of late-onset ataxia. Since then, many heterozygous carriers have been identified, with an estimated allele frequency of 0.7% to 4% in the healthy population. Here, we describe in two affected CANVAS sisters the presence of the nonsense c.724C > T p.(Arg242*) variant in compound heterozygosity with the pathogenic repeat expansion in the RFC1 gene. Further RNA analysis demonstrated a reduced expression of the p.Arg242* allele in patients confirming an efficient nonsense-mediated mRNA decay. We also highlight the importance of considering the sequencing of the RFC1 gene for the diagnosis, especially in patients with CANVAS diagnosis carriers of the AAGGG repeat expansion.
Collapse
Affiliation(s)
- Ana Arteche-López
- Genetics Department, 12 de Octubre University Hospital, Madrid, Spain
- UDISGEN (Unidad de Dismorfología y Genética), 12 de Octubre University Hospital, Madrid, Spain
| | - Almudena Avila-Fernandez
- Genetics Department, Health Research Institute-Jimenez Diaz Foundation University Hospital, Universidad Autónoma de Madrid (IIS-FJD-UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Alejandra Damian
- Genetics Department, Health Research Institute-Jimenez Diaz Foundation University Hospital, Universidad Autónoma de Madrid (IIS-FJD-UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Emma Soengas-Gonda
- Genetics Department, 12 de Octubre University Hospital, Madrid, Spain
- UDISGEN (Unidad de Dismorfología y Genética), 12 de Octubre University Hospital, Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Rubén Pérez de la Fuente
- Genetics Department, 12 de Octubre University Hospital, Madrid, Spain
- UDISGEN (Unidad de Dismorfología y Genética), 12 de Octubre University Hospital, Madrid, Spain
| | | | - Jesús Gallego Merlo
- Genetics Department, Health Research Institute-Jimenez Diaz Foundation University Hospital, Universidad Autónoma de Madrid (IIS-FJD-UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Laura Horcajada Burgos
- Genetics Department, Health Research Institute-Jimenez Diaz Foundation University Hospital, Universidad Autónoma de Madrid (IIS-FJD-UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Jose Miguel Lezana Rosales
- Genetics Department, 12 de Octubre University Hospital, Madrid, Spain
- UDISGEN (Unidad de Dismorfología y Genética), 12 de Octubre University Hospital, Madrid, Spain
| | | | - Juan Francisco Quesada-Espinosa
- Genetics Department, 12 de Octubre University Hospital, Madrid, Spain
- UDISGEN (Unidad de Dismorfología y Genética), 12 de Octubre University Hospital, Madrid, Spain
| | - Marta Corton
- Genetics Department, Health Research Institute-Jimenez Diaz Foundation University Hospital, Universidad Autónoma de Madrid (IIS-FJD-UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | | |
Collapse
|
10
|
Zhao T, Zhong R, Zhang X, Li G, Zhou C, Fang S, Ding Y, Lin W. Efavirenz restored NMDA receptor dysfunction and inhibited epileptic seizures in GluN2A/Grin2a mutant mice. Front Neurosci 2023; 17:1086462. [PMID: 36937661 PMCID: PMC10017539 DOI: 10.3389/fnins.2023.1086462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/02/2023] [Indexed: 03/06/2023] Open
Abstract
Introduction N-methyl-D-aspartate receptor (NMDAR) is one of the main receptor of the excitatory neurotransmitter glutamate in the brain, which is the key determinant of the excitatory/inhibitory balance of neural network. GluN2A/GRIN2A is one of the subunits of NMDAR and plays an important role in epilepsy. Approximately 78% of patients with GluN2A/Grin2a mutations have epilepsy, and the underlying mechanism of this association is not well characterized. Methods We constructed a mouse model of hyperthermic seizure, and conducted in vitro and in vivo electrophysiological and behavioral studies to clarify the pathogenic characteristics and mechanism of GluN2A/GRIN2A-V685G mutation. In addition, the drug efavirenz (EFV), which is used to treat HIV infection, was administrated to mutant animals to assess whether it can restore the loss of function. Results Mutant mice showed no significant change in the mRNA or protein expressions of NMDAR compared with wild type (WT) mice. Mice with GluN2A/GRIN2A-V685G mutation exhibited shorter latency to seizure, increased frequency of seizure-like events, decreased peak current and current area of NMDAR excitatory postsynaptic current, and decreased event frequency of micro-inhibitory postsynaptic current, compared to WT mice. They also exhibited decreased threshold, increased amplitude, increased input resistance, and increased root number of action potential. EFV administration reversed these changes. The loss-of-function (LoF) mutation of NMDAR changed the excitatory/inhibitory balance of neural network, rendering animal more prone to seizures. Discussion EFV was indicated to hold its potential in the treatment of inherited epilepsy.
Collapse
Affiliation(s)
- Teng Zhao
- Department of Neurology, The First Hospital of Jilin University, Changchun, China
| | - Rui Zhong
- Department of Neurology, The First Hospital of Jilin University, Changchun, China
| | - Xinyue Zhang
- Department of Neurology, The First Hospital of Jilin University, Changchun, China
| | - Guangjian Li
- Department of Neurology, The First Hospital of Jilin University, Changchun, China
| | - Chunkui Zhou
- Department of Neurology, The First Hospital of Jilin University, Changchun, China
| | - Shaokuan Fang
- Department of Neurology, The First Hospital of Jilin University, Changchun, China
- Shaokuan Fang,
| | - Ying Ding
- Department of Radiology, The First Hospital of Jilin University, Changchun, China
- Ying Ding,
| | - Weihong Lin
- Department of Neurology, The First Hospital of Jilin University, Changchun, China
- *Correspondence: Weihong Lin,
| |
Collapse
|
11
|
AlTassan R, AlQudairy H, Alromayan R, Alfalah A, AlHarbi OA, González-Álvarez AC, Arold ST, Kaya N. Clinical, Radiological, and Genetic Characterization of a Patient with a Novel Homoallelic Loss-of-Function Variant in DNM1. Genes (Basel) 2022; 13:genes13122252. [PMID: 36553519 PMCID: PMC9777962 DOI: 10.3390/genes13122252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/02/2022] Open
Abstract
Heterozygous pathogenic variants in DNM1 are linked to an autosomal dominant form of epileptic encephalopathy. Recently, homozygous loss-of-function variants in DNM1 were reported to cause an autosomal recessive form of developmental and epileptic encephalopathy in unrelated patients. Here, we investigated a singleton from a first-degree cousin marriage who presented with facial dysmorphism, global developmental delay, seizure disorder, and nystagmus. To identify the involvement of any likely genetic cause, diagnostic clinical exome sequencing was performed. Comprehensive filtering revealed a single plausible candidate variant in DNM1. Sanger sequencing of the trio, the patient, and her parents, confirmed the full segregation of the variant. The variant is a deletion leading to a premature stop codon and is predicted to cause a protein truncation. Structural modeling implicated a complete loss of function of the Dynamin 1 (DNM1). Such mutation is predicted to impair the nucleotide binding, dimer formation, and GTPase activity of DNM1. Our study expands the phenotypic spectrum of pathogenic homozygous loss-of-function variants in DNM1.
Collapse
Affiliation(s)
- Ruqaiah AlTassan
- Department of Medical Genomics, Centre for Genomic Medicine, MBC: 75, P.O. Box 3354, King Faisal Specialist Hospital, and Research Centre, Riyadh 11211, Saudi Arabia
- College of Medicine, P.O. Box 50927, AlFaisal University, Riyadh 11533, Saudi Arabia
| | - Hanan AlQudairy
- Translational Genomic Department, Centre for Genomic Medicine, MBC: 03, P.O. Box 3354, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Rakan Alromayan
- Translational Genomic Department, Centre for Genomic Medicine, MBC: 03, P.O. Box 3354, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
- College of Medicine, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdullah Alfalah
- Department of Medical Genomics, Centre for Genomic Medicine, MBC: 75, P.O. Box 3354, King Faisal Specialist Hospital, and Research Centre, Riyadh 11211, Saudi Arabia
| | - Omar A. AlHarbi
- Department of Radiology, MBC: 28, P.O. Box 3354, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Ana C. González-Álvarez
- Bioengineering Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Stefan T. Arold
- Bioengineering Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational Biology Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université de Montpellier, F-34090 Montpellier, France
| | - Namik Kaya
- Translational Genomic Department, Centre for Genomic Medicine, MBC: 03, P.O. Box 3354, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
- Correspondence: ; Tel.: +966-112162919 (ext. 39612)
| |
Collapse
|
12
|
Wolsan M, Sato JJ. Role of feeding specialization in taste receptor loss: insights from sweet and umami receptor evolution in Carnivora. Chem Senses 2022; 47:6838703. [PMID: 36433799 PMCID: PMC9680018 DOI: 10.1093/chemse/bjac033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Controversy and misunderstanding surround the role of feeding specialization in taste receptor loss in vertebrates. We refined and tested the hypothesis that this loss is caused by feeding specializations. Specifically, feeding specializations were proposed to trigger time-dependent process of taste receptor loss through deprivation of benefit of using the receptor's gustatory function. We propose that this process may be accelerated by abiotic environmental conditions or decelerated/stopped because of extragustatory functions of the receptor's protein(s). As test case we used evolution of the sweet (TAS1R2+TAS1R3) and umami (TAS1R1+TAS1R3) receptors in Carnivora (dogs, cats, and kin). We predicted these receptors' absence/presence using data on presence/absence of inactivating mutations in these receptors' genes and data from behavioral sweet/umami preference tests. We identified 20 evolutionary events of sweet (11) or umami (9) receptor loss. These events affected species with feeding specializations predicted to favor sweet/umami receptor loss (27 and 22 species, respectively). All species with feeding habits predicted to favor sweet/umami receptor retention (11 and 24, respectively) were found to retain that receptor. Six species retained the sweet (5) or umami (1) receptor despite feeding specialization predicted to favor loss of that receptor, which can be explained by the time dependence of sweet/umami receptor loss process and the possible decelerating effect of TAS1R extragustatory functions so that the sweet/umami receptor process is ongoing in these species. Our findings support the idea that feeding specialization leads to taste receptor loss and is the main if not only triggering factor for evolutionary loss of taste receptors.
Collapse
Affiliation(s)
- Mieczyslaw Wolsan
- Corresponding author: Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679 Warszawa, Poland.
| | - Jun J Sato
- Department of Biotechnology, Fukuyama University, Higashimura-cho, Aza, Sanzo, 985-1, Fukuyama 729-0292, Japan
| |
Collapse
|
13
|
Zug R, Uller T. Evolution and dysfunction of human cognitive and social traits: A transcriptional regulation perspective. Evol Hum Sci 2022; 4:e43. [PMID: 37588924 PMCID: PMC10426018 DOI: 10.1017/ehs.2022.42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/11/2022] [Accepted: 09/11/2022] [Indexed: 11/07/2022] Open
Abstract
Evolutionary changes in brain and craniofacial development have endowed humans with unique cognitive and social skills, but also predisposed us to debilitating disorders in which these traits are disrupted. What are the developmental genetic underpinnings that connect the adaptive evolution of our cognition and sociality with the persistence of mental disorders with severe negative fitness effects? We argue that loss of function of genes involved in transcriptional regulation represents a crucial link between the evolution and dysfunction of human cognitive and social traits. The argument is based on the haploinsufficiency of many transcriptional regulator genes, which makes them particularly sensitive to loss-of-function mutations. We discuss how human brain and craniofacial traits evolved through partial loss of function (i.e. reduced expression) of these genes, a perspective compatible with the idea of human self-domestication. Moreover, we explain why selection against loss-of-function variants supports the view that mutation-selection-drift, rather than balancing selection, underlies the persistence of psychiatric disorders. Finally, we discuss testable predictions.
Collapse
Affiliation(s)
- Roman Zug
- Department of Biology, Lund University, Lund, Sweden
| | - Tobias Uller
- Department of Biology, Lund University, Lund, Sweden
| |
Collapse
|
14
|
Baselga-Cervera B, Gettle N, Travisano M. Loss-of-heterozygosity facilitates a fitness valley crossing in experimentally evolved multicellular yeast. Proc Biol Sci 2022; 289:20212722. [PMID: 36547392 PMCID: PMC9185828 DOI: 10.1098/rspb.2021.2722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Determining how adaptive possibilities do or do not become evolutionary realities is central to understanding the tempo and mode of evolutionary change. Some of the simplest evolutionary landscapes arise from underdominance at a single locus where the fitness valley consists of only one less-fit genotype. Despite their potential for rapid evolutionary change, few such examples have been investigated. We capitalized on an experimental system in which a significant evolutionary shift, the transition from uni-to-multicellularity, was observed in asexual diploid populations of Saccharomyces cerevisiae experimentally selected for increased settling rates. The multicellular phenotype results from recessive single-locus mutations that undergo loss-of-heterozygosity (LOH) events. By reconstructing the necessary heterozygous intermediate steps, we found that the evolution of multicellularity involves a decrease in size during the first steps. Heterozygous genotypes are 20% smaller in size than genotypes with functional alleles. Nevertheless, populations of heterozygotes give rise to multicellular genotypes more readily than unicellular genotypes with two functional alleles, by rapid LOH events. LOH drives adaptation that may enable rapid evolution in diploid yeast. Together these results show discordance between the phenotypic and genotypic multicellular transition. The evolutionary path to multicellularity, and the adaptive benefits of increased size, requires initial size reductions.
