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Sangsuwan T, Mannervik M, Haghdoost S. Transgenerational effects of gamma radiation dose and dose rate on Drosophila flies irradiated at an early embryonal stage. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2022; 881:503523. [PMID: 36031335 DOI: 10.1016/j.mrgentox.2022.503523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/26/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Ionizing radiation (IR) kills cells mainly through induction of DNA damages and the surviving cells may suffer from mutations. Transgenerational effects of IR are well documented, but the exact mechanisms underlying them are less well understood; they include induction of mutations in germ cells and epigenetic inheritance. Previously, effects in the offspring of mice and zebrafish exposed to IR have been reported. A few studies also showed indications of transgenerational effects of radiation in humans, particularly in nuclear power workers. In the present project, short- and long-term effects of low-dose-rate (LDR; 50 and 97 mGy/h) and high-dose-rate (HDR; 23.4, 47.1 and 495 Gy/h) IR in Drosophila embryos were investigated. The embryos were irradiated at different doses and dose rates and radiosensitivity at different developmental stages was investigated. Also, the survival of larvae, pupae and adults developed from embryos irradiated at an early stage (30 min after egg laying) were studied. The larval crawling and pupation height assays were applied to investigate radiation effects on larval locomotion and pupation behavior, respectively. In parallel, the offspring from 3 Gy irradiated early-stage embryos were followed up to 12 generations and abnormal phenotypes were studied. Acute exposure of embryos at different stages of development showed that the early stage embryo is the most sensitive. The effects on larval locomotion showed no significant differences between the dose rates but a significant decrease of locomotion activity above 7 Gy was observed. The results indicate that embryos exposed to the low dose rates have shorter eclosion times. At the same cumulative dose (1 up to 7 Gy), HDR is more embryotoxic than LDR. We also found a radiation-induced depigmentation on males (A5 segment of the dorsal abdomen, A5pig-) that can be transmitted up to 12 generations. The phenomenon does not follow the classical Mendelian laws of segregation.
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Affiliation(s)
- Traimate Sangsuwan
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Mattias Mannervik
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Siamak Haghdoost
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden; University of Caen Normandy, Cimap-Aria, Ganil, and Advanced Resource Center for HADrontherapy in Europe (ARCHADE), Caen, France.
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2
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Sertori R, Lin JX, Martinez E, Rana S, Sharo A, Kazemian M, Sunderam U, Andrake M, Shinton S, Truong B, Dunbrack RM, Liu C, Srinivasan R, Brenner SE, Seroogy CM, Puck JM, Leonard WJ, Wiest DL. Investigation of the causal etiology in a patient with T-B+NK+ immunodeficiency. Front Immunol 2022; 13:928252. [PMID: 35967429 PMCID: PMC9372720 DOI: 10.3389/fimmu.2022.928252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/27/2022] [Indexed: 11/24/2022] Open
Abstract
Newborn screening for severe combined immunodeficiency (SCID) has not only accelerated diagnosis and improved treatment for affected infants, but also led to identification of novel genes required for human T cell development. A male proband had SCID newborn screening showing very low T cell receptor excision circles (TRECs), a biomarker for thymic output of nascent T cells. He had persistent profound T lymphopenia, but normal numbers of B and natural killer (NK) cells. Despite an allogeneic hematopoietic stem cell transplant from his brother, he failed to develop normal T cells. Targeted resequencing excluded known SCID genes; however, whole exome sequencing (WES) of the proband and parents revealed a maternally inherited X-linked missense mutation in MED14 (MED14V763A), a component of the mediator complex. Morpholino (MO)-mediated loss of MED14 function attenuated T cell development in zebrafish. Moreover, this arrest was rescued by ectopic expression of cDNA encoding the wild type human MED14 ortholog, but not by MED14V763A , suggesting that the variant impaired MED14 function. Modeling of the equivalent mutation in mouse (Med14V769A) did not disrupt T cell development at baseline. However, repopulation of peripheral T cells upon competitive bone marrow transplantation was compromised, consistent with the incomplete T cell reconstitution experienced by the proband upon transplantation with bone marrow from his healthy male sibling, who was found to have the same MED14V763A variant. Suspecting that the variable phenotypic expression between the siblings was influenced by further mutation(s), we sought to identify genetic variants present only in the affected proband. Indeed, WES revealed a mutation in the L1 cell adhesion molecule (L1CAMQ498H); however, introducing that mutation in vivo in mice did not disrupt T cell development. Consequently, immunodeficiency in the proband may depend upon additional, unidentified gene variants.
