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Duarte RG, Jardim THA, Paulino PG, Dias RJP, Rossi MF, D Agosto M, Peixoto MP, Guedes Junior DS, Gonçalves NP, Massard CL, Santos HA. Molecular diversity and polyparasitism of avian trypanosomes in the Brazilian Atlantic Rainforest. AN ACAD BRAS CIENC 2024; 96:e20230629. [PMID: 38922254 DOI: 10.1590/0001-3765202420230629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/16/2023] [Indexed: 06/27/2024] Open
Abstract
The current study proposes to investigate the diversity and phylogeny of trypanosomes parasitizing wild birds from the Brazilian Atlantic Forest. Cytological examination was carried out by light microscopy of blood smears and positive birds were selected for amplification of the 18S rDNA sequence through PCR. The resulting amplicons were subjected to purification, cloning, and sequencing analysis. Phylogenetic reconstruction was conducted, including all avian trypanosomes representative's lineages. A total of ten bird samples from species of Turdus flavipes (N=1/12), T. albicollis (N=1/8), Tachyphonus coronatus (N=6/121), Thamnophilus caerulescens (N=1/22) and Synallaxis spixi (N=1/8) were positive for Trypanosoma spp. In the six specimens of T. coronatus, five distinct lineages of Trypanosoma spp. 18S-rRNA were observed in ninety sequences obtained, and using the strategy of cloning independent PCR, it was possible to observe that two of them were related to T. avium (JB01/JB02), and three were closed related to T. bennetti (JB03/ JB04/JB05). Addionaly, all fifteen sequences obtained from T. caerulescens/ S. spixi/T. flavipes/T. albicollis were identical. The present research is the first study to access molecular diversity and polyparasitism by avian trypanosomes in Brazil. The current research exhibits the wide genetic variability in avian trypanosomes and its non-specific relationship with its avian hosts.
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Affiliation(s)
- Rodrigo G Duarte
- Universidade Federal Rural do Rio de Janeiro/UFRRJ, Instituto de Veterinária, Departamento de Epidemiologia e Saúde Pública, BR 465, Km 07, 23897-000 Seropédica, RJ, Brazil
| | - Talys Henrique A Jardim
- Universidade Federal Rural do Rio de Janeiro/UFRRJ, Instituto de Veterinária, Departamento de Epidemiologia e Saúde Pública, BR 465, Km 07, 23897-000 Seropédica, RJ, Brazil
| | - Patrícia G Paulino
- Universidade Federal Rural do Rio de Janeiro/UFRRJ, Instituto de Veterinária, Departamento de Epidemiologia e Saúde Pública, BR 465, Km 07, 23897-000 Seropédica, RJ, Brazil
| | - Roberto J P Dias
- Universidade Federal de Juiz de Fora/UFJF, Instituto de Ciências Biológicas, Departamento de Zoologia, Rua José Lourenço Kelmer, s/n, São Pedro, 36036-900 Juiz de Fora, MG, Brazil
| | - Mariana F Rossi
- Universidade Federal de Juiz de Fora/UFJF, Instituto de Ciências Biológicas, Departamento de Zoologia, Rua José Lourenço Kelmer, s/n, São Pedro, 36036-900 Juiz de Fora, MG, Brazil
| | - Marta D Agosto
- Universidade Federal de Juiz de Fora/UFJF, Instituto de Ciências Biológicas, Departamento de Zoologia, Rua José Lourenço Kelmer, s/n, São Pedro, 36036-900 Juiz de Fora, MG, Brazil
| | - Maristela P Peixoto
- Universidade Federal Rural do Rio de Janeiro/UFRRJ, Instituto de Veterinária, Departamento de Parasitologia Animal, BR 465, Km 07, 23897-000 Seropédica, RJ, Brazil
| | - Daniel S Guedes Junior
- Fundação Oswaldo Cruz/FIOCRUZ, Instituto de Tecnologia em Imunobiológicos, Departamento de Controle de Qualidade, Av. Brasil, 4365, Manguinhos, 21040-090 Rio de Janeiro, RJ, Brazil
| | - Natalia P Gonçalves
- Fundação Oswaldo Cruz/FIOCRUZ, Instituto de Tecnologia em Imunobiológicos, Departamento de Controle de Qualidade, Av. Brasil, 4365, Manguinhos, 21040-090 Rio de Janeiro, RJ, Brazil
| | - Carlos L Massard
- Universidade Federal Rural do Rio de Janeiro/UFRRJ, Instituto de Veterinária, Departamento de Parasitologia Animal, BR 465, Km 07, 23897-000 Seropédica, RJ, Brazil
| | - Huarrisson A Santos
- Universidade Federal Rural do Rio de Janeiro/UFRRJ, Instituto de Veterinária, Departamento de Epidemiologia e Saúde Pública, BR 465, Km 07, 23897-000 Seropédica, RJ, Brazil
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Huybrechts Y, Appelman-Dijkstra NM, Steenackers E, Van Beylen W, Mortier G, Hendrickx G, Van Hul W. A Mosaic Variant in CTNNB1/β-catenin as a Novel Cause for Osteopathia Striata With Cranial Sclerosis. J Clin Endocrinol Metab 2024; 109:1891-1898. [PMID: 38173341 DOI: 10.1210/clinem/dgad757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/05/2024]
Abstract
CONTEXT Osteopathia striata with cranial sclerosis (OSCS) is a rare bone disorder with X-linked dominant inheritance, characterized by a generalized hyperostosis in the skull and long bones and typical metaphyseal striations in the long bones. So far, loss-of-function variants in AMER1 (also known as WTX or FAM123B), encoding the APC membrane recruitment protein 1 (AMER1), have been described as the only molecular cause for OSCS. AMER1 promotes the degradation of β-catenin via AXIN stabilization, acting as a negative regulator of the WNT/β-catenin signaling pathway, a central pathway in bone formation. OBJECTIVE In this study, we describe a Dutch adult woman with an OSCS-like phenotype, namely, generalized high bone mass and characteristic metaphyseal striations, but no genetic variant affecting AMER1. RESULTS Whole exome sequencing led to the identification of a mosaic missense variant (c.876A > C; p.Lys292Asn) in CTNNB1, coding for β-catenin. The variant disrupts an amino acid known to be crucial for interaction with AXIN, a key factor in the β-catenin destruction complex. Western blotting experiments demonstrate that the p.Lys292Asn variant does not significantly affect the β-catenin phosphorylation status, and hence stability in the cytoplasm. Additionally, luciferase reporter assays were performed to investigate the effect of p.Lys292Asn β-catenin on canonical WNT signaling. These studies indicate an average 70-fold increase in canonical WNT signaling activity by p.Lys292Asn β-catenin. CONCLUSION In conclusion, this study indicates that somatic variants in the CTNNB1 gene could explain the pathogenesis of unsolved cases of osteopathia striata.
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Affiliation(s)
- Yentl Huybrechts
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium
| | - Natasha M Appelman-Dijkstra
- Department of Internal Medicine, Division Endocrinology, Leiden University Medical Center, 2300 Leiden, The Netherlands
| | - Ellen Steenackers
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium
| | - Wouter Van Beylen
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium
| | - Geert Mortier
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium
- Laboratory for Skeletal Dysplasia Research, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
- Center for Human Genetics, University Hospital Leuven, 3000 Leuven, Belgium
| | - Gretl Hendrickx
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium
- Laboratory for Skeletal Dysplasia Research, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Wim Van Hul
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium
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Shahbazi M, Majka J, Kubíková D, Zwierzykowski Z, Glombik M, Wendel JF, Sharbrough J, Hartmann S, Szecówka M, Doležel J, Bartoš J, Kopecký D, Kneřová J. Cytonuclear interplay in auto- and allopolyploids: a multifaceted perspective from the Festuca-Lolium complex. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1102-1118. [PMID: 38323852 DOI: 10.1111/tpj.16659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/15/2023] [Accepted: 01/22/2024] [Indexed: 02/08/2024]
Abstract
Restoring cytonuclear stoichiometry is necessary after whole-genome duplication (WGD) and interspecific/intergeneric hybridization in plants. We investigated this phenomenon in auto- and allopolyploids of the Festuca-Lolium complex providing insights into the mechanisms governing cytonuclear interactions in early polyploid and hybrid generations. Our study examined the main processes potentially involved in restoring the cytonuclear balance after WGD comparing diploids and new and well-established autopolyploids. We uncovered that both the number of chloroplasts and the number of chloroplast genome copies were significantly higher in the newly established autopolyploids and grew further in more established autopolyploids. The increase in the copy number of the chloroplast genome exceeded the rise in the number of chloroplasts and fully compensated for the doubling of the nuclear genome. In addition, changes in nuclear and organelle gene expression were insignificant. Allopolyploid Festuca × Lolium hybrids displayed potential structural conflicts in parental protein variants within the cytonuclear complexes. While biased maternal allele expression has been observed in numerous hybrids, our results suggest that its role in cytonuclear stabilization in the Festuca × Lolium hybrids is limited. This study provides insights into the restoration of the cytonuclear stoichiometry, yet it emphasizes the need for future research to explore post-transcriptional regulation and its impact on cytonuclear gene expression stoichiometry. Our findings may enhance the understanding of polyploid plant evolution, with broader implications for the study of cytonuclear interactions in diverse biological contexts.
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Affiliation(s)
- Mehrdad Shahbazi
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
| | - Joanna Majka
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
- Department of Environmental Stress Biology, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Denisa Kubíková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Zbigniew Zwierzykowski
- Department of Environmental Stress Biology, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Marek Glombik
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
- Department of Crop Genetics, John Innes Centre, Norwich, NR4 7UH, UK
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, Iowa, USA
| | - Joel Sharbrough
- New Mexico Institute of Mining and Technology, Biology Department, Socorro, New Mexico, 87801, USA
| | - Stephan Hartmann
- Bavarian State Research Center for Agriculture (LfL), Institute for Crop Science and Plant Breeding, Am Gereuth 4, 85354, Freising, Germany
| | - Marek Szecówka
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Jan Bartoš
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - David Kopecký
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Jana Kneřová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
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Todaro AM, Radu CM, Ciccone M, Toffanin S, Serino ML, Campello E, Bulato C, Lunghi B, Gemmati D, Cuneo A, Hackeng TM, Simioni P, Bernardi F, Castoldi E. In vitro and ex vivo rescue of a nonsense mutation responsible for severe coagulation factor V deficiency. J Thromb Haemost 2024; 22:410-422. [PMID: 37866515 DOI: 10.1016/j.jtha.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/24/2023]
Abstract
BACKGROUND Coagulation factor V (FV) deficiency is a rare bleeding disorder that is usually managed with fresh-frozen plasma. Patients with nonsense mutations may respond to treatment with readthrough agents. OBJECTIVES To investigate whether the F5 p.Arg1161Ter mutation, causing severe FV deficiency in several patients, would be amenable to readthrough therapy. METHODS F5 mRNA and protein expression were evaluated in a F5 p.Arg1161Ter-homozygous patient. Five readthrough agents with different mechanisms of action, i.e. G418, ELX-02, PTC-124, 2,6-diaminopurine (2,6-DAP), and Amlexanox, were tested in in vitro and ex vivo models of the mutation. RESULTS The F5 p.Arg1161Ter-homozygous patient showed residual F5 mRNA and functional platelet FV, indicating detectable levels of natural readthrough. COS-1 cells transfected with the FV-Arg1161Ter cDNA expressed 0.7% FV activity compared to wild-type. Treatment with 0-500 μM G418, ELX-02, and 2,6-DAP dose-dependently increased FV activity up to 7.0-fold, 3.1-fold, and 10.8-fold, respectively, whereas PTC-124 and Amlexanox (alone or in combination) were ineffective. These findings were confirmed by thrombin generation assays in FV-depleted plasma reconstituted with conditioned media of treated cells. All compounds except ELX-02 showed some degree of cytotoxicity. Ex vivo differentiated megakaryocytes of the F5 p.Arg1161Ter-homozygous patient, which were negative at FV immunostaining, turned positive after treatment with all 5 readthrough agents. Notably, they were also able to internalize mutant FV rescued with G418 or 2,6-DAP, which would be required to maintain the crucial platelet FV pool in vivo. CONCLUSION These findings provide in vitro and ex vivo proof-of-principle for readthrough-mediated rescue of the F5 p.Arg1161Ter mutation.
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Affiliation(s)
- Alice M Todaro
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands
| | - Claudia M Radu
- Department of Medicine, Thrombotic and Haemorrhagic Diseases Unit, Padua University Medical School, Padua, Italy
| | - Maria Ciccone
- Department of Medical Sciences, Section of Haematology, Sant'Anna Hospital, Ferrara University, Ferrara, Italy
| | - Serena Toffanin
- Department of Medicine, Thrombotic and Haemorrhagic Diseases Unit, Padua University Medical School, Padua, Italy
| | - M Luisa Serino
- Department of Medical Sciences, Section of Haematology, Sant'Anna Hospital, Ferrara University, Ferrara, Italy
| | - Elena Campello
- Department of Medicine, Thrombotic and Haemorrhagic Diseases Unit, Padua University Medical School, Padua, Italy
| | - Cristiana Bulato
- Department of Medicine, Thrombotic and Haemorrhagic Diseases Unit, Padua University Medical School, Padua, Italy
| | - Barbara Lunghi
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, Ferrara University, Ferrara, Italy
| | - Donato Gemmati
- Department of Translational Medicine, Haemostasis & Thrombosis Centre, Ferrara University, Ferrara, Italy
| | - Antonio Cuneo
- Department of Medical Sciences, Section of Haematology, Sant'Anna Hospital, Ferrara University, Ferrara, Italy
| | - Tilman M Hackeng
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands
| | - Paolo Simioni
- Department of Medicine, Thrombotic and Haemorrhagic Diseases Unit, Padua University Medical School, Padua, Italy
| | - Francesco Bernardi
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, Ferrara University, Ferrara, Italy
| | - Elisabetta Castoldi
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands.
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Nguyen ANT, Gorrell R, Kwok T, Connallon T, McDonald MJ. Horizontal gene transfer facilitates the molecular reverse-evolution of antibiotic sensitivity in experimental populations of H. pylori. Nat Ecol Evol 2024; 8:315-324. [PMID: 38177692 DOI: 10.1038/s41559-023-02269-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 11/09/2023] [Indexed: 01/06/2024]
Abstract
Reversing the evolution of traits harmful to humans, such as antimicrobial resistance, is a key ambition of applied evolutionary biology. A major impediment to reverse evolution is the relatively low spontaneous mutation rates that revert evolved genotypes back to their ancestral state. However, the repeated re-introduction of ancestral alleles by horizontal gene transfer (HGT) could make reverse evolution likely. Here we evolve populations of an antibiotic-resistant strain of Helicobacter pylori in growth conditions without antibiotics while introducing an ancestral antibiotic-sensitive allele by HGT. We evaluate reverse evolution using DNA sequencing and find that HGT facilitates the molecular reverse evolution of the antibiotic resistance allele, and that selection for high rates of HGT drives the evolution of increased HGT rates in low-HGT treatment populations. Finally, we use a theoretical model and carry out simulations to infer how the fitness costs of antibiotic resistance, rates of HGT and effects of genetic drift interact to determine the probability and predictability of reverse evolution.
