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Greveniotis V, Bouloumpasi E, Zotis S, Korkovelos A, Kantas D, Ipsilandis CG. Genotype-by-Environment Interaction Analysis for Quantity and Quality Traits in Faba Beans Using AMMI, GGE Models, and Stability Indices. Plants (Basel) 2023; 12:3769. [PMID: 37960125 PMCID: PMC10648669 DOI: 10.3390/plants12213769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/26/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023]
Abstract
Faba beans are considered one of the most important crops for animal feed. The genotype × environment interaction (GEI) has a considerable effect on faba bean seed production. The objectives of this study included assessing multiple locations and genotypes to understand how various ecosystems and faba bean genotypes relate to one another, and suggesting the ideal climatic conditions, crop management system, and genotypes so that they are carefully chosen for their stability. A 2-year experiment was conducted in order to define the stability across four environments based on stability indices for certain characteristics: moisture (%), ash content (%), crude protein content (%), crude fat (%), total starch (%), and crude fiber content (%). Statistically significant differences indicated that GEIs were present. The heritability was generally high for qualitative traits in comparison with quantitative traits. The crude protein content, plant height, and thousand-seed weight were all positively correlated with the seed yield; however, the other qualitative variables were adversely correlated. The crude protein content of the cultivar Tanagra displayed a high stability index, followed by Ste1. Under conventional management, Tanagra demonstrated high values for the seed yield in Giannitsa and Florina. Ste1 and Ste2 are particularly promising genetic materials that showed high values under low-input conditions. The best genotypes to use and the most favorable environments/types of cultivation were the Tanagra cultivar, followed by the Ste2 genotype, according to the additive main effects and multiplicative interaction (AMMI) and genotype plus genotype-by-environment (GGE) biplot models. Earliness showed significant heritability values and very high stability indices, again indicating qualitative behavior according to genetic parameters. With the exception of the number of pods per plant, which demonstrated low heritability while having excellent index values, traits like seed yield showed relatively low-stability-based heritability values. Global efforts aimed at improving the genetics of faba beans might benefit from genotypes that exhibit consistent yields in various conditions.
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Affiliation(s)
- Vasileios Greveniotis
- Hellenic Agricultural Organization Demeter, Institute of Industrial and Forage Crops, GR-41335 Larissa, Greece
- Department of Agricultural Technology, Technological Educational Institute of Western Macedonia, GR-53100 Florina, Greece
| | - Elisavet Bouloumpasi
- Department of Agricultural Biotechnology and Oenology, International Hellenic University, GR-66100 Drama, Greece;
| | - Stylianos Zotis
- Department of Agricultural Technology, Technological Educational Institute of Western Macedonia, GR-53100 Florina, Greece
| | - Athanasios Korkovelos
- Directorate of Water Management of Thessaly, Decentralized Administration of Thessaly—Central Greece, GR-41335 Larissa, Greece;
| | - Dimitrios Kantas
- Department of Animal Science, University of Thessaly, Campus Gaiopolis, GR-41500 Larissa, Greece;
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152
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Bannasch DL, Oertle DT, Vo J, Batcher KL, Stern JA, Kaplan JL, Li RHL, Madden IE, Christen M, Leeb T, Joshi N. Naturally occurring canine laminopathy leading to a dilated and fibrosing cardiomyopathy in the Nova Scotia Duck Tolling Retriever. Sci Rep 2023; 13:19077. [PMID: 37925523 PMCID: PMC10625583 DOI: 10.1038/s41598-023-46601-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 11/02/2023] [Indexed: 11/06/2023] Open
Abstract
Dilated cardiomyopathy (DCM) is characterized by decreased systolic function and dilation of one or both ventricles, often leading to heart failure or sudden death. Two 10-month-old sibling Nova Scotia Duck Tolling Retrievers (NSDTR) died acutely with evidence of dilated cardiomyopathy with myocardial fibrosis. Association analysis using two cases and 35 controls identified three candidate regions homozygous in the two cases. Whole genome sequencing identified a frameshift deletion in the LMNA gene (NC_049228.1:g.41688530del, NP_001274080:p.(Asp576ThrfsTer124)). Three retrospectively identified NSDTRs with sudden death before 2 years of age and severe myocardial fibrosis were also homozygous for the deletion. One 5 year old with sudden death and myocardial fibrosis was heterozygous for the deletion. This variant was not identified in 722 dogs of other breeds, nor was it identified to be homozygous in 784 NSDTR. LMNA codes for lamin A/C proteins, which are type V intermediate filaments that provide structural support to the nuclear membrane. In humans, LMNA variants can cause DCM with sudden death as well as diseases of striated muscles, lipodystrophy, neuropathies, and accelerated aging disorders. This frameshift deletion is predicted to affect processing of prelamin A into lamin A. Pedigree analysis in the NSDTR and functional evaluation of heterozygotes is consistent with a predominantly recessive mode of inheritance and possibly low penetrance in heterozygotes in contrast to people, where most pathogenic LMNA variants are dominantly inherited.
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Affiliation(s)
- Danika L Bannasch
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, USA.
| | - Danielle T Oertle
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Julia Vo
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Kevin L Batcher
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Joshua A Stern
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Joanna L Kaplan
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Ronald H L Li
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Indiana E Madden
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Matthias Christen
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Nikhil Joshi
- Bioinformatics Core, UC Davis Genome Center, University of California, Davis, CA, USA
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153
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Odegard EA, Meeds HL, Kleiboeker SB, Ziady A, Sabulski A, Jodele S, Seif AE, Davies SM, Laskin BL, Blackard JT. BK Polyomavirus Diversity After Hematopoietic Stem Cell Transplantation. J Infect Dis 2023; 228:1208-1218. [PMID: 37165301 PMCID: PMC10629712 DOI: 10.1093/infdis/jiad117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/21/2023] [Indexed: 05/12/2023] Open
Abstract
BK polyomavirus (BKPyV) infection is common after hematopoietic stem cell transplantation (HSCT) and is associated with the development of hemorrhagic cystitis (HC). The role that BKPyV plays in the pathogenesis of HC is not well characterized. We investigated the impact of BKPyV diversity on the development of HC using a previously established cohort of pediatric HSCT patients. There were 147 urine samples with quantifiable BKPyV at month 1 after HSCT; 137 (93.2%) were amplified using our in-house polymerase chain reaction approach and sent for next-generation sequencing. Subtype Ia was most frequent (61.3%), followed by subtype Ib1 (31.4%). The median viral load of subtype Ia samples was higher than for subtype Ib1 at month 1. Across the protein coding regions, APOBEC-induced mutations and signature patterns associated with HC were identified. This is the largest sequencing study of a single cohort of HSCT patients, providing a vast resource of sequence data for future analyses.
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Affiliation(s)
- Elizabeth A Odegard
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Ohio
| | - Heidi L Meeds
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Ohio
| | | | - Assem Ziady
- Department of Pediatrics, University of Cincinnati College of Medicine, Ohio
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Ohio
| | - Anthony Sabulski
- Department of Pediatrics, University of Cincinnati College of Medicine, Ohio
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Ohio
| | - Sonata Jodele
- Department of Pediatrics, University of Cincinnati College of Medicine, Ohio
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Ohio
| | - Alix E Seif
- Perelman School of Medicine, University of Pennsylvania, Pennsylvania
- Division of Oncology, The Children's Hospital of Philadelphia, Pennsylvania
| | - Stella M Davies
- Department of Pediatrics, University of Cincinnati College of Medicine, Ohio
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Ohio
| | - Benjamin L Laskin
- Perelman School of Medicine, University of Pennsylvania, Pennsylvania
- Division of Nephrology, The Children's Hospital of Philadelphia, Pennsylvania
| | - Jason T Blackard
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Ohio
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154
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Li Z, Cheng W, Zi F, Wang J, Huang X, Sheng X, Rong W. Four different gene-related cone-rod dystrophy: clinical and genetic findings in six Chinese families with diverse modes of inheritance. Front Genet 2023; 14:1157156. [PMID: 38028590 PMCID: PMC10652761 DOI: 10.3389/fgene.2023.1157156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Purpose: To investigate pathogenic variants in six families with cone-rod dystrophy (CORD) presenting various inheritance patterns by using whole-exome sequencing (WES) and analyzing phenotypic features. Methods: A total of six families with CORD were enrolled in Ningxia Eye Hospital for this study. The probands and their family members received comprehensive ophthalmic examinations, and DNA was abstracted from patients and family members. Whole-exome sequencing was performed on probands to screen the causative variants, and all suspected pathogenic variants were determined via Sanger sequencing. Furthermore, co-segregation analysis was performed on available family members. The pathogenicity of novel variants was predicted using in silico analysis and evaluated according to the American College of Medical Genetics and Genomics (ACMG) guidelines. Results: Of the six families, two families were assigned as X-linked recessive (XL), two families were assigned as autosomal recessive (AR), and two families were assigned as autosomal dominant (AD). Pathogenic variants were detected in CACNA1F in two X-linked recessive probands, among which family 1 had a hemizygous frameshift variant c.2201del (p.Val734Glyfs*17) and family 2 had a hemizygous missense variant c.245G>A (p.Arg82Gln). Both probands had high myopia, with fundus tessellation accompanied by abnormalities in the outer structure of the macular area. The homozygous splice variant c.2373 + 5G>T in PROM1 and the homozygous nonsense variant c.604C>T (p.Arg202Ter) in ADAM9 were detected in two autosomal recessive families of the probands. Both probands showed different degrees of atrophy in the macular area, and the lesions showed hypofluorescence changes in autofluorescence. The heterozygous variation in CRX c.682C>T (p.Gln228Ter) was detected in two autosomal dominant families. The onset age of the two probands was late, with better vision and severe macular atrophy. According to ACMG guidelines and the analysis of online in silico tools, all variations were labeled as potentially harmful or pathogenic. Conclusion: Pathogenic variants in CACNA1F, PROM1, ADAM9, and CRX genes were identified in six families affected by the diverse inheritance patterns of CORD. Furthermore, the potential impact of the nonsense-mediated decay (NMD) mechanism on the manifestation of CORD phenotypes was examined and addressed. Simultaneously, the spectrum of pathogenic variants and clinical phenotypes associated with the CORD gene was extended.