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Affiliation(s)
- Robert Sertori
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Jian-Xin Lin
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Esteban Martinez
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Sadhna Rana
- Innovation Labs, Tata Consultancy Services, Hyderabad, India
| | - Andrew Sharo
- Center for Computational Biology, University of California, Berkeley, CA, United States
| | - Majid Kazemian
- Departments of Biochemistry and Computer Science, Purdue University, West Lafayette, IN, United States
| | - Uma Sunderam
- Innovation Labs, Tata Consultancy Services, Hyderabad, India
| | - Mark Andrake
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Susan Shinton
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Billy Truong
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Roland M. Dunbrack
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Chengyu Liu
- Transgenic Core, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | | | - Steven E. Brenner
- Center for Computational Biology, University of California, Berkeley, CA, United States
| | - Christine M. Seroogy
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Jennifer M. Puck
- Department of Pediatrics, University of California San Francisco and UCSF Benioff Children’s Hospital, San Francisco, CA, United States
| | - Warren J. Leonard
- Laboratory of Molecular Immunology, Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - David L. Wiest
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, United States
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3
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Kingdom R, Wright CF. Incomplete Penetrance and Variable Expressivity: From Clinical Studies to Population Cohorts. Front Genet 2022; 13:920390. [PMID: 35983412 PMCID: PMC9380816 DOI: 10.3389/fgene.2022.920390] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/09/2022] [Indexed: 12/20/2022] Open
Abstract
The same genetic variant found in different individuals can cause a range of diverse phenotypes, from no discernible clinical phenotype to severe disease, even among related individuals. Such variants can be said to display incomplete penetrance, a binary phenomenon where the genotype either causes the expected clinical phenotype or it does not, or they can be said to display variable expressivity, in which the same genotype can cause a wide range of clinical symptoms across a spectrum. Both incomplete penetrance and variable expressivity are thought to be caused by a range of factors, including common variants, variants in regulatory regions, epigenetics, environmental factors, and lifestyle. Many thousands of genetic variants have been identified as the cause of monogenic disorders, mostly determined through small clinical studies, and thus, the penetrance and expressivity of these variants may be overestimated when compared to their effect on the general population. With the wealth of population cohort data currently available, the penetrance and expressivity of such genetic variants can be investigated across a much wider contingent, potentially helping to reclassify variants that were previously thought to be completely penetrant. Research into the penetrance and expressivity of such genetic variants is important for clinical classification, both for determining causative mechanisms of disease in the affected population and for providing accurate risk information through genetic counseling. A genotype-based definition of the causes of rare diseases incorporating information from population cohorts and clinical studies is critical for our understanding of incomplete penetrance and variable expressivity. This review examines our current knowledge of the penetrance and expressivity of genetic variants in rare disease and across populations, as well as looking into the potential causes of the variation seen, including genetic modifiers, mosaicism, and polygenic factors, among others. We also considered the challenges that come with investigating penetrance and expressivity.