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Affiliation(s)
- An N T Nguyen
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Rebecca Gorrell
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Terry Kwok
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
- Biomedical Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Tim Connallon
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia.
| | - Michael J McDonald
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia.
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia.
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Marano JM, Weger-Lucarelli J. Preexisting inter-serotype immunity drives antigenic evolution of dengue virus serotype 2. Virology 2024; 590:109951. [PMID: 38096749 PMCID: PMC10855010 DOI: 10.1016/j.virol.2023.109951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/10/2023] [Accepted: 11/21/2023] [Indexed: 01/03/2024]
Abstract
Dengue virus (DENV) infects roughly 400 million people annually, causing febrile and hemorrhagic disease. While preexisting inter-serotype immunity (PISI) provides transient protection, it may drive severe disease over time. PISI's impact on virus evolution, however, is less understood. Retrospective epidemiological analyses suggest that PISI may drive DENV evolution. Using in vitro directed evolution, we explored how DENV2 evolves in the presence of DENV3/4 convalescent serum. Two post-passaging mutations (E-I6M and E-N203D) were then studied for fitness effects in mammalian and insect hosts and immune escape. E-I6M resisted neutralization, altered fitness in mammalian cell culture models, and had no effect in Aedes albopictus mosquitoes. E-N203D showed no change in neutralization sensitivity, reduced fitness in a DENV-naïve epithelial model, and no effects in the other models. These results align with surveillance data, where E-I6M emerged and disappeared, while E-203D and E-203 N cocirculate, thus suggesting that PISI can drive DENV evolution.
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Affiliation(s)
- Jeffrey M Marano
- Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Roanoke, VA, United States; Department of Biomedical Sciences and Pathobiology, Virginia Tech, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, VA, United States; Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, United States
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, VA, United States; Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, United States.
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7
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Choi S, Yang JW, Kim JE, Jeon H, Shin S, Wui D, Kim LS, Kim BJ, Son H, Min K. Infectivity and stress tolerance traits affect community assembly of plant pathogenic fungi. Front Microbiol 2023; 14:1234724. [PMID: 37692392 PMCID: PMC10486888 DOI: 10.3389/fmicb.2023.1234724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 07/26/2023] [Indexed: 09/12/2023] Open
Abstract
Understanding how ecological communities assemble is an urgent research priority. In this study, we used a community ecology approach to examine how ecological and evolutionary processes shape biodiversity patterns of plant pathogenic fungi, Fusarium graminearum and F. asiaticum. High-throughput screening revealed that the isolates had a wide range of phenotypic variation in stress tolerance traits. Net Relatedness Index (NRI) and Nearest Taxon Index (NTI) values were computed based on stress-tolerant distance matrices. Certain local regions exhibited positive values of NRI and NTI, indicating phenotypic clustering within the fungal communities. Competition assays of the pooled strains were conducted to investigate the cause of clustering. During stress conditions and wheat colonization, only a few strains dominated the fungal communities, resulting in reduced diversity. Overall, our findings support the modern coexistence theory that abiotic stress and competition lead to phenotypic similarities among coexisting organisms by excluding large, low-competitive clades. We suggest that agricultural environments and competition for host infection lead to locally clustered communities of plant pathogenic fungi in the field.
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Affiliation(s)
- Soyoung Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Jung Wook Yang
- Crop Cultivation and Environment Research Division, National Institute of Crop Science, Rural Development Administration, Suwon, Republic of Korea
| | - Jung-Eun Kim
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeju, Republic of Korea
| | - Hosung Jeon
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Soobin Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Dayoun Wui
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Lee Seul Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Byung Joo Kim
- Crop Cultivation and Environment Research Division, National Institute of Crop Science, Rural Development Administration, Suwon, Republic of Korea
| | - Hokyoung Son
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Kyunghun Min
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
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8
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Nucci A, Rocha EPC, Rendueles O. Latent evolution of biofilm formation depends on life-history and genetic background. NPJ Biofilms Microbiomes 2023; 9:53. [PMID: 37537176 PMCID: PMC10400614 DOI: 10.1038/s41522-023-00422-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/20/2023] [Indexed: 08/05/2023] Open
Abstract
Adaptation to one environment can often generate phenotypic and genotypic changes which impact the future ability of an organism to thrive in other environmental conditions. In the context of host-microbe interactions, biofilm formation can increase survival rates in vivo upon exposure to stresses, like the host's immune system or antibiotic therapy. However, how the generic process of adaptation impacts the ability to form biofilm and how it may change through time has seldomly been studied. To do so, we used a previous evolution experiment with three strains of the Klebsiella pneumoniae species complex, in which we specifically did not select for biofilm formation. We observed that changes in the ability to form biofilm happened very fast at first and afterwards reverted to ancestral levels in many populations. Biofilm changes were associated to changes in population yield and surface polysaccharide production. Genotypically, mutations in the tip adhesin of type III fimbriae (mrkD) or the fim switch of type I fimbriae were shaped by nutrient availability during evolution, and their impact on biofilm formation was dependent on capsule production. Analyses of natural isolates revealed similar mutations in mrkD, suggesting that such mutations also play an important role in adaptation outside the laboratory. Our work reveals that the latent evolution of biofilm formation, and its temporal dynamics, depend on nutrient availability, the genetic background and other intertwined phenotypic and genotypic changes. Ultimately, it suggests that small differences in the environment can alter an organism's fate in more complex niches like the host.
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Affiliation(s)
- Amandine Nucci
- Institut Pasteur, Université de Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université de Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France
| | - Olaya Rendueles
- Institut Pasteur, Université de Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France.
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9
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Darwish AM, Sharaf A, Gaouar SBS, Ali NI, El-Aziz THA, Abushady AM, Kaouadji Z, Othman OE, Obornik M. Biochemical and genotyping analyses of camels (Camelus dromedaries) trypanosomiasis in North Africa. Sci Rep 2023; 13:7176. [PMID: 37137920 PMCID: PMC10156784 DOI: 10.1038/s41598-023-34086-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/24/2023] [Indexed: 05/05/2023] Open
Abstract
Camels are considered an important food source in North Africa. Trypanosomiasis in camels is a life-threatening disease that causes severe economic losses in milk and meat production. Therefore, the objective of this study was to determine the trypanosome genotypes in the North African region. Trypanosome infection rates were determined by microscopic examination of blood smears and polymerase chain reaction (PCR). In addition, total antioxidant capacity (TAC), lipid peroxides (MDA), reduced glutathione (GSH), superoxide dismutase (SOD) and catalase (CAT) were determined in erythrocyte lysate. Furthermore, 18S amplicon sequencing was used to barcode and characterizes the genetic diversity of trypanosome genotypes in camel blood. In addition to Trypanosoma, Babesia and Thelieria were also detected in the blood samples. PCR showed that the trypanosome infection rate was higher in Algerian samples (25.7%) than in Egyptian samples (7.2%). Parameters such as MDA, GSH, SOD and CAT had significantly increased in camels infected with trypanosomes compared to uninfected control animals, while TAC level was not significantly changed. The results of relative amplicon abundance showed that the range of trypanosome infection was higher in Egypt than in Algeria. Moreover, phylogenetic analysis showed that the Trypanosoma sequences of Egyptian and Algerian camels are related to Trypanosoma evansi. Unexpectedly, diversity within T. evansi was higher in Egyptian camels than in Algerian camels. We present here the first molecular report providing a picture of trypanosomiasis in camels, covering wide geographical areas in Egypt and Algeria.
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Affiliation(s)
- Ahmed M Darwish
- Cell Biology Department, Biotechnology Research Institute, National Research Centre, Dokki, 12622, Giza, Egypt.
| | - Abdoallah Sharaf
- SequAna Core Facility, Department of Biology, University of Konstanz, 78464, Konstanz, Germany
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Semir Bechir Suheil Gaouar
- Applied Genetic in Agriculture, Ecology and Public Health Laboratory, SNV/STU Faculty, University of Tlemcen, Chetouane, Algeria
| | - Neama I Ali
- Cell Biology Department, Biotechnology Research Institute, National Research Centre, Dokki, 12622, Giza, Egypt
| | - Tamer H Abd El-Aziz
- Parasitology and Animal Diseases, Veterinary Research Institute, National Research Centre, Dokki, 12622, Giza, Egypt
| | - Asmaa M Abushady
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
- Biotechnology School, Nile University, Sheikh Zayed, Giza, Egypt
| | - Zoubeyda Kaouadji
- Applied Genetic in Agriculture, Ecology and Public Health Laboratory, SNV/STU Faculty, University of Tlemcen, Chetouane, Algeria
| | - Othman E Othman
- Cell Biology Department, Biotechnology Research Institute, National Research Centre, Dokki, 12622, Giza, Egypt
| | - Miroslav Obornik
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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10
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Wedel E, Bernabe-Balas C, Ares-Arroyo M, Montero N, Santos-Lopez A, Mazel D, Gonzalez-Zorn B. Insertion Sequences Determine Plasmid Adaptation to New Bacterial Hosts. mBio 2023:e0315822. [PMID: 37097157 DOI: 10.1128/mbio.03158-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Plasmids facilitate the vertical and horizontal spread of antimicrobial resistance genes between bacteria. The host range and adaptation of plasmids to new hosts determine their impact on the spread of resistance. In this work, we explore the mechanisms driving plasmid adaptation to novel hosts in experimental evolution. Using the small multicopy plasmid pB1000, usually found in Pasteurellaceae, we studied its adaptation to a host from a different bacterial family, Escherichia coli. We observed two different mechanisms of adaptation. One mechanism is single nucleotide polymorphisms (SNPs) in the origin of replication (oriV) of the plasmid, which increase the copy number in E. coli cells, elevating the stability, and resistance profile. The second mechanism consists of two insertion sequences (ISs), IS1 and IS10, which decrease the fitness cost of the plasmid by disrupting an uncharacterized gene on pB1000 that is harmful to E. coli. Both mechanisms increase the stability of pB1000 independently, but only their combination allows long-term maintenance. Crucially, we show that the mechanisms have a different impact on the host range of the plasmid. SNPs in oriV prevent the replication in the original host, resulting in a shift of the host range. In contrast, the introduction of ISs either shifts or expands the host range, depending on the IS. While IS1 leads to expansion, IS10 cannot be reintroduced into the original host. This study gives new insights into the relevance of ISs in plasmid-host adaptation to understand the success in spreading resistance. IMPORTANCE ColE1-like plasmids are small, mobilizable plasmids that can be found across at least four orders of Gammaproteobacteria and are strongly associated with antimicrobial resistance genes. Plasmid pB1000 carries the gene blaROB-1, conferring high-level resistance to penicillins and cefaclor. pB1000 has been described in various species of the family Pasteurellaceae, for example, in Haemophilus influenzae, which can cause diseases such as otitis media, meningitis, and pneumonia. To understand the resistance spread through horizontal transfer, it is essential to study the mechanisms of plasmid adaptation to novel hosts. In this work we identify that a gene from pB1000, which encodes a peptide that is toxic for E. coli, and the low plasmid copy number (PCN) of pB1000 in E. coli cells are essential targets in the described plasmid-host adaptation and therefore limit the spread of pB1000-encoded blaROB-1. Furthermore, we show how the interplay of two adaptation mechanisms leads to successful plasmid maintenance in a different bacterial family.
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Affiliation(s)
- Emilia Wedel
- Antimicrobial Resistance Unit (ARU), Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Cristina Bernabe-Balas
- Antimicrobial Resistance Unit (ARU), Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Manuel Ares-Arroyo
- Antimicrobial Resistance Unit (ARU), Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Natalia Montero
- Antimicrobial Resistance Unit (ARU), Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Alfonso Santos-Lopez
- Antimicrobial Resistance Unit (ARU), Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Didier Mazel
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France
| | - Bruno Gonzalez-Zorn
- Antimicrobial Resistance Unit (ARU), Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
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11
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Al-Jazrawe M, Xu S, Poon R, Wei Q, Przybyl J, Varma S, van de Rijn M, Alman BA. CD142 Identifies Neoplastic Desmoid Tumor Cells, Uncovering Interactions Between Neoplastic and Stromal Cells That Drive Proliferation. CANCER RESEARCH COMMUNICATIONS 2023; 3:697-708. [PMID: 37377751 PMCID: PMC10128091 DOI: 10.1158/2767-9764.crc-22-0403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 01/03/2023] [Accepted: 03/27/2023] [Indexed: 06/29/2023]
Abstract
The interaction between neoplastic and stromal cells within a tumor mass plays an important role in cancer biology. However, it is challenging to distinguish between tumor and stromal cells in mesenchymal tumors because lineage-specific cell surface markers typically used in other cancers do not distinguish between the different cell subpopulations. Desmoid tumors consist of mesenchymal fibroblast-like cells driven by mutations stabilizing beta-catenin. Here we aimed to identify surface markers that can distinguish mutant cells from stromal cells to study tumor-stroma interactions. We analyzed colonies derived from single cells from human desmoid tumors using a high-throughput surface antigen screen, to characterize the mutant and nonmutant cells. We found that CD142 is highly expressed by the mutant cell populations and correlates with beta-catenin activity. CD142-based cell sorting isolated the mutant population from heterogeneous samples, including one where no mutation was previously detected by traditional Sanger sequencing. We then studied the secretome of mutant and nonmutant fibroblastic cells. PTX3 is one stroma-derived secreted factor that increases mutant cell proliferation via STAT6 activation. These data demonstrate a sensitive method to quantify and distinguish neoplastic from stromal cells in mesenchymal tumors. It identifies proteins secreted by nonmutant cells that regulate mutant cell proliferation that could be therapeutically. Significance Distinguishing between neoplastic (tumor) and non-neoplastic (stromal) cells within mesenchymal tumors is particularly challenging, because lineage-specific cell surface markers typically used in other cancers do not differentiate between the different cell subpopulations. Here, we developed a strategy combining clonal expansion with surface proteome profiling to identify markers for quantifying and isolating mutant and nonmutant cell subpopulations in desmoid tumors, and to study their interactions via soluble factors.
