1
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Birk-Bachar M, Cohen H, Sofrin-Drucker E, Kropach-Gilad N, Orenstein N, Lidzbarsky G, Kornreich L, Tal R, Amarilyo G, Levinsky Y, Sokolov M, Raveh E, Gerlic M, Harel L. Discovery of a Novel Missense Variant in NLRP3 Causing Atypical Cryopyrin-Associated Periodic Syndromes With Hearing Loss as the Primary Presentation, Responsive to Anti-Interleukin-1 Therapy. Arthritis Rheumatol 2024; 76:444-454. [PMID: 37738164 DOI: 10.1002/art.42721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/15/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
OBJECTIVE Cryopyrin-associated periodic syndromes (CAPS), also known as NLRP3-associated autoinflammatory diseases, are a spectrum of rare autoinflammatory diseases caused by gain-of-function variants in the NLRP3 gene, resulting in inflammasome hyperactivation and dysregulated release of interleukin-1β (IL-1β). Many patients with CAPS develop progressive sensorineural hearing loss (SNHL) because of cochlear autoinflammation, which may be the sole manifestation in rare cases. This study was undertaken to establish the suspected diagnosis of CAPS in a family presenting with autosomal-dominant progressive/acute SNHL and a novel missense variant in the NLRP3 gene of unknown significance (NM_001079821.3:c.1784G>A p.Ser595Asn). METHODS We conducted an ex vivo functional assessment of the NLRP3 inflammasome in heterozygous individuals (n = 10) and healthy family members (n = 5). RESULTS The assay revealed hyperactivation of the inflammasome among heterozygous individuals, supporting the hypothesis that this missense variant is a pathogenic gain-of-function variant. Administration of IL-1 receptor antagonist resulted in a substantial clinical improvement among pediatric patients, who exhibited near resolution of hearing impairment within 1 to 3 months of treatment. CONCLUSION Our findings highlight the crucial role of early diagnosis and treatment with an anti-IL-1 agent in reversing cochlear damage. Furthermore, our results suggest that high- and ultrahigh-frequency ranges need to be included in the auditory assessment to enable early detection of subclinical SNHL. Finally, incorporating functional inflammasome assessment as part of the clinical evaluation could establish the diagnosis in inconclusive cases.
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Affiliation(s)
| | | | - Efrat Sofrin-Drucker
- Schneider Children's Medical Center of Israel and Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach-Tikva, and Tel-Aviv University, Tel-Aviv, Israel
| | - Nesia Kropach-Gilad
- Schneider Children's Medical Center of Israel and Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach-Tikva, and Tel-Aviv University, Tel-Aviv, Israel
| | - Naama Orenstein
- Schneider Children's Medical Center of Israel and Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach-Tikva, and Tel-Aviv University, Tel-Aviv, Israel
| | - Gabriel Lidzbarsky
- Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach-Tikva, Israel
| | - Liora Kornreich
- Schneider Children's Medical Center of Israel, Petach-Tikva, and Tel-Aviv University, Tel-Aviv, Israel
| | - Rotem Tal
- Schneider Children's Medical Center of Israel, Petach-Tikva, and Tel-Aviv University, Tel-Aviv, Israel
| | - Gil Amarilyo
- Schneider Children's Medical Center of Israel, Petach-Tikva, and Tel-Aviv University, Tel-Aviv, Israel
| | - Yoel Levinsky
- Schneider Children's Medical Center of Israel, Petach-Tikva, and Tel-Aviv University, Tel-Aviv, Israel
| | - Meirav Sokolov
- Schneider Children's Medical Center of Israel, Petach-Tikva, and Tel-Aviv University, Tel-Aviv, Israel
| | - Eyal Raveh
- Schneider Children's Medical Center of Israel, Petach-Tikva, and Tel-Aviv University, Tel-Aviv, Israel
| | | | - Liora Harel
- Schneider Children's Medical Center of Israel, Petach-Tikva, and Tel-Aviv University, Tel-Aviv, Israel
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2
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Sachs N, Wechsberg O, Landau YE, Krause I, Israel Elgali I, Darawshe M, Shomron N, Lidzbarsky G, Orenstein N. A novel SLC25A13 gene splice site variant causes Citrin deficiency in an infant. Gene 2023; 874:147483. [PMID: 37196891 DOI: 10.1016/j.gene.2023.147483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/01/2023] [Accepted: 05/09/2023] [Indexed: 05/19/2023]
Abstract
Citrin deficiency is an autosomal recessive disorder associated with SLC25A13 gene pathogenic variants, with more than a hundred known at present. It manifests in neonates as failure to thrive and acute liver insufficiency. We herein describe a case of a 4-week-old infant who presented with insufficient weight gain and liver failure accompanied by hyperammonemia. She was diagnosed with Citrin deficiency after a thorough biochemical and molecular analysis including amino acid profile, DNA sequencing of genes of interest and RNA splice site evaluation, to reveal a yet unknown damaging variant of the SLC25A13 gene.