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Affiliation(s)
- Rebecca Kingdom
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
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4
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Raldugina GN, Hoang TZ, Ngoc HB, Karpichev IV. An increased proportion of transgenic plants in the progeny of rapeseed (Brassica napus L.) transformants. Vavilovskii Zhurnal Genet Selektsii 2021; 25:147-156. [PMID: 34901712 PMCID: PMC8627876 DOI: 10.18699/vj21.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/23/2021] [Accepted: 01/27/2021] [Indexed: 11/20/2022] Open
Abstract
Cotyledon and leaf explants of two spring rapeseed varieties were transformed with Agrobacterium
tumefaciens harboring a genetic construct with the gfp marker gene. In order to reduce the proportion of hyperhydrated shoots, which appeared during regenerant formation, we optimized sucrose content in the regeneration media. Analysis of the progeny obtained from T0 regenerants showed that in a number of lines the distribution of the gfp marker did not follow Mendelian segregation of a monogenic trait in self-pollinated plants, while in
the progeny of the other lines of transgenic plants, the gfp marker was completely absent, although its presence
had been confirmed in all selected T0 plants. We also found that in individual transformants gfp is randomly
inherited throughout the central peduncle; its presence in the genome of seedlings does not depend on the location of the pod. Thus, both transformed and non-transformed cells were involved in the formation of gametes in
T0 plants. In addition, marker segregation was different in plants of the T1 line obtained by nodal cuttings of a
primary transformant, depending on the location of the cuttings on the stem of the original plant, indicating that
the nature of T1 generation plants was also chimeric. Furthermore, we showed that propagation of plants by cutting followed by propagation by seeds formed as a result of self-pollination led to an increase in the proportion
of transgenic plants in subsequent generations. The results obtained during the course of this study show that
the transformants were chimeric, i. e. their tissues contained both transgenic and non-transgenic cells, and this
chimeric nature was passed on to subsequent generations. We found that, in addition to nutrient media composition, other factors such as plant genotype and explant type also contribute to the rising of chimeric plants during
transformation. Based on these results, we developed a simplified method, which consists of several rounds of a
combination of cutting, seed production by self-pollination, and subsequent culling of wild-type plants, which
significantly enriched descendent populations of the original rapeseed transformants with plants transgenic for
the gfp marker
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Affiliation(s)
- G N Raldugina
- Timiryazev Institute of Plant Physiology of the Russian Academy of Sciences, Moscow, Russia
| | - T Z Hoang
- Timiryazev Institute of Plant Physiology of the Russian Academy of Sciences, Moscow, Russia NKLPCB, Agricultural Genetics Institute, Hanoi, Vietnam
| | - H B Ngoc
- Timiryazev Institute of Plant Physiology of the Russian Academy of Sciences, Moscow, Russia
| | - I V Karpichev
- Timiryazev Institute of Plant Physiology of the Russian Academy of Sciences, Moscow, Russia
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Farrell PM, Langfelder-Schwind E, Farrell MH. Challenging the dogma of the healthy heterozygote: Implications for newborn screening policies and practices. Mol Genet Metab 2021; 134:8-19. [PMID: 34483044 DOI: 10.1016/j.ymgme.2021.08.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022]
Abstract
Heterozygous (carrier) status for an autosomal recessive condition is traditionally considered to lack significance for an individual's health, but this assumption has been challenged by a growing body of evidence. Carriers of several autosomal recessive disorders and some X-linked diseases are potentially at risk for the pathology manifest in homozygotes. This minireview provides an overview of the literature regarding health risks to carriers of two common autosomal recessive conditions on the Recommended Uniform Screening Panel: sickle cell disease [sickle cell trait (SCT)] and cystic fibrosis (CF). We also consider and comment on bioethical and policy implications for newborn blood screening (NBS). Health risks for heterozygotes, while relatively low for individuals, are often influenced by intrinsic (e.g., other genomic variants or co-morbidities) and extrinsic (environmental) factors, which present opportunities for personalized genomic medicine and risk counseling. They create a special challenge, however, for developing screening/follow-up policies and for genetic counseling, particularly after identification and reporting of heterozygote status through NBS. Although more research is needed, this minireview of the SCT and CF literature to date leads us to propose that blanket terms such as "healthy heterozygotes" or "unaffected carriers" should be superseded in communications about NBS results, in favor of a more nuanced paradigm of setting expectations for health outcomes with "genotype-to-risk." In the molecular era of NBS, it remains clear that public health needs to become better prepared for the full range of applied genetics.