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Affiliation(s)
- Mushriq Al-Jazrawe
- Hospital for Sick Children, Program in Developmental & Stem Cell Biology, Toronto, Ontario, Canada
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Steven Xu
- Hospital for Sick Children, Program in Developmental & Stem Cell Biology, Toronto, Ontario, Canada
| | - Raymond Poon
- Hospital for Sick Children, Program in Developmental & Stem Cell Biology, Toronto, Ontario, Canada
| | - Qingxia Wei
- Hospital for Sick Children, Program in Developmental & Stem Cell Biology, Toronto, Ontario, Canada
| | - Joanna Przybyl
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Sushama Varma
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Matt van de Rijn
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Benjamin A. Alman
- Hospital for Sick Children, Program in Developmental & Stem Cell Biology, Toronto, Ontario, Canada
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Orthopedic Surgery, Duke University, Durham, North Carolina
- Regeneration Next Initiative, Duke University, Durham, North Carolina
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12
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Marano JM, Weger-Lucarelli J. Replication in the presence of dengue convalescent serum impacts Zika virus neutralization sensitivity and fitness. Front Cell Infect Microbiol 2023; 13:1130749. [PMID: 36968111 PMCID: PMC10034770 DOI: 10.3389/fcimb.2023.1130749] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/13/2023] [Indexed: 03/11/2023] Open
Abstract
Introduction Flaviviruses like dengue virus (DENV) and Zika virus (ZIKV) are mosquito-borne viruses that cause febrile, hemorrhagic, and neurological diseases in humans, resulting in 400 million infections annually. Due to their co-circulation in many parts of the world, flaviviruses must replicate in the presence of pre-existing adaptive immune responses targeted at serologically closely related pathogens, which can provide protection or enhance disease. However, the impact of pre-existing cross-reactive immunity as a driver of flavivirus evolution, and subsequently the implications on the emergence of immune escape variants, is poorly understood. Therefore, we investigated how replication in the presence of convalescent dengue serum drives ZIKV evolution. Methods We used an in vitro directed evolution system, passaging ZIKV in the presence of serum from humans previously infected with DENV (anti-DENV) or serum from DENV-naïve patients (control serum). Following five passages in the presence of serum, we performed next-generation sequencing to identify mutations that arose during passaging. We studied two non-synonymous mutations found in the anti-DENV passaged population (E-V355I and NS1-T139A) by generating individual ZIKV mutants and assessing fitness in mammalian cells and live mosquitoes, as well as their sensitivity to antibody neutralization. Results and discussion Both viruses had increased fitness in Vero cells with and without the addition of anti-DENV serum and in human lung epithelial and monocyte cells. In Aedes aegypti mosquitoes-using blood meals with and without anti-DENV serum-the mutant viruses had significantly reduced fitness compared to wild-type ZIKV. These results align with the trade-off hypothesis of constrained mosquito-borne virus evolution. Notably, only the NS1-T139A mutation escaped neutralization, while E-V335I demonstrated enhanced neutralization sensitivity to neutralization by anti-DENV serum, indicating that neutralization escape is not necessary for viruses passaged under cross-reactive immune pressures. Future studies are needed to assess cross-reactive immune selection in humans and relevant animal models or with different flaviviruses.
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Affiliation(s)
- Jeffrey M. Marano
- Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Roanoke, VA, United States
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, VA, United States
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, United States
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, VA, United States
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, United States
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13
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Aldea D, Kokalari B, Atsuta Y, Dingwall HL, Zheng Y, Nace A, Cotsarelis G, Kamberov YG. Differential modularity of the mammalian Engrailed 1 enhancer network directs sweat gland development. PLoS Genet 2023; 19:e1010614. [PMID: 36745673 PMCID: PMC9934363 DOI: 10.1371/journal.pgen.1010614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 02/16/2023] [Accepted: 01/13/2023] [Indexed: 02/07/2023] Open
Abstract
Enhancers are context-specific regulators of expression that drive biological complexity and variation through the redeployment of conserved genes. An example of this is the enhancer-mediated control of Engrailed 1 (EN1), a pleiotropic gene whose expression is required for the formation of mammalian eccrine sweat glands. We previously identified the En1 candidate enhancer (ECE) 18 cis-regulatory element that has been highly and repeatedly derived on the human lineage to potentiate ectodermal EN1 and induce our species' uniquely high eccrine gland density. Intriguingly, ECE18 quantitative activity is negligible outside of primates and ECE18 is not required for En1 regulation and eccrine gland formation in mice, raising the possibility that distinct enhancers have evolved to modulate the same trait. Here we report the identification of the ECE20 enhancer and show it has conserved functionality in mouse and human developing skin ectoderm. Unlike ECE18, knock-out of ECE20 in mice reduces ectodermal En1 and eccrine gland number. Notably, we find ECE20, but not ECE18, is also required for En1 expression in the embryonic mouse brain, demonstrating that ECE20 is a pleiotropic En1 enhancer. Finally, that ECE18 deletion does not potentiate the eccrine phenotype of ECE20 knock-out mice supports the secondary incorporation of ECE18 into the regulation of this trait in primates. Our findings reveal that the mammalian En1 regulatory machinery diversified to incorporate both shared and lineage-restricted enhancers to regulate the same phenotype, and also have implications for understanding the forces that shape the robustness and evolvability of developmental traits.
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Affiliation(s)
- Daniel Aldea
- Department of Genetics, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Blerina Kokalari
- Department of Genetics, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Yuji Atsuta
- Genetics Department, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Heather L. Dingwall
- Department of Genetics, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Ying Zheng
- Department of Dermatology, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Arben Nace
- Department of Dermatology, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - George Cotsarelis
- Department of Dermatology, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Yana G. Kamberov
- Department of Genetics, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
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14
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Huang CS, Legett HD, Plough LV, Aguilar R, Fitzgerald C, Gregory B, Heggie K, Lee B, Richie KD, Harbold W, Ogburn MB. Early detection and recovery of river herring spawning habitat use in response to a mainstem dam removal. PLoS One 2023; 18:e0284561. [PMID: 37134118 PMCID: PMC10156059 DOI: 10.1371/journal.pone.0284561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/03/2023] [Indexed: 05/04/2023] Open
Abstract
Historical loss of river and stream habitats due to impassable dams has contributed to the severe decline of many fish species. Anadromous fishes that migrate from the sea to freshwater streams to spawn have been especially impacted as dams restrict these fish from accessing ancestral spawning grounds. In 2018, Bloede Dam was removed from the Patapsco River near Baltimore, Maryland, restoring approximately 100 km of potential habitat for migratory fish. We assessed the response of anadromous river herring, alewife (Alosa pseudoharengus) and blueback herring (Alosa aestivalis), to this dam removal by monitoring environmental DNA (eDNA) and eggs from 2015 to 2021 at locations upstream and downstream of the dam site during their spawning migrations. We additionally assessed the presence of fish by collecting electrofishing samples and tracked the movements of individual adult fish within the river using passive integrated transponder (PIT) tags. No adult river herring, eDNA, or eggs were detected upstream of Bloede Dam in the four years prior to its removal despite the presence of a fish ladder. Our results suggest initial habitat use recovery by spawning river herring in the first year post-removal, although a relatively small proportion of the population in the river used the newly accessible habitat. In the three years post-removal, the likelihood of detecting river herring eDNA upstream of the former dam site increased to 5% for alewife and 13% for blueback herring. Two adult fish were also collected in electrofishing samples upstream of the dam site in 2021. We found no evidence of changes in egg abundance and no tagged fish were detected upstream of the dam site post-removal. While long term monitoring is needed to assess population changes, this study highlights the value of integrating methods for comprehensive understanding of habitat use following dam removal.
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Affiliation(s)
- Claire S Huang
- Nicholas School of the Environment, Duke University Marine Lab, Beaufort, North Carolina, United States of America
- Smithsonian Environmental Research Center, Edgewater, Maryland, United States of America
| | - Henry D Legett
- Smithsonian Environmental Research Center, Edgewater, Maryland, United States of America
| | - Louis V Plough
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, United States of America
| | - Rob Aguilar
- Smithsonian Environmental Research Center, Edgewater, Maryland, United States of America
| | - Catherine Fitzgerald
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, United States of America
| | - Benjamin Gregory
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, United States of America
| | - Keira Heggie
- Smithsonian Environmental Research Center, Edgewater, Maryland, United States of America
| | - Benjamin Lee
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, United States of America
| | - Kimberly D Richie
- Smithsonian Environmental Research Center, Edgewater, Maryland, United States of America
| | - William Harbold
- Maryland Department of Natural Resources, Annapolis, Maryland, United States of America
| | - Matthew B Ogburn
- Smithsonian Environmental Research Center, Edgewater, Maryland, United States of America
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15
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Gao C, Zhou G, Shi J, Shi P, Jin L, Li Y, Wang X, Liao S, Yan H, Wu J, Lu Y, Zhai Y, Zhang J, Zhang H, Zhang H, Yang C, Cao P, Cheng S, Zhou G. The A-to-I editing of KPC1 promotes intrahepatic cholangiocarcinoma by attenuating proteasomal processing of NF-κB1 p105 to p50. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:338. [PMID: 36476255 PMCID: PMC9730630 DOI: 10.1186/s13046-022-02549-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Aberrant RNA editing of adenosine-to-inosine (A-to-I) has been linked to multiple human cancers, but its role in intrahepatic cholangiocarcinoma (iCCA) remains unknown. We conducted an exome-wide investigation to search for dysregulated RNA editing that drive iCCA pathogenesis. METHODS An integrative whole-exome and transcriptome sequencing analysis was performed to elucidate the RNA editing landscape in iCCAs. Putative RNA editing sites were validated by Sanger sequencing. In vitro and in vivo experiments were used to assess the effects of an exemplary target gene Kip1 ubiquitination-promoting complex 1 (KPC1) and its editing on iCCA cells growth and metastasis. Crosstalk between KPC1 RNA editing and NF-κB signaling was analyzed by molecular methods. RESULTS Through integrative omics analyses, we revealed an adenosine deaminases acting on RNA 1A (ADAR1)-mediated over-editing pattern in iCCAs. ADAR1 is frequently amplified and overexpressed in iCCAs and plays oncogenic roles. Notably, we identified a novel ADAR1-mediated A-to-I editing of KPC1 transcript, which results in substitution of methionine with valine at residue 8 (p.M8V). KPC1 p.M8V editing confers loss-of-function phenotypes through blunting the tumor-suppressive role of wild-type KPC1. Mechanistically, KPC1 p.M8V weakens the affinity of KPC1 to its substrate NF-κB1 p105, thereby reducing the ubiquitinating and proteasomal processing of p105 to p50, which in turn enhances the activity of oncogenic NF-κB signaling. CONCLUSIONS Our findings established that amplification-driven ADAR1 overexpression results in overediting of KPC1 p.M8V in iCCAs, leading to progression via activation of the NF-κB signaling pathway, and suggested ADAR1-KPC1-NF-κB axis as a potential therapeutic target for iCCA.
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Affiliation(s)
- Chengming Gao
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Guangming Zhou
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Jie Shi
- grid.414375.00000 0004 7588 8796Eastern Hepatobiliary Surgery Hospital, Navy Military Medical University, 225 Changhai Road, Shanghai, 200433 China
| | - Peipei Shi
- grid.256885.40000 0004 1791 4722Hebei University, Baoding City, China
| | - Liang Jin
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Yuanfeng Li
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Xiaowen Wang
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Lifeomics, Beijing, China
| | - Song Liao
- grid.488137.10000 0001 2267 2324Medical School of Chinese PLA, Beijing, China
| | - Han Yan
- grid.256885.40000 0004 1791 4722Hebei University, Baoding City, China
| | - Junjie Wu
- grid.186775.a0000 0000 9490 772XAnhui Medical University, Hefei City, China
| | - Yiming Lu
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Yun Zhai
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Jinxu Zhang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China ,grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Lifeomics, Beijing, China
| | - Haitao Zhang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Hongxing Zhang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China ,grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Lifeomics, Beijing, China
| | - Chenning Yang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Pengbo Cao
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China
| | - Shuqun Cheng
- grid.414375.00000 0004 7588 8796Eastern Hepatobiliary Surgery Hospital, Navy Military Medical University, 225 Changhai Road, Shanghai, 200433 China
| | - Gangqiao Zhou
- grid.506261.60000 0001 0706 7839State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 China ,grid.256885.40000 0004 1791 4722Hebei University, Baoding City, China ,grid.186775.a0000 0000 9490 772XAnhui Medical University, Hefei City, China ,grid.89957.3a0000 0000 9255 8984Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing City, China
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16
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Robinson JI, Md Yusof MY, Davies V, Wild D, Morgan M, Taylor JC, El-Sherbiny Y, Morris DL, Liu L, Rawstron AC, Buch MH, Plant D, Cordell HJ, Isaacs JD, Bruce IN, Emery P, Barton A, Vyse TJ, Barrett JH, Vital EM, Morgan AW. Comprehensive genetic and functional analyses of Fc gamma receptors influence on response to rituximab therapy for autoimmunity. EBioMedicine 2022; 86:104343. [PMID: 36371989 PMCID: PMC9663864 DOI: 10.1016/j.ebiom.2022.104343] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 10/07/2022] [Accepted: 10/18/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Rituximab is widely used to treat autoimmunity but clinical response varies. Efficacy is determined by the efficiency of B-cell depletion, which may depend on various Fc gamma receptor (FcγR)-dependent mechanisms. Study of FcγR is challenging due to the complexity of the FCGR genetic locus. We sought to assess the effect of FCGR variants on clinical response, B-cell depletion and NK-cell-mediated killing in rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). METHODS A longitudinal cohort study was conducted in 835 patients [RA = 573; SLE = 262]. Clinical outcome measures were two-component disease activity score in 28-joints (2C-DAS28CRP) for RA and British Isles Lupus Assessment Group (BILAG)-2004 major clinical response (MCR) for SLE at 6 months. B-cells were evaluated by highly-sensitive flow cytometry. Single nucleotide polymorphism and copy number variation for genes encoding five FcγRs were measured using multiplex ligation-dependent probe amplification. Ex vivo studies assessed NK-cell antibody-dependent cellular cytotoxicity (ADCC) and FcγR expression. FINDINGS In RA, carriage of FCGR3A-158V and increased FCGR3A-158V copies were associated with greater 2C-DAS28CRP response (adjusted for baseline 2C-DAS28CRP). In SLE, MCR was associated with increased FCGR3A-158V, OR 1.64 (95% CI 1.12-2.41) and FCGR2C-ORF OR 1.93 (95% CI 1.09-3.40) copies. 236/413 (57%) patients with B-cell data achieved complete depletion. Homozygosity for FCGR3A-158V and increased FCGR3A-158V copies were associated with complete depletion in combined analyses. FCGR3A genotype was associated with rituximab-induced ADCC, and increased NK-cell FcγRIIIa expression was associated with improved clinical response and depletion in vivo. Furthermore, disease status and concomitant therapies impacted both NK-cell FcγRIIIa expression and ADCC. INTERPRETATION FcγRIIIa is the major low affinity FcγR associated with rituximab response. Increased copies of the FCGR3A-158V allele (higher affinity for IgG1), influences clinical and biological responses to rituximab in autoimmunity. Enhancing FcγR-effector functions could improve the next generation of CD20-depleting therapies and genotyping may stratify patients for optimal treatment protocols. FUNDING Medical Research Council, National Institute for Health and Care Research, Versus Arthritis.