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Affiliation(s)
- Zhen Li
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Wanyu Cheng
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Feiyin Zi
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Juan Wang
- Department of Ophthalmology, Qingdao West Coast New District Central Hospital, Qingdao, China
| | - Xiaoyu Huang
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | | | - Weining Rong
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
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155
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Ressler AK, Snellings DA, Girard R, Gallione CJ, Lightle R, Allen AS, Awad IA, Marchuk DA. Single-nucleus DNA sequencing reveals hidden somatic loss-of-heterozygosity in Cerebral Cavernous Malformations. Nat Commun 2023; 14:7009. [PMID: 37919320 PMCID: PMC10622526 DOI: 10.1038/s41467-023-42908-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/24/2023] [Indexed: 11/04/2023] Open
Abstract
Cerebral Cavernous Malformations (CCMs) are vascular malformations of the central nervous system which can lead to moderate to severe neurological phenotypes in patients. A majority of CCM lesions are driven by a cancer-like three-hit mutational mechanism, including a somatic, activating mutation in the oncogene PIK3CA, as well as biallelic loss-of-function mutations in a CCM gene. However, standard sequencing approaches often fail to yield a full complement of pathogenic mutations in many CCMs. We suggest this reality reflects the limited sensitivity to identify low-frequency variants and the presence of mutations undetectable with bulk short-read sequencing. Here we report a single-nucleus DNA-sequencing approach that leverages the underlying biology of CCMs to identify lesions with somatic loss-of-heterozygosity, a class of such hidden mutations. We identify an alternative genetic mechanism for CCM pathogenesis and establish a method that can be repurposed to investigate the genetic underpinning of other disorders with multiple somatic mutations.
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Affiliation(s)
- Andrew K Ressler
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA.
| | - Daniel A Snellings
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Romuald Girard
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago Medicine and Biological Sciences, Chicago, IL, USA
| | - Carol J Gallione
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Rhonda Lightle
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago Medicine and Biological Sciences, Chicago, IL, USA
| | - Andrew S Allen
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, 27710, USA
| | - Issam A Awad
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago Medicine and Biological Sciences, Chicago, IL, USA
| | - Douglas A Marchuk
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA.
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156
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Mier-Mota J, Ponce-González JG, Perez-Bey A, Cabanas-Sánchez V, Veiga-Núñez O, Santiago-Dorrego C, Gómez-Gallego F, Castro-Piñero J. Longitudinal effects of FTO gene polymorphism on body composition, cardiorespiratory fitness, physical activity, inflammatory markers, and cardiovascular risk in children and adolescents. "The UP & DOWN study". Scand J Med Sci Sports 2023; 33:2261-2272. [PMID: 37647022 DOI: 10.1111/sms.14469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 07/13/2023] [Accepted: 08/03/2023] [Indexed: 09/01/2023]
Abstract
The role of polymorphism rs9939609 of the FTO gene has been related with fat mass and cardiovascular risk in adults, but it remains unclear in children and adolescents. Hence, the main aim of this study was to determine the FTO polymorphism effects on body composition, cardiorespiratory fitness (CRF), physical activity (PA), inflammatory markers, and cardiovascular risk both in cross-sectional analysis and after two-years of follow-up in children and adolescents. A total of 2129 participants were included in this study. The rs9939609 polymorphism was genotyped. Body composition measurements, CRF, and moderate-to-vigorous PA (MVPA) were determined at baseline and after two-year of follow-up. Moreover, plasma leptin and adiponectin were also determined as inflammatory markers. Furthermore, an index of cardiovascular disease risk factors (CVDRF-I) was calculated. Codominant (TT vs. TA vs. AA) and dominant (AA+AT vs. TT) models were applied for statistical analysis. The results showed a main effect of the FTO genotype on body composition measures in both first and third year (p < 0.05), with lower adiposity in TT compared with AA or AA+AT group. These differences were maintained after accounting for pubertal maturity, sex, age, VO2 max, and MVPA. Moreover, lower leptin level was observed in TT compared to AA+AT group in the third year. An interaction in Gene*Time*Sex was found in height and neck circumference in dominant model (p = 0.047; p = 0.020, respectively). No differences were found in CRF, MVPA nor CVDRF-I between groups. Hence, homozygous TT allele could be a protective factor against weight gain from early childhood.
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Affiliation(s)
| | - Jesús G Ponce-González
- ExPhy Research Group, Department of Physical Education, Faculty of Education Sciences, University of Cadiz, Cádiz, Spain
- Research Unit, Biomedical Research and Innovation Institute of Cadiz (INiBICA), Puerta Del Mar University Hospital, University of Cadiz, Cádiz, Spain
| | - Alejandro Perez-Bey
- Research Unit, Biomedical Research and Innovation Institute of Cadiz (INiBICA), Puerta Del Mar University Hospital, University of Cadiz, Cádiz, Spain
- GALENO Research Group, Department of Physical Education, School of Education, University of Cádiz, Puerto Real, Spain
| | - Verónica Cabanas-Sánchez
- Department of Preventive Medicine and Public Health. School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
- CIBERESP (CIBER of Epidemiology and Public Health), Madrid, Spain
- IMDEA-Food Institute. CEI UAM+CSIC, Madrid, Spain
| | - Oscar Veiga-Núñez
- Department of Preventive Medicine and Public Health. School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
| | - Catalina Santiago-Dorrego
- Faculty of Physical Activity, Sport Sciences and Physiotherapy, Universidad Europea de Madrid, Madrid, Spain
| | - Félix Gómez-Gallego
- Department of Basic Health Sciences, Universidad Rey Juan Carlos, Madrid, Spain
| | - José Castro-Piñero
- Research Unit, Biomedical Research and Innovation Institute of Cadiz (INiBICA), Puerta Del Mar University Hospital, University of Cadiz, Cádiz, Spain
- GALENO Research Group, Department of Physical Education, School of Education, University of Cádiz, Puerto Real, Spain
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157
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Arline Diana I, Tan EC, Gondokaryono SP, Koh MJA, Dwiyana RF, Rahardja JI, Yogya Y, Rafi'ee K, Suwarsa O. Phenotype and genotype correlation of inherited epidermolysis bullosa in Indonesia. Australas J Dermatol 2023; 64:e327-e332. [PMID: 37452458 DOI: 10.1111/ajd.14121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/20/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Inherited epidermolysis bullosa (EB) is a group of genodermatoses with considerable clinical and genetic heterogeneity. Clinical diagnosis of the EB subtypes is frequently imprecise and requires confirmation with genetic testing. There is still limited study using genetic testing to identify EB subtypes in Indonesia. This study aims to identify the pathogenic variants of inherited EB patients at the Department of Dermatology and Venereology, Universitas Padjadjaran-Dr Hasan Sadikin General Hospital in Bandung, West Java, Indonesia and to describe the correlation between the phenotype and genotype of our patients. METHODS Twelve patients clinically diagnosed with EB were included in this study. Genetic testing was performed in collaboration with KK Women's and Children's Hospital, Singapore. RESULTS Pathogenic variants were identified in the COL7A1 gene in seven patients, namely Dominant Dystrophic EB (DDEB) with mutation types c.5945G>T, c.6218G>A, Recessive Dystrophic EB (RDEB) c.2005C>T, c.6081dup, c.1268C>T, c.1784C>T which are all known mutations. Novel mutations were found in the COL7A1 gene in two patients namely DDEB c.6253G>T and RDEB c.6740C>T. Two EB Simplex (EBS) patients showed mutation KRT14 gene as c.356T>C, c.373C>T which are known mutation. In addition, a novel mutation in LAMA3 gene c.2649del was found in one Junctional EB (JEB) patient. CONCLUSION The molecular diagnoses of 12 Indonesian EB patients were identified, of which three were novel pathogenic variants. Concordance between the initial clinical diagnosis and genetic testing was only 33%. This demonstrated the importance of early genetic testing for accurate diagnosis, prognostication, management and genetic counselling.
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Affiliation(s)
- Inne Arline Diana
- Department of Dermatology and Venereology, Faculty of Medicine, Universitas Padjadjaran-Dr. Hasan Sadikin General Hospital, Bandung, Indonesia
| | - Ene-Choo Tan
- Research Laboratory, KK Women's & Children Hospital, Singapore, Singapore
| | - Srie Prihianti Gondokaryono
- Department of Dermatology and Venereology, Faculty of Medicine, Universitas Padjadjaran-Dr. Hasan Sadikin General Hospital, Bandung, Indonesia
| | - Mark Jean-Aan Koh
- Department of Dermatology, KK Women's & Children's Hospital, Singapore, Singapore
| | - Reiva Farah Dwiyana
- Department of Dermatology and Venereology, Faculty of Medicine, Universitas Padjadjaran-Dr. Hasan Sadikin General Hospital, Bandung, Indonesia
| | - July Iriani Rahardja
- Department of Dermatology and Venereology, Faculty of Medicine, Universitas Padjadjaran-Dr. Hasan Sadikin General Hospital, Bandung, Indonesia
| | - Yuri Yogya
- Department of Dermatology and Venereology, Faculty of Medicine, Universitas Padjadjaran-Dr. Hasan Sadikin General Hospital, Bandung, Indonesia
| | - Khadijah Rafi'ee
- Research Laboratory, KK Women's & Children Hospital, Singapore, Singapore
| | - Oki Suwarsa
- Department of Dermatology and Venereology, Faculty of Medicine, Universitas Padjadjaran-Dr. Hasan Sadikin General Hospital, Bandung, Indonesia
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158
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Crincoli E, Leoni C, Viscogliosi G, Onesimo R, Mattei R, Tartaglia M, Catania F, Rizzo S, Zampino G, Salerni A. Systematic ophthalmologic evaluation in cardio-facio-cutaneous syndrome: A genotype-endophenotype correlation. Am J Med Genet A 2023; 191:2783-2792. [PMID: 37697822 DOI: 10.1002/ajmg.a.63395] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 07/18/2023] [Accepted: 08/23/2023] [Indexed: 09/13/2023]
Abstract
Cardio-facio-cutaneous syndrome (CFCS) is a rare genetic disorder belonging to the RASopathies, a group of developmental syndromes caused by upregulated RAS/MAPK signaling. Pathogenic variants affecting four genes, KRAS, BRAF, MAP2K1 and MAP2K2, encoding core signal transducers of the pathway, underlie the condition. Major clinical features include a distinctive facies, ectodermal and cardiac anomalies, reduced postnatal growth, intellectual disability, and musculoskeletal abnormalities. Similar to other RASopathies, reports of visual impairment, high refractive error, optic nerve pallor, and other ocular abnormalities have been anecdotally reported in the literature. The aim of our study is to report the prevalence of ophthalmologic abnormalities in a large monocentric cohort of individuals affected by CFCS and explore the occurrence of genotype-endophenotype correlations in this series of patients. We observed that BRAF mutations are associated to a higher prevalence of anisometropia >3D (11.8% vs. 0%) and high astigmatism (29.4% vs. 0%; both p < 0.001) while patients with mutations in other genes had a significantly higher prevalence of myopia >6 D (60% vs. 5.9%; p = 0.012). Pale optic disc was associated with higher prevalence of inferior oblique muscle (IO) overaction (33.3% vs. 0%) and lower prevalence of ptosis (0% vs. 11.8%; both p < 0.001). Combined exotropia, IO overaction and nystagmus were frequent in patients with pale optic nerve. Our findings might suggest the need for earlier ophthalmologic referral for CFCS patients due to high risk of amblyopia, especially those expressing BRAF mutations.