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Affiliation(s)
- Philip M Farrell
- Departments of Pediatrics and Population Health Sciences, University of Wisconsin School of Medicine and Public Health, 600 Highland Avenue, Clinical Sciences Center (K4/948), Madison, WI 53792, USA.
| | - Elinor Langfelder-Schwind
- The Cystic Fibrosis Center, Mount Sinai Beth Israel, Department of Pulmonary, Critical Care, and Sleep Medicine, Icahn School of Medicine at Mount Sinai, 1st Ave at 16th Street, 8F18, New York, NY 10003, USA.
| | - Michael H Farrell
- Departments of Internal Medicine and Pediatrics, University of Minnesota Medical School, Division of General Internal Medicine (MMC 741), 420 Delaware St SE, Minneapolis, MN 55455, USA.
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Abstract
Electronic health records (EHRs) are a rich source of data for researchers, but extracting meaningful information out of this highly complex data source is challenging. Phecodes represent one strategy for defining phenotypes for research using EHR data. They are a high-throughput phenotyping tool based on ICD (International Classification of Diseases) codes that can be used to rapidly define the case/control status of thousands of clinically meaningful diseases and conditions. Phecodes were originally developed to conduct phenome-wide association studies to scan for phenotypic associations with common genetic variants. Since then, phecodes have been used to support a wide range of EHR-based phenotyping methods, including the phenotype risk score. This review aims to comprehensively describe the development, validation, and applications of phecodes and suggest some future directions for phecodes and high-throughput phenotyping.
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Affiliation(s)
- Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA;
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7
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Liu J. Giant cells: Linking McClintock's heredity to early embryogenesis and tumor origin throughout millennia of evolution on Earth. Semin Cancer Biol 2021; 81:176-192. [PMID: 34116161 DOI: 10.1016/j.semcancer.2021.06.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/12/2021] [Accepted: 06/06/2021] [Indexed: 02/08/2023]
Abstract
The "life code" theory postulates that egg cells, which are giant, are the first cells in reproduction and that damaged or aged giant somatic cells are the first cells in tumorigenesis. However, the hereditary basis for giant cells remains undefined. Here I propose that stress-induced genomic reorganization proposed by Nobel Laureate Barbara McClintock may represent the underlying heredity for giant cells, referred to as McClintock's heredity. Increase in cell size may serve as a response to environmental stress via switching proliferative mitosis to intranuclear replication for reproduction. Intranuclear replication activates McClintock's heredity to reset the genome following fertilization for reproduction or restructures the somatic genome for neoplastic transformation via formation of polyploid giant cancer cells (PGCCs). The genome-based McClintock heredity functions together with gene-based Mendel's heredity to regulate the genomic stability at two different stages of life cycle or tumorigenesis. Thus, giant cells link McClintock's heredity to both early embryogenesis and tumor origin. Cycling change in cell size together with ploidy number switch may represent the most fundamental mechanism on how both germ and soma for coping with environmental stresses for the survival across the tree of life which evolved over millions of years on Earth.
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Affiliation(s)
- Jinsong Liu
- Department of Anatomical Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, United States.
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Vinkšel M, Writzl K, Maver A, Peterlin B. Improving diagnostics of rare genetic diseases with NGS approaches. J Community Genet 2021; 12:247-256. [PMID: 33452619 PMCID: PMC8141085 DOI: 10.1007/s12687-020-00500-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 12/08/2020] [Indexed: 01/08/2023] Open
Abstract
According to a rough estimate, one in fifteen people worldwide is affected by a rare disease. Rare diseases are therefore common in clinical practice; however, timely diagnosis of rare diseases is still challenging. Introduction of novel methods based on next-generation sequencing (NGS) technology offers a successful diagnosis of genetically heterogeneous disorders, even in case of unclear clinical diagnostic hypothesis. However, the application of novel technology differs among the centres and health systems significantly. Our goal is to discuss the impact of the implementation of NGS in the diagnosis of rare diseases and present advantages along with challenges of diagnostic approach. Systematic implementation of NGS in health systems can significantly improve the access of patients with rare diseases to diagnosis and reduce the dependence of national health systems for cross-border collaboration.