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Affiliation(s)
- James I Robinson
- School of Medicine, University of Leeds and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, UK
| | - Md Yuzaiful Md Yusof
- School of Medicine, University of Leeds and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, UK
| | - Vinny Davies
- School of Medicine, University of Leeds and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, UK; School of Mathematics and Statistics, University of Glasgow, UK
| | - Dawn Wild
- School of Medicine, University of Leeds and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, UK
| | - Michael Morgan
- School of Medicine, University of Leeds and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, UK; Cancer Research UK Cambridge Institute, University of Cambridge, UK
| | - John C Taylor
- School of Medicine, University of Leeds and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, UK
| | - Yasser El-Sherbiny
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, UK; Department of Clinical Pathology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - David L Morris
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, UK
| | - Lu Liu
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, UK
| | - Andy C Rawstron
- Haematological Malignancy Diagnostic Service, Leeds Teaching Hospitals NHS Trust, UK
| | - Maya H Buch
- School of Medicine, University of Leeds and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, UK; Versus Arthritis Centre for Genetics and Genomics, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, The University of Manchester and NIHR Manchester BRC, Manchester University NHS Foundation Trust, UK
| | - Darren Plant
- Versus Arthritis Centre for Genetics and Genomics, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, The University of Manchester and NIHR Manchester BRC, Manchester University NHS Foundation Trust, UK
| | | | - John D Isaacs
- Translational and Clinical Research Institute, Newcastle University and Musculoskeletal Unit, Newcastle upon Tyne Hospitals NHS Foundation Trust, UK
| | - Ian N Bruce
- Versus Arthritis Centre for Genetics and Genomics, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, The University of Manchester and NIHR Manchester BRC, Manchester University NHS Foundation Trust, UK
| | - Paul Emery
- School of Medicine, University of Leeds and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, UK; NIHR Leeds Medtech and In vitro Diagnostics Co-operative, Leeds Teaching Hospitals NHS Trust, UK
| | - Anne Barton
- Versus Arthritis Centre for Genetics and Genomics, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, The University of Manchester and NIHR Manchester BRC, Manchester University NHS Foundation Trust, UK
| | - Timothy J Vyse
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, UK
| | - Jennifer H Barrett
- School of Medicine, University of Leeds and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, UK
| | - Edward M Vital
- School of Medicine, University of Leeds and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, UK
| | - Ann W Morgan
- School of Medicine, University of Leeds and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, UK; NIHR Leeds Medtech and In vitro Diagnostics Co-operative, Leeds Teaching Hospitals NHS Trust, UK.
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17
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Taylor MB, Skophammer R, Warwick AR, Geck RC, Boyer JM, Walson M, Large CRL, Hickey ASM, Rowley PA, Dunham MJ. yEvo: experimental evolution in high school classrooms selects for novel mutations that impact clotrimazole resistance in Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2022; 12:jkac246. [PMID: 36173330 PMCID: PMC9635649 DOI: 10.1093/g3journal/jkac246] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/15/2022] [Indexed: 11/18/2022]
Abstract
Antifungal resistance in pathogenic fungi is a growing global health concern. Nonpathogenic laboratory strains of Saccharomyces cerevisiae are an important model for studying mechanisms of antifungal resistance that are relevant to understanding the same processes in pathogenic fungi. We have developed a series of laboratory modules in which high school students used experimental evolution to study antifungal resistance by isolating azole-resistant S. cerevisiae mutants and examining the genetic basis of resistance. We have sequenced 99 clones from these experiments and found that all possessed mutations previously shown to impact azole resistance, validating our approach. We additionally found recurrent mutations in an mRNA degradation pathway and an uncharacterized mitochondrial protein (Csf1) that have possible mechanistic connections to azole resistance. The scale of replication in this initiative allowed us to identify candidate epistatic interactions, as evidenced by pairs of mutations that occur in the same clone more frequently than expected by chance (positive epistasis) or less frequently (negative epistasis). We validated one of these pairs, a negative epistatic interaction between gain-of-function mutations in the multidrug resistance transcription factors Pdr1 and Pdr3. This high school-university collaboration can serve as a model for involving members of the broader public in the scientific process to make meaningful discoveries in biomedical research.
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Affiliation(s)
- Matthew Bryce Taylor
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Program in Biology, Loras College, Dubuque, IA 52001, USA
| | | | - Alexa R Warwick
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA
| | - Renee C Geck
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Josephine M Boyer
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - yEvo Students
- Westridge School, Pasadena, CA 91105, USA
- Moscow High School, Moscow, ID 83843, USA
| | - Margaux Walson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Christopher R L Large
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- UW Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Angela Shang-Mei Hickey
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Present address: Department of Genetics, Stanford University, Biomedical Innovations Building, Palo Alto, CA 94304, USA
| | - Paul A Rowley
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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18
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Shoop WK, Gorsuch CL, Bacman SR, Moraes CT. Precise and simultaneous quantification of mitochondrial DNA heteroplasmy and copy number by digital PCR. J Biol Chem 2022; 298:102574. [PMID: 36209825 PMCID: PMC9650046 DOI: 10.1016/j.jbc.2022.102574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/01/2022] [Accepted: 10/05/2022] [Indexed: 11/09/2022] Open
Abstract
Mitochondrial DNA (mtDNA) is present in multiple copies and phenotypic consequences of mtDNA mutations depend on the mutant load surpassing a specific threshold. Additionally, changes in mtDNA copy number can impact mitochondrial ATP production, resulting in disease. Therefore, the precise determination of mtDNA heteroplasmy and copy number is crucial to the study of mitochondrial diseases. However, current methods can be imprecise, and quantifying small changes in either heteroplasmy or copy number is challenging. We developed a new approach to measure mtDNA heteroplasmy using a single digital PCR (dPCR) probe. This method is based on the observation that fluorescent-labeled probes in dPCR exhibit different intensities depending on the presence of a single nucleotide change in the sequence bound by the probe. This finding allowed us to precisely and simultaneously determine mtDNA copy number and heteroplasmy levels using duplex dPCR. We tested this approach in two different models (human and mouse), which proved faster and more internally controlled when compared to other published methods routinely used in the mitochondrial genetics field. We believe this approach could be broadly applicable to the detection and quantification of other mixed genetic variations.
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Affiliation(s)
- Wendy K Shoop
- Precision BioSciences, Durham, North Carolina, USA; University of Miami Miller School of Medicine, Miami, Florida, USA.
| | | | - Sandra R Bacman
- University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Carlos T Moraes
- University of Miami Miller School of Medicine, Miami, Florida, USA.
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19
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Feng C, Cao X, Du Y, Chen Y, Xin K, Zou J, Jin Q, Xu JR, Liu H. Uncovering Cis-Regulatory Elements Important for A-to-I RNA Editing in Fusarium graminearum. mBio 2022; 13:e0187222. [PMID: 36102513 PMCID: PMC9600606 DOI: 10.1128/mbio.01872-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/25/2022] [Indexed: 11/20/2022] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing independent of adenosine deaminase acting on RNA (ADAR) enzymes was discovered in fungi recently, and shown to be crucial for sexual reproduction. However, the underlying mechanism for editing is unknown. Here, we combine genome-wide comparisons, proof-of-concept experiments, and machine learning to decipher cis-regulatory elements of A-to-I editing in Fusarium graminearum. We identified plenty of RNA primary sequences and secondary structural features that affect editing specificity and efficiency. Although hairpin loop structures contribute importantly to editing, unlike in animals, the primary sequences have more profound influences on editing than secondary structures. Nucleotide preferences at adjacent positions of editing sites are the most important features, especially preferences at the -1 position. Unexpectedly, besides the number of positions with preferred nucleotides, the combination of preferred nucleotides with depleted ones at different positions are also important for editing. Some cis-sequence features have distinct importance for editing specificity and efficiency. Machine learning models built from diverse sequence and secondary structural features can accurately predict genome-wide editing sites but not editing levels, indicating that the cis-regulatory principle of editing efficiency is more complex than that of editing specificity. Nevertheless, our model interpretation provides insights into the quantitative contribution of each feature to the prediction of both editing sites and levels. We found that efficient editing of FG3G34330 transcripts depended on the full-length RNA molecule, suggesting that additional RNA structural elements may also contribute to editing efficiency. Our work uncovers multidimensional cis-regulatory elements important for A-to-I RNA editing in F. graminearum, helping to elucidate the fungal editing mechanism. IMPORTANCE A-to-I RNA editing is a new epigenetic phenomenon that is crucial for sexual reproduction in fungi. Deciphering cis-regulatory elements of A-to-I RNA editing can help us elucidate the editing mechanism and develop a model that accurately predicts RNA editing. In this study, we discovered multiple RNA sequence and secondary structure features important for A-to-I editing in Fusarium graminearum. We also identified the cis-sequence features with distinct importance for editing specificity and efficiency. The potential importance of full-length RNA molecules for editing efficiency is also revealed. This study represents the first comprehensive investigation of the cis-regulatory principles of A-to-I RNA editing in fungi.
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Affiliation(s)
- Chanjing Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Xinyu Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA
| | - Yanfei Du
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Yitong Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Kaiyun Xin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Jingwen Zou
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Qiaojun Jin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Jin-Rong Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
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20
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Schuster J, Klar J, Khalfallah A, Laan L, Hoeber J, Fatima A, Sequeira VM, Jin Z, Korol SV, Huss M, Nordgren A, Anderlid BM, Gallant C, Birnir B, Dahl N. ZEB2 haploinsufficient Mowat-Wilson syndrome induced pluripotent stem cells show disrupted GABAergic transcriptional regulation and function. Front Mol Neurosci 2022; 15:988993. [PMID: 36353360 PMCID: PMC9637781 DOI: 10.3389/fnmol.2022.988993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/20/2022] [Indexed: 07/30/2023] Open
Abstract
Mowat-Wilson syndrome (MWS) is a severe neurodevelopmental disorder caused by heterozygous variants in the gene encoding transcription factor ZEB2. Affected individuals present with structural brain abnormalities, speech delay and epilepsy. In mice, conditional loss of Zeb2 causes hippocampal degeneration, altered migration and differentiation of GABAergic interneurons, a heterogeneous population of mainly inhibitory neurons of importance for maintaining normal excitability. To get insights into GABAergic development and function in MWS we investigated ZEB2 haploinsufficient induced pluripotent stem cells (iPSC) of MWS subjects together with iPSC of healthy donors. Analysis of RNA-sequencing data at two time points of GABAergic development revealed an attenuated interneuronal identity in MWS subject derived iPSC with enrichment of differentially expressed genes required for transcriptional regulation, cell fate transition and forebrain patterning. The ZEB2 haploinsufficient neural stem cells (NSCs) showed downregulation of genes required for ventral telencephalon specification, such as FOXG1, accompanied by an impaired migratory capacity. Further differentiation into GABAergic interneuronal cells uncovered upregulation of transcription factors promoting pallial and excitatory neurons whereas cortical markers were downregulated. The differentially expressed genes formed a neural protein-protein network with extensive connections to well-established epilepsy genes. Analysis of electrophysiological properties in ZEB2 haploinsufficient GABAergic cells revealed overt perturbations manifested as impaired firing of repeated action potentials. Our iPSC model of ZEB2 haploinsufficient GABAergic development thus uncovers a dysregulated gene network leading to immature interneurons with mixed identity and altered electrophysiological properties, suggesting mechanisms contributing to the neuropathogenesis and seizures in MWS.
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Affiliation(s)
- Jens Schuster
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Joakim Klar
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Ayda Khalfallah
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Loora Laan
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Jan Hoeber
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Ambrin Fatima
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Velin Marita Sequeira
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Zhe Jin
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Sergiy V. Korol
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Mikael Huss
- Wallenberg Long-Term Bioinformatics Support, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Britt Marie Anderlid
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Caroline Gallant
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Bryndis Birnir
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
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21
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Santos FM, Sano NY, Liberal SC, Dario MA, Nantes WAG, Alves FM, da Silva AR, De Oliveira CE, Roque ALR, Herrera HM, Jansen AM. Kinetoplastid Species Maintained by a Small Mammal Community in the Pantanal Biome. Pathogens 2022; 11:pathogens11101205. [PMID: 36297262 PMCID: PMC9612235 DOI: 10.3390/pathogens11101205] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/15/2022] [Accepted: 10/18/2022] [Indexed: 11/24/2022] Open
Abstract
Kinetoplastids include species economically important in agriculture, livestock, and human health. We evaluated the richness of kinetoplastids that infect small mammals in patches of unflooded forests in the Pantanal biome, an area where we hypothesize that its diversity is higher than currently recognized. Hemocultures (HC) and Next Generation Sequencing (NGS) targeting the 18S rDNA gene were employed for the detection of kinetoplastids. We grouped the positive samples into pools for each small mammal species (Monodelphis domestica, Thylamys macrurus, Oecomys mamorae, Thrichomys fosteri, Clyomys laticeps, and Holochilus chacarius). Eight parasite species were identified: Leishmania amazonensis, L. infantum; Trypanosoma cascavelli (HC + NGS), T. cruzi, T. lainsoni, T. rangeli (HC + NGS), Trypanosoma sp. DID, and Neobodo sp. The use of a tool as sensitive as NGS has increased our awareness of the diversity of kinetoplastids, as well as their host range, with emphasis on the species O. mamorae (seven kinetoplastid species, excepting T. cascavelli in a pool of nine individuals) and T. macrurus (four kinetoplastid species in a single individual). Furthermore, L. infantum and L. amazonensis infections were described in small mammals from this region for the first time. These findings make it mandatory to revisit the kinetoplastids/host associations proposed so far.
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Affiliation(s)
- Filipe Martins Santos
- Programa de Pós-Graduação em Ciências Ambientais e Sustentabilidade Agropecuária, Universidade Católica Dom Bosco (UCDB), Campo Grande 79117-010, Brazil
- Correspondence:
| | - Nayara Yoshie Sano
- Programa de Pós-Graduação em Ecologia e Conservação, Universidade Federal do Mato Grosso do Sul (UFMS), Campo Grande 79070-900, Brazil
| | - Sany Caroline Liberal
- Programa de Pós-Graduação em Ciências Ambientais e Sustentabilidade Agropecuária, Universidade Católica Dom Bosco (UCDB), Campo Grande 79117-010, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco (UCDB), Campo Grande 79117-010, Brazil
| | - Maria Augusta Dario
- Laboratório de Biologia de Tripanossomatídeos, Instituto Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
| | - Wesley Arruda Gimenes Nantes
- Programa de Pós-Graduação em Ciências Ambientais e Sustentabilidade Agropecuária, Universidade Católica Dom Bosco (UCDB), Campo Grande 79117-010, Brazil
| | - Fernanda Moreira Alves
- Laboratório de Biologia de Tripanossomatídeos, Instituto Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
- Programa de Pós-Graduação em Biologia Parasitária, Instituto Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
| | | | - Carina Elisei De Oliveira
- Programa de Pós-Graduação em Ciências Ambientais e Sustentabilidade Agropecuária, Universidade Católica Dom Bosco (UCDB), Campo Grande 79117-010, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco (UCDB), Campo Grande 79117-010, Brazil
| | - André Luiz Rodrigues Roque
- Laboratório de Biologia de Tripanossomatídeos, Instituto Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
| | - Heitor Miraglia Herrera
- Programa de Pós-Graduação em Ciências Ambientais e Sustentabilidade Agropecuária, Universidade Católica Dom Bosco (UCDB), Campo Grande 79117-010, Brazil
- Programa de Pós-Graduação em Ecologia e Conservação, Universidade Federal do Mato Grosso do Sul (UFMS), Campo Grande 79070-900, Brazil
- Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco (UCDB), Campo Grande 79117-010, Brazil
| | - Ana Maria Jansen
- Programa de Pós-Graduação em Ciências Ambientais e Sustentabilidade Agropecuária, Universidade Católica Dom Bosco (UCDB), Campo Grande 79117-010, Brazil
- Laboratório de Biologia de Tripanossomatídeos, Instituto Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
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22
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Al-Mutairi DA, Alsabah BH, Alkhaledi BA, Pennekamp P, Omran H. Identification of a novel founder variant in DNAI2 cause primary ciliary dyskinesia in five consanguineous families derived from a single tribe descendant of Arabian Peninsula. Front Genet 2022; 13:1017280. [PMID: 36303540 PMCID: PMC9596166 DOI: 10.3389/fgene.2022.1017280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/23/2022] [Indexed: 11/24/2022] Open
Abstract
Introduction: Primary ciliary dyskinesia (PCD) is caused by dysfunction of motile cilia resulting in insufficient mucociliary clearance of the lungs. The overall aim of this study is to identify disease causing genetic variants for PCD patients in the Kuwaiti population. Methods: A cohort of multiple consanguineous PCD families was identified from Kuwaiti patients and genomic DNA from the family members was analysed for variant screening. Transmission electron microscopy (TEM) and immunofluorescent (IF) analyses were performed on nasal brushings to detect specific structural abnormalities within ciliated cells. Results: All the patients inherited the same founder variant in DNAI2 and exhibited PCD symptoms. TEM analysis demonstrated lack of outer dynein arms (ODA) in all analysed samples. IF analysis confirmed absence of DNAI1, DNAI2, and DNAH5 from the ciliary axoneme. Whole exome sequencing, autozygosity mapping and segregation analysis confirmed that seven patients carry the same homozygous missense variant (DNAI2:c.740G>A; p.Arg247Gln; rs755060592). Conclusion:DNAI2:c.740G>A is the founder variant causing PCD in patients belonging to a particular Arabian tribe which practices consanguineous marriages.