Collapse
Affiliation(s)
- Beatriz Baselga-Cervera
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, MN 55108, USA,Minnesota Center for Philosophy of Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Noah Gettle
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Michael Travisano
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, MN 55108, USA,The BioTechnology Institute, University of Minnesota, St Paul, MN 55108, USA,Minnesota Center for Philosophy of Science, University of Minnesota, Minneapolis, MN 55455, USA
| |
Collapse
|
15
|
Tian Y, Zhai QX, Li XJ, Shi Z, Cheng CF, Fan CX, Tang B, Zhang Y, He YY, Li WB, Luo S, Hou C, Chen WX, Liao WP, Wang J. ATP6V0C Is Associated With Febrile Seizures and Epilepsy With Febrile Seizures Plus. Front Mol Neurosci 2022; 15:889534. [PMID: 35600075 PMCID: PMC9120599 DOI: 10.3389/fnmol.2022.889534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/12/2022] [Indexed: 11/13/2022] Open
Abstract
Purpose To identify novel genetic causes of febrile seizures (FS) and epilepsy with febrile seizures plus (EFS+). Methods We performed whole-exome sequencing in a cohort of 32 families, in which at least two individuals were affected by FS or EFS+. The probands, their parents, and available family members were recruited to ascertain whether the genetic variants were co-segregation. Genes with repetitively identified variants with segregations were selected for further studies to define the gene-disease association. Results We identified two heterozygous ATP6V0C mutations (c.64G > A/p.Ala22Thr and c.361_373del/p.Thr121Profs*7) in two unrelated families with six individuals affected by FS or EFS+. The missense mutation was located in the proteolipid c-ring that cooperated with a-subunit forming the hemichannel for proton transferring. It also affected the hydrogen bonds with surround residues and the protein stability, implying a damaging effect. The frameshift mutation resulted in a loss of function by yielding a premature termination of 28 residues at the C-terminus of the protein. The frequencies of ATP6V0C mutations identified in this cohort were significantly higher than that in the control populations. All the six affected individuals suffered from their first FS at the age of 7-8 months. The two probands later manifested afebrile seizures including myoclonic seizures that responded well to lamotrigine. They all displayed favorable outcomes without intellectual or developmental abnormalities, although afebrile seizures or frequent seizures occurred. Conclusion This study suggests that ATP6V0C is potentially a candidate pathogenic gene of FS and EFS+. Screening for ATP6V0C mutations would help differentiating patients with Dravet syndrome caused by SCN1A mutations, which presented similar clinical manifestation but different responses to antiepileptic treatment.
Collapse
Affiliation(s)
- Yang Tian
- Department of Neurology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Qiong-Xiang Zhai
- Department of Pediatrics, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xiao-Jing Li
- Department of Neurology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Zhen Shi
- Department of Neurology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Chuan-Fang Cheng
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, Ministry of Education of China, Guangzhou, China
| | - Cui-Xia Fan
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, Ministry of Education of China, Guangzhou, China
| | - Bin Tang
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, Ministry of Education of China, Guangzhou, China
| | - Ying Zhang
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yun-Yan He
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, Ministry of Education of China, Guangzhou, China
| | - Wen-Bin Li
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, Ministry of Education of China, Guangzhou, China
| | - Sheng Luo
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, Ministry of Education of China, Guangzhou, China
| | - Chi Hou
- Department of Neurology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Wen-Xiong Chen
- Department of Neurology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Wei-Ping Liao
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, Ministry of Education of China, Guangzhou, China
| | - Jie Wang
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, Ministry of Education of China, Guangzhou, China
| |
Collapse
|
16
|
Holling T, Lisfeld J, Johannsen J, Matschke J, Song F, Altmeppen HC, Kutsche K. Autosomal dominantly inherited myopathy likely caused by the TNNT1 variant p.(Asp65Ala). Hum Mutat 2022; 43:1224-1233. [PMID: 35510366 DOI: 10.1002/humu.24397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 04/25/2022] [Accepted: 05/01/2022] [Indexed: 11/12/2022]
Abstract
Nemaline myopathies (NEM) are genetically and clinically heterogenous. Biallelic or monoallelic variants in TNNT1, encoding slow skeletal troponin T1 (TnT1), cause NEM. We report a 2-year-old patient and his mother carrying the heterozygous TNNT1 variant c.194A>C/p.(Asp65Ala) that occurred de novo in the mother. Both had muscle hypotrophy and muscle weakness. Muscle pathology in the proband's mother revealed slow twitch type 1 fiber hypotrophy and fast twitch type 2 fiber hypertrophy that was confirmed by a reduced ratio of slow skeletal myosin to fast skeletal myosin type 2a. RT-PCR and immunoblotting data demonstrated increased levels of high-molecular-weight TnT1 isoforms in skeletal muscle of the proband's mother that were also observed in some controls. In an overexpression system, complex formation of TnT1-D65A with tropomyosin 3 (TPM3) was enhanced. The previously reported TnT1-E104V and TnT1-L96P mutants showed reduced or no co-immunoprecipitation with TPM3. Our studies support pathogenicity of the TNNT1 p.(Asp65Ala) variant. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Tess Holling
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jasmin Lisfeld
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jessika Johannsen
- Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jakob Matschke
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Feizhi Song
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| |
Collapse
|
17
|
Koprulu M, Zhao Y, Wheeler E, Dong L, Rocha N, Li C, Griffin JD, Patel S, Van de Streek M, Glastonbury CA, Stewart ID, Day FR, Luan J, Bowker N, Wittemans LBL, Kerrison ND, Cai L, Lucarelli DME, Barroso I, McCarthy MI, Scott RA, Saudek V, Small KS, Wareham NJ, Semple RK, Perry JRB, O’Rahilly S, Lotta LA, Langenberg C, Savage DB. Identification of Rare Loss-of-Function Genetic Variation Regulating Body Fat Distribution. J Clin Endocrinol Metab 2022; 107:1065-1077. [PMID: 34875679 PMCID: PMC8947777 DOI: 10.1210/clinem/dgab877] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Indexed: 11/25/2022]
Abstract
CONTEXT Biological and translational insights from large-scale, array-based genetic studies of fat distribution, a key determinant of metabolic health, have been limited by the difficulty in linking predominantly noncoding variants to specific gene targets. Rare coding variant analyses provide greater confidence that a specific gene is involved, but do not necessarily indicate whether gain or loss of function (LoF) would be of most therapeutic benefit. OBJECTIVE This work aimed to identify genes/proteins involved in determining fat distribution. METHODS We combined the power of genome-wide analysis of array-based rare, nonsynonymous variants in 450 562 individuals in the UK Biobank with exome-sequence-based rare LoF gene burden testing in 184 246 individuals. RESULTS The data indicate that the LoF of 4 genes (PLIN1 [LoF variants, P = 5.86 × 10-7], INSR [LoF variants, P = 6.21 × 10-7], ACVR1C [LoF + moderate impact variants, P = 1.68 × 10-7; moderate impact variants, P = 4.57 × 10-7], and PDE3B [LoF variants, P = 1.41 × 10-6]) is associated with a beneficial effect on body mass index-adjusted waist-to-hip ratio and increased gluteofemoral fat mass, whereas LoF of PLIN4 (LoF variants, P = 5.86 × 10-7 adversely affects these parameters. Phenotypic follow-up suggests that LoF of PLIN1, PDE3B, and ACVR1C favorably affects metabolic phenotypes (eg, triglycerides [TGs] and high-density lipoprotein [HDL] cholesterol concentrations) and reduces the risk of cardiovascular disease, whereas PLIN4 LoF has adverse health consequences. INSR LoF is associated with lower TG and HDL levels but may increase the risk of type 2 diabetes. CONCLUSION This study robustly implicates these genes in the regulation of fat distribution, providing new and in some cases somewhat counterintuitive insight into the potential consequences of targeting these molecules therapeutically.
Collapse
Affiliation(s)
- Mine Koprulu
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
| | - Yajie Zhao
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
| | - Eleanor Wheeler
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
| | - Liang Dong
- University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
| | - Nuno Rocha
- University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
| | - Chen Li
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
| | - John D Griffin
- Internal Medicine Research Unit, Pfizer Worldwide Research, Development, and Medical, Cambridge, Massachusetts 02139, USA
| | - Satish Patel
- University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
| | - Marcel Van de Streek
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Campus, London, SE1 7EH, UK
| | | | - Isobel D Stewart
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
| | - Felix R Day
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
| | - Jian’an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
| | - Nicholas Bowker
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
| | - Laura B L Wittemans
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
- Big Data Institute at the Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, OX3 7LF, UK
- Nuffield Department of Women’s and Reproductive Health, Medical Sciences Division, University of Oxford, Oxford, OX3 9DU, UK
| | - Nicola D Kerrison
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
| | - Lina Cai
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
| | - Debora M E Lucarelli
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
- D.M.E.L. is currently an employee of Enhanc3D Genomics Ltd
| | - Inês Barroso
- Exeter Centre of Excellence for Diabetes Research (EXCEED), Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, EX1 2HZ, UK
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- M.McM.’s current address is Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Robert A Scott
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
| | - Vladimir Saudek
- University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Campus, London, SE1 7EH, UK
| | - Nicholas J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
| | - Robert K Semple
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, EH16 4TJ, UK
| | - John R B Perry
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
| | - Stephen O’Rahilly
- University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
| | - Luca A Lotta
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
- Computational Medicine, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, 10117 Berlin, Germany
- Correspondence: Claudia Langenberg, MD, Dr Med, PhD, MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Box 285, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.
| | - David B Savage
- University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge, CB2 0QQ, UK
- David B. Savage, MBCHB, PhD, University of Cambridge Metabolic Research Laboratories, Wellcome Trust–MRC Institute of Metabolic Science, Box 289, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.
| |
Collapse
|
18
|
Rhinn H, Tatton N, McCaughey S, Kurnellas M, Rosenthal A. Progranulin as a therapeutic target in neurodegenerative diseases. Trends Pharmacol Sci 2022; 43:641-652. [PMID: 35039149 DOI: 10.1016/j.tips.2021.11.015] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/12/2021] [Accepted: 11/18/2021] [Indexed: 01/02/2023]
Abstract
Progranulin (PGRN, encoded by the GRN gene) plays a key role in the development, survival, function, and maintenance of neurons and microglia in the mammalian brain. It regulates lysosomal biogenesis, inflammation, repair, stress response, and aging. GRN loss-of-function mutations cause neuronal ceroid lipofuscinosis or frontotemporal dementia-GRN (FTD-GRN) in a gene dosage-dependent manner. Mutations that reduce PGRN levels increase the risk for developing Alzheimer's disease, Parkinson's disease, and limbic-predominant age-related transactivation response DNA-binding protein 43 encephalopathy, as well as exacerbate the progression of amyotrophic lateral sclerosis (ALS) and FTD caused by the hexanucleotide repeat expansion in the C9orf72 gene. Elevating and/or restoring PGRN levels is an attractive therapeutic strategy and is being investigated for neurodegenerative diseases through multiple mechanisms of action.
Collapse
Affiliation(s)
- Herve Rhinn
- Alector, Inc., South San Francisco, CA 94080, USA
| | | | | | | | | |
Collapse
|
19
|
Xiong J, Liu Z, Chen S, Kessi M, Chen B, Duan H, Deng X, Yang L, Peng J, Yin F. Correlation Analyses of Clinical Manifestations and Variant Effects in KCNB1-Related Neurodevelopmental Disorder. Front Pediatr 2022; 9:755344. [PMID: 35071126 PMCID: PMC8767024 DOI: 10.3389/fped.2021.755344] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 12/14/2021] [Indexed: 12/24/2022] Open
Abstract
Objective: Vitro functional analyses of KCNB1 variants have been done to disclose possible pathogenic mechanisms in KCNB1-related neurodevelopmental disorder. "Complete or partial loss of function (LoF)," "dominant-negative (DN) effect" are applied to describe KCNB1 variant's molecular phenotypes. The study here aimed to investigate clinical presentations and variant effects associations in the disorder. Methods: We reported 10 Chinese pediatric patients with KCNB1-related neurodevelopmental disorder here. Functional experiments on newly reported variants, including electrophysiology and protein expression, were performed in vitro. Phenotypic, functional, and genetic data in the cohort and published literature were collected. According to their variants' molecular phenotypes, patients were grouped into complete or partial LoF, and DN effect or non-dominant-negative (non-DN) effect to compare their clinical features. Results: Nine causative KCNB1 variants in 10 patients were identified in the cohort, including eight novel and one reported. Epilepsy (9/10), global developmental delay (10/10), and behavior issues (7/10) were common clinical features in our patients. Functional analyses of 8 novel variants indicated three partial and five complete LoF variants, five DN and three non-DN effect variants. Patient 1 in our series with truncated variants, whose functional results supported haploinsufficiency, had the best prognosis. Cases in complete LoF group had earlier seizure onset age (64.3 vs. 16.7%, p = 0.01) and worse seizure outcomes (18.8 vs. 66.7%, p = 0.03), and patients in DN effect subgroup had multiple seizure types compared to those in non-DN effect subgroup (65.5 vs. 30.8%, p = 0.039). Conclusion: Patients with KCNB1 variants in the Asian cohort have similar clinical manifestations to those of other races. Truncated KCNB1 variants exhibiting with haploinsufficiency molecular phenotype are linked to milder phenotypes. Individuals with complete LoF and DN effect KCNB1 variants have more severe seizure attacks than the other two subgroups.