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Affiliation(s)
- Mateja Vinkšel
- Clinical Institute of Genomic Medicine, University medical Centre Ljubljana, Zaloška cesta 7, Ljubljana, Slovenia
| | - Karin Writzl
- Clinical Institute of Genomic Medicine, University medical Centre Ljubljana, Zaloška cesta 7, Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University medical Centre Ljubljana, Zaloška cesta 7, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University medical Centre Ljubljana, Zaloška cesta 7, Ljubljana, Slovenia.
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Gimenez MD, Vazquez DV, Trepat F, Cambiaso V, Rodríguez GR. Fruit quality and DNA methylation are affected by parental order in reciprocal crosses of tomato. PLANT CELL REPORTS 2021; 40:171-186. [PMID: 33079280 DOI: 10.1007/s00299-020-02624-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 10/03/2020] [Indexed: 06/11/2023]
Abstract
Reciprocal effects were found for tomato fruit quality and DNA methylation. The epigenetic identity of reciprocal hybrids indicates that DNA methylation might be one of the mechanisms involved in POEs. Crosses between different genotypes and even between different species are commonly used in plant breeding programs. Reciprocal hybrids are obtained by changing the cross direction (or the sexual role) of parental genotypes in a cross. Phenotypic differences between these hybrids constitute reciprocal effects (REs). The aim of this study was to evaluate phenotypic differences in tomato fruit traits and DNA methylation profiles in three inter- and intraspecific reciprocal crosses. REs were detected for 13 of the 16 fruit traits analyzed. The number of traits with REs was the lowest in the interspecific cross, whereas the highest was found in the cross between recombinant inbred lines (RILs) derived from the same interspecific cross. An extension of gene action analysis was proposed to incorporate parent-of-origin effects (POEs). Maternal and paternal dominance were found in four fruit traits. REs and paternal inheritance were found for epiloci located at coding and non-coding regions. The epigenetic identity displayed by the reciprocal hybrids accounts for the phenotypic differences among them, indicating that DNA methylation might be one of the mechanisms involved in POEs.
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Affiliation(s)
- Magalí Diana Gimenez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
- CIGEOBIO, (CONICET-UNSJ), Complejo Universitario "Islas Malvinas", FCEFN, Universidad de San Juan, Av. Ignacio de la Roza 590, J5402DCS, Rivadavia, San Juan, Argentina
| | - Dana Valeria Vazquez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
| | - Felipe Trepat
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
| | - Vladimir Cambiaso
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina
| | - Gustavo Rubén Rodríguez
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina.
- Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Santa Fe, Argentina.
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Chadwick BJ, Lin X. On the History and Applications of Congenic Strains in Cryptococcus Research. Pathogens 2020; 9:pathogens9090750. [PMID: 32942570 PMCID: PMC7560043 DOI: 10.3390/pathogens9090750] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 01/23/2023] Open
Abstract
Congenic strains have been utilized in numerous model organisms to determine the genetic underpinning of various phenotypic traits. Congenic strains are usually derived after 10 backcrosses to a recipient parent, at which point they are 99.95% genetically identical to the parental strain. In recent decades, congenic pairs have provided an invaluable tool for genetics and molecular biology research in the Cryptococcus neoformans species complex. Here, we summarize the history of Cryptococcus congenic pairs and their application in Cryptococcus research on topics including the impact of the mating type locus on unisexual reproduction, virulence, tissue tropism, uniparental mitochondrial inheritance, and the genetic underpinning of other various traits. We also discuss the limitations of these approaches and other biological questions, which could be explored by employing congenic pairs.