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Affiliation(s)
- Emanuele Crincoli
- Ophthalmology Unit, "Fondazione Policlinico Universitario A. Gemelli IRCCS", Rome, Italy
| | - Chiara Leoni
- Center for Rare Diseases and Birth Defect, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Germana Viscogliosi
- Center for Rare Diseases and Birth Defect, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Roberta Onesimo
- Center for Rare Diseases and Birth Defect, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Roberta Mattei
- Ophthalmology Unit, "Fondazione Policlinico Universitario A. Gemelli IRCCS", Rome, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Fiammetta Catania
- Department of Ophthalmology, Hopital Fondation Adolphe De Rothschild, Paris, France
| | - Stanislao Rizzo
- Ophthalmology Unit, "Fondazione Policlinico Universitario A. Gemelli IRCCS", Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
- "Consiglio Nazionale delle Ricerche, Istituto di Neuroscienze", Pisa, Italy
| | - Giuseppe Zampino
- Center for Rare Diseases and Birth Defect, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Annabella Salerni
- Ophthalmology Unit, "Fondazione Policlinico Universitario A. Gemelli IRCCS", Rome, Italy
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159
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Lera-Ramírez M, Bähler J, Mata J, Rutherford K, Hoffman CS, Lambert S, Oliferenko S, Martin SG, Gould KL, Du LL, Sabatinos SA, Forsburg SL, Nielsen O, Nurse P, Wood V. Revised fission yeast gene and allele nomenclature guidelines for machine readability. Genetics 2023; 225:iyad143. [PMID: 37758508 PMCID: PMC10627252 DOI: 10.1093/genetics/iyad143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/24/2023] [Indexed: 09/30/2023] Open
Abstract
Standardized nomenclature for genes, gene products, and isoforms is crucial to prevent ambiguity and enable clear communication of scientific data, facilitating efficient biocuration and data sharing. Standardized genotype nomenclature, which describes alleles present in a specific strain that differ from those in the wild-type reference strain, is equally essential to maximize research impact and ensure that results linking genotypes to phenotypes are Findable, Accessible, Interoperable, and Reusable (FAIR). In this publication, we extend the fission yeast clade gene nomenclature guidelines to support the curation efforts at PomBase (www.pombase.org), the Schizosaccharomyces pombe Model Organism Database. This update introduces nomenclature guidelines for noncoding RNA genes, following those set forth by the Human Genome Organisation Gene Nomenclature Committee. Additionally, we provide a significant update to the allele and genotype nomenclature guidelines originally published in 1987, to standardize the diverse range of genetic modifications enabled by the fission yeast genetic toolbox. These updated guidelines reflect a community consensus between numerous fission yeast researchers. Adoption of these rules will improve consistency in gene and genotype nomenclature, and facilitate machine-readability and automated entity recognition of fission yeast genes and alleles in publications or datasets. In conclusion, our updated guidelines provide a valuable resource for the fission yeast research community, promoting consistency, clarity, and FAIRness in genetic data sharing and interpretation.
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Affiliation(s)
- Manuel Lera-Ramírez
- University College London, Department of Genetics Evolution and Environment, Darwin Building, 99-105 Gower Street, London WC1E 6BT, UK
| | - Jürg Bähler
- University College London, Department of Genetics Evolution and Environment, Darwin Building, 99-105 Gower Street, London WC1E 6BT, UK
| | - Juan Mata
- University of Cambridge, Department of Biochemistry, Cambridge CB2 1GA, UK
| | - Kim Rutherford
- University of Cambridge, Department of Biochemistry, Cambridge CB2 1GA, UK
| | | | - Sarah Lambert
- Institut Curie, Université Paris-Saclay, CNRS UMR3348, Orsay 91400, France
| | - Snezhana Oliferenko
- The Francis Crick Institute, London NW1 1AT, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London SE1 1UL, UK
| | - Sophie G Martin
- University of Geneva, Department of Molecular and Cellular Biology, Geneva 1211, Switzerland
| | - Kathleen L Gould
- Vanderbilt University School of Medicine, Department of Cell and Developmental Biology, Nashville, TN 37232, USA
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing 102206, China
| | - Sarah A Sabatinos
- Toronto Metropolitan University, Department of Chemistry & Biology, Toronto M5B 2K3, Canada
| | - Susan L Forsburg
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
| | - Olaf Nielsen
- Department of Biology, Cell cycle and genome stability Group, University of Copenhagen, Copenhagen N DK2100, Denmark
| | - Paul Nurse
- The Francis Crick Institute, London NW1 1AT, UK
| | - Valerie Wood
- University of Cambridge, Department of Biochemistry, Cambridge CB2 1GA, UK
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Duan H, Li J, Jiang Z, Shi X, Hu Y. Noninvasive screening of fetal RHD genotype in Chinese pregnant women with serologic RhD-negative phenotype. Transfusion 2023; 63:2152-2158. [PMID: 37698267 DOI: 10.1111/trf.17545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 09/13/2023]
Abstract
BACKGROUND Noninvasive fetal RHD genotyping has been provided to nonimmunized RhD-negative pregnant women to guide anti-D prophylaxis. Among the Chinese, more than 30% of the RhD-negative phenotype is associated with variant RHD alleles, which would limit the accuracy of fetal RHD status prediction; thus, more targeting and proper programs need to be developed. STUDY DESIGN AND METHODS Fluorescence quantitative polymerase chain reaction PCR (qPCR) or Sanger sequencing on all RHD exons was used to detect maternal RHD genotypes. For pregnant women with RHD*01N.01 or RHD*01N.03 alleles, the presence of RHD exons 5 and 10 in cell-free DNA was determined by qPCR. For pregnant women with the RHD(1227G>A) allele, high-throughput sequencing on exon 9 of the RHD gene and RHCE gene was used to predict fetal RhD phenotype. RESULTS Among 65 cases of Chinese pregnant women with the serologic RhD-negative phenotype, three major genotypes were identified: RHD*01N.01/RHD*01N.01 (61.5%), RHD*01N.01/RHD(1227G>A) or RHD*01N.03/RHD(1227G>A) (20%), and RHD*01N.01/RHD*01N.03 (13.8%), along with three cases of minor genotypes (4.6%). For 43 pregnant women with the RHD*01N.01 or RHD*01N.03 alleles, qPCR on maternal cell-free DNA yielded a 98.5% (42/43) accuracy rate and 100% successful prediction rate. High-throughput sequencing was successfully used to predict fetal RhD phenotypes for 13 pregnant women with RHD(1227G>A). CONCLUSION On the basis of maternal RHD genotyping, fetal genotyping through qPCR or high-throughput sequencing can improve the accuracy and success rate of prenatal fetal RhD phenotype prediction among Chinese pregnant women. It plays a potential role in guiding anti-D prophylaxis and pregnancy management in Chinese pregnant women.
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Affiliation(s)
- Honglei Duan
- Center for Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Jie Li
- Center for Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Zihan Jiang
- Center for Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Xiaohong Shi
- Center for Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Yali Hu
- Center for Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
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Zhang T, Xu Y. Update on Surgical Management of FAP. Clin Colon Rectal Surg 2023; 36:385-390. [PMID: 37795461 PMCID: PMC10547540 DOI: 10.1055/s-0043-1767707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
Familial adenomatous polyposis (FAP) is an autosomal dominant disease caused by pathogenic germline adenomatous polyposis coli mutation, and characterized with multiple adenomas in the colon and the rectum. Various genetic variants have been confirmed to be associated with corresponding FAP phenotypes, which play important roles in the diagnosis and surgical treatment of FAP. Generally, proctocolectomy is recommended for FAP patients at the age of 20s. Exceptionally, for patients with attenuated FAP, high-risk of desmoid, chemoprevention therapy, or other circumstances, surgery can be postponed. With the wide application of minimal invasive surgery in colorectal cancer, laparoscopic, robotic surgery, and natural orifice specimen extraction are proved to be feasible for FAP patients, but high-level evidences are needed to confirm their safety and advantages. In the times of precise medicine, the surgical management of FAP should vary with individuals based on genotype, phenotype, and clinical practice. Therefore, in addition to innovation in surgical procedures, investigation in links between genetic features and phenotypes will be helpful to optimize the surgical management of FAP in the future.