Collapse
Affiliation(s)
- Juan Xiong
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
- Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Zhonghua Liu
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Shimeng Chen
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
- Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Miriam Kessi
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
- Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Baiyu Chen
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
- Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Haolin Duan
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
- Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Xiaolu Deng
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
- Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Lifen Yang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
- Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
- Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fei Yin
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
- Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| |
Collapse
|
20
|
Benussi L, Longobardi A, Kocoglu C, Carrara M, Bellini S, Ferrari C, Nicsanu R, Saraceno C, Bonvicini C, Fostinelli S, Zanardini R, Catania M, Moisse M, Van Damme P, Di Fede G, Binetti G, Van Broeckhoven C, van der Zee J, Ghidoni R. Investigating the Endo-Lysosomal System in Major Neurocognitive Disorders Due to Alzheimer's Disease, Frontotemporal Lobar Degeneration and Lewy Body Disease: Evidence for SORL1 as a Cross-Disease Gene. Int J Mol Sci 2021; 22:13633. [PMID: 34948429 DOI: 10.3390/ijms222413633] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/26/2022] Open
Abstract
Dysfunctions in the endo-lysosomal system have been hypothesized to underlie neurodegeneration in major neurocognitive disorders due to Alzheimer's disease (AD), Frontotemporal Lobar Degeneration (FTLD), and Lewy body disease (DLB). The aim of this study is to investigate whether these diseases share genetic variability in the endo-lysosomal pathway. In AD, DLB, and FTLD patients and in controls (948 subjects), we performed a targeted sequencing of the top 50 genes belonging to the endo-lysosomal pathway. Genetic analyses revealed (i) four previously reported disease-associated variants in the SORL1 (p.N1246K, p.N371T, p.D2065V) and DNAJC6 genes (p.M133L) in AD, FTLD, and DLB, extending the previous knowledge attesting SORL1 and DNAJC6 as AD- and PD-related genes, respectively; (ii) three predicted null variants in AD patients in the SORL1 (p.R985X in early onset familial AD, p.R1207X) and PPT1 (p.R48X in early onset familial AD) genes, where loss of function is a known disease mechanism. A single variant and gene burden analysis revealed some nominally significant results of potential interest for SORL1 and DNAJC6 genes. Our data highlight that genes controlling key endo-lysosomal processes (i.e., protein sorting/transport, clathrin-coated vesicle uncoating, lysosomal enzymatic activity regulation) might be involved in AD, FTLD and DLB pathogenesis, thus suggesting an etiological link behind these diseases.
Collapse
|
21
|
Uribe KB, Chemello K, Larrea-Sebal A, Benito-Vicente A, Galicia-Garcia U, Bourane S, Jaafar AK, Lambert G, Martín C. A Systematic Approach to Assess the Activity and Classification of PCSK9 Variants. Int J Mol Sci 2021; 22:ijms222413602. [PMID: 34948399 PMCID: PMC8706470 DOI: 10.3390/ijms222413602] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/03/2021] [Accepted: 12/16/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Gain of function (GOF) mutations of PCSK9 cause autosomal dominant familial hypercholesterolemia as they reduce the abundance of LDL receptor (LDLR) more efficiently than wild-type PCSK9. In contrast, PCSK9 loss of function (LOF) variants are associated with a hypocholesterolemic phenotype. Dozens of PCSK9 variants have been reported, but most remain of unknown significance since their characterization has not been conducted. OBJECTIVE Our aim was to make the most comprehensive assessment of PCSK9 variants and to determine the simplest approach for the classification of these variants. METHODS The expression, maturation, secretion, and activity of nine well-established PCSK9 variants were assessed in transiently transfected HEK293 cells by Western blot and flow cytometry. Their extracellular activities were determined in HepG2 cells incubated with the purified recombinant PCSK9 variants. Their binding affinities toward the LDLR were determined by solid-phase immunoassay. RESULTS LDLR expression increased when cells were transfected with LOF variants and reduced when cells were transfected with GOF variants compared with wild-type PCSK9. Extracellular activities measurements yielded exactly similar results. GOF and LOF variants had increased, respectively reduced, affinities for the LDLR compared with wild-type PCSK9 with the exception of one GOF variant (R218S) that showed complete resistance to inactivation by furin. All variants were expressed at similar levels and underwent normal maturation and secretion patterns except for two LOF and two GOF mutants. CONCLUSIONS We propose that transient transfections of HEK293 cells with a plasmid encoding a PCSK9 variant followed by LDLR expression assessment by flow cytometry is sufficient to reliably determine its GOF or LOF status. More refined experiments should only be used to determine the underlying mechanism(s) at hand.
Collapse
Affiliation(s)
- Kepa B. Uribe
- Department of Molecular Biophysics, Biofisika Institute, University of Basque Country and Consejo Superior de Investigaciones Científicas (UPV/EHU, CSIC), 48940 Leioa, Spain; (K.B.U.); (A.L.-S.); (A.B.-V.); (U.G.-G.)
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), 20014 Donostia San Sebastian, Spain
| | - Kevin Chemello
- Inserm, UMR 1188 Diabète Athérothrombose Thérapies Réunion Océan Indien (DéTROI), Université de La Réunion, 97400 Saint-Denis de La Reunion, France; (K.C.); (S.B.); (A.K.J.)
| | - Asier Larrea-Sebal
- Department of Molecular Biophysics, Biofisika Institute, University of Basque Country and Consejo Superior de Investigaciones Científicas (UPV/EHU, CSIC), 48940 Leioa, Spain; (K.B.U.); (A.L.-S.); (A.B.-V.); (U.G.-G.)
- Fundación Biofisika Bizkaia, 48940 Leioa, Spain
| | - Asier Benito-Vicente
- Department of Molecular Biophysics, Biofisika Institute, University of Basque Country and Consejo Superior de Investigaciones Científicas (UPV/EHU, CSIC), 48940 Leioa, Spain; (K.B.U.); (A.L.-S.); (A.B.-V.); (U.G.-G.)
- Department of Biochemistry and Molecular Biology, Universidad del País Vasco UPV/EHU, 48080 Bilbao, Spain
| | - Unai Galicia-Garcia
- Department of Molecular Biophysics, Biofisika Institute, University of Basque Country and Consejo Superior de Investigaciones Científicas (UPV/EHU, CSIC), 48940 Leioa, Spain; (K.B.U.); (A.L.-S.); (A.B.-V.); (U.G.-G.)
- Fundación Biofisika Bizkaia, 48940 Leioa, Spain
| | - Steeve Bourane
- Inserm, UMR 1188 Diabète Athérothrombose Thérapies Réunion Océan Indien (DéTROI), Université de La Réunion, 97400 Saint-Denis de La Reunion, France; (K.C.); (S.B.); (A.K.J.)
| | - Ali K. Jaafar
- Inserm, UMR 1188 Diabète Athérothrombose Thérapies Réunion Océan Indien (DéTROI), Université de La Réunion, 97400 Saint-Denis de La Reunion, France; (K.C.); (S.B.); (A.K.J.)
| | - Gilles Lambert
- Inserm, UMR 1188 Diabète Athérothrombose Thérapies Réunion Océan Indien (DéTROI), Université de La Réunion, 97400 Saint-Denis de La Reunion, France; (K.C.); (S.B.); (A.K.J.)
- Correspondence: (G.L.); (C.M.); Tel.: +94-601-8053 (C.M.)
| | - César Martín
- Department of Molecular Biophysics, Biofisika Institute, University of Basque Country and Consejo Superior de Investigaciones Científicas (UPV/EHU, CSIC), 48940 Leioa, Spain; (K.B.U.); (A.L.-S.); (A.B.-V.); (U.G.-G.)
- Department of Biochemistry and Molecular Biology, Universidad del País Vasco UPV/EHU, 48080 Bilbao, Spain
- Correspondence: (G.L.); (C.M.); Tel.: +94-601-8053 (C.M.)
| |
Collapse
|
22
|
Szpak M, Collins SC, Li Y, Liu X, Ayub Q, Fischer MC, Vancollie VE, Lelliott CJ, Xue Y, Yalcin B, Yang H, Tyler-Smith C. A Positively Selected MAGEE2 LoF Allele Is Associated with Sexual Dimorphism in Human Brain Size and Shows Similar Phenotypes in Magee2 Null Mice. Mol Biol Evol 2021; 38:5655-5663. [PMID: 34464968 PMCID: PMC8662591 DOI: 10.1093/molbev/msab243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A nonsense allele at rs1343879 in human MAGEE2 on chromosome X has previously been reported as a strong candidate for positive selection in East Asia. This premature stop codon causing ∼80% protein truncation is characterized by a striking geographical pattern of high population differentiation: common in Asia and the Americas (up to 84% in the 1000 Genomes Project East Asians) but rare elsewhere. Here, we generated a Magee2 mouse knockout mimicking the human loss-of-function mutation to study its functional consequences. The Magee2 null mice did not exhibit gross abnormalities apart from enlarged brain structures (13% increased total brain area, P = 0.0022) in hemizygous males. The area of the granular retrosplenial cortex responsible for memory, navigation, and spatial information processing was the most severely affected, exhibiting an enlargement of 34% (P = 3.4×10-6). The brain size in homozygous females showed the opposite trend of reduced brain size, although this did not reach statistical significance. With these insights, we performed human association analyses between brain size measurements and rs1343879 genotypes in 141 Chinese volunteers with brain MRI scans, replicating the sexual dimorphism seen in the knockout mouse model. The derived stop gain allele was significantly associated with a larger volume of gray matter in males (P = 0.00094), and smaller volumes of gray (P = 0.00021) and white (P = 0.0015) matter in females. It is unclear whether or not the observed neuroanatomical phenotypes affect behavior or cognition, but it might have been the driving force underlying the positive selection in humans.
Collapse
Affiliation(s)
- Michał Szpak
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Stephan C Collins
- Inserm UMR1231, Genetics of Developmental Disorders Laboratory, University of Bourgogne Franche-Comté, Dijon, France.,IGBMC, UMR7104, Illkirch, Inserm, France
| | - Yan Li
- BGI-Shenzhen, Shenzhen, China
| | - Xiao Liu
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Qasim Ayub
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.,Monash University Malaysia Genomics Facility, School of Science, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | | | | | | | - Yali Xue
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Binnaz Yalcin
- Inserm UMR1231, Genetics of Developmental Disorders Laboratory, University of Bourgogne Franche-Comté, Dijon, France.,IGBMC, UMR7104, Illkirch, Inserm, France
| | | | - Chris Tyler-Smith
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| |
Collapse
|
23
|
Nicole S, Lory P. New Challenges Resulting From the Loss of Function of Na v1.4 in Neuromuscular Diseases. Front Pharmacol 2021; 12:751095. [PMID: 34671263 PMCID: PMC8521073 DOI: 10.3389/fphar.2021.751095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/16/2021] [Indexed: 11/13/2022] Open
Abstract
The voltage-gated sodium channel Nav1.4 is a major actor in the excitability of skeletal myofibers, driving the muscle force in response to nerve stimulation. Supporting further this key role, mutations in SCN4A, the gene encoding the pore-forming α subunit of Nav1.4, are responsible for a clinical spectrum of human diseases ranging from muscle stiffness (sodium channel myotonia, SCM) to muscle weakness. For years, only dominantly-inherited diseases resulting from Nav1.4 gain of function (GoF) were known, i.e., non-dystrophic myotonia (delayed muscle relaxation due to myofiber hyperexcitability), paramyotonia congenita and hyperkalemic or hypokalemic periodic paralyses (episodic flaccid muscle weakness due to transient myofiber hypoexcitability). These last 5 years, SCN4A mutations inducing Nav1.4 loss of function (LoF) were identified as the cause of dominantly and recessively-inherited disorders with muscle weakness: periodic paralyses with hypokalemic attacks, congenital myasthenic syndromes and congenital myopathies. We propose to name this clinical spectrum sodium channel weakness (SCW) as the mirror of SCM. Nav1.4 LoF as a cause of permanent muscle weakness was quite unexpected as the Na+ current density in the sarcolemma is large, securing the ability to generate and propagate muscle action potentials. The properties of SCN4A LoF mutations are well documented at the channel level in cellular electrophysiological studies However, much less is known about the functional consequences of Nav1.4 LoF in skeletal myofibers with no available pertinent cell or animal models. Regarding the therapeutic issues for Nav1.4 channelopathies, former efforts were aimed at developing subtype-selective Nav channel antagonists to block myofiber hyperexcitability. Non-selective, Nav channel blockers are clinically efficient in SCM and paramyotonia congenita, whereas patient education and carbonic anhydrase inhibitors are helpful to prevent attacks in periodic paralyses. Developing therapeutic tools able to counteract Nav1.4 LoF in skeletal muscles is then a new challenge in the field of Nav channelopathies. Here, we review the current knowledge regarding Nav1.4 LoF and discuss the possible therapeutic strategies to be developed in order to improve muscle force in SCW.
Collapse
Affiliation(s)
- Sophie Nicole
- Institut de Génomique Fonctionnelle (IGF), Université de Montpellier, CNRS, INSERM, Montpellier, France.,LabEx 'Ion Channel Science and Therapeutics (ICST), Montpellier, France
| | - Philippe Lory
- Institut de Génomique Fonctionnelle (IGF), Université de Montpellier, CNRS, INSERM, Montpellier, France.,LabEx 'Ion Channel Science and Therapeutics (ICST), Montpellier, France
| |
Collapse
|
24
|
Shamseldin HE, AlAbdi L, Maddirevula S, Alsaif HS, Alzahrani F, Ewida N, Hashem M, Abdulwahab F, Abuyousef O, Kuwahara H, Gao X, Alkuraya FS. Lethal variants in humans: lessons learned from a large molecular autopsy cohort. Genome Med 2021; 13:161. [PMID: 34645488 PMCID: PMC8511862 DOI: 10.1186/s13073-021-00973-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/17/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Molecular autopsy refers to DNA-based identification of the cause of death. Despite recent attempts to broaden its scope, the term remains typically reserved to sudden unexplained death in young adults. In this study, we aim to showcase the utility of molecular autopsy in defining lethal variants in humans. METHODS We describe our experience with a cohort of 481 cases in whom the cause of premature death was investigated using DNA from the index or relatives (molecular autopsy by proxy). Molecular autopsy tool was typically exome sequencing although some were investigated using targeted approaches in the earlier stages of the study; these include positional mapping, targeted gene sequencing, chromosomal microarray, and gene panels. RESULTS The study includes 449 cases from consanguineous families and 141 lacked family history (simplex). The age range was embryos to 18 years. A likely causal variant (pathogenic/likely pathogenic) was identified in 63.8% (307/481), a much higher yield compared to the general diagnostic yield (43%) from the same population. The predominance of recessive lethal alleles allowed us to implement molecular autopsy by proxy in 55 couples, and the yield was similarly high (63.6%). We also note the occurrence of biallelic lethal forms of typically non-lethal dominant disorders, sometimes representing a novel bona fide biallelic recessive disease trait. Forty-six disease genes with no OMIM phenotype were identified in the course of this study. The presented data support the candidacy of two other previously reported novel disease genes (FAAH2 and MSN). The focus on lethal phenotypes revealed many examples of interesting phenotypic expansion as well as remarkable variability in clinical presentation. Furthermore, important insights into population genetics and variant interpretation are highlighted based on the results. CONCLUSIONS Molecular autopsy, broadly defined, proved to be a helpful clinical approach that provides unique insights into lethal variants and the clinical annotation of the human genome.