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Affiliation(s)
- Benjamin J. Chadwick
- Department of Plant Biology, Franklin College of Arts and Sciences, University of Georgia, Athens, GA 30602, USA;
| | - Xiaorong Lin
- Department of Plant Biology, Franklin College of Arts and Sciences, University of Georgia, Athens, GA 30602, USA;
- Department of Microbiology, Franklin College of Arts and Sciences, University of Georgia, Athens, GA 30602, USA
- Correspondence:
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Snanoudj S, Molin A, Colson C, Coudray N, Paulien S, Mittre H, Gérard M, Schaefer E, Goldenberg A, Bacchetta J, Odent S, Naudion S, Demeer B, Faivre L, Gruchy N, Kottler ML, Richard N. Maternal Transmission Ratio Distortion of GNAS Loss-of-Function Mutations. J Bone Miner Res 2020; 35:913-919. [PMID: 31886927 DOI: 10.1002/jbmr.3948] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 12/09/2019] [Accepted: 12/14/2019] [Indexed: 12/14/2022]
Abstract
Pseudohypoparathyroidism type 1A (PHP1A) and pseudopseudohypoparathyroidism (PPHP) are two rare autosomal dominant disorders caused by loss-of-function mutations in the imprinted Guanine Nucleotide Binding Protein, Alpha Stimulating Activity (GNAS) gene, coding Gs α. PHP1A is caused by mutations in the maternal allele and results in Albright's hereditary osteodystrophy (AHO) and hormonal resistance, mainly to the parathormone (PTH), whereas PPHP, with AHO features and no hormonal resistance, is linked to mutations in the paternal allele. This study sought to investigate parental transmission of GNAS mutations. We conducted a retrospective study in a population of 204 families with 361 patients harboring GNAS mutations. To prevent ascertainment bias toward a higher proportion of affected children due to the way in which data were collected, we excluded from transmission analysis all probands in the ascertained sibships. After bias correction, the distribution ratio of the mutated alleles was calculated from the observed genotypes of the offspring of nuclear families and was compared to the expected ratio of 50% according to Mendelian inheritance (one-sample Z-test). Sex ratio, phenotype of the transmitting parent, and transmission depending on the severity of the mutation were also analyzed. Transmission analysis was performed in 114 nuclear families and included 250 descendants. The fertility rates were similar between male and female patients. We showed an excess of transmission from mother to offspring of mutated alleles (59%, p = .022), which was greater when the mutations were severe (61.7%, p = .023). Similarly, an excess of transmission was found when the mother had a PHP1A phenotype (64.7%, p = .036). By contrast, a Mendelian distribution was observed when the mutations were paternally inherited. Higher numbers of females within the carriers, but not in noncarriers, were also observed. The mother-specific transmission ratio distortion (TRD) and the sex-ratio imbalance associated to PHP1A point to a role of Gs α in oocyte biology or embryogenesis, with implications for genetic counseling. © 2019 American Society for Bone and Mineral Research.
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Affiliation(s)
- Sarah Snanoudj
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Arnaud Molin
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Cindy Colson
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Nadia Coudray
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Sylvie Paulien
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Hervé Mittre
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Marion Gérard
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Elise Schaefer
- Department of Genetics, CHU de Strasbourg, Strasbourg, France
| | | | - Justine Bacchetta
- Department of Pediatric Nephrology, Rheumatology and Dermatology, CHU de Lyon, Bron, France
| | - Sylvie Odent
- Department of Genetics, CHU de Rennes, Rennes, France
| | - Sophie Naudion
- Department of Genetics, CHU de Bordeaux, Bordeaux, France
| | | | | | - Nicolas Gruchy
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Marie-Laure Kottler
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
| | - Nicolas Richard
- Normandie Université, UNICAEN, CHU de Caen Normandie, Department of Genetics, Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism, EA7450 BioTARGen, Caen, France
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12
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Rahit KMTH, Tarailo-Graovac M. Genetic Modifiers and Rare Mendelian Disease. Genes (Basel) 2020; 11:E239. [PMID: 32106447 PMCID: PMC7140819 DOI: 10.3390/genes11030239] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 02/21/2020] [Indexed: 12/11/2022] Open
Abstract
Despite advances in high-throughput sequencing that have revolutionized the discovery of gene defects in rare Mendelian diseases, there are still gaps in translating individual genome variation to observed phenotypic outcomes. While we continue to improve genomics approaches to identify primary disease-causing variants, it is evident that no genetic variant acts alone. In other words, some other variants in the genome (genetic modifiers) may alleviate (suppress) or exacerbate (enhance) the severity of the disease, resulting in the variability of phenotypic outcomes. Thus, to truly understand the disease, we need to consider how the disease-causing variants interact with the rest of the genome in an individual. Here, we review the current state-of-the-field in the identification of genetic modifiers in rare Mendelian diseases and discuss the potential for future approaches that could bridge the existing gap.