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Affiliation(s)
- Nimrod Sachs
- Department of Pediatrics C, Schneider Children's Medical Center of Israel, Petah Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Oded Wechsberg
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petah Tikva, Israel; Maccabi Healthcare Services, Tel Aviv, Israel
| | - Yuval E Landau
- Metabolic Disease Service, Schneider Children's Medical Center of Israel, Petah Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Irit Krause
- Department of Pediatrics C, Schneider Children's Medical Center of Israel, Petah Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ifat Israel Elgali
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Malak Darawshe
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gabriel Lidzbarsky
- The Raphael Recanati Genetic institute, Rabin Medical Center, Beilinson hospital, Petah Tikva, Israel
| | - Naama Orenstein
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
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3
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Michelson M, Lidzbarsky G, Nishri D, Israel-Elgali I, Berger R, Gafner M, Shomron N, Lev D, Goldberg Y. Microdeletion of 16q24.1-q24.2-A unique etiology of Lymphedema-Distichiasis syndrome and neurodevelopmental disorder. Am J Med Genet A 2022; 188:1990-1996. [PMID: 35312147 PMCID: PMC9314700 DOI: 10.1002/ajmg.a.62730] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 12/09/2021] [Accepted: 01/28/2022] [Indexed: 01/15/2023]
Abstract
Interstitial deletions of 16q24.1–q24.2 are associated with alveolar capillary dysplasia, congenital renal malformations, neurodevelopmental disorders, and congenital abnormalities. Lymphedema–Distichiasis syndrome (LDS; OMIM # 153400) is a dominant condition caused by heterozygous pathogenic variants in FOXC2. Usually, lymphedema and distichiasis occur in puberty or later on, and affected individuals typically achieve normal developmental milestones. Here, we describe a boy with congenital lymphedema, distichiasis, bilateral hydronephrosis, and global developmental delay, with a de novo microdeletion of 894 kb at 16q24.1–q24.2. This report extends the phenotype of both 16q24.1–q24.2 microdeletion syndrome and of LDS. Interestingly, the deletion involves only the 3′‐UTR part of FOXC2.
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Affiliation(s)
- Marina Michelson
- Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel.,The Genetic Institute of Maccabi Health Medicinal Organization, Tel-Aviv, Israel.,Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Gabriel Lidzbarsky
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel
| | - Daniella Nishri
- Child Developmental Center of Maccabi Health Medicinal Organization, Tel-Aviv, Israel
| | - Ifat Israel-Elgali
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel
| | - Rachel Berger
- The Genetic Institute of Maccabi Health Medicinal Organization, Tel-Aviv, Israel
| | - Michal Gafner
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Noam Shomron
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel
| | - Dorit Lev
- Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel.,The Genetic Institute of Maccabi Health Medicinal Organization, Tel-Aviv, Israel.,Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Yael Goldberg
- The Genetic Institute of Maccabi Health Medicinal Organization, Tel-Aviv, Israel.,Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel
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4
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Michaeli O, Ladany H, Erez A, Shachar SB, Izraeli S, Lidzbarsky G, Basel-Salmon L, Biskup S, Maruvka YE, Toledano H, Goldberg Y. Di-genic inheritance of germline POLE and PMS2 pathogenic variants causes a unique condition associated with pediatric cancer predisposition. Clin Genet 2021; 101:442-447. [PMID: 34967012 DOI: 10.1111/cge.14106] [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: 10/16/2021] [Revised: 12/12/2021] [Accepted: 12/25/2021] [Indexed: 11/25/2022]