Collapse
Affiliation(s)
- Hanan E Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Lama AlAbdi
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hessa S Alsaif
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Center of Excellence for Biomedicine, King Abdulaziz City for Science and Technology, Riyadh, 12354, Saudi Arabia
| | - Fatema Alzahrani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nour Ewida
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Omar Abuyousef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hiroyuki Kuwahara
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
| |
Collapse
|
25
|
Sassi A, Désir J, Duerinckx S, Soblet J, Van Dooren S, Bonduelle M, Abramowicz M, Delbaere A. Compound heterozygous null mutations of NOBOX in sisters with delayed puberty and primary amenorrhea. Mol Genet Genomic Med 2021; 9:e1776. [PMID: 34480423 PMCID: PMC8580073 DOI: 10.1002/mgg3.1776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/02/2021] [Accepted: 07/09/2021] [Indexed: 11/25/2022] Open
Abstract
Background Premature ovarian insufficiency (POI) is a heterogeneous clinical syndrome defined by a premature loss of ovarian function that associates menstrual disturbances and hypergonatropic hypogonadism. POI is a major cause of female infertility affecting 1% of women before the age of 40 and up to 0.01% before the age of 20. The etiology of POI may be iatrogenic, auto‐immune or genetic but remains however undetermined in a large majority of cases. An underlying genetic etiology has to be searched in idiopathic cases, particularly in the context of a family history of POI. Methods Whole exome sequencing (WES) was performed in trio in a Belgian patient presenting POI and in her two parents. The patient presented delayed puberty and primary amenorrhea with hypergonadotropic hypogonadism. Results WES identified two novel compound heterozygous truncating mutations in the Newborn oogenesis homeobox (NOBOX) gene, c.826C>T (p.(Arg276Ter)) and c.1421del (p.(Gly474AlafsTer76)). Both mutations were confirmed by Sanger sequencing in the proband's sister who presented the same phenotype. Both variants were pathogenic and very likely responsible for the severe POI in this family. Conclusion We report here for the first time compound heterozygous truncating mutations of NOBOX in outbred patients, generalizing biallelic NOBOX null mutations as a cause of severe POI with primary amenorrhea. In addition, our findings also suggest that NOBOX haploinsufficiency is tolerated.
Collapse
Affiliation(s)
- Asma Sassi
- Fertility Clinic, Department of Obstetrics and Gynecology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Julie Désir
- Department of Genetics, Erasme Hospital, ULB Center of Human Genetics, Université Libre de Bruxelles, Brussels, Belgium
| | - Sarah Duerinckx
- Institute of Interdisciplinary Research in Human and Molecular Biology, Human Genetics, IRIBHM, Université Libre de Bruxelles, Brussels, Belgium
| | - Julie Soblet
- Department of Genetics, Erasme Hospital, ULB Center of Human Genetics, Université Libre de Bruxelles, Brussels, Belgium.,Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, ULB Center of Human Genetics, Université Libre de Bruxelles, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles, Brussels, Belgium
| | - Sonia Van Dooren
- Brussels Interuniversity Genomics High Throughput core (Bright Core), Brussels, Belgium
| | - Maryse Bonduelle
- Centre for Medical Genetics, Reproduction and Genetics, Reproduction and Genetics and Regenerative Medicine, UZ Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Marc Abramowicz
- Department of Genetics, Erasme Hospital, ULB Center of Human Genetics, Université Libre de Bruxelles, Brussels, Belgium.,Institute of Interdisciplinary Research in Human and Molecular Biology, Human Genetics, IRIBHM, Université Libre de Bruxelles, Brussels, Belgium
| | - Anne Delbaere
- Fertility Clinic, Department of Obstetrics and Gynecology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| |
Collapse
|
26
|
Arana-Rueda E, Pezzotti MR, Pedrote A, Acosta J, Frutos-López M, Varela LM, García-Fernández N, Castellano A. Brugada syndrome masked by complete left bundle branch block: A clinical and functional study of its association with the p.1449Y>H SCN5A variant. J Cardiovasc Electrophysiol 2021; 32:2785-2790. [PMID: 34411358 DOI: 10.1111/jce.15215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/24/2021] [Accepted: 07/22/2021] [Indexed: 11/27/2022]
Abstract
SCN5A gene variants are associated with both Brugada syndrome and conduction disturbances, sometimes expressing an overlapping phenotype. Functional consequences of SCN5A variants assessed by patch-clamp electrophysiology are particularly beneficial for correct pathogenic classification and are related to disease penetrance and severity. Here, we identify a novel SCN5A loss of function variant, p.1449Y>H, which presented with high penetrance and complete left bundle branch block, totally masking the typical findings on the electrocardiogram. We highlight the possibility of this overlap combination that makes impossible an electrocardiographic diagnosis and, through a functional analysis, associate the p.1449Y>H variant to SCN5A pathogenicity.
Collapse
Affiliation(s)
- Eduardo Arana-Rueda
- Department of Cardiology, Arrhythmia Unit, Virgen del Rocío University Hospital, Sevilla, Spain.,Departamento de Fisiología Médica y Biofísica, Instituto de Biomedicina de Sevilla (IBiS)/Hospital Universitario Virgen del Rocío/CSIC, Universidad de Sevilla, Sevilla, Spain
| | - María R Pezzotti
- Departamento de Fisiología Médica y Biofísica, Instituto de Biomedicina de Sevilla (IBiS)/Hospital Universitario Virgen del Rocío/CSIC, Universidad de Sevilla, Sevilla, Spain
| | - Alonso Pedrote
- Department of Cardiology, Arrhythmia Unit, Virgen del Rocío University Hospital, Sevilla, Spain
| | - Juan Acosta
- Department of Cardiology, Arrhythmia Unit, Virgen del Rocío University Hospital, Sevilla, Spain
| | - Manuel Frutos-López
- Department of Cardiology, Arrhythmia Unit, Virgen del Rocío University Hospital, Sevilla, Spain
| | - Lourdes-María Varela
- Departamento de Fisiología Médica y Biofísica, Instituto de Biomedicina de Sevilla (IBiS)/Hospital Universitario Virgen del Rocío/CSIC, Universidad de Sevilla, Sevilla, Spain
| | - Noelia García-Fernández
- Departamento de Fisiología Médica y Biofísica, Instituto de Biomedicina de Sevilla (IBiS)/Hospital Universitario Virgen del Rocío/CSIC, Universidad de Sevilla, Sevilla, Spain
| | - Antonio Castellano
- Departamento de Fisiología Médica y Biofísica, Instituto de Biomedicina de Sevilla (IBiS)/Hospital Universitario Virgen del Rocío/CSIC, Universidad de Sevilla, Sevilla, Spain.,CIBERCV, ISCIII, Madrid, Spain
| |
Collapse
|
27
|
Liu Y, Ding H, Yan T, Liu L, Yu L, Huang Y, Li F, Zeng Y, Huang W, Zhang Y, Yin A. A Novel Multi-Exon Deletion of PACS1 in a Three-Generation Pedigree: Supplements to PACS1 Neurodevelopmental Disorder Spectrum. Front Genet 2021; 12:690216. [PMID: 34373684 PMCID: PMC8346485 DOI: 10.3389/fgene.2021.690216] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/30/2021] [Indexed: 01/18/2023] Open
Abstract
PACS1 neurodevelopmental disorder (PACS1-NDD) is a category of rare disorder characterized by intellectual disability, speech delay, dysmorphic facial features, and developmental delay. Other various physical abnormalities of PACS1-NDD might involve all organs and systems. Notably, there were only two unique missense mutations [c.607C > T (p.Arg203Trp) and c.608G > A (p.Arg203Gln)] in PACS1 that had been identified as pathogenic variants for PACS1-NDD or Schuurs-Hoeijmakers syndrome (SHMS). Previous reports suggested that these common missense variants were likely to act through dominant-negative or gain-of-function effects manner. It is still uncertain whether the intragenic deletion or duplication in PACS1 will be disease-causing. By using whole-exome sequencing, we first identified a novel heterozygous multi-exon deletion covering exons 12-24 in PACS1 (NM_018026) in four individuals (two brothers and their father and grandfather) in a three-generation family. The younger brother was referred to our center prenatally and was evaluated before and after the birth. Unlike SHMS, no typical dysmorphic facial features, intellectual problems, and structural brain anomalies were observed among these four individuals. The brothers showed a mild hypermyotonia of their extremities at the age of 3 months old and recovered over time. Mild speech and cognitive delay were also noticed in the two brothers at the age of 13 and 27 months old, respectively. However, their father and grandfather showed normal language and cognitive competence. This study might supplement the spectrum of PACS1-NDD and demonstrates that the loss of function variation in PACS1 displays no contributions to the typical SHMS which is caused by the recurrent c.607C > T (p.Arg203Trp) variant.
Collapse
Affiliation(s)
- Yuan Liu
- Medical Genetics Centre, Guangdong Women and Children Hospital, Guangzhou, China
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Hongke Ding
- Medical Genetics Centre, Guangdong Women and Children Hospital, Guangzhou, China
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Tizhen Yan
- Department of Medical Genetics, Liuzhou Key Laboratory of Birth Defects Prevention and Control, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
| | - Ling Liu
- Medical Genetics Centre, Guangdong Women and Children Hospital, Guangzhou, China
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Lihua Yu
- Medical Genetics Centre, Guangdong Women and Children Hospital, Guangzhou, China
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yanlin Huang
- Medical Genetics Centre, Guangdong Women and Children Hospital, Guangzhou, China
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Fake Li
- Medical Genetics Centre, Guangdong Women and Children Hospital, Guangzhou, China
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yukun Zeng
- Medical Genetics Centre, Guangdong Women and Children Hospital, Guangzhou, China
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Weiwei Huang
- Medical Genetics Centre, Guangdong Women and Children Hospital, Guangzhou, China
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yan Zhang
- Medical Genetics Centre, Guangdong Women and Children Hospital, Guangzhou, China
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Aihua Yin
- Medical Genetics Centre, Guangdong Women and Children Hospital, Guangzhou, China
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, China
| |
Collapse
|
28
|
Jiao WB, Patel V, Klasen J, Liu F, Pecinkova P, Ferrand M, Gy I, Camilleri C, Effgen S, Koornneef M, Pecinka A, Loudet O, Schneeberger K. The Evolutionary Dynamics of Genetic Incompatibilities Introduced by Duplicated Genes in Arabidopsis thaliana. Mol Biol Evol 2021; 38:1225-1240. [PMID: 33247726 PMCID: PMC8042742 DOI: 10.1093/molbev/msaa306] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although gene duplications provide genetic backup and allow genomic changes under relaxed selection, they may potentially limit gene flow. When different copies of a duplicated gene are pseudofunctionalized in different genotypes, genetic incompatibilities can arise in their hybrid offspring. Although such cases have been reported after manual crosses, it remains unclear whether they occur in nature and how they affect natural populations. Here, we identified four duplicated-gene based incompatibilities including one previously not reported within an artificial Arabidopsis intercross population. Unexpectedly, however, for each of the genetic incompatibilities we also identified the incompatible alleles in natural populations based on the genomes of 1,135 Arabidopsis accessions published by the 1001 Genomes Project. Using the presence of incompatible allele combinations as phenotypes for GWAS, we mapped genomic regions that included additional gene copies which likely rescue the genetic incompatibility. Reconstructing the geographic origins and evolutionary trajectories of the individual alleles suggested that incompatible alleles frequently coexist, even in geographically closed regions, and that their effects can be overcome by additional gene copies collectively shaping the evolutionary dynamics of duplicated genes during population history.
Collapse
Affiliation(s)
- Wen-Biao Jiao
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Vipul Patel
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jonas Klasen
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Fang Liu
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Petra Pecinkova
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Department of Cell Biology and Genetics, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Marina Ferrand
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Isabelle Gy
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Christine Camilleri
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Sigi Effgen
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Maarten Koornneef
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Laboratory of Genetics, Wageningen University & Research, Wageningen, The Netherlands
| | - Ales Pecinka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Institute of Experimental Botany (IEB), Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Olomouc, Czech Republic
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| |
Collapse
|
29
|
Kellner S, Abbasi A, Carmi I, Heinrich R, Garin-Shkolnik T, Hershkovitz T, Giladi M, Haitin Y, Johannesen KM, Steensbjerre Møller R, Berlin S. Two de novo GluN2B mutations affect multiple NMDAR-functions and instigate severe pediatric encephalopathy. eLife 2021; 10:67555. [PMID: 34212862 PMCID: PMC8260228 DOI: 10.7554/elife.67555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 06/27/2021] [Indexed: 12/15/2022] Open
Abstract
The N-methyl-D-aspartate receptors (NMDARs; GluNRS) are glutamate receptors, commonly located at excitatory synapses. Mutations affecting receptor function often lead to devastating neurodevelopmental disorders. We have identified two toddlers with different heterozygous missense mutations of the same, and highly conserved, glycine residue located in the ligand-binding-domain of GRIN2B: G689C and G689S. Structure simulations suggest severely impaired glutamate binding, which we confirm by functional analysis. Both variants show three orders of magnitude reductions in glutamate EC50, with G689S exhibiting the largest reductions observed for GRIN2B (~2000-fold). Moreover, variants multimerize with, and upregulate, GluN2Bwt-subunits, thus engendering a strong dominant-negative effect on mixed channels. In neurons, overexpression of the variants instigates suppression of synaptic GluNRs. Lastly, while exploring spermine potentiation as a potential treatment, we discovered that the variants fail to respond due to G689’s novel role in proton-sensing. Together, we describe two unique variants with extreme effects on channel function. We employ protein-stability measures to explain why current (and future) LBD mutations in GluN2B primarily instigate Loss-of-Function.