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Affiliation(s)
- Tianqi Zhang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China
| | - Ye Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China
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Liñán-Barroso JM, Mantrana-Bermejo ME, Durán-Romero AJ, Ortiz-Álvarez J, Monserrat-García MT, Jiménez-Thomas GJ, Conejo-Mir Sánchez J, Bernabéu-Wittel J. Genetic and dermoscopic findings in a case series of children with oculocutaneous albinism. Pediatr Dermatol 2023; 40:1081-1085. [PMID: 37872643 DOI: 10.1111/pde.15463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 10/05/2023] [Indexed: 10/25/2023]
Abstract
Oculocutaneous albinism (OCA) is a genetic disease caused by disorders in melanin synthesis or distribution. In this descriptive study conducted in a tertiary care pediatric hospital, patients with a clinical diagnosis of OCA and genetic study were retrospectively recruited and underwent dermatological and ophthalmological exam, including optical coherence tomography (OCT) and digital dermoscopy. Our findings revealed milder OCA phenotypic expression in individuals harboring single pathogenic mutations in conjunction with polymorphisms, as well as in those with mutations of uncertain significance. Regardless OCA subgroup, severe phenotypes of OCA were associated with a higher number of mutations/polymorphisms in melanin biosynthesis genes and paler dermoscopic patterns, such as vascular pattern, which was the most common pattern in our series.
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Affiliation(s)
| | | | | | - Juan Ortiz-Álvarez
- Dermatology Department, Virgen del Rocío University Hospital, Seville, Spain
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Esa E, Mohamad AS, Hamzah R, Hamid FSA, Aziz NA, Sevaratnam V, Sathar J, Chen G, Yasin NM. Clinical and haematological characteristics of 38 individuals with Hb G-Makassar in Malaysia. EJHaem 2023; 4:940-948. [PMID: 38024609 PMCID: PMC10660101 DOI: 10.1002/jha2.750] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/02/2023] [Accepted: 06/20/2023] [Indexed: 12/01/2023]
Abstract
Haemoglobin (Hb) G-Makassar is a rare Hb variant. It presents a diagnostic challenge as it imitates sickle Hb (Hb S) in standard electrophoresis and high-performance liquid chromatography assays requiring DNA analysis to confirm diagnosis. Both have point mutations in codon 6, exon 1 in the β-globin (HBB) gene with different pathogenicities. This study describes the clinical phenotype, haematology and genotype of Hb G-Makassar. Clinical and laboratory data of 38 cases of Hb G-Makassar over 8 years were analysed. Hb G-Makassar was confirmed by a direct sequencing of HBB gene and co-inheritance of α-thalassaemia determined through multiplex gap-PCR and multiplex Amplification Refractory Mutation System polymerase chain reaction. All cases were Malays, predominantly from Terengganu (n = 20, 52.6%). There were 14 (36.8%) males and 24 (63.2%) females with median age of 25 years. Majority (n = 33, 86.8%) had features of thalassaemia trait with mean ± SD for Hb, mean cell volume (MCV) and mean cell haemoglobin (MCH) as 13.21 g/dL ± 1.69, 73.06 ± 4.48 fL and 24.71 ± 1.82 pg, respectively. None had evidence of haemolysis or thromboembolic complications. Six genotypes were identified; ßG-Makassar/ß,αα/αα (n = 19, 50.0%), ßG-Makassar/ßE,αα/αα (n = 4, 10.5%), ßG-Makassar/ßNewYork,αα/αα (n = 1, 2.6%), ßG-Makassar/ß,αα/-α (n = 11, 28.9%), ßG-Makassar/ß,αα/αAdanaα (n = 2, 5.3%) and ßG-Makassar/ß,αα/-SEA (n = 1, 2.6%). The ßG-Makassar/ß,αα/αα showed that features of thalassaemia trait with mean ± SD for Hb, MCV and MCH were 13.74 g/dL ± 2.40, 76.18 ± 6.02 fL and 25.79 ± 2.41 pg, respectively. This is the largest study reporting a significant number of Hb G-Makassar in Malaysia. Although the mutation is similar to Hb S, the phenotype is benign.
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Affiliation(s)
- Ezalia Esa
- Institute for Medical ResearchSetia AlamSelangorMalaysia
| | - Ahmad Sabry Mohamad
- Medical EngineeringUniversiti Kuala Lumpur British Malaysian InstituteGombakSelangorMalaysia
| | | | | | | | | | - Jameela Sathar
- Hematology DepartmentAmpang HospitalAmpangSelangorMalaysia
| | - Guo Chen
- Beam Therapeutics Inc.CambridgeMassachusettsUSA
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Kim M, Lee MH, Hong SJ, Yu J, Cho J, Suh DI, Kim HY, Kim HY, Jung S, Lee E, Lee S, Jeong K, Shim JY, Kim JH, Chung HL, Jang YY, Kwon JW, Seo JH, Kim JH, Ahn JY, Song KB, Song KS, Kim SY, Kim SY, Kil HR, Chung EH. Clinical Manifestations and Genotype of Primary Ciliary Dyskinesia Diagnosed in Korea: Multicenter Study. Allergy Asthma Immunol Res 2023; 15:757-766. [PMID: 37957793 PMCID: PMC10643857 DOI: 10.4168/aair.2023.15.6.757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 05/10/2023] [Accepted: 06/13/2023] [Indexed: 11/15/2023]
Abstract
PURPOSE Primary ciliary dyskinesia (PCD) is a genetically heterogeneous disorder that leads to secondary ciliary dysfunction. PCD is a rare disease, and data on it are limited in Korea. This study systematically evaluated the clinical symptoms, diagnostic characteristics, and treatment modalities of pediatric PCD in Korea. METHODS This Korean nationwide, multicenter study, conducted between January 2000 and August 2022, reviewed the medical records of pediatric patients diagnosed with PCD. Prospective studies have been added to determine whether additional genetic testing is warranted in some patients. RESULTS Overall, 41 patients were diagnosed with PCD in 15 medical institutions. The mean age at diagnosis was 11.8 ± 5.4 years (range: 0.5 months-18.9 years). Most patients (40/41) were born full term, 15 (36.6%) had neonatal respiratory symptoms, and 12 (29.3%) had a history of admission to the neonatal intensive care unit. The most common complaint (58.5%) was chronic nasal symptoms. Thirty-three patients were diagnosed with transmission electron microscopy (TEM) and 12 patients by genetic studies. TEM mostly identified outer dynein arm defects (alone or combined with inner dynein arm defects, n = 17). The genes with the highest mutation rates were DNAH5 (3 cases) and DNAAF1 (3 cases). Rare genotypes (RPGR, HYDIN, NME5) were found as well. Chest computed tomography revealed bronchiectasis in 33 out of 41 patients. Among them, 15 patients had a PrImary CiliAry DyskinesiA Rule score of over 5 points. CONCLUSIONS To our knowledge, this is the first multicenter study to report the clinical characteristics, diagnostic methods, and genotypes of PCD in Korea. These results can be used as basic data for further PCD research.
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Affiliation(s)
- Minji Kim
- Department of Pediatrics, Chungnam National University Sejong Hospital, Chungnam National University School of Medicine, Sejong, Korea
| | - Mi-Hee Lee
- Department of Pediatrics, Incheon Medical Center, Incheon, Korea
| | - Soo-Jong Hong
- Department of Pediatrics, Asan Medical Center, University of Ulsan, College of Medicine, Seoul, Korea
| | - Jinho Yu
- Department of Pediatrics, Asan Medical Center, University of Ulsan, College of Medicine, Seoul, Korea
| | - Joongbum Cho
- Department of Pediatrics, Department of Critical Care Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Dong In Suh
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
| | - Hyung Young Kim
- Department of Pediatrics, Dongnam Institute of Radiology and Medical Sciences, Busan, Korea
| | - Hye-Young Kim
- Integrated & Respite Care Center for Children, Seoul National University Hospital, Seoul, Korea
| | - Sungsu Jung
- Department of Pediatrics, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, College of Medicine, Pusan National University, Yangsan, Korea
| | - Eun Lee
- Department of Pediatrics, Chonnam National University Hospital, Chonnam National University Medical School, Gwangju, Korea
| | - Sooyoung Lee
- Department of Pediatrics, Ajou University School of Medicine, Suwon, Korea
| | - Kyunguk Jeong
- Department of Pediatrics, Ajou University School of Medicine, Suwon, Korea
| | - Jung Yeon Shim
- Department of Pediatrics, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jeong Hee Kim
- Department of Pediatrics, College of Medicine, Inha University, Incheon, Korea
| | - Hai Lee Chung
- Department of Pediatrics, Daegu Catholic University Medical Center, Daegu, Korea
| | - Yoon Young Jang
- Department of Pediatrics, Daegu Catholic University Medical Center, Daegu, Korea
| | - Ji-Won Kwon
- Department of Pediatrics, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Ju-Hee Seo
- Department of Pediatrics, Dankook University Medical School, Cheonan, Korea
| | - Ju Hee Kim
- Department of Pediatrics, Kyung Hee University Medical Center, Seoul, Korea
| | - Ji Young Ahn
- Department of Pediatrics, Yeungnam University College of Medicine, Daegu, Korea
| | - Kun-Baek Song
- Department of Pediatrics, Soonchunhyang University Cheonan Hospital, Cheonan, Korea
| | - Kyu-Sang Song
- Department of Pathology, Chungnam National University School of Medicine, Daejeon, Korea
| | - So Yeon Kim
- Department of Laboratory Medicine, National Medical Center, Seoul, Korea
| | - Seon Young Kim
- Department of Laboratory Medicine, Chungnam National University School of Medicine, Daejeon, Korea.
| | - Hong Ryang Kil
- Department of Pediatrics, Chungnam National University School of Medicine, Daejeon, Korea
| | - Eun Hee Chung
- Department of Pediatrics, Chungnam National University School of Medicine, Daejeon, Korea.
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Li W, Wang X, Zhang X, Li F, Zhang D, Li X, Zhang Y, Zhao Y, Zhao L, Xu D, Cheng J, Wang J, Zhou B, Lin C, Wang W. Polymorphism of sheep PRKAA2 gene and its association with growth traits. Anim Biotechnol 2023; 34:1324-1330. [PMID: 34971343 DOI: 10.1080/10495398.2021.2021215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Small ruminants farming plays an important role in the livelihood of a large part of the population. Herein we aimed to analyze the effects of single nucleotide polymorphisms in PRKAA2 gene on the growth-related traits of Hu sheep and Dorper sheep. The body weight and body type of 1254 sheep were measured at 80, 100, 120, 140, 160 and 180d, and 37620 phenotypic data were collected. RT-qPCR analysis was performed to test PRKAA2 gene expressed in different tissues of sheep, with the highest expression level in spleen, followed by kidney. In the present study, the PRKAA2 gene sequencing revealed one polymorphism located on Chr1 (Oar_rambouillet_v1.0), termed as chr1:32832382 G > A, and were significantly associated with growth traits of sheep (p < 0.05). The body weight, body length, chest circumference, and cannon circumference of individuals with AA genotype were significantly higher than those with the GG and GA genotypes (p < 0.05). Our findings reveal that PRKAA2 gene could be used as a marker-assisted selection to improve the growth-related traits of sheep.