Abstract
Polymerase proofreading-associated polyposis (PPAP) and Lynch syndrome, caused by mutated POLE and mismatch repair (MMR) genes, respectively, are associated with adult-onset cancer. PPAP and MMR-deficient tumors are both hypermutated, and each has a unique mutational signature. We describe a 4.5-year-old boy with multiple café au lait spots who presented with metastatic Sonic Hedgehog-activated medulloblastoma, with partial response to intensive chemotherapy and immunotherapy. Tumor showed microsatellite stability, loss of PMS2 nuclear expression, and an exceptionally high tumor mutational burden of 276 Mut/Mb. Germline molecular analysis revealed an inherited heterozygous pathogenic POLE variant and a de novo heterozygous PMS2 pathogenic variant. The tumor featured the MMR, POLE, and POLE+MMR mutational signatures. This is the first description of a di-genic condition, which we named "POL-LYNCH syndrome", manifested by an aggressive ultra-mutant pediatric medulloblastoma with a unique genomic signature. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Orli Michaeli
- Department of Pediatric Hematology and Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Hagay Ladany
- Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Ayelet Erez
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Shay Ben Shachar
- Clalit Research Institute & Department of Genetics, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Shai Izraeli
- Department of Pediatric Hematology and Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gabriel Lidzbarsky
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel
| | - Lina Basel-Salmon
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel
| | - Saskia Biskup
- CeGaT Center for Genomics and Transcriptomics, Tuebingen, Germany
| | - Yosef E Maruvka
- Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Helen Toledano
- Department of Pediatric Hematology and Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yael Goldberg
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel
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5
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Goldberg Y, Laitman Y, Ben David M, Bazak L, Lidzbarsky G, Salmon LB, Shkedi-Rafid S, Barshack I, Avivi C, Darawshe M, Shomron N, Bruchim R, Vinkler C, Yannoukakos D, Fostira F, Bernstein-Molho R, Friedman E. Re-evaluating the pathogenicity of the c.783+2T>C BAP1 germline variant. Hum Mutat 2021; 42:592-599. [PMID: 33600035 DOI: 10.1002/humu.24189] [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: 12/07/2020] [Revised: 02/09/2021] [Accepted: 02/15/2021] [Indexed: 12/13/2022]
Abstract
BAP1 germline pathogenic sequence variants (PSVs) underlie a unique tumor predisposition syndrome (BAP1-TPDS) associated with an increased lifetime risk for developing primarily pleural and peritoneal mesothelioma and uveal and cutaneous melanoma. Overwhelmingly, BAP1 PSVs are unique, family-specific inactivating variants. We identified seven families, six of Jewish Iraqi origin, harboring an identical BAP1 splice variant (c.783+2T>C), currently assigned a "likely pathogenic" status. Given a nonclassical BAP1-TPDS tumor type clustering and low penetrance in these families, the pathogenicity of this variant was re-evaluated by a combined approach including literature analysis, revised bioinformatics analysis, allelic loss, effect on the transcript, and tumor protein expression patterns. None of the three available tumors showed an allelic loss, there was no discernable effect on alternative splicing based on reverse-transcription polymerase chain reaction, and there was no decrease or loss of somatic protein expression in 2/3 analyzed tumors. This led to assigning a Benign Strong (BS) criteria, BS4, supporting BS3 criteria, and weakening the Pathogenic Supporting (PP) criteria PP5. Combined, these data suggest that this sequence variant should be reclassified as a variant of unknown significance by American College of Medical Genetics (ACMG) criteria.