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Affiliation(s)
- Dalal A. Al-Mutairi
- Department of Pathology, Faculty of Medicine, Health Sciences Center, Kuwait University, Kuwait City, Kuwait
- *Correspondence: Dalal A. Al-Mutairi,
| | | | | | - Petra Pennekamp
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Heymut Omran
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
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23
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Sofronova V, Fukushima Y, Masuno M, Naka M, Nagata M, Ishihara Y, Miyashita Y, Asano Y, Moriwaki T, Iwata R, Terawaki S, Yamanouchi Y, Otomo T. A novel nonsense variant in ARID1B causing simultaneous RNA decay and exon skipping is associated with Coffin-Siris syndrome. Hum Genome Var 2022; 9:26. [PMID: 35879281 PMCID: PMC9314373 DOI: 10.1038/s41439-022-00203-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/08/2022] [Accepted: 06/27/2022] [Indexed: 01/12/2023] Open
Abstract
Coffin-Siris syndrome (CSS) is a congenital disorder that is characterized by an absent/hypoplastic fifth distal phalanx, psychomotor developmental delay, and coarse facial features. One of the causative genes, ARID1B (AT-rich interactive domain-containing protein 1B), encodes components of the BAF chromatin remodeling complexes. Here, we report a case of a 3-year 8-month-old male with a novel nonsense variant (NM_001374820.1:c.4282C > T, p.(Gln1428*)) in the ARID1B gene, which was identified with whole-exome sequencing. He showed clinical symptoms of cleft soft palate, distinctive facial features (flat nasal bridge, thick eyebrows, and long eyelashes), right cryptorchidism, and hypertrichosis that partially overlapped with CSS. One of the most characteristic features of CSS is absent/hypoplastic fifth distal phalanx. He showed no obvious clinical finding in the lengths of his fingers or in the formation of his fingernails. However, radiographic analyses of the metacarpophalangeal bones revealed shortening of all the distal phalanges and fifth middle phalanges, suggesting brachydactyly. We performed mRNA analyses and revealed that both nonsense-mediated decay and nonsense-associated altered splicing were simultaneously caused by the c.4282C > T nonsense variant. The proband's clinical manifestations fit the previously reported criteria of disease for CSS or intellectual disability with ARID1B variant. Altogether, we suggest that c.4282C > T is a pathogenic variant that causes this clinical phenotype.
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Affiliation(s)
- Viktoriia Sofronova
- grid.415086.e0000 0001 1014 2000Department of Molecular and Genetic Medicine, Kawasaki Medical School, Kurashiki, Japan ,grid.440700.70000 0004 0556 741XLaboratory of Molecular Medicine and Human Genetics, North-Eastern Federal University, Yakutsk, Russia
| | - Yu Fukushima
- grid.415664.40000 0004 0641 4765Division of Neonatology, National Hospital Organization Okayama Medical Center, Okayama, Japan
| | - Mitsuo Masuno
- grid.415106.70000 0004 0641 4861Department of Medical Genetics, Kawasaki Medical School Hospital, Kurashiki, Japan ,grid.412082.d0000 0004 0371 4682Genetic Counseling Program, Graduate School of Health and Welfare, Kawasaki University of Medical Welfare, Kurashiki, Japan
| | - Mami Naka
- grid.412082.d0000 0004 0371 4682Genetic Counseling Program, Graduate School of Health and Welfare, Kawasaki University of Medical Welfare, Kurashiki, Japan
| | - Miho Nagata
- grid.136593.b0000 0004 0373 3971Department of Cardiovascular Medicine (IRUD Analysis Center), Osaka University Graduate School of Medicine, Suita, Japan
| | - Yasuki Ishihara
- grid.136593.b0000 0004 0373 3971Department of Cardiovascular Medicine (IRUD Analysis Center), Osaka University Graduate School of Medicine, Suita, Japan
| | - Yohei Miyashita
- grid.136593.b0000 0004 0373 3971Department of Cardiovascular Medicine (IRUD Analysis Center), Osaka University Graduate School of Medicine, Suita, Japan
| | - Yoshihiro Asano
- grid.136593.b0000 0004 0373 3971Department of Cardiovascular Medicine (IRUD Analysis Center), Osaka University Graduate School of Medicine, Suita, Japan
| | - Takahito Moriwaki
- grid.415086.e0000 0001 1014 2000Department of Molecular and Genetic Medicine, Kawasaki Medical School, Kurashiki, Japan
| | - Rina Iwata
- grid.415086.e0000 0001 1014 2000Department of Molecular and Genetic Medicine, Kawasaki Medical School, Kurashiki, Japan
| | - Seigo Terawaki
- grid.415086.e0000 0001 1014 2000Department of Molecular and Genetic Medicine, Kawasaki Medical School, Kurashiki, Japan
| | - Yasuko Yamanouchi
- grid.415106.70000 0004 0641 4861Department of Medical Genetics, Kawasaki Medical School Hospital, Kurashiki, Japan ,grid.412082.d0000 0004 0371 4682Genetic Counseling Program, Graduate School of Health and Welfare, Kawasaki University of Medical Welfare, Kurashiki, Japan
| | - Takanobu Otomo
- grid.415086.e0000 0001 1014 2000Department of Molecular and Genetic Medicine, Kawasaki Medical School, Kurashiki, Japan ,grid.415106.70000 0004 0641 4861Department of Medical Genetics, Kawasaki Medical School Hospital, Kurashiki, Japan
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24
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Marciano DC, Wang C, Hsu TK, Bourquard T, Atri B, Nehring RB, Abel NS, Bowling EA, Chen TJ, Lurie PD, Katsonis P, Rosenberg SM, Herman C, Lichtarge O. Evolutionary action of mutations reveals antimicrobial resistance genes in Escherichia coli. Nat Commun 2022; 13:3189. [PMID: 35680894 PMCID: PMC9184624 DOI: 10.1038/s41467-022-30889-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 05/24/2022] [Indexed: 11/08/2022] Open
Abstract
Since antibiotic development lags, we search for potential drug targets through directed evolution experiments. A challenge is that many resistance genes hide in a noisy mutational background as mutator clones emerge in the adaptive population. Here, to overcome this noise, we quantify the impact of mutations through evolutionary action (EA). After sequencing ciprofloxacin or colistin resistance strains grown under different mutational regimes, we find that an elevated sum of the evolutionary action of mutations in a gene identifies known resistance drivers. This EA integration approach also suggests new antibiotic resistance genes which are then shown to provide a fitness advantage in competition experiments. Moreover, EA integration analysis of clinical and environmental isolates of antibiotic resistant of E. coli identifies gene drivers of resistance where a standard approach fails. Together these results inform the genetic basis of de novo colistin resistance and support the robust discovery of phenotype-driving genes via the evolutionary action of genetic perturbations in fitness landscapes.
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Affiliation(s)
- David C Marciano
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Chen Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Teng-Kuei Hsu
- The Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Thomas Bourquard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Benu Atri
- Structural and Computational Biology & Molecular Biophysics Program, Baylor College of Medicine, Houston, TX, 77030, USA
- Clara Analytics Inc., 451 El Camino Real #201, Santa Clara, CA, 95050, USA
| | - Ralf B Nehring
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- The Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nicholas S Abel
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Elizabeth A Bowling
- The Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Taylor J Chen
- Integrative Molecular & Biomedical Biosciences Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pamela D Lurie
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- The Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Integrative Molecular & Biomedical Biosciences Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Structural and Computational Biology & Molecular Biophysics Program, Baylor College of Medicine, Houston, TX, 77030, USA.
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX, 77030, USA.
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25
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Wang L, Wang Y, Makhmoudova A, Nitschke F, Tetlow IJ, Emes MJ. CRISPR-Cas9-mediated editing of starch branching enzymes results in altered starch structure in Brassica napus. PLANT PHYSIOLOGY 2022; 188:1866-1886. [PMID: 34850950 PMCID: PMC8968267 DOI: 10.1093/plphys/kiab535] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/20/2021] [Indexed: 05/24/2023]
Abstract
Starch branching enzymes (SBEs) are one of the major classes of enzymes that catalyze starch biosynthesis in plants. Here, we utilized the clustered regularly interspaced short palindromic repeats-CRISPR associated protein 9 (CRISPR-Cas9)-mediated gene editing system to investigate the effects of SBE mutation on starch structure and turnover in the oilseed crop Brassica napus. Multiple single-guide RNA (sgRNA) expression cassettes were assembled into a binary vector and two rounds of transformation were employed to edit all six BnaSBE genes. All mutations were heterozygous monoallelic or biallelic, and no chimeric mutations were detected from a total of 216 editing events. Previously unannotated gene duplication events associated with two BnaSBE genes were characterized through analysis of DNA sequencing chromatograms, reflecting the complexity of genetic information in B. napus. Five Cas9-free homozygous mutant lines carrying two to six mutations of BnaSBE were obtained, allowing us to compare the effect of editing different BnaSBE isoforms. We also found that in the sextuple sbe mutant, although indels were introduced at the genomic DNA level, an alternate transcript of one BnaSBE2.1 gene bypassed the indel-induced frame shift and was translated to a modified full-length protein. Subsequent analyses showed that the sextuple mutant possesses much lower SBE enzyme activity and starch branching frequency, higher starch-bound phosphate content, and altered pattern of amylopectin chain length distribution relative to wild-type (WT) plants. In the sextuple mutant, irregular starch granules and a slower rate of starch degradation during darkness were observed in rosette leaves. At the pod-filling stage, the sextuple mutant was distinguishable from WT plants by its thick main stem. This work demonstrates the applicability of the CRISPR-Cas9 system for the study of multi-gene families and for investigation of gene-dosage effects in the oil crop B. napus. It also highlights the need for rigorous analysis of CRISPR-Cas9-mutated plants, particularly with higher levels of ploidy, to ensure detection of gene duplications.
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Affiliation(s)
- Liping Wang
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - You Wang
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Amina Makhmoudova
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Felix Nitschke
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ian J Tetlow
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Michael J Emes
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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26
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Cochin M, Luciani L, Touret F, Driouich JS, Petit PR, Moureau G, Baronti C, Laprie C, Thirion L, Maes P, Boudewijns R, Neyts J, de Lamballerie X, Nougairède A. The SARS-CoV-2 Alpha variant exhibits comparable fitness to the D614G strain in a Syrian hamster model. Commun Biol 2022; 5:225. [PMID: 35273335 PMCID: PMC8913834 DOI: 10.1038/s42003-022-03171-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 02/14/2022] [Indexed: 12/14/2022] Open
Abstract
Late 2020, SARS-CoV-2 Alpha variant emerged in United Kingdom and gradually replaced G614 strains initially involved in the global spread of the pandemic. In this study, we use a Syrian hamster model to compare a clinical strain of Alpha variant with an ancestral G614 strain. The Alpha variant succeed to infect animals and to induce a pathology that mimics COVID-19. However, both strains replicate to almost the same level and induced a comparable disease and immune response. A slight fitness advantage is noted for the G614 strain during competition and transmission experiments. These data do not corroborate the epidemiological situation observed during the first half of 2021 in humans nor reports that showed a more rapid replication of Alpha variant in human reconstituted bronchial epithelium. This study highlights the need to combine data from different laboratories using various animal models to decipher the biological properties of newly emerging SARS-CoV-2 variants.
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Affiliation(s)
- Maxime Cochin
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Léa Luciani
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Franck Touret
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Jean-Sélim Driouich
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Paul-Rémi Petit
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Grégory Moureau
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Cécile Baronti
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | | | - Laurence Thirion
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Piet Maes
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, Leuven, Belgium
| | - Robbert Boudewijns
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Antoine Nougairède
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France.
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27
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Lineage Divergence and Vector-Specific Adaptation Have Driven Chikungunya Virus onto Multiple Adaptive Landscapes. mBio 2021; 12:e0273821. [PMID: 34749526 PMCID: PMC8576524 DOI: 10.1128/mbio.02738-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previous studies have shown that the adaptation of Indian Ocean lineage (IOL) chikungunya virus (CHIKV) strains for Aedes albopictus transmission was mediated by an E1-A226V substitution, followed by either a single substitution in E2 or synergistic substitutions in the E2 and E3 envelope glycoproteins. Here, we examined whether Asian lineage strains, including those that descended from the 2014 Caribbean introduction, are likely to acquire these A. albopictus-adaptive E2 substitutions. Because Asian lineage strains cannot adapt through the E1-A226V substitution due to an epistatic constraint, we first determined that the beneficial effect of these E2 mutations in IOL strains is independent of E1-A226V. We then introduced each of these E2 adaptive mutations into the Asian lineage backbone to determine if they improve infectivity for A. albopictus. Surprisingly, our results indicated that in the Asian lineage backbone, these E2 mutations significantly decreased CHIKV fitness in A. albopictus. Furthermore, we tested the effects of these mutations in Aedes aegypti and observed different results from those in A. albopictus, suggesting that mosquito species-specific factors that interact with the envelope proteins are involved in vector infection efficiency. Overall, our results indicate that the divergence between Asian lineage and IOL CHIKVs has led them onto different adaptive landscapes with differing potentials to expand their vector host range. IMPORTANCE Since its introduction into the Caribbean in October 2013, CHIKV has rapidly spread to almost the entire neotropical region. However, its potential to further spread globally, including into more temperate climates, depends in part on its ability to be transmitted efficiently by Aedes albopictus, which can survive colder winters than A. aegypti. We examined in an Asian lineage backbone A. albopictus-adaptive mutations that arose from 2005 to 2009 in Indian Ocean lineage (IOL) strains. Our results predict that the Asian CHIKV lineage now in the Americas will not readily adapt for enhanced A. albopictus transmission via the same mechanisms or adaptive mutations used previously by IOL strains. The vector species- and CHIKV lineage-specific effects caused by adaptive CHIKV envelope glycoprotein substitutions may elucidate our understanding of the mechanisms of mosquito infection and spread.