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Affiliation(s)
- Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaojuan Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fadi Li
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- Engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province, Minqin, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Bubo Zhou
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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Paganini J, Faux P, Beley S, Picard C, Chiaroni J, Di Cristofaro J. HLA-F transcriptional and protein differential expression according to its genetic polymorphisms. HLA 2023; 102:578-589. [PMID: 37166140 DOI: 10.1111/tan.15087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/21/2023] [Accepted: 04/20/2023] [Indexed: 05/12/2023]
Abstract
Many specificities single out HLA-F: its structure, expression regulation at cell membrane and function. HLA-F mRNA is detected in the most cell types and the protein is localized in the ER and Golgi apparatus. When expressed at cell surface, HLA-F may be associated to β2-microglobulin and peptide or expressed as an open-conformer molecule. HLA-F reaches the membrane upon activation of different primary cell types and cell-lines. HLA-F has its highest affinity for the KIR3DS1-activating NK receptor, but also binds inhibitory immune receptors. Some studies reported that HLA-F expression is associated with its genotype. Higher HLA-F mRNA expression associated with F*01:01:02, and 3 noncoding SNPs, rs1362126, rs2523405, and rs2523393, located in HLA-F-AS1 or upstream the HLA-F sequence were associated with HLA-F mRNA expression. Given the implication of HLA-F in many clinical setting, and the undisclosed process of its expression regulation, we aim to confirm the effect of the aforementioned SNPs with HLA-F transcriptional and protein expression. We analyzed the distribution, frequency and linkage disequilibrium of these SNPs at worldwide scale in the 1000 Genomes Project samples. Influence on the genotype of each SNP on HLA-F expression was explored using RNAseq data from the 1000 Genomes Project, and using Q-PCR and intracellular cytometry in PBMC from healthy individuals. Our results show that the SNPs under studied displayed remarkably different allelic proportion according to geography and confirm that rs1362126, rs2523405, and rs2523393 displayed the most concordant results, with the highest effect size and a double-dose effect.
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Affiliation(s)
| | - Pierre Faux
- GenPhySE, Université de Toulouse, INRAE, INPT, INP-ENVT, Castanet Tolosan, France
- Aix Marseille University, CNRS, EFS, ADES, UMR7268, Marseille, France
| | - Sophie Beley
- Aix Marseille University, CNRS, EFS, ADES, UMR7268, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
| | - Christophe Picard
- Aix Marseille University, CNRS, EFS, ADES, UMR7268, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
| | - Jacques Chiaroni
- Aix Marseille University, CNRS, EFS, ADES, UMR7268, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
| | - Julie Di Cristofaro
- Aix Marseille University, CNRS, EFS, ADES, UMR7268, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
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167
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Liang X, Jin P, Zhan C, Zhao L, Zi X, Zhi L, Yu K. Glucocorticoid-Induced Transcript 1(GLCCI1) SNP rs37937 Is Associated With the Risk of Developing Allergic Rhinitis and the Response to Intranasal Corticosteroids in a Chinese Han Population. Am J Rhinol Allergy 2023; 37:751-757. [PMID: 37553950 DOI: 10.1177/19458924231193156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
BACKGROUND Evidence has shown that glucocorticoid-induced transcript 1 (GLCCI1) single nucleotide polymorphism (SNP) rs37937 is associated with asthma. OBJECTIVES The objective of this study was to investigate whether the GLCCI1 SNP rs37937 is a risk factor for allergic rhinitis (AR) in a Chinese Han population. METHODS A total of 220 individuals including 109 AR patients and 111 healthy subjects were included. The genotyping of GLCCI1 rs37973 was performed by the SNaPshot method. The correlations of rs37973 polymorphism, AR risk, and clinical characteristics were further analyzed, as well as the treatment response to intranasal corticosteroids (INCS) in AR patients of different genotypes. RESULTS Three GLCCI1 rs37973 SNP genotypes were identified in both AR patients and healthy subjects. Significant association between rs37973 polymorphism and AR under allele model, dominant model, heterozygote model, and homozygote model were shown. The A allele frequency of SNP rs37973 in AR was significantly higher than that in controls. The serum total immunoglobulin E (IgE) in AR patients of AA genotype was significantly higher than in patients of GA and GG genotype, and the serum total IgE in GA genotype was significantly higher than in GG genotype. Interestingly, after 4 weeks of INCS treatment for AR patients, the improvement of the nasal itching score, sneezing score, runny nose score, total nasal symptom score, and visual analog scale score of the GG genotype were worse than the AA or GA genotype. CONCLUSION The GLCCI1 rs37937 polymorphism is associated with the risk of developing AR and the response to INCS treatment in the Chinese Han population.
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Affiliation(s)
- Xu Liang
- Department of Otolaryngology, The Second Hospital of Shandong University, Jinan, China
| | - Peng Jin
- Department of Otolaryngology, The Second Hospital of Shandong University, Jinan, China
| | - Changcui Zhan
- Department of Otolaryngology, Dongping County People's Hospital, Taian, China
| | - Li Zhao
- Department of Otolaryngology, The Second Hospital of Shandong University, Jinan, China
| | - Xiaoxue Zi
- Department of Otolaryngology, The Second Hospital of Shandong University, Jinan, China
| | - Lili Zhi
- Department of Allergy, Shandong Provincial Qianfoshan Hospital, The First Affiliated Hospital of Shandong First Medical University, Shandong Institute of Respiratory Diseases, Jinan, China
| | - Kena Yu
- Department of Otolaryngology, The Second Hospital of Shandong University, Jinan, China
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Daglish MRC, Reilly SR, Mostafa S, Edwards C, O'Gorman TM, Hayllar JS. Cytochrome P450-2D6 activity in people with codeine use disorder. Pharmacogenomics J 2023; 23:195-200. [PMID: 37940651 PMCID: PMC10661737 DOI: 10.1038/s41397-023-00319-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 10/22/2023] [Accepted: 10/26/2023] [Indexed: 11/10/2023]
Abstract
Compound-analgesics containing codeine (CACC) have been a common source of codeine for people seeking opioid replacement therapy (ORT) for codeine use disorder (CUD). Our previous work demonstrated no relationship between pre-treatment CACC and ORT buprenorphine doses; we hypothesised that CYP2D6 activity would partially account for this disconnection. One hundred six participants with CUD were compared to a published population sample of 5408 Australian patients. Mean age of participants with CUD at treatment entry was 35 years, with mean 6.1 years duration of CUD. Mean codeine dose was 660 mg/day (range 40-2700 mg). Mean calculated CYP2D6 activity scores were significantly higher in the codeine group (CUD 1.65 + 0.63 vs. Gen pop 1.39 + 0.65, Wilcoxon W = 347,001, p < 0.001). Pre-treatment CACC dose weakly predicted sublingual buprenorphine doses overall; there was a stronger relationship within ultrarapid metabolisers. While normal and ultrarapid metabolisers of codeine were more likely to have a diagnosis of CUD, poor or intermediate CYP2D6 metaboliser status may protect against CUD.
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Affiliation(s)
- Mark R C Daglish
- Alcohol & Drug Service, The Prince Charles Hospital, Metro North Health, Brisbane, QLD, Australia.
- Hospital Alcohol & Drug Service, Royal Brisbane and Women's Hospital, Metro North Health, Brisbane, QLD, Australia.
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.
| | - Sarah R Reilly
- Alcohol & Drug Service, The Prince Charles Hospital, Metro North Health, Brisbane, QLD, Australia
| | - Sam Mostafa
- myDNA Life, Australia Ltd, South Yarra, VIC, Australia
- Centre for Medicine Use and Safety, Monash University, Parkville, VIC, Australia
| | - Cameron Edwards
- Alcohol & Drug Service, The Prince Charles Hospital, Metro North Health, Brisbane, QLD, Australia
| | - Thomas M O'Gorman
- Alcohol & Drug Service, The Prince Charles Hospital, Metro North Health, Brisbane, QLD, Australia
| | - Jeremy S Hayllar
- Alcohol & Drug Service, The Prince Charles Hospital, Metro North Health, Brisbane, QLD, Australia
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169
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Montalban-Bravo G, Kanagal-Shamanna R, Li Z, Hammond D, Chien K, Rodriguez-Sevilla JJ, Sasaki K, Jabbour E, DiNardo C, Takahashi K, Short N, Issa GC, Pemmaraju N, Kadia T, Ravandi F, Daver N, Borthakur G, Loghavi S, Pierce S, Bueso-Ramos C, Kantarjian H, Garcia-Manero G. Phenotypic subtypes of leukaemic transformation in chronic myelomonocytic leukaemia. Br J Haematol 2023; 203:581-592. [PMID: 37608562 DOI: 10.1111/bjh.19060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/24/2023]
Abstract
Chronic myelomonocytic leukaemia (CMML) is a haematological disorder with high risk of transformation to acute myeloid leukaemia (AML). To characterize the phenotypic and genomic patterns of CMML progression, we evaluated a cohort of 189 patients with AML evolving from CMML. We found that transformation occurs through distinct trajectories characterized by genomic profiles and clonal evolution: monocytic (Mo-AML, 53%), immature myeloid (My-AML, 43%) or erythroid (Ery-AML, 2%). Mo-AML, characterized by expansion of monoblasts and promonocytes (low CD34, CD117 expression; high CD14, CD33, CD56 and CD64 expression), were defined by SRSF2, TET2 and RAS pathway mutation co-dominance and were more likely to evolve from SRSF2-TET2 co-mutant CMML through emergence/expansion of RAS pathway mutant clones. Conversely, My-AML, characterized by expansion of immature myeloid blasts (high frequency of CD34, CD38, CD117; low frequency of CD14, CD64 and CD56 expression) were less likely to exhibit SRSF2-TET2 co-mutations or RAS pathway mutations and had higher frequency of CEBPA mutations. Ery-AML was defined by complex karyotypes and TP53 mutations. A trend towards improved OS and EFS with hypomethylating agent-venetoclax combination was observed in My-AML, but not Mo-AML. These findings define distinct progression of CMML and set the basis for future studies evaluating the role of phenotype-specific therapeutics.