Collapse
Affiliation(s)
- Shai Kellner
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Abeer Abbasi
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ido Carmi
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ronit Heinrich
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | | | | | - Moshe Giladi
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yoni Haitin
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Katrine M Johannesen
- Department of Epilepsy Genetics and Personalized Treatment, the Danish Epilepsy Centre, Dianalund, Denmark.,Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Rikke Steensbjerre Møller
- Department of Epilepsy Genetics and Personalized Treatment, the Danish Epilepsy Centre, Dianalund, Denmark.,Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Shai Berlin
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| |
Collapse
|
30
|
Canosa A, Lomartire A, De Marco G, Grassano M, Brunetti M, Manera U, Vasta R, Salamone P, Fuda G, Sbaiz L, Gallone S, Moglia C, Calvo A, Chiò A. A novel splice site FUS mutation in a familial ALS case: effects on protein expression. Amyotroph Lateral Scler Frontotemporal Degener 2021; 23:128-136. [PMID: 33879000 DOI: 10.1080/21678421.2021.1909065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Objective: To investigate the impact of a novel heterozygous FUS mutation in the acceptor splice site of intron 14 (c.1542 - 1 g > t) on protein expression in Peripheral Blood Mononuclear Cells (PBMC) from a familial ALS patient. Methods: PBMC were isolated for mRNA analysis (cDNA synthesis, sequencing and one-step RT-PCR), Western Immunoblot (WI), and Immunofluorescence (IF). Results: cDNA analysis revealed the skipping of exon 15 and a premature stop codon at c.228. RT-PCR showed reduced FUS mRNA by more than half compared to a healthy control (HC) and an ALS patient without genetic mutations (wtALS). In WI FUS band intensity in the proband was 30-50% compared to HC and wtALS. An antibody expected to detect only the wild-type protein did not reveal any reduction of FUS band intensity compared to the other antibodies. IF showed no difference among HC, wtALS, and the proband. Discussion: The reduction of FUS mRNA and protein in PBMC suggests the absence of the truncated protein, probably due to nonsense-mediated decay, leading to loss of function.
Collapse
Affiliation(s)
- Antonio Canosa
- "Rita Levi Montalcini" Department of Neuroscience, ALS Centre, University of Turin, Turin, Italy.,Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Neurology Unit 1, Turin, Italy
| | - Annarosa Lomartire
- "Rita Levi Montalcini" Department of Neuroscience, ALS Centre, University of Turin, Turin, Italy
| | - Giovanni De Marco
- "Rita Levi Montalcini" Department of Neuroscience, ALS Centre, University of Turin, Turin, Italy.,Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Neurology Unit 1, Turin, Italy
| | - Maurizio Grassano
- "Rita Levi Montalcini" Department of Neuroscience, ALS Centre, University of Turin, Turin, Italy
| | - Maura Brunetti
- "Rita Levi Montalcini" Department of Neuroscience, ALS Centre, University of Turin, Turin, Italy
| | - Umberto Manera
- "Rita Levi Montalcini" Department of Neuroscience, ALS Centre, University of Turin, Turin, Italy
| | - Rosario Vasta
- "Rita Levi Montalcini" Department of Neuroscience, ALS Centre, University of Turin, Turin, Italy
| | - Paolina Salamone
- "Rita Levi Montalcini" Department of Neuroscience, ALS Centre, University of Turin, Turin, Italy
| | - Giuseppe Fuda
- "Rita Levi Montalcini" Department of Neuroscience, ALS Centre, University of Turin, Turin, Italy
| | - Luca Sbaiz
- Department of Clinical Pathology, Laboratory of Genetics, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Turin, Italy
| | - Salvatore Gallone
- Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Neurology Unit 1, Turin, Italy
| | - Cristina Moglia
- "Rita Levi Montalcini" Department of Neuroscience, ALS Centre, University of Turin, Turin, Italy.,Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Neurology Unit 1, Turin, Italy
| | - Andrea Calvo
- "Rita Levi Montalcini" Department of Neuroscience, ALS Centre, University of Turin, Turin, Italy.,Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Neurology Unit 1, Turin, Italy.,Neuroscience Institute of Turin (NIT), Turin, Italy, and
| | - Adriano Chiò
- "Rita Levi Montalcini" Department of Neuroscience, ALS Centre, University of Turin, Turin, Italy.,Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Neurology Unit 1, Turin, Italy.,Neuroscience Institute of Turin (NIT), Turin, Italy, and.,Institute of Cognitive Sciences and Technologies, C.N.R., Rome, Italy
| |
Collapse
|
31
|
Wang J, Qiao JD, Liu XR, Liu DT, Chen YH, Wu Y, Sun Y, Yu J, Ren RN, Mei Z, Liu YX, Shi YW, Jiang M, Lin SM, He N, Li B, Bian WJ, Li BM, Yi YH, Su T, Liu HK, Gu WY, Liao WP. UNC13B variants associated with partial epilepsy with favourable outcome. Brain 2021; 144:3050-3060. [PMID: 33876820 PMCID: PMC8634081 DOI: 10.1093/brain/awab164] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/25/2021] [Accepted: 04/03/2021] [Indexed: 11/12/2022] Open
Abstract
The unc-13 homolog B (UNC13B) gene encodes a presynaptic protein, mammalian uncoordinated 13-2 (Munc13-2), that is highly expressed in the brain-predominantly in the cerebral cortex-and plays an essential role in synaptic vesicle priming and fusion, potentially affecting neuronal excitability. However, the functional significance of UNC13B mutation in human disease is not known. In this study we screened for novel genetic variants in a cohort of 446 unrelated cases (families) with partial epilepsy without acquired causes by trio-based whole-exome sequencing. UNC13B variants were identified in 12 individuals affected by partial epilepsy and/or febrile seizures from eight unrelated families. The eight probands all had focal seizures and focal discharges in EEG recordings, including two patients who experienced frequent daily seizures and one who showed abnormalities in the hippocampus by brain MRI; however, all of the patients showed favorable outcome without intellectual or developmental abnormalities. The identified UNC13B variants included one nonsense variant, two variants at or around a splice site, one compound heterozygous missense variant, and four missense variants that cosegregated in the families. The frequency of UNC13B variants identified in the present study was significantly higher than that in a control cohort of Han Chinese and controls of the East Asian and all populations in the Genome Aggregation Database. Computational modeling, including hydrogen bond and docking analyses, suggested that the variants lead to functional impairment. In Drosophila, seizure rate and duration were increased by Unc13b knockdown compared to wild-type flies, but these effects were less pronounced than in sodium voltage-gated channel alpha subunit 1 (Scn1a) knockdown Drosophila. Electrophysiologic recordings showed that excitatory neurons in Unc13b-deficient flies exhibited increased excitability. These results suggest that UNC13B is potentially associated with epilepsy. The frequent daily seizures and hippocampal abnormalities but ultimately favorable outcome under antiepileptic therapy in our patients indicate that partial epilepsy caused by UNC13B variant is a clinically manageable condition.
Collapse
Affiliation(s)
- Jie Wang
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Jing-Da Qiao
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Xiao-Rong Liu
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - De-Tian Liu
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Yan-Hui Chen
- Department of Pediatrics, Fujian Medical University Union Hospital, Fujian, China
| | - Yi Wu
- Department of Pediatrics, Fujian Medical University Union Hospital, Fujian, China
| | - Yan Sun
- Department of Pediatrics, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
| | - Jing Yu
- Department of Pediatrics, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
| | - Rong-Na Ren
- Department of Pediatrics and Neurosurgery, 900 Hospital of the Joint Logistics Team, Fujian, China
| | - Zhen Mei
- Department of Pediatrics and Neurosurgery, 900 Hospital of the Joint Logistics Team, Fujian, China
| | - Yu-Xi Liu
- Department of Neurology, The First Affiliated Hospital of Shanxi Medical University, Shanxi, China
| | - Yi-Wu Shi
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Mi Jiang
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Si-Mei Lin
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Na He
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Bin Li
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Wen-Jun Bian
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Bing-Mei Li
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Yong-Hong Yi
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Tao Su
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | | | - Wei-Yue Gu
- Chigene (Beijing) Translational Medical Research Center Co., Beijing, China
| | - Wei-Ping Liao
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | | |
Collapse
|
32
|
Dong HL, Ma Y, Yu H, Wei Q, Li JQ, Liu GL, Li HF, Chen L, Chen DF, Bai G, Wu ZY. Bi-allelic loss of function variants in COX20 gene cause autosomal recessive sensory neuronopathy. Brain 2021; 144:2457-2470. [PMID: 33751098 DOI: 10.1093/brain/awab135] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/18/2021] [Accepted: 01/30/2021] [Indexed: 12/24/2022] Open
Abstract
Sensory neuronopathies are a rare and distinct subgroup of peripheral neuropathies, characterized by degeneration of the dorsal root ganglia neurons. About 50% of sensory neuronopathies are idiopathic and genetic causes remain to be clarified. Through a combination of homozygosity mapping and whole exome sequencing, we linked an autosomal recessive sensory neuronopathy to pathogenic variants in COX20 gene. We identified 8 unrelated families from the eastern China population carrying a founder variant c.41A>G (p. Lys14Arg) within COX20 in either a homozygous or compound heterozygous state. All patients displayed sensory ataxia with non-length-dependent sensory potentials decrease. COX20 encodes a key transmembrane protein implicated in the assembly of mitochondrial complex IV. We showed that COX20 variants lead to reduction of COX20 protein in patient's fibroblasts and transfected cell lines, consistent with a loss-of-function mechanism. Knockdown of COX20 expression in ND7/23 sensory neuron cells resulted in complex IV deficiency and perturbed assembly of complex IV, which subsequently compromised cell spare respiratory capacity and reduced cell proliferation under metabolic stress. Consistent with mitochondrial dysfunction in knockdown cells, reduced complex IV assembly, enzyme activity and oxygen consumption rate were also found in patients' fibroblasts. We speculated that the mechanism of COX20 was similar to other causative genes (e.g. SURF1, COX6A1, COA3 and SCO2) for peripheral neuropathies, all of which were functionally important in the structure and assembly of complex IV. Our study identifies a novel causative gene for the autosomal recessive sensory neuronopathy, whose vital function in complex IV and high expression in the proprioceptive sensory neuron further underlines loss of COX20 contributing to mitochondrial bioenergetic dysfunction as a mechanism in peripheral sensory neuron disease.
Collapse
Affiliation(s)
- Hai-Lin Dong
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, Hangzhou, China
| | - Yin Ma
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, Hangzhou, China
| | - Hao Yu
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, Hangzhou, China
| | - Qiao Wei
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, Hangzhou, China
| | - Jia-Qi Li
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, Hangzhou, China
| | - Gong-Lu Liu
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, Hangzhou, China
| | - Hong-Fu Li
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, Hangzhou, China
| | - Lei Chen
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, Hangzhou, China.,Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Dian-Fu Chen
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, Hangzhou, China.,Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Ge Bai
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, Hangzhou, China.,Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China.,NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, China
| | - Zhi-Ying Wu
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, Hangzhou, China.,Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China.,NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai, China
| |
Collapse
|
33
|
Heidari E, Harrison AN, Jafarinia E, Tavasoli AR, Almadani N, Molday RS, Garshasbi M. Novel variants in critical domains of ATP8A2 and expansion of clinical spectrum. Hum Mutat 2021; 42:491-497. [PMID: 33565221 DOI: 10.1002/humu.24180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 01/17/2021] [Accepted: 02/07/2021] [Indexed: 12/12/2022]
Abstract
ATP8A2 is a P4-ATPase that flips phosphatidylserine across membranes to generate and maintain transmembrane phospholipid asymmetry. Loss-of-function variants cause severe neurodegenerative and developmental disorders. We have identified three ATP8A2 variants in unrelated Iranian families that cause intellectual disability, dystonia, below-average head circumference, mild optic atrophy, and developmental delay. Additionally, all the affected individuals displayed tooth abnormalities associated with defects in teeth development. Two variants (p.Asp825His and p.Met438Val) reside in critical functional domains of ATP8A2. These variants express at very low levels and lack ATPase activity. Inhibitor studies indicate that these variants are misfolded and degraded by the cellular proteasome. We conclude that Asp825, which coordinates with the Mg2+ ion within the ATP binding site, and Met438 are essential for the proper folding of ATP8A2 into a functional flippase. We also provide evidence on the association of tooth abnormalities with defects in ATP8A2, thereby expanding the clinical spectrum of the associated disease.