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28
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The N501Y spike substitution enhances SARS-CoV-2 infection and transmission. Nature 2021; 602:294-299. [PMID: 34818667 DOI: 10.1038/s41586-021-04245-0] [Citation(s) in RCA: 256] [Impact Index Per Article: 85.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 11/12/2021] [Indexed: 11/08/2022]
Abstract
Beginning in the summer of 2020, a variant of SARS-CoV-2, the cause of the COVID-19 pandemic, emerged in the United Kingdom. This B.1.1.7 variant, also known as Alpha, increased rapidly in prevalence, attributed to an increase in infection and/or transmission efficiency1. The Alpha variant has 19 nonsynonymous mutations across its viral genome, including 8 substitutions or deletions in the spike protein, which interacts with cellular receptors to mediate infection and tropism. Here, using a reverse genetics approach, we show that, of the 8 individual spike protein substitutions, only N501Y exhibited consistent fitness gains for replication in the upper airway in the hamster model as well as primary human airway epithelial cells. The N501Y substitution recapitulated the phenotype of enhanced viral transmission seen with the combined 8 Alpha spike mutations, suggesting it is a major determinant of increased transmission of this variant. Mechanistically, the N501Y substitution improved the affinity of the viral spike protein for cellular receptors. As suggested by its convergent evolution in Brazil, South Africa, and elsewhere2,3, our results indicate that N501Y substitution is a major adaptive spike mutation of major concern.
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29
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Ferenczi A, Chew YP, Kroll E, von Koppenfels C, Hudson A, Molnar A. Mechanistic and genetic basis of single-strand templated repair at Cas12a-induced DNA breaks in Chlamydomonas reinhardtii. Nat Commun 2021; 12:6751. [PMID: 34799578 PMCID: PMC8604939 DOI: 10.1038/s41467-021-27004-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/26/2021] [Indexed: 12/12/2022] Open
Abstract
Single-stranded oligodeoxynucleotides (ssODNs) are widely used as DNA repair templates in CRISPR/Cas precision genome editing. However, the underlying mechanisms of single-strand templated DNA repair (SSTR) are inadequately understood, constraining rational improvements to precision editing. Here we study SSTR at CRISPR/Cas12a-induced DNA double-strand breaks (DSBs) in the eukaryotic model green microalga Chlamydomonas reinhardtii. We demonstrate that ssODNs physically incorporate into the genome during SSTR at Cas12a-induced DSBs. This process is genetically independent of the Rad51-dependent homologous recombination and Fanconi anemia pathways, is strongly antagonized by non-homologous end-joining, and is mediated almost entirely by the alternative end-joining enzyme polymerase θ. These findings suggest differences in SSTR between C. reinhardtii and animals. Our work illustrates the promising potentially of C. reinhardtii as a model organism for studying nuclear DNA repair.
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Affiliation(s)
- Aron Ferenczi
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Yen Peng Chew
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Erika Kroll
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | | | - Andrew Hudson
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Attila Molnar
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK.
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30
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Cottrell KA, Soto-Torres L, Dizon MG, Weber JD. 8-azaadenosine and 8-chloroadenosine are not selective inhibitors of ADAR. CANCER RESEARCH COMMUNICATIONS 2021; 1:56-64. [PMID: 35586115 PMCID: PMC9113518 DOI: 10.1158/2767-9764.crc-21-0027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The RNA editing enzyme ADAR, is an attractive therapeutic target for multiple cancers. Through its deaminase activity, ADAR edits adenosine to inosine in dsRNAs. Loss of ADAR in some cancer cell lines causes activation of the type I interferon pathway and the PKR translational repressor, leading to inhibition of proliferation and stimulation of cell death. As such, inhibition of ADAR function is a viable therapeutic strategy for many cancers. However, there are no FDA approved inhibitors of ADAR. Two small molecules have been previously shown to inhibit ADAR or reduce its expression: 8-azaadenosine and 8-chloroadenosine. Here we show that neither molecule is a selective inhibitor of ADAR. Both 8-azaadenosine and 8-chloroadenosine show similar toxicity to ADAR-dependent and independent cancer cell lines. Furthermore, the toxicity of both small molecules is comparable between cell lines with either knockdown or overexpression of ADAR, and cells with unperturbed ADAR expression. Treatment with neither molecule causes activation of PKR. Finally, treatment with either molecule has no effect on A-to-I editing of multiple ADAR substrates. Together these data show that 8-azaadenosine and 8-chloroadenosine are not suitable small molecules for therapies that require selective inhibition of ADAR, and neither should be used in preclinical studies as ADAR inhibitors.
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Affiliation(s)
- Kyle A. Cottrell
- Department of Medicine, Division of Molecular Oncology, Siteman Cancer Center, Washington University School of Medicine, Saint Louis, Missouri
| | - Luisangely Soto-Torres
- Department of Medicine, Division of Molecular Oncology, Siteman Cancer Center, Washington University School of Medicine, Saint Louis, Missouri
| | - Michael G. Dizon
- Department of Medicine, Division of Molecular Oncology, Siteman Cancer Center, Washington University School of Medicine, Saint Louis, Missouri
| | - Jason D. Weber
- Department of Medicine, Division of Molecular Oncology, Siteman Cancer Center, Washington University School of Medicine, Saint Louis, Missouri.,Department of Cell Biology and Physiology, Siteman Cancer Center, Washington University School of Medicine, Saint Louis, Missouri.,Corresponding Author: Jason D. Weber, Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8069, St. Louis, MO 63110. Phone: 314-747-3896; E-mail:
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31
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Lee DE, Kim HC, Chong ST, Klein TA, Kim JH, Lee SH. Prediction of species composition ratios in pooled specimens of the Anopheles Hyrcanus group using quantitative sequencing. Malar J 2021; 20:338. [PMID: 34362388 PMCID: PMC8349024 DOI: 10.1186/s12936-021-03868-y] [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: 03/30/2021] [Accepted: 07/27/2021] [Indexed: 11/21/2022] Open
Abstract
Background Plasmodium vivax is transmitted by members of the Anopheles Hyrcanus Group that includes six species in the Republic of Korea: Anopheles sinensis sensu stricto (s.s.), Anopheles pullus, Anopheles kleini, Anopheles belenrae, Anopheles lesteri, and Anopheles sineroides. Individual Anopheles species within the Hyrcanus Group demonstrate differences in their geographical distributions, vector competence and insecticide resistance, making it crucial for accurate species identification. Conventional species identification conducted using individual genotyping (or barcoding) based on species-specific molecular markers requires extensive time commitment and financial resources. Results A population-based quantitative sequencing (QS) protocol developed in this study provided a rapid estimate of species composition ratios among pooled mosquitoes as a cost-effective alternative to individual genotyping. This can be accomplished by using species- or group-specific nucleotide sequences of the mitochondrial cytochrome C oxidase subunit I (COI) and the ribosomal RNA internal transcribed spacer 2 (ITS2) region as species identification alleles in a two-step prediction protocol. Standard genomic DNA fragments of COI and ITS2 genes were amplified from each Anopheles species using group-specific universal primer sets. Following sequencing of the COI or ITS2 amplicons generated from sets of standard DNA mixtures, equations were generated via linear regression to predict species-specific nucleotide sequence frequencies at different positions. Species composition ratios between An. sineroides, An. pullus and An. lesteri were estimated from QS of the COI amplicons based on the mC.260A, mC.122C and mC.525C alleles at the first step, followed by the prediction of species composition ratios between An. sinensis, An. kleini and An. belenrae based on QS of the ITS2 amplicons using the rI.370G and rI.389T alleles. The COI copy number was not significantly different between species, suggesting the reliability of COI-based prediction. In contrast, ITS2 showed a slightly but significantly higher copy number in An. belenrae, requiring an adjustment of its predicted composition ratio. A blind test proved that predicted species composition ratios either from pooled DNA specimens or pooled mosquito specimens were not statistically different from the actual values, demonstrating that the QS-based prediction is accurate and reliable. Conclusions This two-step prediction protocol will facilitate rapid estimation of the species composition ratios in field-collected Anopheles Hyrcanus Group populations and is particularly useful for studying the vector ecology of Anopheles population and epidemiology of malaria. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-021-03868-y.
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Affiliation(s)
- Do Eun Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Heung-Chul Kim
- Medical Department Activity-Korea/65th Medical Brigade, Force Health Protection and Preventive Medicine, Unit 15281, APO, 96271-5281, AP, USA
| | - Sung-Tae Chong
- Medical Department Activity-Korea/65th Medical Brigade, Force Health Protection and Preventive Medicine, Unit 15281, APO, 96271-5281, AP, USA
| | - Terry A Klein
- Medical Department Activity-Korea/65th Medical Brigade, Force Health Protection and Preventive Medicine, Unit 15281, APO, 96271-5281, AP, USA
| | - Ju Hyeon Kim
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Si Hyeock Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea. .,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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32
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Badawi M, Mori T, Kurihara T, Yoshizawa T, Nohara K, Kouyama-Suzuki E, Yanagawa T, Shirai Y, Tabuchi K. Risperidone Mitigates Enhanced Excitatory Neuronal Function and Repetitive Behavior Caused by an ASD-Associated Mutation of SIK1. Front Mol Neurosci 2021; 14:706494. [PMID: 34295222 PMCID: PMC8289890 DOI: 10.3389/fnmol.2021.706494] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 05/27/2021] [Indexed: 12/28/2022] Open
Abstract
Six mutations in the salt-inducible kinase 1 (SIK1)-coding gene have been identified in patients with early infantile epileptic encephalopathy (EIEE-30) accompanied by autistic symptoms. Two of the mutations are non-sense mutations that truncate the C-terminal region of SIK1. It has been shown that the C-terminal-truncated form of SIK1 protein affects the subcellular distribution of SIK1 protein, tempting to speculate the relevance to the pathophysiology of the disorders. We generated SIK1-mutant (SIK1-MT) mice recapitulating the C-terminal-truncated mutations using CRISPR/Cas9-mediated genome editing. SIK1-MT protein was distributed in the nucleus and cytoplasm, whereas the distribution of wild-type SIK1 was restricted to the nucleus. We found the disruption of excitatory and inhibitory (E/I) synaptic balance due to an increase in excitatory synaptic transmission and enhancement of neural excitability in the pyramidal neurons in layer 5 of the medial prefrontal cortex in SIK1-MT mice. We also found the increased repetitive behavior and social behavioral deficits in SIK1-MT mice. The risperidone administration attenuated the neural excitability and excitatory synaptic transmission, but the disrupted E/I synaptic balance was unchanged, because it also reduced the inhibitory synaptic transmission. Risperidone also eliminated the repetitive behavior but not social behavioral deficits. These results indicate that risperidone has a role in decreasing neuronal excitability and excitatory synapses, ameliorating repetitive behavior in the SIK1-truncated mice.
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Affiliation(s)
- Moataz Badawi
- Department of Molecular and Cellular Physiology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Takuma Mori
- Department of Molecular and Cellular Physiology, Shinshu University School of Medicine, Matsumoto, Japan.,Department of NeuroHealth Innovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto, Japan
| | - Taiga Kurihara
- Department of Molecular and Cellular Physiology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Takahiro Yoshizawa
- Research Center for Supports to Advanced Science, Shinshu University, Matsumoto, Japan
| | - Katsuhiro Nohara
- Department of Molecular and Cellular Physiology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Emi Kouyama-Suzuki
- Department of Molecular and Cellular Physiology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Toru Yanagawa
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yoshinori Shirai
- Department of Molecular and Cellular Physiology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Katsuhiko Tabuchi
- Department of Molecular and Cellular Physiology, Shinshu University School of Medicine, Matsumoto, Japan.,Department of NeuroHealth Innovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto, Japan
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33
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Smyth M, Khamina K, Popa A, Gudipati V, Agerer B, Lercher A, Kosack L, Endler L, Baazim H, Viczenczova C, Huppa JB, Bergthaler A. Characterization of CD8 T Cell-Mediated Mutations in the Immunodominant Epitope GP33-41 of Lymphocytic Choriomeningitis Virus. Front Immunol 2021; 12:638485. [PMID: 34194424 PMCID: PMC8236698 DOI: 10.3389/fimmu.2021.638485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Cytotoxic T lymphocytes (CTLs) represent key immune effectors of the host response against chronic viruses, due to their cytotoxic response to virus-infected cells. In response to this selection pressure, viruses may accumulate escape mutations that evade CTL-mediated control. To study the emergence of CTL escape mutations, we employed the murine chronic infection model of lymphocytic choriomeningitis virus (LCMV). We developed an amplicon-based next-generation sequencing pipeline to detect low frequency mutations in the viral genome and identified non-synonymous mutations in the immunodominant LCMV CTL epitope, GP33-41, in infected wildtype mice. Infected Rag2-deficient mice lacking CTLs did not contain such viral mutations. By using transgenic mice with T cell receptors specific to GP33-41, we characterized the emergence of viral mutations in this epitope under varying selection pressure. We investigated the two most abundant viral mutations by employing reverse genetically engineered viral mutants encoding the respective mutations. These experiments provided evidence that these mutations prevent activation and expansion of epitope-specific CD8 T cells. Our findings on the mutational dynamics of CTL escape mutations in a widely-studied viral infection model contributes to our understanding of how chronic viruses interact with their host and evade the immune response. This may guide the development of future treatments and vaccines against chronic infections.
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Affiliation(s)
- Mark Smyth
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Kseniya Khamina
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alexandra Popa
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Venugopal Gudipati
- Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, Austria
| | - Benedikt Agerer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alexander Lercher
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Lindsay Kosack
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Lukas Endler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Hatoon Baazim
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Csilla Viczenczova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Johannes B Huppa
- Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, Austria
| | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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Repeated mutation of a developmental enhancer contributed to human thermoregulatory evolution. Proc Natl Acad Sci U S A 2021; 118:2021722118. [PMID: 33850016 PMCID: PMC8072367 DOI: 10.1073/pnas.2021722118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Humans sweat to cool their bodies and have by far the highest eccrine sweat gland density among primates. Humans' high eccrine gland density has long been recognized as a hallmark human evolutionary adaptation, but its genetic basis has been unknown. In humans, expression of the Engrailed 1 (EN1) transcription factor correlates with the onset of eccrine gland formation. In mice, regulation of ectodermal En1 expression is a major determinant of natural variation in eccrine gland density between strains, and increased En1 expression promotes the specification of more eccrine glands. Here, we show that regulation of EN1 has evolved specifically on the human lineage to promote eccrine gland formation. Using comparative genomics and validation of ectodermal enhancer activity in mice, we identified a human EN1 skin enhancer, hECE18. We showed that multiple epistatically interacting derived substitutions in the human ECE18 enhancer increased its activity compared with nonhuman ape orthologs in cultured keratinocytes. Repression of hECE18 in human cultured keratinocytes specifically attenuated EN1 expression, indicating this element positively regulates EN1 in this context. In a humanized enhancer knock-in mouse, hECE18 increased developmental En1 expression in the skin to induce the formation of more eccrine glands. Our study uncovers a genetic basis contributing to the evolution of one of the most singular human adaptations and implicates multiple interacting mutations in a single enhancer as a mechanism for human evolutionary change.