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Affiliation(s)
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ziyi Li
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Danielle Hammond
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kelly Chien
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Koji Sasaki
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Elias Jabbour
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Courtney DiNardo
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Koichi Takahashi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Nicholas Short
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ghayas C Issa
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Naveen Pemmaraju
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Tapan Kadia
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Farhad Ravandi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Naval Daver
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Gautam Borthakur
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sanam Loghavi
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sherry Pierce
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Carlos Bueso-Ramos
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hagop Kantarjian
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Guillermo Garcia-Manero
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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170
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Warner IA, Kok WJ, Martinelli N, Yang Z, Goodall ECA, Henderson I. Microbial Primer: Transposon directed insertion site sequencing (TraDIS): A high throughput method for linking genotype to phenotype. Microbiology (Reading) 2023; 169. [PMID: 37909267 DOI: 10.1099/mic.0.001385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Genetic screens are a key tool for linking phenotype and genotype. Transposon mutagenesis was one of the first genetic methodologies to associate genetic loci with phenotypes. The advent of next-generation sequencing transformed the use of this technique allowing rapid interrogation of whole genomes for genes that correlate with phenotype. One method is transposon directed insertion-site sequencing (TraDIS). Here we describe the method, recent developments in technology, and the advantages and disadvantages of this method compared to other genetic screening tools.
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Affiliation(s)
- Isabel A Warner
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
| | - Weine J Kok
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
| | - Nicole Martinelli
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
| | - Zihao Yang
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
| | - Emily C A Goodall
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
| | - Ian Henderson
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
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171
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Durán-Manuel EM, Bello-López JM, Salinas-Bobadilla AD, Vargas-De-León C, Nieto-Velázquez NG, Moreno-Eutimio MA, Pastelin-Palacios R, Calzada-Mendoza CC, Blanco-Hernández DMR. Molecular Characterization of Bacterial Agents Causing External Ocular Infections Isolates of Patients in a Third Level Hospital. Pathogens 2023; 12:1294. [PMID: 38003759 PMCID: PMC10675722 DOI: 10.3390/pathogens12111294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
Empirical use of antibiotics in the treatment of eye infections leads to bacterial pathogens becoming resistant to antibiotics; consequently, treatment failure and eye health complications occur. The aim of this study was to describe the phenotype and genotype of the resistance and adherence of bacterial agents causing eye infections in patients at Hospital Juárez de México. An observational, prospective, cross-sectional, and descriptive study was carried out in patients with signs and symptoms of ocular infection. Bacterial agents were isolated and identified by classical microbiology and mass spectrometry. Antibiotic resistance and adherence profiles were determined. Finally, resistance (mecA/SCCmec) and virulence (icaA and icaD) genes were detected in the Gram-positive population. The results showed that blepharitis was the most prevalent condition in the study population. A MALDI-TOF analysis revealed that Staphylococcus and Pseudomonas genus were the most prevalent as causal agents of infection. Resistances to β-lactams were detected of 44 to 100%, followed by clindamycins, aminoglycosides, folate inhibitors, and nitrofurans. A multiple correspondence analysis showed a relationship between mecA genotype and β-lactams resistance. The identification of SCCmecIII and SCCmecIV elements suggested community and hospital sources of infection. Finally, the coexistence of icaA+/icaD+/mecA(SCCmecIII) and icaA+/icaD+/mecA(SCCmecIV) genotypes was detected in S. aureus. The identification of resistant and virulent isolates highlights the importance of developing protocols that address the timely diagnosis of ocular infections. Herein, implications for the failure of antimicrobial therapy in the treatment of ocular infections in susceptible patients are analysed and discussed.
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Affiliation(s)
- Emilio Mariano Durán-Manuel
- Hospital Juárez de México, Mexico City 07760, Mexico
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | | | | | - Cruz Vargas-De-León
- Hospital Juárez de México, Mexico City 07760, Mexico
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | | | - Mario Adán Moreno-Eutimio
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City 04510, Mexico
| | - Rodolfo Pastelin-Palacios
- Facultad de Estudios Superiores Zaragoza, Universidad Nacional Autónoma de México, Mexico City 09230, Mexico
| | - Claudia Camelia Calzada-Mendoza
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico
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172
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Ludwig K, Lai F, Wiley V, Ravine A, Srinivasan S. Genotyping in patients with congenital adrenal hyperplasia by sequencing of newborn bloodspot samples. J Pediatr Endocrinol Metab 2023; 36:966-973. [PMID: 37728028 DOI: 10.1515/jpem-2023-0044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 09/01/2023] [Indexed: 09/21/2023]
Abstract
OBJECTIVES Genotype-phenotype correlation in congenital adrenal hyperplasia (CAH) caused by 21-hydroxylase deficiency ranges from 45 to 97 %. We performed massively parallel sequencing of CYP21A2 on stored newborn bloodspot samples to catalogue the genotypes present in our patients with CAH and enable genotype-phenotype comparison. METHODS Participants ≤15 years old with clinically diagnosed CAH were recruited from The Sydney Children's Hospitals Network. Phenotype was classified from clinical and biochemical details in the medical record as salt wasting (SW), simple virilising (SV), non-classic (NC) or an intermediate phenotype (SW/SV; SV/NC). Amplicon-based sequencing for CYP21A2 was performed on stored newborn bloodspot samples by the New South Wales Newborn Bloodspot Screening Laboratory on MiSeq™Dx (Illumina, California). Available genetic test results were also obtained from the medical records. RESULTS Samples from 67 participants (43 % female, age 0.3-15 years) were sequenced, including 9 sibships. SW phenotype was present in 33/67 participants (49 %), SV in 9 (13 %) and NC in 16 (24 %). Intermediate phenotypes included SW/SV in seven participants (10 %) and SV/NC in two (3 %). Variants were identified in 90/116 alleles (78 %). A complete genotype was available in 47/67 participants (70 %). The most common genotype was homozygous c.293-13A/C>G (I2G) in 7/47 participants (15 %). Genotype correlated with the most commonly reported phenotype in 36/44 cases (82 %). Correlation was higher in SW and NC phenotypes. CONCLUSIONS This study uses genetic testing of newborn bloodspots to identify and characterise the genotypes present in an ethnically diverse Australian population with CAH. It further strengthens our knowledge of genotype-phenotype correlations in CAH.
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Affiliation(s)
- Karissa Ludwig
- Department of Endocrinology, Queensland Children's Hospital, South Brisbane, QLD, Australia
| | - Fei Lai
- Faculty of Child and Adolescent Health, The University of Sydney, Camperdown, NSW, Australia
- NSW Newborn Screening Programme, Westmead, NSW, Australia
| | - Veronica Wiley
- Faculty of Child and Adolescent Health, The University of Sydney, Camperdown, NSW, Australia
- NSW Newborn Screening Programme, Westmead, NSW, Australia
| | - Anja Ravine
- Faculty of Child and Adolescent Health, The University of Sydney, Camperdown, NSW, Australia
- Molecular Genetics, Western Sydney Genetics Program, Westmead, NSW, Australia
| | - Shubha Srinivasan
- Faculty of Child and Adolescent Health, The University of Sydney, Camperdown, NSW, Australia
- Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Westmead, NSW, Australia
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173
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Zhao H, Li X, Xiao X, Wang T, Liu L, Li C, Wu H, Shan Z, Wu Q. Evaluating Tartary Buckwheat Genotypes with High Callus Induction Rates and the Transcriptomic Profiling during Callus Formation. Plants (Basel) 2023; 12:3663. [PMID: 37960020 PMCID: PMC10647830 DOI: 10.3390/plants12213663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023]
Abstract
Due to their complex genotypes, low in vitro regeneration rates, and difficulty in obtaining transgenic plants, studies concerning basic biological research and molecular breeding in Tartary buckwheat (TB) are greatly limited. In this study, the hypocotyls of 60 genotypes of TB (TBC1~60) were used as explants. Of these, TBC14 was selected due to a high callus induction rate of 97.78% under dark and a proliferation coefficient (PC) of 28.2 when cultured on MS medium supplemented with 2.0 mg/L of 2,4-D and 1.5 mg/L of 6-BA. Subsequently, the samples of the calli obtained from TBC14 were collected at 0, 10, 20, and 30 d, and their transcriptomes were sequenced where identified. GO enrichment led to the detection of the most significant active gene set, which was the DNA binding transcription factor activity. The DEGs related to the pathways concerning metabolism, the biosynthesis of secondary metabolites, and hormone signal transduction were the most enriched in the KEGG database. The sets of MYB, AP2/ERF, and bHLH TFs exhibited the highest number of DEGs. Using this enrichment analysis, 421 genes encoding TFs, 47 auxin- and cytokinin-related genes, and 6 signal transduction-associated genes were screened that may play significant roles in callus formation (CF) in TB. Furthermore, FtPinG0008123200.01 (bZIP), a key gene promoting CF, was screened in terms of the weighted gene co-expression network associated with the various stages of CF. Our study not only provides valuable information about the molecular mechanism of CF but also reveals new genes involved in this process.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Qi Wu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya’an 625014, China; (H.Z.); (X.L.); (X.X.); (T.W.); (L.L.); (C.L.); (H.W.); (Z.S.)