Collapse
Affiliation(s)
- Erfan Heidari
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Alexander N Harrison
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ehsan Jafarinia
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ali Reza Tavasoli
- Division of Pediatric Neurology, Myelin Disorders Clinic, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Navid Almadani
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Robert S Molday
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| |
Collapse
|
34
|
Steinberg C, Pilote S, Philippon F, Laksman ZW, Champagne J, Simard C, Krahn AD, Drolet B. SCN5A-C683R exhibits combined gain-of-function and loss-of-function properties related to adrenaline-triggered ventricular arrhythmia. Exp Physiol 2021; 106:683-699. [PMID: 33480457 DOI: 10.1113/ep089088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/11/2021] [Indexed: 12/14/2022]
Abstract
NEW FINDINGS What is the role of SCN5A-C683R? SCN5A-C683R is a novel variant associated with an uncommon phenotype of adrenaline-triggered ventricular arrhythmia in the absence of a distinct ECG phenotype. What is the main finding and its importance? Functional studies demonstrated that NaV 1.5/C683R results in a mixed electrophysiological phenotype with gain-of-function (GOF) and loss-of-function (LOF) properties compared with NaV 1.5/wild type. Gain-of-function properties are characterized by a significant increase of the maximal current density and a hyperpolarizing shift of the steady-state activation. The LOF effect of NaV 1.5/C683R is characterized by increased closed-state inactivation. Electrophysiological properties and clinical manifestation of SCN5A-C683R are different from long-QT-3 or Brugada syndrome and might represent a distinct inherited arrhythmia syndrome. ABSTRACT Mutations of SCN5Ahave been identified as the genetic substrate of various inherited arrhythmia syndromes, including long-QT-3 and Brugada syndrome. We recently identified a novel SCN5A variant (C683R) in two genetically unrelated families. The index patients of both families experienced adrenaline-triggered ventricular arrhythmia with cardiac arrest but did not show a specific ECG phenotype, raising the hypothesis that SCN5A-C683R might be a susceptibility variant and the genetic substrate of distinct inherited arrhythmia. We conducted functional cellular studies to characterize the electrophysiological properties of NaV 1.5/C683R in order to explore the potential pathogenicity of this novel variant. The C683R variant was engineered by site-directed mutagenesis. NaV 1.5/wild type (WT) and NaV 1.5/C683R were expressed in tsA201 cells. Electrophysiological characterization of C683R was performed using the whole-cell patch-clamp technique. Adrenergic stimulation was mimicked by exposure to the protein kinase A activator 8-CPT-cAMP. The impact of β-blockers was tested by exposing NaV 1.5/WT and NaV 1.5/C683R currents to propranolol and nadolol. C683R resulted in a co-association of gain-of-function and loss-of-function properties of NaV 1.5. Gain-of-function properties were characterized by a significant increase of the maximal NaV 1.5 current density compared with NaV 1.5/WT (861 ± 309 vs. 627 ± 489 pA/pF; P < 0.05, n ≥ 9) that was potentiated in NaV 1.5/C683R with 8-CPT-cAMP stimulation (869 ± 287 vs. 607 ± 320 pA/pF; P < 0.05, n ≥ 12). C683R also resulted in a significant hyperpolarizing shift in the voltage of steady-state activation (-65.4 ± 3.0 vs. -57.2 ± 4.8 mV; P < 0.001), resulting in an increased window current compared with WT. The loss-of-function effect of NaV 1.5/C683R was characterized by significantly increased closed-state inactivation compared with NaV 1.5/WT (P < 0.05). C683R is a novel SCN5A variant resulting in a co-association of gain-of-function and loss-of-function properties of the cardiac sodium channel NaV 1.5. The phenotype is characterized by adrenaline-triggered ventricular arrhythmias. Electrophysiological properties and clinical manifestations are different from long-QT-3 or Brugada syndrome and might represent a distinct inherited arrhythmia syndrome.
Collapse
Affiliation(s)
- Christian Steinberg
- Division of Cardiology, Electrophysiology Service, Institut universitaire de cardiologie et de pneumologie de Québec, IUCPQ-UL), Laval University, Québec, QC, Canada.,IUCPQ-UL Research Center, Laval University, Québec, QC, Canada
| | - Sylvie Pilote
- IUCPQ-UL Research Center, Laval University, Québec, QC, Canada.,Faculty of Pharmacy, Laval University, Québec, QC, Canada
| | - François Philippon
- Division of Cardiology, Electrophysiology Service, Institut universitaire de cardiologie et de pneumologie de Québec, IUCPQ-UL), Laval University, Québec, QC, Canada.,IUCPQ-UL Research Center, Laval University, Québec, QC, Canada
| | - Zachary W Laksman
- Heart Rhythm Services, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Jean Champagne
- Division of Cardiology, Electrophysiology Service, Institut universitaire de cardiologie et de pneumologie de Québec, IUCPQ-UL), Laval University, Québec, QC, Canada.,IUCPQ-UL Research Center, Laval University, Québec, QC, Canada
| | - Chantale Simard
- IUCPQ-UL Research Center, Laval University, Québec, QC, Canada.,Faculty of Pharmacy, Laval University, Québec, QC, Canada
| | - Andrew D Krahn
- Heart Rhythm Services, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Benoît Drolet
- IUCPQ-UL Research Center, Laval University, Québec, QC, Canada.,Faculty of Pharmacy, Laval University, Québec, QC, Canada
| |
Collapse
|
35
|
Sawan ZA, Almehaidib A, Binamer Y, Monies D, Alsaleem KA, Aldekhail W, Alkuraya FS, Abanemai M. PLACK syndrome is potentially treatable with intralipids. Clin Genet 2021; 99:572-576. [PMID: 33410500 DOI: 10.1111/cge.13919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 11/29/2022]
Abstract
We describe an 11-year-old girl with PLACK Syndrome (peeling skin, leukonychia, acral punctate keratosis, cheilitis, and knuckle pads), who was found to have a novel homozygous variant in CAST, the pathogenicity of which was confirmed using blood-derived RNA. There is no established treatment for PLACK syndrome. However, we demonstrate for the first time that this condition is associated with low levels of vitamin A and essential fatty acids, which prompted us to consider a potential treatment strategy. Indeed, we initiated this patient on intravenous lipid infusion (Vitalipid®; an emulsion of fat-soluble vitamins and lipofundin-MCT/LCT 20%) and the response was dramatic. Following the fourth monthly course of treatment, pruritis disappeared and the skin lesions showed remarkable objective improvement. PLACK syndrome is a very rare genodermatosis and only six families have been described to date with pathogenic CAST variants. This is the first report of an objective response to a therapeutic agent, which suggests that PLACK is a potentially treatable condition. The remarkable response we report and the relative safety of the intervention should prompt healthcare providers who care for PLACK syndrome patients to explore this as a potential treatment strategy in future studies.
Collapse
Affiliation(s)
- Zinab A Sawan
- Department of Pediatrics, King Abduaziz University, Faculty of Medicine, Jeddah, Kingdom of Saudi Arabia.,Department of Pediatrics, Division of Gastroenterology, King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Ali Almehaidib
- Department of Pediatrics, Division of Gastroenterology, King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Yousef Binamer
- Department of Dermatology, King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Dorota Monies
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia.,Saudi Human Genome Program, King Abdul-Aziz City for Science and Technology, Riyadh, Kingdom of Saudi Arabia
| | - Khalid A Alsaleem
- Department of Pediatrics, Division of Gastroenterology, King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Wajeeh Aldekhail
- Department of Pediatrics, Division of Gastroenterology, King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Mohammed Abanemai
- Department of Pediatrics, Division of Gastroenterology, King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| |
Collapse
|
36
|
Daniloski Z, Jordan TX, Wessels HH, Hoagland DA, Kasela S, Legut M, Maniatis S, Mimitou EP, Lu L, Geller E, Danziger O, Rosenberg BR, Phatnani H, Smibert P, Lappalainen T, tenOever BR, Sanjana NE. Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells. Cell 2021; 184:92-105.e16. [PMID: 33147445 PMCID: PMC7584921 DOI: 10.1016/j.cell.2020.10.030] [Citation(s) in RCA: 367] [Impact Index Per Article: 122.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/25/2020] [Accepted: 10/20/2020] [Indexed: 12/21/2022]
Abstract
To better understand host-virus genetic dependencies and find potential therapeutic targets for COVID-19, we performed a genome-scale CRISPR loss-of-function screen to identify host factors required for SARS-CoV-2 viral infection of human alveolar epithelial cells. Top-ranked genes cluster into distinct pathways, including the vacuolar ATPase proton pump, Retromer, and Commander complexes. We validate these gene targets using several orthogonal methods such as CRISPR knockout, RNA interference knockdown, and small-molecule inhibitors. Using single-cell RNA-sequencing, we identify shared transcriptional changes in cholesterol biosynthesis upon loss of top-ranked genes. In addition, given the key role of the ACE2 receptor in the early stages of viral entry, we show that loss of RAB7A reduces viral entry by sequestering the ACE2 receptor inside cells. Overall, this work provides a genome-scale, quantitative resource of the impact of the loss of each host gene on fitness/response to viral infection.
Collapse
Affiliation(s)
- Zharko Daniloski
- New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | - Tristan X Jordan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hans-Hermann Wessels
- New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | - Daisy A Hoagland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Silva Kasela
- New York Genome Center, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA
| | - Mateusz Legut
- New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | | | - Eleni P Mimitou
- Technology Innovation Lab, New York Genome Center, New York, NY, USA
| | - Lu Lu
- New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | - Evan Geller
- New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | - Oded Danziger
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brad R Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hemali Phatnani
- New York Genome Center, New York, NY, USA; Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Peter Smibert
- Technology Innovation Lab, New York Genome Center, New York, NY, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA
| | - Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Neville E Sanjana
- New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA.
| |
Collapse
|
37
|
Jones LB, Peters CH, Rosch RE, Owers M, Hughes E, Pal DK, Ruben PC. The L1624Q Variant in SCN1A Causes Familial Epilepsy Through a Mixed Gain and Loss of Channel Function. Front Pharmacol 2021; 12:788192. [PMID: 34925043 PMCID: PMC8675213 DOI: 10.3389/fphar.2021.788192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/17/2021] [Indexed: 11/13/2022] Open
Abstract
Variants of the SCN1A gene encoding the neuronal voltage-gated sodium channel NaV1.1 cause over 85% of all cases of Dravet syndrome, a severe and often pharmacoresistent epileptic encephalopathy with mostly infantile onset. But with the increased availability of genetic testing for patients with epilepsy, variants in SCN1A have now also been described in a range of other epilepsy phenotypes. The vast majority of these epilepsy-associated variants are de novo, and most are either nonsense variants that truncate the channel or missense variants that are presumed to cause loss of channel function. However, biophysical analysis has revealed a significant subset of missense mutations that result in increased excitability, further complicating approaches to precision pharmacotherapy for patients with SCN1A variants and epilepsy. We describe clinical and biophysical data of a familial SCN1A variant encoding the NaV1.1 L1624Q mutant. This substitution is located on the extracellular linker between S3 and S4 of Domain IV of NaV1.1 and is a rare case of a familial SCN1A variant causing an autosomal dominant frontal lobe epilepsy. We expressed wild-type (WT) and L1642Q channels in CHO cells. Using patch-clamp to characterize channel properties at several temperatures, we show that the L1624Q variant increases persistent current, accelerates fast inactivation onset and decreases current density. While SCN1A-associated epilepsy is typically considered a loss-of-function disease, our results put L1624Q into a growing set of mixed gain and loss-of-function variants in SCN1A responsible for epilepsy.
Collapse
Affiliation(s)
- Laura B Jones
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Colin H Peters
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Richard E Rosch
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, United Kingdom.,Department of Paediatric Neurology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Maxine Owers
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Elaine Hughes
- Department of Paediatric Neurosciences, King's College Hospital, London, United Kingdom.,Department of Paediatric Neurosciences, Evelina London Children's Hospital, London, United Kingdom
| | - Deb K Pal
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, United Kingdom.,Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, United Kingdom
| | - Peter C Ruben
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| |
Collapse
|
38
|
Van AAN, Kunkel MT, Baffi TR, Lordén G, Antal CE, Banerjee S, Newton AC. Protein kinase C fusion proteins are paradoxically loss of function in cancer. J Biol Chem 2021; 296:100445. [PMID: 33617877 PMCID: PMC8008189 DOI: 10.1016/j.jbc.2021.100445] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 02/11/2021] [Accepted: 02/18/2021] [Indexed: 12/02/2022] Open
Abstract
Within the AGC kinase superfamily, gene fusions resulting from chromosomal rearrangements have been most frequently described for protein kinase C (PKC), with gene fragments encoding either the C-terminal catalytic domain or the N-terminal regulatory moiety fused to other genes. Kinase fusions that eliminate regulatory domains are typically gain of function and often oncogenic. However, several quality control pathways prevent accumulation of aberrant PKC, suggesting that PKC fusions may paradoxically be loss of function. To explore this topic, we used biochemical, cellular, and genome editing approaches to investigate the function of fusions that retain the portion of the gene encoding either the catalytic domain or regulatory domain of PKC. Overexpression studies revealed that PKC catalytic domain fusions were constitutively active but vulnerable to degradation. Genome editing of endogenous genes to generate a cancer-associated PKC fusion resulted in cells with detectable levels of fusion transcript but no detectable protein. Hence, PKC catalytic domain fusions are paradoxically loss of function as a result of their instability, preventing appreciable accumulation of protein in cells. Overexpression of a PKC regulatory domain fusion suppressed both basal and agonist-induced endogenous PKC activity, acting in a dominant-negative manner by competing for diacylglycerol. For both catalytic and regulatory domain fusions, the PKC component of the fusion proteins mediated the effects of the full-length fusions on the parameters examined, suggesting that the partner protein is dispensable in these contexts. Taken together, our findings reveal that PKC gene fusions are distinct from oncogenic fusions and present a mechanism by which loss of PKC function occurs in cancer.
Collapse
Affiliation(s)
- An-Angela N Van
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA; Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, California, USA
| | - Maya T Kunkel
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA
| | - Timothy R Baffi
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA; Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, California, USA
| | - Gema Lordén
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA
| | - Corina E Antal
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA; Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, California, USA
| | - Sourav Banerjee
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA
| | - Alexandra C Newton
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA.
| |
Collapse
|
39
|
Suzuki H, Kinoshita G, Tsunoi T, Noju K, Araki K. Mouse Hair Significantly Lightened Through Replacement of the Cysteine Residue in the N-Terminal Domain of Mc1r Using the CRISPR/Cas9 System. J Hered 2020; 111:640-645. [PMID: 33252683 DOI: 10.1093/jhered/esaa054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/27/2020] [Indexed: 11/13/2022] Open
Abstract
A loss-of-function mutation in the melanocortin 1 receptor gene (MC1R), which switches off the eumelanin production, causes yellowish coat color variants in mammals. In a wild population of sables (Martes zibellina) in Hokkaido, Japan, the mutation responsible for a bright yellow coat color variant was inferred to be a cysteine replacement at codon 35 of the N-terminal extracellular domain of the Mc1r receptor. In the present study, we validated these findings by applying genome editing on Mc1r in mouse strains C3H/HeJ and C57BL/6N, altering the codon for cysteine (Cys33Phe). The resulting single amino acid substitution (Cys33Phe) and unintentionally generated frameshift mutations yielded a color variant exhibiting substantially brighter body color, indicating that the Cys35 replacement produced sufficient MC1R loss of function to confirm that this mutation is responsible for producing the Hokkaido sable yellow color variant. Notably, the yellowish mutant mouse phenotype exhibited brown coloration in subapical hair on the dorsal side in both the C3H/HeJ and C57BL/6N strains, despite the inability of the latter to produce the agouti signaling protein (Asip). This darker hair and body coloration was not apparent in the Hokkaido sable variant, implying the presence of an additional genetic system shaping yellowish hair variability.