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Plante JA, Liu Y, Liu J, Xia H, Johnson BA, Lokugamage KG, Zhang X, Muruato AE, Zou J, Fontes-Garfias CR, Mirchandani D, Scharton D, Bilello JP, Ku Z, An Z, Kalveram B, Freiberg AN, Menachery VD, Xie X, Plante KS, Weaver SC, Shi PY. Spike mutation D614G alters SARS-CoV-2 fitness. Nature 2021; 592:116-121. [PMID: 33106671 PMCID: PMC8158177 DOI: 10.1038/s41586-020-2895-3] [Citation(s) in RCA: 1096] [Impact Index Per Article: 365.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/20/2020] [Indexed: 11/09/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein substitution D614G became dominant during the coronavirus disease 2019 (COVID-19) pandemic1,2. However, the effect of this variant on viral spread and vaccine efficacy remains to be defined. Here we engineered the spike D614G substitution in the USA-WA1/2020 SARS-CoV-2 strain, and found that it enhances viral replication in human lung epithelial cells and primary human airway tissues by increasing the infectivity and stability of virions. Hamsters infected with SARS-CoV-2 expressing spike(D614G) (G614 virus) produced higher infectious titres in nasal washes and the trachea, but not in the lungs, supporting clinical evidence showing that the mutation enhances viral loads in the upper respiratory tract of COVID-19 patients and may increase transmission. Sera from hamsters infected with D614 virus exhibit modestly higher neutralization titres against G614 virus than against D614 virus, suggesting that the mutation is unlikely to reduce the ability of vaccines in clinical trials to protect against COVID-19, and that therapeutic antibodies should be tested against the circulating G614 virus. Together with clinical findings, our work underscores the importance of this variant in viral spread and its implications for vaccine efficacy and antibody therapy.
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Affiliation(s)
- Jessica A Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Yang Liu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jianying Liu
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Bryan A Johnson
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Kumari G Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xianwen Zhang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Antonio E Muruato
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Camila R Fontes-Garfias
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Divya Mirchandani
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Dionna Scharton
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | | | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Birte Kalveram
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Alexander N Freiberg
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Vineet D Menachery
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Kenneth S Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Scott C Weaver
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
| | - Pei-Yong Shi
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
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Liu Y, Liu J, Plante KS, Plante JA, Xie X, Zhang X, Ku Z, An Z, Scharton D, Schindewolf C, Menachery VD, Shi PY, Weaver SC. The N501Y spike substitution enhances SARS-CoV-2 transmission. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33758836 PMCID: PMC7986995 DOI: 10.1101/2021.03.08.434499] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Beginning in the summer of 2020, a variant of SARS-CoV-2, the cause of the COVID-19 pandemic, emerged in the United Kingdom (UK). This B.1.1.7 variant increased rapidly in prevalence among sequenced strains, attributed to an increase in infection and/or transmission efficiency. The UK variant has 19 nonsynonymous mutations across its viral genome including 8 substitutions or deletions in the spike protein, which interacts with cellular receptors to mediate infection and tropism. Here, using a reverse genetics approach, we show that, of the 8 individual spike protein substitutions, only N501Y exhibited consistent fitness gains for replication in the upper airway in the hamster model as well as primary human airway epithelial cells. The N501Y substitution recapitulated the phenotype of enhanced viral transmission seen with the combined 8 UK spike mutations, suggesting it is a major determinant responsible for increased transmission of this variant. Mechanistically, the N501Y substitution improved the affinity of the viral spike protein for cellular receptors. As suggested by its convergent evolution in Brazil and South Africa, our results indicate that N501Y substitution is a major adaptive spike mutation of major concern.
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Sparber P, Krylova T, Repina S, Demina N, Rudenskaya G, Sharkova I, Sharkov A, Kadyshev V, Kanivets I, Korostelev S, Pomerantseva E, Kaimonov V, Mikhailova S, Zakharova E, Skoblov M. Retrospective analysis of 17 patients with mitochondrial membrane protein-associated neurodegeneration diagnosed in Russia. Parkinsonism Relat Disord 2021; 84:98-104. [DOI: 10.1016/j.parkreldis.2021.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 01/26/2021] [Accepted: 02/01/2021] [Indexed: 12/14/2022]
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Seroussi E. Estimating Copy-Number Proportions: The Comeback of Sanger Sequencing. Genes (Basel) 2021; 12:283. [PMID: 33671263 PMCID: PMC7922598 DOI: 10.3390/genes12020283] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 12/28/2022] Open
Abstract
Determination of the relative copy numbers of mixed molecular species in nucleic acid samples is often the objective of biological experiments, including Single-Nucleotide Polymorphism (SNP), indel and gene copy-number characterization, and quantification of CRISPR-Cas9 base editing, cytosine methylation, and RNA editing. Standard dye-terminator chromatograms are a widely accessible, cost-effective information source from which copy-number proportions can be inferred. However, the rate of incorporation of dye terminators is dependent on the dye type, the adjacent sequence string, and the secondary structure of the sequenced strand. These variable rates complicate inferences and have driven scientists to resort to complex and costly quantification methods. Because these complex methods introduce their own biases, researchers are rethinking whether rectifying distortions in sequencing trace files and using direct sequencing for quantification will enable comparable accurate assessment. Indeed, recent developments in software tools (e.g., TIDE, ICE, EditR, BEEP and BEAT) indicate that quantification based on direct Sanger sequencing is gaining in scientific acceptance. This commentary reviews the common obstacles in quantification and the latest insights and developments relevant to estimating copy-number proportions based on direct Sanger sequencing, concluding that bidirectional sequencing and sophisticated base calling are the keys to identifying and avoiding sequence distortions.
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Affiliation(s)
- Eyal Seroussi
- Institute of Animal Science, Agricultural Research Organization (ARO), HaMaccabim Road, P.O.B 15159, Rishon LeTsiyon 7528809, Israel
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39
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Liu J, Liu Y, Shan C, Nunes BTD, Yun R, Haller SL, Rafael GH, Azar SR, Andersen CR, Plante K, Vasilakis N, Shi PY, Weaver SC. Role of mutational reversions and fitness restoration in Zika virus spread to the Americas. Nat Commun 2021; 12:595. [PMID: 33500409 PMCID: PMC7838395 DOI: 10.1038/s41467-020-20747-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 12/15/2020] [Indexed: 01/30/2023] Open
Abstract
Zika virus (ZIKV) emerged from obscurity in 2013 to spread from Asia to the South Pacific and the Americas, where millions of people were infected, accompanied by severe disease including microcephaly following congenital infections. Phylogenetic studies have shown that ZIKV evolved in Africa and later spread to Asia, and that the Asian lineage is responsible for the recent epidemics in the South Pacific and Americas. However, the reasons for the sudden emergence of ZIKV remain enigmatic. Here we report evolutionary analyses that revealed four mutations, which occurred just before ZIKV introduction to the Americas, represent direct reversions of previous mutations that accompanied earlier spread from Africa to Asia and early circulation there. Our experimental infections of Aedes aegypti mosquitoes, human cells, and mice using ZIKV strains with and without these mutations demonstrate that the original mutations reduced fitness for urban, human-amplifed transmission, while the reversions restored fitness, increasing epidemic risk. These findings include characterization of three transmission-adaptive ZIKV mutations, and demonstration that these and one identified previously restored fitness for epidemic transmission soon before introduction into the Americas. The initial mutations may have followed founder effects and/or drift when the virus was introduced decades ago into Asia.
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Affiliation(s)
- Jianying Liu
- World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infections and Immunity, and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Yang Liu
- Department of Biochemistry and Molecular Biology and Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Chao Shan
- Department of Biochemistry and Molecular Biology and Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Bruno T D Nunes
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil
| | - Ruimei Yun
- World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infections and Immunity, and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Sherry L Haller
- World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infections and Immunity, and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Grace H Rafael
- World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infections and Immunity, and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Sasha R Azar
- World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infections and Immunity, and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Clark R Andersen
- Department of Preventive Medicine and Community Health, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Kenneth Plante
- World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infections and Immunity, and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Nikos Vasilakis
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, World Reference Center for Emerging Viruses and Arboviruses, and Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology and Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, 77555, USA.
| | - Scott C Weaver
- World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infections and Immunity, and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
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40
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Malik TN, Cartailler JP, Emeson RB. Quantitative Analysis of Adenosine-to-Inosine RNA Editing. Methods Mol Biol 2021; 2181:97-111. [PMID: 32729077 DOI: 10.1007/978-1-0716-0787-9_7] [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] [Indexed: 12/30/2022]
Abstract
The conversion of adenosine to inosine (A to I) by RNA editing represents a common posttranscriptional mechanism for diversification of both the transcriptome and proteome, and is a part of the cellular response for innate immune tolerance. Due to its preferential base-pairing with cytosine (C), inosine (I) is recognized as guanosine (G) by reverse transcriptase, as well as the cellular splicing and translation machinery. A-to-I editing events appear as A-G discrepancies between genomic DNA and cDNA sequences. Molecular analyses of RNA editing have leveraged these nucleoside differences to quantify RNA editing in ensemble populations of RNA transcripts and within individual cDNAs using high-throughput sequencing or Sanger sequencing-derived analysis of electropherogram peak heights. Here, we briefly review and compare these methods of RNA editing quantification, as well as provide experimental protocols by which such analyses may be achieved.
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Affiliation(s)
- Turnee N Malik
- Training Program in Neuroscience, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jean-Philippe Cartailler
- Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ronald B Emeson
- Training Program in Neuroscience, Vanderbilt University School of Medicine, Nashville, TN, USA. .,Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA. .,Departments of Pharmacology, Biochemistry and Psychiatry & Behavioral Sciences, Vanderbilt University School of Medicine, Nashville, TN, USA.
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41
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Targeted Next-Generation Sequencing and Informatics as an Effective Tool to Establish the Composition of Bovine Piroplasm Populations in Endemic Regions. Microorganisms 2020; 9:microorganisms9010021. [PMID: 33374586 PMCID: PMC7822421 DOI: 10.3390/microorganisms9010021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/12/2020] [Accepted: 12/19/2020] [Indexed: 12/16/2022] Open
Abstract
Protists of the genera Babesia and Theileria (piroplasms) cause some of the most prevalent and debilitating diseases for bovines worldwide. In this study, we established and used a next-generation sequencing-informatic approach to explore the composition of Babesia and Theileria populations in cattle and water buffalo in a country (Pakistan) endemic for these pathogens. We collected individual blood samples from cattle (n = 212) and water buffalo (n = 154), extracted genomic DNAs, PCR-amplified the V4 hypervariable region of 18S small subunit rRNA gene from piroplasms, sequenced amplicons using Illumina technology, and then analysed data using bioinformatic platforms. The results revealed piroplasms in 68.9% (252/366) samples, with overall occurrence being markedly higher in cattle (85.8%) than in water buffaloes (45.5%). Babesia (B.) occultans and Theileria (T.) lestoquardi-like species were recorded for the first time in Pakistan, and, overall, T. annulata was most commonly detected (65.8%) followed by B. bovis (7.1%), B. bigemina (4.4%), and T. orientalis (0.5%), with the genetic variability within B. bovis being pronounced. The occurrence and composition of piroplasm species varied markedly across different agro-ecological zones. The high detection of T. annulata in asymptomatic animals suggested a relatively high level of endemic stability of tropical theileriosis in the bovine population.
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Welter L, Xu L, McKinley D, Dago AE, Prabakar RK, Restrepo-Vassalli S, Xu K, Rodriguez-Lee M, Kolatkar A, Nevarez R, Ruiz C, Nieva J, Kuhn P, Hicks J. Treatment response and tumor evolution: lessons from an extended series of multianalyte liquid biopsies in a metastatic breast cancer patient. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005819. [PMID: 33203646 PMCID: PMC7784493 DOI: 10.1101/mcs.a005819] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/15/2020] [Indexed: 12/17/2022] Open
Abstract
Currently, clinical characterization of metastatic breast cancer is based on tissue samples taken at time of diagnosis. However, tissue biopsies are invasive and tumors are continuously evolving, which indicates the need for minimally invasive longitudinal assessment of the tumor. Blood-based liquid biopsies provide minimal invasive means for serial sampling over the course of treatment and the opportunity to adjust therapies based on molecular markers. Here, we aim to identify cellular changes that occur in breast cancer over the lifespan of an affected patient through single-cell proteomic and genomic analysis of longitudinally sampled solid and liquid biopsies. Three solid and 17 liquid biopsies from peripheral blood of an ER+/HER2− metastatic breast cancer patient collected over 4 years and eight treatment regimens were analyzed for morphology, protein expression, copy-number alterations, and single-nucleotide variations. Analysis of 563 single morphometrically similar circulating tumor cells (CTCs) and 13 cell-free DNA (cfDNA) samples along with biopsies of the primary and metastatic tumor revealed progressive genomic evolution away from the primary tumor profiles, along with changes in ER expression and the appearance of resistance mutations. Both the abundance and the genomic alterations of CTCs and cfDNA were highly correlated and consistent with genomic alterations in the tissue samples. We demonstrate that genomic evolution and acquisition of drug resistance can be detected in real time and at single-cell resolution through liquid biopsy analytes and highlight the utility of liquid biopsies to guide treatment decisions.
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Affiliation(s)
- Lisa Welter
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Liya Xu
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Dillon McKinley
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Angel E Dago
- The Scripps Research Institute, La Jolla, California 92037, USA
| | - Rishvanth K Prabakar
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Sara Restrepo-Vassalli
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Kevin Xu
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Mariam Rodriguez-Lee
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Anand Kolatkar
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Rafael Nevarez
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Carmen Ruiz
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Jorge Nieva
- Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
| | - Peter Kuhn
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA.,Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA.,Viterbi School of Engineering, University of Southern California, Los Angeles, California 90089, USA
| | - James Hicks
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
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Shi PY, Plante J, Liu Y, Liu J, Xia H, Johnson B, Lokugamage K, Zhang X, Muruato A, Zou J, Fontes-Garfias C, Mirchandani D, Scharton D, Kalveram B, Bilello J, Ku Z, An Z, Freiberg A, Menachery V, Xie X, Plante K, Weaver S. Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. RESEARCH SQUARE 2020:rs.3.rs-70482. [PMID: 32935091 PMCID: PMC7491579 DOI: 10.21203/rs.3.rs-70482/v1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A spike protein mutation D614G became dominant in SARS-CoV-2 during the COVID-19 pandemic. However, the mutational impact on viral spread and vaccine efficacy remains to be defined. Here we engineer the D614G mutation in the SARS-CoV-2 USA-WA1/2020 strain and characterize its effect on viral replication, pathogenesis, and antibody neutralization. The D614G mutation significantly enhances SARS-CoV-2 replication on human lung epithelial cells and primary human airway tissues, through an improved infectivity of virions with the spike receptor-binding domain in an "up" conformation for binding to ACE2 receptor. Hamsters infected with D614 or G614 variants developed similar levels of weight loss. However, the G614 virus produced higher infectious titers in the nasal washes and trachea, but not lungs, than the D614 virus. The hamster results confirm clinical evidence that the D614G mutation enhances viral loads in the upper respiratory tract of COVID-19 patients and may increases transmission. For antibody neutralization, sera from D614 virus-infected hamsters consistently exhibit higher neutralization titers against G614 virus than those against D614 virus, indicating that (i) the mutation may not reduce the ability of vaccines in clinical trials to protect against COVID-19 and (ii) therapeutic antibodies should be tested against the circulating G614 virus before clinical development.