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174
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Flasco MT, Fuchs MF. Two Distinct Genotypes of Spissistilus festinus (Say, 1830) Reproduce and Differentially Transmit Grapevine Red Blotch Virus. Insects 2023; 14:831. [PMID: 37887843 PMCID: PMC10607809 DOI: 10.3390/insects14100831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/28/2023]
Abstract
Two phenotypically similar but genetically distinct genotypes of Spissistilus festinus (Say, 1830) (Hemiptera: Membracidae), a pest of legume crops in Southern United States and a vector of grapevine red blotch virus (GRBV) in California vineyards, exist. No information is available on whether the two S. festinus genotypes, i.e., California (CA) and Southeastern (SE), are sexually compatible or whether the SE genotype can transmit GRBV. In this study, we established mixed mating S. festinus pairs for which the F1 offspring varied phenotypically compared with the offspring of same genotype pairs but acquired GRBV isolate NY175 at similar rates (p = 0.96) and with a similar viral genome copy number (p = 0.34). Likewise, rates of GRBV acquisition were alike for the two parental CA (58%, 61/105) and SE (61%, 65/106) genotypes (p = 0.74), though the GRBV copy number in the salivary glands was overall significantly higher for SE than CA individuals (p = 0.02). Furthermore, the GRBV transmission rate was significantly higher for the SE genotype (89%, 16/18) than the CA genotype (50%, 8/16) (p = 0.04). These results revealed the existence of two sexually compatible S. festinus genotypes with distinct GRBV transmission abilities, suggesting the need to study GRBV ecology in Southeastern United States and areas where the two genotypes might co-exist.
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Affiliation(s)
- Madison T. Flasco
- Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA;
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175
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Ham H, Park DS. Novel approach toward the understanding of genetic diversity based on the two types of amino acid repeats in Erwinia amylovora. Sci Rep 2023; 13:17876. [PMID: 37857695 PMCID: PMC10587187 DOI: 10.1038/s41598-023-44558-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023] Open
Abstract
Erwinia amylovora is a notorious plant pathogenic bacterium of global concern that has devastated the apple and pear production industry worldwide. Nevertheless, the approaches available currently to understand the genetic diversity of E. amylovora remain unsatisfactory because of the lack of a trustworthy index and data covering the globally occurring E. amylovora strains; thus, their origin and distribution pattern remains ambiguous. Therefore, there is a growing need for robust approaches for obtaining this information via the comparison of the genomic structure of Amygdaloideae-infecting strains to understand their genetic diversity and distribution. Here, the whole-genome sequences of 245 E. amylovora strains available from the NCBI database were compared to identify intraspecific genes for use as an improved index for the simple classification of E. amylovora strains regarding their distribution. Finally, we discovered two kinds of strain-typing protein-encoding genes, i.e., the SAM-dependent methyltransferase and electron transport complex subunit RsxC. Interestingly, both of these proteins carried an amino acid repeat in these strains: SAM-dependent methyltransferase comprised a single-amino-acid repeat (asparagine), whereas RsxC carried a 40-amino-acid repeat, which was differentially distributed among the strains. These noteworthy findings and approaches may enable the exploration of the genetic diversity of E. amylovora from a global perspective.
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Affiliation(s)
- Hyeonheui Ham
- Crop Protection Division, Department of Agro-Food Safety and Crop Protection, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Dong Suk Park
- Crop Protection Division, Department of Agro-Food Safety and Crop Protection, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365, Republic of Korea.
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176
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Yadava YK, Chaudhary P, Yadav S, Rizvi AH, Kumar T, Srivastava R, Soren KR, Bharadwaj C, Srinivasan R, Singh NK, Jain PK. Genetic mapping of quantitative trait loci associated with drought tolerance in chickpea (Cicer arietinum L.). Sci Rep 2023; 13:17623. [PMID: 37848483 PMCID: PMC10582051 DOI: 10.1038/s41598-023-44990-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/14/2023] [Indexed: 10/19/2023] Open
Abstract
Elucidation of the genetic basis of drought tolerance is vital for genomics-assisted breeding of drought tolerant crop varieties. Here, we used genotyping-by-sequencing (GBS) to identify single nucleotide polymorphisms (SNPs) in recombinant inbred lines (RILs) derived from a cross between a drought tolerant chickpea variety, Pusa 362 and a drought sensitive variety, SBD 377. The GBS identified a total of 35,502 SNPs and subsequent filtering of these resulted in 3237 high-quality SNPs included in the eight linkage groups. Fifty-one percent of these SNPs were located in the genic regions distributed throughout the genome. The high density linkage map has total map length of 1069 cm with an average marker interval of 0.33 cm. The linkage map was used to identify 9 robust and consistent QTLs for four drought related traits viz. membrane stability index, relative water content, seed weight and yield under drought, with percent variance explained within the range of 6.29%-90.68% and LOD scores of 2.64 to 6.38, which were located on five of the eight linkage groups. A genomic region on LG 7 harbors quantitative trait loci (QTLs) explaining > 90% phenotypic variance for membrane stability index, and > 10% PVE for yield. This study also provides the first report of major QTLs for physiological traits such as membrane stability index and relative water content for drought stress in chickpea. A total of 369 putative candidate genes were identified in the 6.6 Mb genomic region spanning these QTLs. In-silico expression profiling based on the available transcriptome data revealed that 326 of these genes were differentially expressed under drought stress. KEGG analysis resulted in reduction of candidate genes from 369 to 99, revealing enrichment in various signaling pathways. Haplotype analysis confirmed 5 QTLs among the initially identified 9 QTLs. Two QTLs, qRWC1.1 and qYLD7.1, were chosen based on high SNP density. Candidate gene-based analysis revealed distinct haplotypes in qYLD7.1 associated with significant phenotypic differences, potentially linked to pathways for secondary metabolite biosynthesis. These identified candidate genes bolster defenses through flavonoids and phenylalanine-derived compounds, aiding UV protection, pathogen resistance, and plant structure.The study provides novel genomic regions and candidate genes which can be utilized in genomics-assisted breeding of superior drought tolerant chickpea cultivars.
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Affiliation(s)
- Yashwant K Yadava
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - Pooja Chaudhary
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - Sheel Yadav
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - Aqeel Hasan Rizvi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Tapan Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Rachna Srivastava
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - K R Soren
- ICAR-Indian Institute of Pulses Research, Kanpur, 208024, India
| | - C Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - R Srinivasan
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - N K Singh
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - P K Jain
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India.
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177
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Soejima M, Koda Y. FUT1 variants responsible for Bombay or para-Bombay phenotypes in a database. Sci Rep 2023; 13:17447. [PMID: 37838738 PMCID: PMC10576827 DOI: 10.1038/s41598-023-44731-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/11/2023] [Indexed: 10/16/2023] Open
Abstract
Rare individuals with Bombay and para-Bombay phenotypes lack or have weak expression of the ABO(H) antigens on surface of red blood cells due to no or very weak H-type α(1,2)fucosyltransferase activity encoded by FUT1. These phenotypes are clinically important because subjects with these phenotypes can only accept transfusions of autologous blood or blood from subjects with the same phenotypes due to the anti-H antibody. To survey FUT1 alleles involved in Bombay and para-Bombay phenotypes, the effect of 22 uncharacterized nonsynonymous SNPs in the Erythrogene database on the α(1,2)fucosyltransferase activity were examined by transient expression studies and in silico analysis using four different online software tools. Two nonfunctional alleles (FUT1 with c.503C>G and c.749G>C) and one weakly functional allele (with c.799T>C) were identified in transient expression studies, while the software predicted that the proteins encoded by more alleles including these would be impaired. Because both nonfunctional FUT1 alleles appear to link to the nonsecretor alleles, homozygotes of these alleles would be of the Bombay phenotype. The present results suggest that functional assays are useful for characterization of nonsynonymous SNPs of FUT1 when their phenotypes are not available.
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Affiliation(s)
- Mikiko Soejima
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume, 830-0011, Japan
| | - Yoshiro Koda
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume, 830-0011, Japan.
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178
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Chu MJ, Huang LY, Miao WY, Song YF, Lin YS, Li SA, Zhou DH. First Molecular Detection and Genotype Identification of Toxoplasma gondii in Chickens from Farmers' Markets in Fujian Province, Southeastern China. Pathogens 2023; 12:1243. [PMID: 37887759 PMCID: PMC10609706 DOI: 10.3390/pathogens12101243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 10/28/2023] Open
Abstract
Toxoplasma gondii is an opportunistic pathogenic protozoan that can infect all nucleated cells in almost all warm-blooded animals, including humans. T. gondii infection has been reported in many food animals worldwide. However, the prevalence and genotypes of T. gondii in chickens from farmers' markets in Fujian province in southeastern China remain unreported. In the present study, four tissue samples from each of the 577 chickens (namely, the heart, liver, lungs, and muscles) were collected from farmers' markets in five regions of Fujian province (Zhangzhou, Sanming, Quanzhou, Fuzhou, and Longyan). We first analyzed the prevalence and genotypes of T. gondii using PCR targeting of the B1 gene of T. gondii. Of the 577 chickens, thirty-two (5.5%) tested positive for the B1 gene. Among the five regions, Sanming had the highest infection rate (16.8%, 16/95), followed by Quanzhou (8.0%, 8/100), Longyan (5.0%, 5/100), Zhangzhou (1.1%, 2/182), and Fuzhou (1.0%, 1/100). Among these thirty-two T. gondii-positive chickens, the infection rates of the lungs, heart, liver, and muscles were 68.8% (22/32), 34.4% (11/32), 28.1% (9/32), and 9.4% (3/32), respectively. Significant differences in prevalence were found among the different regions (χ2 = 35.164, p < 0.05) and tissues (χ2 = 25.874, p < 0.05). A total of 128 tissue and organ samples of the thirty-two T. gondii-positive chickens from the different regions were analyzed using PCR-restriction fragment length polymorphism (PCR-RFLP) on the basis of 10 genetic markers. Seven tissue samples (lung samples from five chickens, heart samples from one chicken, and liver samples from one chicken) underwent successful amplification at all the genetic markers, and all the T. gondii genotypes were identified as genotype I (ToxoDB #10). These findings serve as a foundation for evaluating the risk of T. gondii contamination in chicken products intended for human consumption and offer insight into preventing the transmission of the parasite from chickens to humans.