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Affiliation(s)
- Yael Goldberg
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel.,Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Yael Laitman
- Susanne Levy Gertner Oncogenetics Unit, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | - Merav Ben David
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Radiation Oncology Unit, Assuta Medical Center, Tel-Aviv, Israel
| | - Lily Bazak
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
| | - Gabriel Lidzbarsky
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
| | - Lina B Salmon
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel.,Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Shiri Shkedi-Rafid
- Department of Genetics, Hadassah-Hebrew University Hospital, Jerusalem, Israel.,Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Iris Barshack
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Pathology Institute, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | - Camila Avivi
- Pathology Institute, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | - Malak Darawshe
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Noam Shomron
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Revital Bruchim
- Naot Clinic, Maccabi Health Care Organization, Tel-Aviv, Israel
| | - Chana Vinkler
- Onco Genetis Unit, Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research "Demokritos", Athens, Greece
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research "Demokritos", Athens, Greece
| | - Rinat Bernstein-Molho
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Breast Cancer Unit, Institute of Oncology, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | - Eitan Friedman
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Susanne Levy Gertner Oncogenetics Unit, Chaim Sheba Medical Center, Tel-Hashomer, Israel
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6
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Fellner A, Lossos A, Kogan E, Argov Z, Gonzaga-Jauregui C, Shuldiner AR, Darawshe M, Bazak L, Lidzbarsky G, Shomron N, Basel-Salmon L, Goldberg Y. Two intronic cis-acting variants in both alleles of the POLR3A gene cause progressive spastic ataxia with hypodontia. Clin Genet 2021; 99:713-718. [PMID: 33491183 DOI: 10.1111/cge.13929] [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: 11/13/2020] [Revised: 01/02/2021] [Accepted: 01/19/2021] [Indexed: 12/14/2022]
Abstract
POLR3A encodes the largest subunit of the DNA-dependent RNA polymerase III. Pathogenic variants in this gene are associated with dysregulation of tRNA production and other non-coding RNAs. POLR3A-related disorders include variable phenotypes. The genotype-phenotype correlation is still unclear. Phenotypic analysis and exome sequencing were performed in four affected siblings diagnosed clinically with hereditary spastic ataxia, two healthy siblings and their unaffected mother. All four affected siblings (ages 46-55) had similar clinical features of early childhood-onset hypodontia and adolescent-onset progressive spastic ataxia. None had progeria, gonadal dysfunction or dysmorphism. All affected individuals had biallelic POLR3A pathogenic variants composed by two cis-acting intronic splicing-altering variants, c.1909 + 22G > A and c.3337-11 T > C. The two healthy siblings had wild-type alleles. The mother and another unaffected sibling were heterozygous for the allele containing both variants. This is the first report addressing the clinical consequence associated with homozygosity for a unique pathogenic intronic allele in the POLR3A gene. This allele was previously reported in compound heterozygous combinations in patients with Wiedemann-Rautenstrauch syndrome, a severe progeroid POLR3A-associated phenotype. We show that homozygosity for this allele is associated with spastic ataxia with hypodontia, and not with progeroid features. These findings contribute to the characterization of genotype-phenotype correlation in POLR3A-related disorders.
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Affiliation(s)
- Avi Fellner
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel.,Department of Neurology, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Alexander Lossos
- Department of Neurology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Elena Kogan
- Department of Neurology, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Zohar Argov
- Department of Neurology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | | | | | - Malak Darawshe
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Lily Bazak
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Gabriel Lidzbarsky
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Lina Basel-Salmon
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Felsenstein Medical Research Center, Petah Tikva, Israel
| | - Yael Goldberg
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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7
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Fellner A, Ruhrman-Shahar N, Orenstein N, Lidzbarsky G, Shuldiner AR, Gonzaga-Jauregui C, Brown-Shalev H, Hagari-Bechar O, Bazak L, Basel-Salmon L. The role of phenotype-based search approaches using public online databases in diagnostics of Mendelian disorders. Genet Med 2021; 23:1095-1100. [PMID: 33473205 DOI: 10.1038/s41436-020-01085-7] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 11/09/2022] Open
Abstract
PURPOSE To investigate the effectiveness of phenotype-based search approaches using publicly available online databases. METHODS We included consecutively solved cases from our exome database. For each case, the combination of Human Phenotype Ontology terms reported by the referring clinician was used to perform a search in three commonly used databases: OMIM (first 300 results), Phenolyzer (first 300 results), and Mendelian (all 100 results). RESULTS One hundred cases were included (43 females; mean age: 10 years). The actual molecular diagnosis identified through exome sequencing was not included in the search results of any of the queried databases in 33% of cases. In 85% of cases it was not found within the top five search results. When included, its median rank was 61 (range: 1-295), 21 (1-270), and 29 (1-92) in OMIM, Phenolyzer and Mendelian, respectively. CONCLUSION This study demonstrates that, in most cases, phenotype-based search approaches using public online databases is ineffective in providing a probable diagnosis for Mendelian conditions. Genotype-first approach through molecular-guided diagnostics with backward phenotyping may be a more appropriate approach for these disorders, unless a specific diagnosis is considered a priori based on highly unique phenotypic features or a specific facial gestalt.