Collapse
Affiliation(s)
- Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
| | - Gohta Kinoshita
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Takeru Tsunoi
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
| | - Koki Noju
- Graduate School of Science, Hokkaido University, Sapporo, Japan
| | - Kimi Araki
- and Division of Developmental Genetics, Institute of Resource Development and Analysis, Kumamoto University, Honjo, Kumamoto, Japan
| |
Collapse
|
40
|
Pantazis A, Kaneko M, Angelini M, Steccanella F, Westerlund AM, Lindström SH, Nilsson M, Delemotte L, Saitta SC, Olcese R. Tracking the motion of the K V1.2 voltage sensor reveals the molecular perturbations caused by a de novo mutation in a case of epilepsy. J Physiol 2020; 598:5245-5269. [PMID: 32833227 PMCID: PMC8923147 DOI: 10.1113/jp280438] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/14/2020] [Indexed: 12/28/2022] Open
Abstract
KEY POINTS KV1.2 channels, encoded by the KCNA2 gene, regulate neuronal excitability by conducting K+ upon depolarization. A new KCNA2 missense variant was discovered in a patient with epilepsy, causing amino acid substitution F302L at helix S4, in the KV1.2 voltage-sensing domain. Immunocytochemistry and flow cytometry showed that F302L does not impair KCNA2 subunit surface trafficking. Molecular dynamics simulations indicated that F302L alters the exposure of S4 residues to membrane lipids. Voltage clamp fluorometry revealed that the voltage-sensing domain of KV1.2-F302L channels is more sensitive to depolarization. Accordingly, KV1.2-F302L channels opened faster and at more negative potentials; however, they also exhibited enhanced inactivation: that is, F302L causes both gain- and loss-of-function effects. Coexpression of KCNA2-WT and -F302L did not fully rescue these effects. The proband's symptoms are more characteristic of patients with loss of KCNA2 function. Enhanced KV1.2 inactivation could lead to increased synaptic release in excitatory neurons, steering neuronal circuits towards epilepsy. ABSTRACT An exome-based diagnostic panel in an infant with epilepsy revealed a previously unreported de novo missense variant in KCNA2, which encodes voltage-gated K+ channel KV1.2. This variant causes substitution F302L, in helix S4 of the KV1.2 voltage-sensing domain (VSD). F302L does not affect KCNA2 subunit membrane trafficking. However, it does alter channel functional properties, accelerating channel opening at more hyperpolarized membrane potentials, indicating gain of function. F302L also caused loss of KV1.2 function via accelerated inactivation onset, decelerated recovery and shifted inactivation voltage dependence to more negative potentials. These effects, which are not fully rescued by coexpression of wild-type and mutant KCNA2 subunits, probably result from the enhancement of VSD function, as demonstrated by optically tracking VSD depolarization-evoked conformational rearrangements. In turn, molecular dynamics simulations suggest altered VSD exposure to membrane lipids. Compared to other encephalopathy patients with KCNA2 mutations, the proband exhibits mild neurological impairment, more characteristic of patients with KCNA2 loss of function. Based on this information, we propose a mechanism of epileptogenesis based on enhanced KV1.2 inactivation leading to increased synaptic release preferentially in excitatory neurons, and hence the perturbation of the excitatory/inhibitory balance of neuronal circuits.
Collapse
Affiliation(s)
- Antonios Pantazis
- Division of Molecular Medicine, Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
- Division of Neurobiology, Department of Biomedical and Clinical Sciences (BKV), Linköping University, Linköping, Sweden
- Wallenberg Center for Molecular Medicine, Linköping University, Linköping, Sweden
| | - Maki Kaneko
- Center for Personalized Medicine, Children's Hospital, Los Angeles, Los Angeles, CA, USA
- Division of Genomic Medicine, Department of Pathology, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Marina Angelini
- Division of Molecular Medicine, Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Federica Steccanella
- Division of Molecular Medicine, Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Annie M Westerlund
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Sarah H Lindström
- Division of Neurobiology, Department of Biomedical and Clinical Sciences (BKV), Linköping University, Linköping, Sweden
| | - Michelle Nilsson
- Division of Neurobiology, Department of Biomedical and Clinical Sciences (BKV), Linköping University, Linköping, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Sulagna C Saitta
- Department of Obstetrics and Gynecology and Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Riccardo Olcese
- Division of Molecular Medicine, Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
- Department of Physiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
- Brain Research Institute, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| |
Collapse
|
41
|
Kim G, Gautier O, Tassoni-Tsuchida E, Ma XR, Gitler AD. ALS Genetics: Gains, Losses, and Implications for Future Therapies. Neuron 2020; 108:822-42. [PMID: 32931756 DOI: 10.1016/j.neuron.2020.08.022] [Citation(s) in RCA: 171] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/01/2020] [Accepted: 08/21/2020] [Indexed: 02/06/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder caused by the loss of motor neurons from the brain and spinal cord. The ALS community has made remarkable strides over three decades by identifying novel familial mutations, generating animal models, elucidating molecular mechanisms, and ultimately developing promising new therapeutic approaches. Some of these approaches reduce the expression of mutant genes and are in human clinical trials, highlighting the need to carefully consider the normal functions of these genes and potential contribution of gene loss-of-function to ALS. Here, we highlight known loss-of-function mechanisms underlying ALS, potential consequences of lowering levels of gene products, and the need to consider both gain and loss of function to develop safe and effective therapeutic strategies.
Collapse
|
42
|
Berecki G, Helbig KL, Ware TL, Grinton B, Skraban CM, Marsh ED, Berkovic SF, Petrou S. Novel Missense CACNA1G Mutations Associated with Infantile-Onset Developmental and Epileptic Encephalopathy. Int J Mol Sci 2020; 21:E6333. [PMID: 32878331 DOI: 10.3390/ijms21176333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/29/2020] [Accepted: 08/29/2020] [Indexed: 11/17/2022] Open
Abstract
The CACNA1G gene encodes the low-voltage-activated Cav3.1 channel, which is expressed in various areas of the CNS, including the cerebellum. We studied two missense CACNA1G variants, p.L208P and p.L909F, and evaluated the relationships between the severity of Cav3.1 dysfunction and the clinical phenotype. The presentation was of a developmental and epileptic encephalopathy without evident cerebellar atrophy. Both patients exhibited axial hypotonia, developmental delay, and severe to profound cognitive impairment. The patient with the L909F mutation had initially refractory seizures and cerebellar ataxia, whereas the L208P patient had seizures only transiently but was overall more severely affected. In transfected mammalian cells, we determined the biophysical characteristics of L208P and L909F variants, relative to the wild-type channel and a previously reported gain-of-function Cav3.1 variant. The L208P mutation shifted the activation and inactivation curves to the hyperpolarized direction, slowed the kinetics of inactivation and deactivation, and reduced the availability of Ca2+ current during repetitive stimuli. The L909F mutation impacted channel function less severely, resulting in a hyperpolarizing shift of the activation curve and slower deactivation. These data suggest that L909F results in gain-of-function, whereas L208P exhibits mixed gain-of-function and loss-of-function effects due to opposing changes in the biophysical properties. Our study expands the clinical spectrum associated with CACNA1G mutations, corroborating further the causal association with distinct complex phenotypes.
Collapse
|
43
|
Boyarskikh UA, Gulyaeva LF, Avdalyan AM, Kechin AA, Khrapov EA, Lazareva DG, Kushlinskii NE, Melkonyan A, Arakelyan A, Filipenko ML. Spectrum of TP53 Mutations in BRCA1/2 Associated High-Grade Serous Ovarian Cancer. Front Oncol 2020; 10:1103. [PMID: 32766142 PMCID: PMC7378769 DOI: 10.3389/fonc.2020.01103] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/02/2020] [Indexed: 12/11/2022] Open
Abstract
Objective: Mutations in TP53 lead to loss of function (LOF) or gain of function (GOF) of the corresponding protein p53 and produce a different effect on the tumor. Our goal was to determine the spectrum of somatic TP53 variants in BRCA1/2 associated high-grade serous ovarian cancer (HGSOC). Methods: The population under study comprised of HGSOCs with pathogenic variants in BRCA1 (n = 78) or BRCA2 (n = 21). Only chemo-naive and platinum-sensitive patients were included in this study. The case group of the IARC database (n = 1249) with HGSOC not stratified by BRCA status was used as a reference. A custom NGS panel was used for sequencing TP53 and mutational hot-spots of other genes, and p53 expression was evaluated by immunohistochemistry for 68 cases of HGSOCs. Results: Somatic TP53 variants (95) or inhibition of wild-type p53 expression (3) were observed in 98 cases. The sample with normal p53 had CDKNA1 variants. The frequency of truncating variants was significantly higher than in the reference cohort (30.3 vs. 21.0%, p = 0.01). Most of the samples (41/68) demonstrated low (or absent) expression of p53, and 17 samples overexpressed p53. LOH was typical for TP53 nonsense variants (14/15). In total, 68/95 samples were LOH positive and showed LOH in all tumorous cells, thus indicating the driver effect of TP53 mutations. Three specimens had KRAS, BAX, APC, and CTNNB1 subclones variants. Conclusion: High frequency of TP53 truncating variants, the low expression of mutant p53, and low incidence of oncogene mutations show potential GOF properties of p53 to be poorly represented in BRCA1/2 associated HGSOC.
Collapse
Affiliation(s)
- Ulyana A Boyarskikh
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - L F Gulyaeva
- Institute for Medicine and Psychology, Novosibirsk State University, Novosibirsk, Russia.,Institute of Molecular Biology and Biophysics, Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | | | - A A Kechin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - E A Khrapov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - D G Lazareva
- Altai Territorial Cancer Control Center, Barnaul, Russia
| | - N E Kushlinskii
- N.N. Blokhin National Medical Research Center of Oncology, Moscow, Russia
| | - A Melkonyan
- Group of Bioinformatics, Institute of Molecular Biology, Armenian National Academy of Sciences (NAS RA), Yerevan, Armenia
| | - A Arakelyan
- Group of Bioinformatics, Institute of Molecular Biology, Armenian National Academy of Sciences (NAS RA), Yerevan, Armenia
| | - Maxim Leonidovich Filipenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| |
Collapse
|
44
|
Cen Z, Chen Y, Chen S, Wang H, Yang D, Zhang H, Wu H, Wang L, Tang S, Ye J, Shen J, Wang H, Fu F, Chen X, Xie F, Liu P, Xu X, Cao J, Cai P, Pan Q, Li J, Yang W, Shan PF, Li Y, Liu JY, Zhang B, Luo W. Biallelic loss-of-function mutations in JAM2 cause primary familial brain calcification. Brain 2020; 143:491-502. [PMID: 31851307 DOI: 10.1093/brain/awz392] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/15/2019] [Accepted: 10/29/2019] [Indexed: 12/23/2022] Open
Abstract
Primary familial brain calcification is a monogenic disease characterized by bilateral calcifications in the basal ganglia and other brain regions, and commonly presents motor, psychiatric, and cognitive symptoms. Currently, four autosomal dominant (SLC20A2, PDGFRB, PDGFB, XPR1) and one autosomal recessive (MYORG) causative genes have been identified. Compared with patients with autosomal dominant primary familial brain calcification, patients with the recessive form of the disease present with more severe clinical and imaging phenotypes, and deserve more clinical and research attention. Biallelic mutations in MYORG cannot explain all autosomal recessive primary familial brain calcification cases, indicating the existence of novel autosomal recessive genes. Using homozygosity mapping and whole genome sequencing, we detected a homozygous frameshift mutation (c.140delT, p.L48*) in the JAM2 gene in a consanguineous family with two affected siblings diagnosed with primary familial brain calcification. Further genetic screening in a cohort of 398 probands detected a homozygous start codon mutation (c.1A>G, p.M1?) and compound heterozygous mutations [c.504G>C, p.W168C and c.(67+1_68-1)_(394+1_395-1), p.Y23_V131delinsL], respectively, in two unrelated families. The clinical phenotypes of the four patients included parkinsonism (3/4), dysarthria (3/4), seizures (1/4), and probable asymptomatic (1/4), with diverse onset ages. All patients presented with severe calcifications in the cortex in addition to extensive calcifications in multiple brain areas (lenticular nuclei, caudate nuclei, thalamus, cerebellar hemispheres, ± brainstem; total calcification scores: 43-77). JAM2 encodes junctional adhesion molecule 2, which is highly expressed in neurovascular unit-related cell types (endothelial cells and astrocytes) and is predominantly localized on the plasma membrane. It may be important in cell-cell adhesion and maintaining homeostasis in the CNS. In Chinese hamster ovary cells, truncated His-tagged JAM2 proteins were detected by western blot following transfection of p.Y23_V131delinsL mutant plasmid, while no protein was detected following transfection of p.L48* or p.1M? mutant plasmids. In immunofluorescence experiments, the p.W168C mutant JAM2 protein failed to translocate to the plasma membrane. We speculated that mutant JAM2 protein resulted in impaired cell-cell adhesion functions and reduced integrity of the neurovascular unit. This is similar to the mechanisms of other causative genes for primary familial brain calcification or brain calcification syndromes (e.g. PDGFRB, PDGFB, MYORG, JAM3, and OCLN), all of which are highly expressed and functionally important in the neurovascular unit. Our study identifies a novel causative gene for primary familial brain calcification, whose vital function and high expression in the neurovascular unit further supports impairment of the neurovascular unit as the root of primary familial brain calcification pathogenesis.