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Affiliation(s)
- K. M. Tahsin Hassan Rahit
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Maja Tarailo-Graovac
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
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13
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Lev A, Simon AJ, Barel O, Eyal E, Glick-Saar E, Nayshool O, Birk O, Stauber T, Hochberg A, Broides A, Almashanu S, Hendel A, Lee YN, Somech R. Reduced Function and Diversity of T Cell Repertoire and Distinct Clinical Course in Patients With IL7RA Mutation. Front Immunol 2019; 10:1672. [PMID: 31379863 PMCID: PMC6650764 DOI: 10.3389/fimmu.2019.01672] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/04/2019] [Indexed: 01/01/2023] Open
Abstract
The alpha subunit of IL-7 receptor (IL7R7α) is critical for the differentiation of T cells, specifically for the development and maintenance of γδT cells. Mutations in IL7RA are associated with Severe Combined Immunodeficiency (SCID). Infants with IL7RA deficiency can be identified through newborn screening program. We aimed at defining the immunological and genetic parameters that are directly affected by the IL7RA mutation on the immune system of five unrelated patients which were identified by our newborn screening program for SCID. The patients were found to have a novel identical homozygote mutation in IL7RA (n.c.120 C>G; p.F40L). Both surface expression of IL7Rα and functionality of IL-7 signaling were impaired in patients compared to controls. Structural modeling demonstrated instability of the protein structure due to the mutation. Lastly the TRG immune repertoire of the patients showed reduced diversity, increased clonality and differential CDR3 characteristics. Interestingly, the patients displayed significant different clinical outcome with two displaying severe clinical picture of immunodeficiency and three had spontaneous recovery. Our data supports that the presented IL7RA mutation affects the IL-7 signaling and shaping of the TRG repertoire, reinforcing the role of IL7RA in the immune system, while non-genetic factors may exist that attribute to the ultimate clinical presentation and disease progression.
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Affiliation(s)
- Atar Lev
- The National Lab for Diagnosing SCID - The Israeli Newborn Screening Program, Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Sheba Medical Center, Edmond and Lily Safra Children's Hospital, Israel Ministry of Health, Tel HaShomer, Israel.,The Mina and Everard Goodman Faculty of Life Sciences, Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Amos J Simon
- Sheba Cancer Research Center and Institute of Hematology, Sheba Medical Center, Tel HaShomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ortal Barel
- Sheba Cancer Research Center and Institute of Hematology, Sheba Medical Center, Tel HaShomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eran Eyal
- Sheba Cancer Research Center and Institute of Hematology, Sheba Medical Center, Tel HaShomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel HaShomer, Israel
| | - Efrat Glick-Saar
- Sheba Cancer Research Center and Institute of Hematology, Sheba Medical Center, Tel HaShomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel HaShomer, Israel
| | - Omri Nayshool
- Sheba Cancer Research Center and Institute of Hematology, Sheba Medical Center, Tel HaShomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel HaShomer, Israel
| | - Ohad Birk
- Soroka Medical Center, Genetics Institute, The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Tali Stauber
- The National Lab for Diagnosing SCID - The Israeli Newborn Screening Program, Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Sheba Medical Center, Edmond and Lily Safra Children's Hospital, Israel Ministry of Health, Tel HaShomer, Israel
| | - Amit Hochberg
- Department of Pediatrics, Hillel Yaffe Medical Center, Hadera, Israel
| | - Arnon Broides
- Faculty of Health Sciences, Soroka University Medical Center, Pediatric Immunology Clinic, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Shlomo Almashanu
- The National Center for Newborn Screening, Israel Ministry of Health, Tel HaShomer, Israel
| | - Ayal Hendel
- The Mina and Everard Goodman Faculty of Life Sciences, Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Yu Nee Lee
- The National Lab for Diagnosing SCID - The Israeli Newborn Screening Program, Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Sheba Medical Center, Edmond and Lily Safra Children's Hospital, Israel Ministry of Health, Tel HaShomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Raz Somech
- The National Lab for Diagnosing SCID - The Israeli Newborn Screening Program, Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Sheba Medical Center, Edmond and Lily Safra Children's Hospital, Israel Ministry of Health, Tel HaShomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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14