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Affiliation(s)
- Avi Fellner
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel. .,The Neurology Department, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel.
| | - Noa Ruhrman-Shahar
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Naama Orenstein
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
| | - Gabriel Lidzbarsky
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
| | | | | | - Hadar Brown-Shalev
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
| | - Ofir Hagari-Bechar
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
| | - Lily Bazak
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
| | - Lina Basel-Salmon
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Laboratory of Immunology and Genetics, Felsenstein Medical Research Center, Petah Tikva, Israel
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8
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Stern T, Orenstein N, Fellner A, Lev-El Halabi N, Shuldiner AR, Gonzaga-Jauregui C, Lidzbarsky G, Basel-Salmon L, Goldberg-Stern H. Epilepsy and electroencephalogram evolution in YWHAG gene mutation: A new phenotype and review of the literature. Am J Med Genet A 2021; 185:901-908. [PMID: 33393734 DOI: 10.1002/ajmg.a.62026] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 02/02/2023]
Abstract
A male patient with a de novo mutation in the YWHAG gene and mild phenotype is presented. He had normal delivery and normal development, with normal speech and social milestones. At the age of 9 months, myoclonic seizures started, with generalized epileptiform discharges. The child responded well to levetiracetam monotherapy with complete seizure resolution. Levetiracetam was stopped and he remained seizure-free for 10 months. His development was appropriate for age according to psychological evaluation and he attended a regular kindergarten. At the age of approximately 4 years, the seizures reappeared with different semiology of staring with eye blinking. Electroencephalogram (EEG) showed multifocal spikes. Brain magnetic resonance imaging did not reveal any structural abnormality. Genetic analysis revealed a de novo likely pathogenic missense variant in the YWHAG gene (c.619G>A p.Glu207Lys). We compared our case to the other cases published in the literature. Our case is unique in its seizure semiology and evolution of EEG. Moreover, in contrast to our case, the majority of cases described in the literature have dysmorphism and intellectual disability or autistic spectrum disorder. This report emphasizes the phenotypic heterogeneity of YWHAG mutation as is the case in other developmental encephalopathies.
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Affiliation(s)
- Tomer Stern
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Naama Orenstein
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Avi Fellner
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel.,Department of Neurology, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
| | - Noa Lev-El Halabi
- The Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
| | | | | | - Gabriel Lidzbarsky
- Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Lina Basel-Salmon
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel.,Department of Neurology, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel.,Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Hadassa Goldberg-Stern
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Epilepsy Center, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
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9
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Gutman D, Lidzbarsky G, Milman S, Gao T, Sin-Chan P, Gonzaga‐Jauregui C, Deelen J, Shuldiner AR, Barzilai N, Atzmon G. Similar burden of pathogenic coding variants in exceptionally long-lived individuals and individuals without exceptional longevity. Aging Cell 2020; 19:e13216. [PMID: 32860726 PMCID: PMC7576295 DOI: 10.1111/acel.13216] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 06/22/2020] [Accepted: 07/12/2020] [Indexed: 12/13/2022] Open
Abstract
Centenarians (exceptionally long‐lived individuals—ELLI) are a unique segment of the population, exhibiting long human lifespan and healthspan, despite generally practicing similar lifestyle habits as their peers. We tested disease‐associated mutation burden in ELLI genomes by determining the burden of pathogenic variants reported in the ClinVar and HGMD databases using data from whole exome sequencing (WES) conducted in a cohort of ELLI, their offspring, and control individuals without antecedents of familial longevity (n = 1879), all descendent from the founder population of Ashkenazi Jews. The burden of pathogenic variants did not differ between the three groups. Additional analyses of variants subtypes and variant effect predictor (VEP) biotype frequencies did not reveal a decrease of pathogenic or loss‐of‐function (LoF) variants in ELLI and offspring compared to the control group. Case–control pathogenic variants enrichment analyses conducted in ELLI and controls also did not identify significant differences in any of the variants between the groups and polygenic risk scores failed to provide a predictive model. Interestingly, cancer and Alzheimer's disease‐associated variants were significantly depleted in ELLI compared to controls, suggesting slower accumulation of mutation. That said, polygenic risk score analysis failed to find any predictive variants among the functional variants tested. The high similarity in the burden of pathogenic variation between ELLI and individuals without familial longevity supports the notion that extension of lifespan and healthspan in ELLI is not a consequence of pathogenic variant depletion but rather a result of other genomic, epigenomic, or potentially nongenomic properties.