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Affiliation(s)
- Pei-Yong Shi
- The University of Texas Medical Branch at Galveston
| | | | - Yang Liu
- University of Texas Medical Branch
| | | | | | | | | | | | | | | | | | | | | | | | | | - Zhiqiang Ku
- The University of Texas Health Science Center at Houston
| | - Zhiqiang An
- University of Texas Health Science Center at Houston
| | | | | | | | | | - Scott Weaver
- The University of Texas Medical Branch at Galveston
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44
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Plante JA, Liu Y, Liu J, Xia H, Johnson BA, Lokugamage KG, Zhang X, Muruato AE, Zou J, Fontes-Garfias CR, Mirchandani D, Scharton D, Bilello JP, Ku Z, An Z, Kalveram B, Freiberg AN, Menachery VD, Xie X, Plante KS, Weaver SC, Shi PY. Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.09.01.278689. [PMID: 32908978 PMCID: PMC7480025 DOI: 10.1101/2020.09.01.278689] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A spike protein mutation D614G became dominant in SARS-CoV-2 during the COVID-19 pandemic. However, the mutational impact on viral spread and vaccine efficacy remains to be defined. Here we engineer the D614G mutation in the SARS-CoV-2 USA-WA1/2020 strain and characterize its effect on viral replication, pathogenesis, and antibody neutralization. The D614G mutation significantly enhances SARS-CoV-2 replication on human lung epithelial cells and primary human airway tissues, through an improved infectivity of virions with the spike receptor-binding domain in an "up" conformation for binding to ACE2 receptor. Hamsters infected with D614 or G614 variants developed similar levels of weight loss. However, the G614 virus produced higher infectious titers in the nasal washes and trachea, but not lungs, than the D614 virus. The hamster results confirm clinical evidence that the D614G mutation enhances viral loads in the upper respiratory tract of COVID-19 patients and may increases transmission. For antibody neutralization, sera from D614 virus-infected hamsters consistently exhibit higher neutralization titers against G614 virus than those against D614 virus, indicating that (i) the mutation may not reduce the ability of vaccines in clinical trials to protect against COVID-19 and (ii) therapeutic antibodies should be tested against the circulating G614 virus before clinical development.
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Affiliation(s)
- Jessica A. Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | - Yang Liu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, USA
| | - Jianying Liu
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, USA
| | - Bryan A. Johnson
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
| | - Kumari G. Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | - Xianwen Zhang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, USA
| | - Antonio E. Muruato
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, USA
| | - Camila R. Fontes-Garfias
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, USA
| | - Divya Mirchandani
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | - Dionna Scharton
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | | | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, USA
| | - Birte Kalveram
- Department of Pathology, University of Texas Medical Branch, Galveston TX, USA
| | - Alexander N. Freiberg
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
- Department of Pathology, University of Texas Medical Branch, Galveston TX, USA
- Center for Biodefense & Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Vineet D. Menachery
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, USA
| | - Kenneth S. Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | - Scott C. Weaver
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA
- Center for Biodefense & Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, USA
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA
- Center for Biodefense & Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
- Lead Contact
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Targeting CD70 with cusatuzumab eliminates acute myeloid leukemia stem cells in patients treated with hypomethylating agents. Nat Med 2020; 26:1459-1467. [PMID: 32601337 DOI: 10.1038/s41591-020-0910-8] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 04/27/2020] [Indexed: 01/22/2023]
Abstract
Acute myeloid leukemia (AML) is driven by leukemia stem cells (LSCs) that resist conventional chemotherapy and are the major cause of relapse1,2. Hypomethylating agents (HMAs) are the standard of care in the treatment of older or unfit patients with AML, but responses are modest and not durable3-5. Here we demonstrate that LSCs upregulate the tumor necrosis factor family ligand CD70 in response to HMA treatment resulting in increased CD70/CD27 signaling. Blocking CD70/CD27 signaling and targeting CD70-expressing LSCs with cusatuzumab, a human αCD70 monoclonal antibody with enhanced antibody-dependent cellular cytotoxicity activity, eliminated LSCs in vitro and in xenotransplantation experiments. Based on these preclinical results, we performed a phase 1/2 trial in previously untreated older patients with AML with a single dose of cusatuzumab monotherapy followed by a combination therapy with the HMA azacitidine ( NCT03030612 ). We report results from the phase 1 dose escalation part of the clinical trial. Hematological responses in the 12 patients enrolled included 8 complete remission, 2 complete remission with incomplete blood count recovery and 2 partial remission with 4 patients achieving minimal residual disease negativity by flow cytometry at <10-3. Median time to response was 3.3 months. Median progression-free survival was not reached yet at the time of the data cutoff. No dose-limiting toxicities were reported and the maximum tolerated dose of cusatuzumab was not reached. Importantly, cusatuzumab treatment substantially reduced LSCs and triggered gene signatures related to myeloid differentiation and apoptosis.
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Holtgräwe D, Rosleff Soerensen T, Hausmann L, Pucker B, Viehöver P, Töpfer R, Weisshaar B. A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock 'Börner' ( Vitis riparia × Vitis cinerea) and Its Exploitation for Marker Development and Targeted Mapping. FRONTIERS IN PLANT SCIENCE 2020; 11:156. [PMID: 32194587 PMCID: PMC7064618 DOI: 10.3389/fpls.2020.00156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/31/2020] [Indexed: 06/10/2023]
Abstract
Grapevine breeding has become highly relevant due to upcoming challenges like climate change, a decrease in the number of available fungicides, increasing public concern about plant protection, and the demand for a sustainable production. Downy mildew caused by Plasmopara viticola is one of the most devastating diseases worldwide of cultivated Vitis vinifera. In modern breeding programs, therefore, genetic marker technologies and genomic data are used to develop new cultivars with defined and stacked resistance loci. Potential sources of resistance are wild species of American or Asian origin. The interspecific hybrid of Vitis riparia Gm 183 x Vitis cinerea Arnold, available as the rootstock cultivar 'Börner,' carries several relevant resistance loci. We applied next-generation sequencing to enable the reliable identification of simple sequence repeats (SSR), and we also generated a draft genome sequence assembly of 'Börner' to access genome-wide sequence variations in a comprehensive and highly reliable way. These data were used to cover the 'Börner' genome with genetic marker positions. A subset of these marker positions was used for targeted mapping of the P. viticola resistance locus, Rpv14, to validate the marker position list. Based on the reference genome sequence PN40024, the position of this resistance locus can be narrowed down to less than 0.5 Mbp on chromosome 5.
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Affiliation(s)
- Daniela Holtgräwe
- Faculty of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | | | - Ludger Hausmann
- Institute for Grapevine Breeding Geilweilerhof, Julius Kuehn-Institute, Federal Research Centre for Cultivated Plants, Siebeldingen, Germany
| | - Boas Pucker
- Faculty of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Prisca Viehöver
- Faculty of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Reinhard Töpfer
- Institute for Grapevine Breeding Geilweilerhof, Julius Kuehn-Institute, Federal Research Centre for Cultivated Plants, Siebeldingen, Germany
| | - Bernd Weisshaar
- Faculty of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
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Rosenberg A, Luth MR, Winzeler EA, Behnke M, Sibley LD. Evolution of resistance in vitro reveals mechanisms of artemisinin activity in Toxoplasma gondii. Proc Natl Acad Sci U S A 2019; 116:26881-26891. [PMID: 31806760 PMCID: PMC6936365 DOI: 10.1073/pnas.1914732116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Artemisinins are effective against a variety of parasites and provide the first line of treatment for malaria. Laboratory studies have identified several mechanisms for artemisinin resistance in Plasmodium falciparum, including mutations in Kelch13 that are associated with delayed clearance in some clinical isolates, although other mechanisms are likely involved. To explore other potential mechanisms of resistance in parasites, we took advantage of the genetic tractability of Toxoplasma gondii, a related parasite that shows moderate sensitivity to artemisinin. Resistant populations of T. gondii were selected by culture in increasing concentrations and whole-genome sequencing identified several nonconservative point mutations that emerged in the population and were fixed over time. Genome editing using CRISPR/Cas9 was used to introduce point mutations conferring amino acid changes in a serine protease homologous to DegP and a serine/threonine protein kinase of unknown function. Single and double mutations conferred a competitive advantage over wild-type parasites in the presence of drug, despite not changing EC50 values. Additionally, the evolved resistant lines showed dramatic amplification of the mitochondria genome, including genes encoding cytochrome b and cytochrome c oxidase I. Prior studies in yeast and mammalian tumor cells implicate the mitochondrion as a target of artemisinins, and treatment of wild-type parasites with high concentrations of drug decreased mitochondrial membrane potential, a phenotype that was stably altered in the resistant parasites. These findings extend the repertoire of mutations associated with artemisinin resistance and suggest that the mitochondrion may be an important target of inhibition of resistance in T. gondii.
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Affiliation(s)
- Alex Rosenberg
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Madeline R. Luth
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Elizabeth A. Winzeler
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Michael Behnke
- Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803
| | - L. David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
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48
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Radzio-Basu J, Council O, Cong ME, Ruone S, Newton A, Wei X, Mitchell J, Ellis S, Petropoulos CJ, Huang W, Spreen W, Heneine W, García-Lerma JG. Drug resistance emergence in macaques administered cabotegravir long-acting for pre-exposure prophylaxis during acute SHIV infection. Nat Commun 2019; 10:2005. [PMID: 31043606 PMCID: PMC6494879 DOI: 10.1038/s41467-019-10047-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/19/2019] [Indexed: 12/17/2022] Open
Abstract
A long-acting injectable formulation of the HIV integrase inhibitor cabotegravir (CAB-LA) is currently in clinical development for PrEP. Although the long plasma half-life of CAB-LA is an important attribute for PrEP, it also raises concerns about drug resistance emergence if someone becomes infected with HIV, or if PrEP is initiated during undiagnosed acute infection. Here we use a macaque model of SHIV infection to model risks of drug resistance to CAB-LA PrEP. Six macaques infected with SHIV received CAB-LA before seroconversion. We show integrase mutations G118R, E92G/Q, or G140R in plasma from 3/6 macaques as early as day 57, and identify G118R and E92Q in viruses from vaginal and rectal fluids. G118R and G140R confer > 800-fold resistance to CAB and cross-resistance to all licensed integrase inhibitors. Our results emphasize the need for appropriate HIV testing strategies before and possibly shortly after initiating CAB LA PrEP to exclude acute infection. Long-acting formulation of the integrase inhibitor cabotegravir (CAB LA) is in clinical development for HIV pre-exposure prophylaxis (PrEP). Here, using a SHIV macaque model, the authors show emergence of integrase mutations associated to CAB LA PrEP that confer pan-integrase inhibitor resistance.
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Affiliation(s)
- Jessica Radzio-Basu
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Olivia Council
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Mian-Er Cong
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Susan Ruone
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Alicia Newton
- Monogram Biosciences, 345 Oyster Point Blvd, San Francisco, CA, 94080, USA
| | - Xierong Wei
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - James Mitchell
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Shanon Ellis
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | | | - Wei Huang
- Monogram Biosciences, 345 Oyster Point Blvd, San Francisco, CA, 94080, USA
| | | | - Walid Heneine
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - J Gerardo García-Lerma
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA.
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49
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Mosquera S, Chen LH, Aegerter B, Miyao E, Salvucci A, Chang TC, Epstein L, Stergiopoulos I. Cloning of the Cytochrome b Gene From the Tomato Powdery Mildew Fungus Leveillula taurica Reveals High Levels of Allelic Variation and Heteroplasmy for the G143A Mutation. Front Microbiol 2019; 10:663. [PMID: 31024474 PMCID: PMC6467933 DOI: 10.3389/fmicb.2019.00663] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/18/2019] [Indexed: 11/13/2022] Open
Abstract
Leveillula taurica is a major pathogen of tomato and several other crops that can cause substantial yield losses in favorable conditions for the fungus. Quinone outside inhibitor fungicides (QoIs) are routinely used for the control of the pathogen in tomato fields across California, but their recurrent use could lead to the emergence of resistance against these compounds. Here, we partially cloned the cytochrome b gene from L. taurica (Lt cytb) and searched within populations of the fungus collected from tomato fields across California for mutations that confer resistance to QoIs. A total of 21 single nucleotide polymorphisms (SNPs) were identified within a 704 bp fragment of the Lt cytb gene analyzed, of which five were non-synonymous substitutions. Among the most frequent SNPs encountered within field populations of the pathogen was the G143A substitution that confers high levels of resistance against QoIs in several fungi. The other four amino acid substitutions were novel mutations, whose effect on QoI resistance is currently unknown. Sequencing of the Lt cytb gene from individual single-cell conidia of the fungus further revealed that most SNPs, including the one leading to the G143A substitution, were present in a heteroplasmic state, indicating the co-existence of multiple mitotypes in single cells. Analysis of the field samples showed that the G143A substitution is predominantly heteroplasmic also within field populations of L. taurica in California, suggesting that QoI resistance in this fungus is likely to be quantitative rather than qualitative.
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Affiliation(s)
- Sandra Mosquera
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Li-Hung Chen
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Brenna Aegerter
- University of California Cooperative Extension, Stockton, CA, United States
| | - Eugene Miyao
- University of California Cooperative Extension, Woodland, CA, United States
| | - Anthony Salvucci
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Ti-Cheng Chang
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Lynn Epstein
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Ioannis Stergiopoulos
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
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50
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Ibal JC, Pham HQ, Park CE, Shin JH. Information about variations in multiple copies of bacterial 16S rRNA genes may aid in species identification. PLoS One 2019; 14:e0212090. [PMID: 30768621 PMCID: PMC6377111 DOI: 10.1371/journal.pone.0212090] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 01/28/2019] [Indexed: 11/19/2022] Open
Abstract
Variable region analysis of 16S rRNA gene sequences is the most common tool in bacterial taxonomic studies. Although used for distinguishing bacterial species, its use remains limited due to the presence of variable copy numbers with sequence variation in the genomes. In this study, 16S rRNA gene sequences, obtained from completely assembled whole genome and Sanger electrophoresis sequencing of cloned PCR products from Serratia fonticola GS2, were compared. Sanger sequencing produced a combination of sequences from multiple copies of 16S rRNA genes. To determine whether the variant copies of 16S rRNA genes affected Sanger sequencing, two ratios (5:5 and 8:2) with different concentrations of cloned 16S rRNA genes were used; it was observed that the greater the number of copies with similar sequences the higher its chance of amplification. Effect of multiple copies for taxonomic classification of 16S rRNA gene sequences was investigated using the strain GS2 as a model. 16S rRNA copies with the maximum variation had 99.42% minimum pairwise similarity and this did not have an effect on species identification. Thus, PCR products from genomes containing variable 16S rRNA gene copies can provide sufficient information for species identification except from species which have high similarity of sequences in their 16S rRNA gene copies like the case of Bacillus thuringiensis and Bacillus cereus. In silico analysis of 1,616 bacterial genomes from long-read sequencing was also done. The average minimum pairwise similarity for each phylum was reported with their average genome size and average "unique copies" of 16S rRNA genes and we found that the phyla Proteobacteria and Firmicutes showed the highest amount of variation in their copies of their 16S rRNA genes. Overall, our results shed light on how the variations in the multiple copies of the 16S rRNA genes of bacteria can aid in appropriate species identification.
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Affiliation(s)
- Jerald Conrad Ibal
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Huy Quang Pham
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Chang Eon Park
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jae-Ho Shin
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
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