Collapse
Affiliation(s)
- Zhidong Cen
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - You Chen
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Si Chen
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Hong Wang
- Department of Neurology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Dehao Yang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Hongmei Zhang
- Department of Neurology, Ningbo Fourth Hospital, Ningbo, Zhejiang, China
| | - Hongwei Wu
- Department of Neurology, Lishui People's Hospital, Lishui, Zhejiang, China
| | - Lebo Wang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Siyang Tang
- Children's Hospital and Department of Biophysics, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jia Ye
- Children's Hospital and Department of Biophysics, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jian Shen
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Haotian Wang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Feng Fu
- Department of Neurology, Zhuji People's Hospital of Zhejiang Province, Shaoxing, Zhejiang, China
| | - Xinhui Chen
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Fei Xie
- Department of Neurology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Peng Liu
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xuan Xu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jianzhi Cao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Pan Cai
- Department of Neurology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Qinqing Pan
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Department of Neurology, Wuyi First People's Hospital, Jinhua, Zhejiang, China
| | - Jieying Li
- Department of Neurology, Guiyang Second People's Hospital, Guiyang, Guizhou, China
| | - Wei Yang
- Department of Biophysics, Institute of Neuroscience, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Peng-Fei Shan
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yuezhou Li
- Children's Hospital and Department of Biophysics, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jing-Yu Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Baorong Zhang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Wei Luo
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| |
Collapse
|
45
|
Rausell A, Luo Y, Lopez M, Seeleuthner Y, Rapaport F, Favier A, Stenson PD, Cooper DN, Patin E, Casanova JL, Quintana-Murci L, Abel L. Common homozygosity for predicted loss-of-function variants reveals both redundant and advantageous effects of dispensable human genes. Proc Natl Acad Sci U S A 2020; 117:13626-13636. [PMID: 32487729 PMCID: PMC7306792 DOI: 10.1073/pnas.1917993117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Humans homozygous or hemizygous for variants predicted to cause a loss of function (LoF) of the corresponding protein do not necessarily present with overt clinical phenotypes. We report here 190 autosomal genes with 207 predicted LoF variants, for which the frequency of homozygous individuals exceeds 1% in at least one human population from five major ancestry groups. No such genes were identified on the X and Y chromosomes. Manual curation revealed that 28 variants (15%) had been misannotated as LoF. Of the 179 remaining variants in 166 genes, only 11 alleles in 11 genes had previously been confirmed experimentally to be LoF. The set of 166 dispensable genes was enriched in olfactory receptor genes (41 genes). The 41 dispensable olfactory receptor genes displayed a relaxation of selective constraints similar to that observed for other olfactory receptor genes. The 125 dispensable nonolfactory receptor genes also displayed a relaxation of selective constraints consistent with greater redundancy. Sixty-two of these 125 genes were found to be dispensable in at least three human populations, suggesting possible evolution toward pseudogenes. Of the 179 LoF variants, 68 could be tested for two neutrality statistics, and 8 displayed robust signals of positive selection. These latter variants included a known FUT2 variant that confers resistance to intestinal viruses, and an APOL3 variant involved in resistance to parasitic infections. Overall, the identification of 166 genes for which a sizeable proportion of humans are homozygous for predicted LoF alleles reveals both redundancies and advantages of such deficiencies for human survival.
Collapse
Affiliation(s)
- Antonio Rausell
- Clinical Bioinformatics Laboratory, INSERM UMR1163, Necker Hospital for Sick Children, 75015 Paris, France;
- University of Paris, Imagine Institute, 75015 Paris, France
| | - Yufei Luo
- Clinical Bioinformatics Laboratory, INSERM UMR1163, Necker Hospital for Sick Children, 75015 Paris, France
- University of Paris, Imagine Institute, 75015 Paris, France
| | - Marie Lopez
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Paris 75015, France
| | - Yoann Seeleuthner
- University of Paris, Imagine Institute, 75015 Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Necker Hospital for Sick Children, 75015 Paris, France
| | - Franck Rapaport
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
| | - Antoine Favier
- Clinical Bioinformatics Laboratory, INSERM UMR1163, Necker Hospital for Sick Children, 75015 Paris, France
- University of Paris, Imagine Institute, 75015 Paris, France
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, CF14 4XN Cardiff, United Kingdom
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, CF14 4XN Cardiff, United Kingdom
| | - Etienne Patin
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Paris 75015, France
| | - Jean-Laurent Casanova
- University of Paris, Imagine Institute, 75015 Paris, France;
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Necker Hospital for Sick Children, 75015 Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
- Howard Hughes Medical Institute, New York, NY 10065
- Pediatric Hematology and Immunology Unit, Necker Hospital for Sick Children, 75015 Paris, France
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Paris 75015, France
- Human Genomics and Evolution, Collège de France, Paris 75005, France
| | - Laurent Abel
- University of Paris, Imagine Institute, 75015 Paris, France;
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Necker Hospital for Sick Children, 75015 Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
| |
Collapse
|
46
|
Gokhman D, Mishol N, de Manuel M, de Juan D, Shuqrun J, Meshorer E, Marques-Bonet T, Rak Y, Carmel L. Reconstructing Denisovan Anatomy Using DNA Methylation Maps. Cell 2019; 179:180-192.e10. [PMID: 31539495 DOI: 10.1016/j.cell.2019.08.035] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/24/2019] [Accepted: 08/20/2019] [Indexed: 12/26/2022]
Abstract
Denisovans are an extinct group of humans whose morphology remains unknown. Here, we present a method for reconstructing skeletal morphology using DNA methylation patterns. Our method is based on linking unidirectional methylation changes to loss-of-function phenotypes. We tested performance by reconstructing Neanderthal and chimpanzee skeletal morphologies and obtained >85% precision in identifying divergent traits. We then applied this method to the Denisovan and offer a putative morphological profile. We suggest that Denisovans likely shared with Neanderthals traits such as an elongated face and a wide pelvis. We also identify Denisovan-derived changes, such as an increased dental arch and lateral cranial expansion. Our predictions match the only morphologically informative Denisovan bone to date, as well as the Xuchang skull, which was suggested by some to be a Denisovan. We conclude that DNA methylation can be used to reconstruct anatomical features, including some that do not survive in the fossil record.
Collapse
|
47
|
Paraiso KD, Blitz IL, Zhou JJ, Cho KWY. Morpholinos Do Not Elicit an Innate Immune Response during Early Xenopus Embryogenesis. Dev Cell 2020; 49:643-650.e3. [PMID: 31112700 DOI: 10.1016/j.devcel.2019.04.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 03/14/2019] [Accepted: 04/16/2019] [Indexed: 02/06/2023]
Abstract
It has recently been reported that a common side effect of translation-blocking morpholino antisense oligonucleotides is the induction of a set of innate immune response genes in Xenopus embryos and that splicing-blocking morpholinos lead to unexpected off-target mis-splicing events. Here, we present an analysis of all publicly available Xenopus RNA sequencing (RNA-seq) data in a reexamination of the effects of translation-blocking morpholinos on the innate immune response. Our analysis does not support the authors' general conclusion, which was based on a limited number of RNA-seq datasets. Moreover, the strong induction of an immune response appears to be specific to the tbxt/tbxt2 morpholinos. The more comprehensive study presented here indicates that using morpholinos for targeted gene knockdowns remains of considerable value for the rapid identification of gene function.
Collapse
Affiliation(s)
- Kitt D Paraiso
- Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Ira L Blitz
- Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Jeff J Zhou
- Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Ken W Y Cho
- Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA.
| |
Collapse
|
48
|
Abstract
Natural or synthetic genetic modules can lose their function over long-term evolution if the function is costly. How populations can evolve to restore such broken function is poorly understood. To test the reversibility of evolutionary breakdown, we use yeast cell populations with a chromosomally integrated synthetic gene circuit. In previous evolution experiments the gene circuit lost its costly function through various mutations. By exposing such mutant populations to conditions where regaining gene circuit function would be beneficial, we find adaptation scenarios with or without repairing lost gene circuit function. These results are important for drug resistance or future synthetic biology applications where evolutionary loss and regain of function play a significant role. Evolutionary reversibility—the ability to regain a lost function—is an important problem both in evolutionary and synthetic biology, where repairing natural or synthetic systems broken by evolutionary processes may be valuable. Here, we use a synthetic positive-feedback (PF) gene circuit integrated into haploid Saccharomyces cerevisiae cells to test if the population can restore lost PF function. In previous evolution experiments, mutations in a gene eliminated the fitness costs of PF activation. Since PF activation also provides drug resistance, exposing such compromised or broken mutants to both drug and inducer should create selection pressure to regain drug resistance and possibly PF function. Indeed, evolving 7 PF mutant strains in the presence of drug revealed 3 adaptation scenarios through genomic, PF-external mutations that elevate PF basal expression, possibly by affecting transcription, translation, degradation, and other fundamental cellular processes. Nonfunctional mutants gained drug resistance without ever developing high expression, while quasifunctional and dysfunctional PF mutants developed high expression nongenetically, which then diminished, although more slowly for dysfunctional mutants where revertant clones arose. These results highlight how intracellular context, such as the growth rate, can affect regulatory network dynamics and evolutionary dynamics, which has important consequences for understanding the evolution of drug resistance and developing future synthetic biology applications.
Collapse
|
49
|
Angus M, Peters CH, Poburko D, Brimble E, Spelbrink EM, Ruben PC. Case studies in neuroscience: a novel amino acid duplication in the NH 2-terminus of the brain sodium channel Na V1.1 underlying Dravet syndrome. J Neurophysiol 2019; 122:1975-1980. [PMID: 31533007 DOI: 10.1152/jn.00491.2019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Dravet syndrome is a severe form of childhood epilepsy characterized by frequent temperature-sensitive seizures and delays in cognitive development. In the majority (80%) of cases, Dravet syndrome is caused by mutations in the SCN1A gene, encoding the voltage-gated sodium channel NaV1.1, which is abundant in the central nervous system. Dravet syndrome can be caused by either gain-of-function mutation or loss of function in NaV1.1, making it necessary to characterize each novel mutation. Here we use a combination of patch-clamp recordings and immunocytochemistry to characterize the first known NH2-terminal amino acid duplication mutation found in a patient with Dravet syndrome, M72dup. M72dup does not significantly alter rate of fast inactivation recovery or rate of fast inactivation onset at any measured membrane potential. M72dup significantly shifts the midpoint of the conductance voltage relationship to more hyperpolarized potentials. Most interestingly, M72dup significantly reduces peak current of NaV1.1 and reduces membrane expression. This suggests that M72dup acts as a loss-of-function mutation primarily by impacting the ability of the channel to localize to the plasma membrane.NEW & NOTEWORTHY Genetic screening of a patient with Dravet syndrome revealed a novel mutation in SCN1A. Of over 700 SCN1A mutations known to cause Dravet syndrome, M72dup is the first to be identified in the NH2-terminus of NaV1.1. We studied M72dup using patch-clamp electrophysiology and immunocytochemistry. M72dup causes a decrease in membrane expression of NaV1.1 and overall loss of function, consistent with the role of the NH2-terminal region in membrane trafficking of NaV1.1.
Collapse
Affiliation(s)
- Madeline Angus
- Department of Biomedical Physiology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Colin H Peters
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Damon Poburko
- Department of Biomedical Physiology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Elise Brimble
- Department of Neurology and Neurological Sciences, Stanford Medicine, Palo Alto, California
| | - Emily M Spelbrink
- Department of Neurology and Neurological Sciences, Stanford Medicine, Palo Alto, California
| | - Peter C Ruben
- Department of Biomedical Physiology, Simon Fraser University, Burnaby, British Columbia, Canada
| |
Collapse
|
50
|
Weinreich M, Shepheard SR, Verber N, Wyles M, Heath PR, Highley JR, Kirby J, Shaw PJ. Neuropathological characterization of a novel TANK binding kinase (TBK1) gene loss of function mutation associated with amyotrophic lateral sclerosis. Neuropathol Appl Neurobiol 2019; 46:279-291. [PMID: 31498468 DOI: 10.1111/nan.12578] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/17/2019] [Indexed: 12/12/2022]
Abstract
AIMS Mutations in TANK binding kinase gene (TBK1) are causative in amyotrophic lateral sclerosis (ALS), however correlations between clinical features and TBK1 mutations have not been fully elucidated. We aimed to identify and compare TBK1 mutations to clinical features in a cohort of ALS patients from Northern England. METHODS TBK1 mutations were analysed in 290 ALS cases. Immunohistochemistry was performed in brain and spinal cord of one case with a novel in-frame deletion. RESULTS Seven TBK1 variants were identified, including one novel in-frame deletion (p.85delIle). In silico analysis and literature suggested four variants were pathogenic, and three were variants of uncertain significance or benign. Post-mortem immunohistochemistry established an individual with the novel in-frame deletion had classical ALS and Type B FTLD-TDP pathology, with no changes in TBK1 staining or interferon regulatory factor IRF3. CONCLUSIONS TBK1 mutations were present in 1.38% of our cohort, and screening showed no clear genotype-phenotype associations compared to other genetic and sporadic ALS cases. TBK1 immunohistochemistry was consistent with previously published literature and we are the first to show no differential expression of interferon regulatory factor IRF3, a downstream effector of TBK1 in the immune pathway, in the TBK1-mutant tissue, compared to controls.
Collapse
Affiliation(s)
- M Weinreich
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - S R Shepheard
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - N Verber
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - M Wyles
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - P R Heath
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - J R Highley
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - J Kirby
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - P J Shaw
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| |
Collapse
|