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Affiliation(s)
- Danielle Gutman
- Faculty of Natural Sciences University of Haifa Haifa Israel
| | | | - Sofiya Milman
- Department of Medicine Albert Einstein College of Medicine Bronx New York USA
| | - Tina Gao
- Department of Medicine Albert Einstein College of Medicine Bronx New York USA
| | | | | | - Joris Deelen
- Max Planck Institute for Biology of Ageing Cologne Germany
- Molecular Epidemiology Department of Biochemical Data Sciences Leiden University Medical Center Leiden The Netherlands
| | | | - Nir Barzilai
- Department of Medicine Albert Einstein College of Medicine Bronx New York USA
- Genetic, Institute for Aging Research and the Diabetes Research Center Albert Einstein College of Medicine Bronx New York USA
| | - Gil Atzmon
- Faculty of Natural Sciences University of Haifa Haifa Israel
- Department of Medicine Albert Einstein College of Medicine Bronx New York USA
- Genetic, Institute for Aging Research and the Diabetes Research Center Albert Einstein College of Medicine Bronx New York USA
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10
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Fatiukha A, Filler N, Lupo I, Lidzbarsky G, Klymiuk V, Korol AB, Pozniak C, Fahima T, Krugman T. Grain protein content and thousand kernel weight QTLs identified in a durum × wild emmer wheat mapping population tested in five environments. Theor Appl Genet 2020. [PMID: 31562566 DOI: 10.1101/601773] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Genetic dissection of GPC and TKW in tetraploid durum × WEW RIL population, based on high-density SNP genetic map, revealed 12 GPC QTLs and 11 TKW QTLs, with favorable alleles for 11 and 5 QTLs, respectively, derived from WEW. Wild emmer wheat (Triticum turgidum ssp. dicoccoides, WEW) was shown to exhibit high grain protein content (GPC) and therefore possess a great potential for improvement of cultivated wheat nutritional value. Genetic dissection of thousand kernel weight (TKW) and grain protein content (GPC) was performed using a high-density genetic map constructed based on a recombinant inbred line (RIL) population derived from a cross between T. durum var. Svevo and WEW acc. Y12-3. Genotyping of 208 F6 RILs with a 15 K wheat single nucleotide polymorphism (SNP) array yielded 4166 polymorphic SNP markers, of which 1510 were designated as skeleton markers. A total map length of 2169 cM was obtained with an average distance of 1.5 cM between SNPs. A total of 12 GPC QTLs and 11 TKW QTLs were found under five different environments. No significant correlations were found between GPC and TKW across all environments. Four major GPC QTLs with favorable alleles from WEW were found on chromosomes 4BS, 5AS, 6BS and 7BL. The 6BS GPC QTL coincided with the physical position of the NAC transcription factor TtNAM-B1, underlying the cloned QTL, Gpc-B1. Comparisons of the physical intervals of the GPC QTLs described here with the results previously reported in other durum × WEW RIL population led to the discovery of seven novel GPC QTLs. Therefore, our research emphasizes the importance of GPC QTL dissection in diverse WEW accessions as a source of novel alleles for improvement of GPC in cultivated wheat.
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Affiliation(s)
- Andrii Fatiukha
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
| | - Naveh Filler
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
| | - Itamar Lupo
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
| | - Gabriel Lidzbarsky
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
| | - Valentyna Klymiuk
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
| | - Abraham B Korol
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
| | - Curtis Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel.
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel.
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel.