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Huang MY, Woolford CA, May G, McManus CJ, Mitchell AP. Circuit diversification in a biofilm regulatory network. PLoS Pathog 2019; 15:e1007787. [PMID: 31116789 PMCID: PMC6530872 DOI: 10.1371/journal.ppat.1007787] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/23/2019] [Indexed: 11/18/2022] Open
Abstract
Genotype-phenotype relationships can vary extensively among members of a species. One cause of this variation is circuit diversification, the alteration of gene regulatory relationships among members of a species. Circuit diversification is thought to be a starting point for the circuit divergence or rewiring that occurs during speciation. How widespread is circuit diversification? Here we address this question with the fungal pathogen Candida albicans, which forms biofilms rich in distinctive hyphal cells as a prelude to infection. Our understanding of the biofilm/hyphal regulatory network comes primarily from studies of one clinical isolate, strain SC5314, and its marked derivatives. We used CRISPR-based methods to create mutations of four key biofilm transcription factor genes–BCR1, UME6, BRG1, and EFG1 –in SC5314 and four additional clinical isolates. Phenotypic analysis revealed that mutations in BCR1 or UME6 have variable impact across strains, while mutations in BRG1 or EFG1 had uniformly severe impact. Gene expression, sampled with Nanostring probes and examined comprehensively for EFG1 via RNA-Seq, indicates that regulatory relationships are highly variable among isolates. Our results suggest that genotype-phenotype relationships vary in this strain panel in part because of differences in control of BRG1 by BCR1, a hypothesis that is supported through engineered constitutive expression of BRG1. Overall, the data show that circuit diversification is the rule, not the exception, in this biofilm/hyphal regulatory network. Much of what we know about microbial pathogens is derived from in-depth analysis of one or a few standard laboratory strains. This statement is especially true for the fungal pathogen Candida albicans, because most studies have centered on strain SC5314 and its genetically marked derivatives. Here we examine the functional impact of mutations of four key biofilm regulators across five different clinical isolates. We observe that functional impact of the mutations, based on biological phenotypes and gene expression effects, varies extensively among the isolates. Our results support the idea that gene function should be validated with multiple strain isolates. In addition, our results indicate that a core regulatory network, which comprises regulatory relationships common to multiple isolates, may be enriched for functionally relevant genes.
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Affiliation(s)
- Manning Y. Huang
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - Carol A. Woolford
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - Gemma May
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - C. Joel McManus
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - Aaron P. Mitchell
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States of America
- * E-mail:
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15
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Strande NT, Brnich SE, Roman TS, Berg JS. Navigating the nuances of clinical sequence variant interpretation in Mendelian disease. Genet Med 2018; 20:918-926. [PMID: 29988079 PMCID: PMC6679919 DOI: 10.1038/s41436-018-0100-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/12/2018] [Indexed: 12/24/2022] Open
Abstract
Understanding clinical genetic test results in the era of next-generation sequencing has become increasingly complex, necessitating clear and thorough guidelines for sequence variant interpretation. To meet this need the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) published guidelines for a systematic approach for sequence variant interpretation in 2015. This framework is intended to be adaptable to any Mendelian condition, promoting transparency and consistency in variant interpretation, yet its comprehensive nature yields important challenges and caveats that end users must understand. In this review, we address some of these nuances and discuss the evolving efforts to refine and adapt this framework. We also consider the added complexity of distinguishing between variant-level interpretations and case-level conclusions, particularly in the context of the large gene panel approach to clinical diagnostics.
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Affiliation(s)
- Natasha T Strande
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah E Brnich
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Tamara S Roman
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jonathan S Berg
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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