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11
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Fatiukha A, Filler N, Lupo I, Lidzbarsky G, Klymiuk V, Korol AB, Pozniak C, Fahima T, Krugman T. Grain protein content and thousand kernel weight QTLs identified in a durum × wild emmer wheat mapping population tested in five environments. Theor Appl Genet 2020; 133:119-131. [PMID: 31562566 DOI: 10.1007/s00122-019-03444-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 09/18/2019] [Indexed: 05/14/2023]
Abstract
Genetic dissection of GPC and TKW in tetraploid durum × WEW RIL population, based on high-density SNP genetic map, revealed 12 GPC QTLs and 11 TKW QTLs, with favorable alleles for 11 and 5 QTLs, respectively, derived from WEW. Wild emmer wheat (Triticum turgidum ssp. dicoccoides, WEW) was shown to exhibit high grain protein content (GPC) and therefore possess a great potential for improvement of cultivated wheat nutritional value. Genetic dissection of thousand kernel weight (TKW) and grain protein content (GPC) was performed using a high-density genetic map constructed based on a recombinant inbred line (RIL) population derived from a cross between T. durum var. Svevo and WEW acc. Y12-3. Genotyping of 208 F6 RILs with a 15 K wheat single nucleotide polymorphism (SNP) array yielded 4166 polymorphic SNP markers, of which 1510 were designated as skeleton markers. A total map length of 2169 cM was obtained with an average distance of 1.5 cM between SNPs. A total of 12 GPC QTLs and 11 TKW QTLs were found under five different environments. No significant correlations were found between GPC and TKW across all environments. Four major GPC QTLs with favorable alleles from WEW were found on chromosomes 4BS, 5AS, 6BS and 7BL. The 6BS GPC QTL coincided with the physical position of the NAC transcription factor TtNAM-B1, underlying the cloned QTL, Gpc-B1. Comparisons of the physical intervals of the GPC QTLs described here with the results previously reported in other durum × WEW RIL population led to the discovery of seven novel GPC QTLs. Therefore, our research emphasizes the importance of GPC QTL dissection in diverse WEW accessions as a source of novel alleles for improvement of GPC in cultivated wheat.
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Affiliation(s)
- Andrii Fatiukha
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
| | - Naveh Filler
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
| | - Itamar Lupo
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
| | - Gabriel Lidzbarsky
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
| | - Valentyna Klymiuk
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
| | - Abraham B Korol
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
| | - Curtis Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel.
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel.
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel.
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12
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Klymiuk V, Yaniv E, Huang L, Raats D, Fatiukha A, Chen S, Feng L, Frenkel Z, Krugman T, Lidzbarsky G, Chang W, Jääskeläinen MJ, Schudoma C, Paulin L, Laine P, Bariana H, Sela H, Saleem K, Sørensen CK, Hovmøller MS, Distelfeld A, Chalhoub B, Dubcovsky J, Korol AB, Schulman AH, Fahima T. Cloning of the wheat Yr15 resistance gene sheds light on the plant tandem kinase-pseudokinase family. Nat Commun 2018; 9:3735. [PMID: 30282993 PMCID: PMC6170490 DOI: 10.1038/s41467-018-06138-9] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/26/2018] [Indexed: 01/11/2023] Open
Abstract
Yellow rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating fungal disease threatening much of global wheat production. Race-specific resistance (R)-genes are used to control rust diseases, but the rapid emergence of virulent Pst races has prompted the search for a more durable resistance. Here, we report the cloning of Yr15, a broad-spectrum R-gene derived from wild emmer wheat, which encodes a putative kinase-pseudokinase protein, designated as wheat tandem kinase 1, comprising a unique R-gene structure in wheat. The existence of a similar gene architecture in 92 putative proteins across the plant kingdom, including the barley RPG1 and a candidate for Ug8, suggests that they are members of a distinct family of plant proteins, termed here tandem kinase-pseudokinases (TKPs). The presence of kinase-pseudokinase structure in both plant TKPs and the animal Janus kinases sheds light on the molecular evolution of immune responses across these two kingdoms.
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Affiliation(s)
- Valentina Klymiuk
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
| | - Elitsur Yaniv
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Lin Huang
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Triticeae Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Dina Raats
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
| | - Andrii Fatiukha
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
| | - Shisheng Chen
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Lihua Feng
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
| | - Zeev Frenkel
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
| | - Gabriel Lidzbarsky
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
| | - Wei Chang
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Marko J Jääskeläinen
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Christian Schudoma
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR4 7UZ, UK
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Pia Laine
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Harbans Bariana
- The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
| | - Hanan Sela
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- The Institute for Cereal Crops Improvement, Tel Aviv University, P.O. Box 39040, 6139001, Tel Aviv, Israel
| | - Kamran Saleem
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | | | - Mogens S Hovmøller
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Assaf Distelfeld
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- School of Plant Sciences and Food Security, Tel Aviv University, P.O. Box 39040, 6139001, Tel Aviv, Israel
| | - Boulos Chalhoub
- Institute of System and Synthetic Biology-Organization and Evolution of Complex Genomes, 2 rue Gaston Crémieux CP 5708, 91057, Evry Cedex, France
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD, 20815, USA
| | - Abraham B Korol
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel
| | - Alan H Schulman
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Viikinkaari 1, P.O. Box 65, FI-00014, Helsinki, Finland
- Natural Resources Institute Finland (Luke), Latokartanonkaari 9, FI-00790, Helsinki, Finland
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel.
- Department of Evolutionary and Environmental Biology, University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838, Haifa, Israel.
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13
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Lidzbarsky G, Gutman D, Shekhidem HA, Sharvit L, Atzmon G. Genomic Instabilities, Cellular Senescence, and Aging: In Vitro, In Vivo and Aging-Like Human Syndromes. Front Med (Lausanne) 2018; 5:104. [PMID: 29719834 PMCID: PMC5913290 DOI: 10.3389/fmed.2018.00104] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [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: 01/07/2018] [Accepted: 03/29/2018] [Indexed: 12/20/2022] Open
Abstract
As average life span and elderly people prevalence in the western world population is gradually increasing, the incidence of age-related diseases such as cancer, heart diseases, diabetes, and dementia is increasing, bearing social and economic consequences worldwide. Understanding the molecular basis of aging-related processes can help extend the organism’s health span, i.e., the life period in which the organism is free of chronic diseases or decrease in basic body functions. During the last few decades, immense progress was made in the understanding of major components of aging and healthy aging biology, including genomic instability, telomere attrition, epigenetic changes, proteostasis, nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, and intracellular communications. This progress has been made by three spear-headed strategies: in vitro (cell and tissue culture from various sources), in vivo (includes diverse model and non-model organisms), both can be manipulated and translated to human biology, and the study of aging-like human syndromes and human populations. Herein, we will focus on current repository of genomic “senescence” stage of aging, which includes health decline, structural changes of the genome, faulty DNA damage response and DNA damage, telomere shortening, and epigenetic alterations. Although aging is a complex process, many of the “hallmarks” of aging are directly related to DNA structure and function. This review will illustrate the variety of these studies, done in in vitro, in vivo and human levels, and highlight the unique potential and contribution of each research level and eventually the link between them.
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Affiliation(s)
| | - Danielle Gutman
- Department of Human Biology, University of Haifa, Haifa, Israel
| | | | - Lital Sharvit
- Department of Human Biology, University of Haifa, Haifa, Israel
| | - Gil Atzmon
- Department of Human Biology, University of Haifa, Haifa, Israel
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14
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Huang L, Raats D, Sela H, Klymiuk V, Lidzbarsky G, Feng L, Krugman T, Fahima T. Evolution and Adaptation of Wild Emmer Wheat Populations to Biotic and Abiotic Stresses. Annu Rev Phytopathol 2016; 54:279-301. [PMID: 27296141 DOI: 10.1146/annurev-phyto-080614-120254] [Citation(s) in RCA: 28] [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] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The genetic bottlenecks associated with plant domestication and subsequent selection in man-made agroecosystems have limited the genetic diversity of modern crops and increased their vulnerability to environmental stresses. Wild emmer wheat, the tetraploid progenitor of domesticated wheat, distributed along a wide range of ecogeographical conditions in the Fertile Crescent, has valuable "left behind" adaptive diversity to multiple diseases and environmental stresses. The biotic and abiotic stress responses are conferred by series of genes and quantitative trait loci (QTLs) that control complex resistance pathways. The study of genetic diversity, genomic organization, expression profiles, protein structure and function of biotic and abiotic stress-resistance genes, and QTLs could shed light on the evolutionary history and adaptation mechanisms of wild emmer populations for their natural habitats. The continuous evolution and adaptation of wild emmer to the changing environment provide novel solutions that can contribute to safeguarding food for the rapidly growing human population.
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Affiliation(s)
- Lin Huang
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Dina Raats
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Hanan Sela
- The Institute for Cereal Crops Improvement, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Valentina Klymiuk
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Gabriel Lidzbarsky
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Lihua Feng
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Tamar Krugman
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Tzion Fahima
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
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