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Affiliation(s)
- Meng-Jie Chu
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-J.C.); (L.-Y.H.); (W.-Y.M.); (Y.-F.S.)
| | - Li-Yuan Huang
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-J.C.); (L.-Y.H.); (W.-Y.M.); (Y.-F.S.)
| | - Wen-Yuan Miao
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-J.C.); (L.-Y.H.); (W.-Y.M.); (Y.-F.S.)
| | - Ya-Fei Song
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-J.C.); (L.-Y.H.); (W.-Y.M.); (Y.-F.S.)
| | - Ying-Sheng Lin
- Zhangzhou Animal Husbandry Technical Service Station, Zhangzhou 363000, China;
| | - Si-Ang Li
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-J.C.); (L.-Y.H.); (W.-Y.M.); (Y.-F.S.)
| | - Dong-Hui Zhou
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-J.C.); (L.-Y.H.); (W.-Y.M.); (Y.-F.S.)
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Tsai CW, Chang WS, Yueh TC, Wang YC, Chin YT, Yang MD, Hung YC, Mong MC, Yang YC, Gu J, Bau DT. The Significant Impacts of Interleukin-8 Genotypes on the Risk of Colorectal Cancer in Taiwan. Cancers (Basel) 2023; 15:4921. [PMID: 37894288 PMCID: PMC10605288 DOI: 10.3390/cancers15204921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
Interleukin-8 (IL-8), a pro-inflammatory cytokine, is upregulated in CRC and plays an important role in its development and progression. Genetic variants in the IL-8 gene may impact the risk of CRC by modulating IL-8 levels. Our primary objective was to investigate the role of IL-8 genotypes in the development of CRC. To accomplish this, we employed the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method to analyze the genotypes of IL-8 rs4017, rs2227306, rs2227543, and rs1126647 in 362 CRC patients and 362 controls. Additionally, we evaluated the interactions between these genotypes and factors such as age, gender, smoking, alcohol consumption, and body mass index (BMI) status in relation to the risk of CRC. Furthermore, we utilized quantitative reverse transcription-PCR to measure the serum IL-8. The results demonstrated a significant difference in the distribution of rs4017 genotypes between the control and case groups (p for trend = 0.0059). Logistic regression analysis revealed that individuals with variant AA genotype had a 1.92-fold higher CRC risk (95% confidence interval [CI] = 1.28-2.89, p = 0.0023). Moreover, carriers of the IL-8 rs4017 AT + AA genotypes exhibited a significant association with CRC risk (odds ratio [OR] = 1.39, 95% CI = 1.02-1.91, p = 0.0460). Additionally, individuals with IL-8 rs4017 AA genotype displayed significantly elevated serum IL-8 compared to those with TT genotype at a 1.73-fold level (p < 0.0001), indicating a correlation between genotype and phenotype. In conclusion, the genotypes of IL-8 rs4017, along with their associated expression levels, can potentially serve as predictive markers for the risk of CRC.
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Affiliation(s)
- Chia-Wen Tsai
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404333, Taiwan; (C.-W.T.); (W.-S.C.); (Y.-C.W.); (Y.-T.C.); (Y.-C.H.)
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Terry Fox Cancer Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung 404327, Taiwan; (T.-C.Y.); (M.-D.Y.)
| | - Wen-Shin Chang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404333, Taiwan; (C.-W.T.); (W.-S.C.); (Y.-C.W.); (Y.-T.C.); (Y.-C.H.)
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Terry Fox Cancer Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung 404327, Taiwan; (T.-C.Y.); (M.-D.Y.)
| | - Te-Cheng Yueh
- Terry Fox Cancer Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung 404327, Taiwan; (T.-C.Y.); (M.-D.Y.)
- Division of Colon and Rectal Surgery, Department of Surgery, Taichung Armed Forces General Hospital, Taichung 41152, Taiwan
- National Defense Medical Center, Taipei 11490, Taiwan
| | - Yun-Chi Wang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404333, Taiwan; (C.-W.T.); (W.-S.C.); (Y.-C.W.); (Y.-T.C.); (Y.-C.H.)
- Terry Fox Cancer Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung 404327, Taiwan; (T.-C.Y.); (M.-D.Y.)
| | - Yu-Ting Chin
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404333, Taiwan; (C.-W.T.); (W.-S.C.); (Y.-C.W.); (Y.-T.C.); (Y.-C.H.)
- Terry Fox Cancer Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung 404327, Taiwan; (T.-C.Y.); (M.-D.Y.)
| | - Mei-Due Yang
- Terry Fox Cancer Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung 404327, Taiwan; (T.-C.Y.); (M.-D.Y.)
- Department of General Surgery, China Medical University Hospital, Taichung 404332, Taiwan
| | - Yi-Chih Hung
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404333, Taiwan; (C.-W.T.); (W.-S.C.); (Y.-C.W.); (Y.-T.C.); (Y.-C.H.)
- Terry Fox Cancer Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung 404327, Taiwan; (T.-C.Y.); (M.-D.Y.)
| | - Mei-Chin Mong
- Department of Food Nutrition and Health Biotechnology, Asia University, Taichung 41354, Taiwan; (M.-C.M.); (Y.-C.Y.)
| | - Ya-Chen Yang
- Department of Food Nutrition and Health Biotechnology, Asia University, Taichung 41354, Taiwan; (M.-C.M.); (Y.-C.Y.)
| | - Jian Gu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Da-Tian Bau
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404333, Taiwan; (C.-W.T.); (W.-S.C.); (Y.-C.W.); (Y.-T.C.); (Y.-C.H.)
- Terry Fox Cancer Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung 404327, Taiwan; (T.-C.Y.); (M.-D.Y.)
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung 41354, Taiwan
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180
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Wang L, Campino S, Phelan J, Clark TG. Mixed infections in genotypic drug-resistant Mycobacterium tuberculosis. Sci Rep 2023; 13:17100. [PMID: 37816829 PMCID: PMC10564873 DOI: 10.1038/s41598-023-44341-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/06/2023] [Indexed: 10/12/2023] Open
Abstract
Tuberculosis disease (TB), caused by Mycobacterium tuberculosis, is a major global public health problem, resulting in more than 1 million deaths each year. Drug resistance (DR), including multi-drug (MDR-TB), is making TB control difficult and accounts for 16% of new and 48% of previously treated cases. To further complicate treatment decision-making, many clinical studies have reported patients harbouring multiple distinct strains of M. tuberculosis across the main lineages (L1 to L4). The extent to which drug-resistant strains can be deconvoluted within mixed strain infection samples is understudied. Here, we analysed M. tuberculosis isolates with whole genome sequencing data (n = 50,723), which covered the main lineages (L1 9.1%, L2 27.6%, L3 11.8%, L4 48.3%), with genotypic resistance to isoniazid (HR-TB; n = 9546 (29.2%)), rifampicin (RR-TB; n = 7974 (24.4%)), and at least MDR-TB (n = 5385 (16.5%)). TB-Profiler software revealed 531 (1.0%) isolates with potential mixed sub-lineage infections, including some with DR mutations (RR-TB 21/531; HR-TB 59/531; at least MDR-TB 173/531). To assist with the deconvolution of such mixtures, we adopted and evaluated a statistical Gaussian Mixture model (GMM) approach. By simulating 240 artificial mixtures of different ratios from empirical data across L1 to L4, a GMM approach was able to accurately estimate the DR profile of each lineage, with a low error rate for the estimated mixing proportions (mean squared error 0.012) and high accuracy for the DR predictions (93.5%). Application of the GMM model to the clinical mixtures (n = 531), found that 33.3% (188/531) of samples consisted of DR and sensitive lineages, 20.2% (114/531) consisted of lineages with only DR mutations, and 40.6% (229/531) consisted of lineages with genotypic pan-susceptibility. Overall, our work demonstrates the utility of combined whole genome sequencing data and GMM statistical analysis approaches for providing insights into mono and mixed M. tuberculosis infections, thereby potentially assisting diagnosis, treatment decision-making, drug resistance and transmission mapping for infection control.
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Affiliation(s)
- Linfeng Wang
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK
| | - Susana Campino
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK
| | - Jody Phelan
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK.
| | - Taane G Clark
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK.
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK.
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Johnson B, Addolorato G, Lesch O, Liu L, Rodd ZA. A critical scientific evaluation of a purportedly negative data report - response to Seneviratne et al. 2022. Front Psychiatry 2023; 14:1271229. [PMID: 37860166 PMCID: PMC10582924 DOI: 10.3389/fpsyt.2023.1271229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/19/2023] [Indexed: 10/21/2023] Open
Abstract
A core principle in the pursuit of scientific knowledge is that science is self-correcting and that important results should be replicable. Hypotheses need to be reinforced, adjusted, or rejected when novel results are obtained. Replication of results confirms hypotheses and enhances their integration into scientific practice. In contrast, publication of substantiated and replicated negative findings (i.e., non-significant or opposite findings) can be the basis to reject erroneous hypotheses or develop alternative strategies for investigation. Replication is a problem in all research fields. The Psychology Reproductivity Project reported that only 36% of 'highly influential' published research in highly ranked journals were reproduced. Similar to positive data, negative data can be flawed. Errors in a negative data set can be based on methodology, statistics, conceptual defects, and flawed peer review. The peer review process has received progressive scrutiny. A large-scale review of the peer review process of manuscripts submitted to the British Medical Journal group indicated that the process could be characterized as inconsistent, inaccurate, and biased. Further analysis indicated that the peer process is easily manipulated, indicative of a failed system, is a major factor behind the lack of replication in science (acceptance of flawed manuscripts), suppresses opposing scientific evidence and views, and causes gaps in and lack of growth of science. Complicating the integrity of scientific publication is the role of Editors/Researchers. Ethical guidelines exist for major publishing houses about editorial ethics, behavior, and practice.
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Affiliation(s)
- Bankole Johnson
- Adial Pharmaceuticals, Inc., Charlottesville, VA, United States
| | - Giovanni Addolorato
- Internal Medicine and Alcohol Related Disease Unit, Department of Medical and Surgical Sciences, Columbus-Gemelli Hospital, Fondazione Policlinico Universitario A. Gemelli IRCCS, Catholic University of Rome, Rome, Italy
- CEMAD Digestive Disease Center, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, Catholic University of Rome, Rome, Italy
| | - Otto Lesch
- Medical University of Vienna, Vienna, Austria
| | - Lei Liu
- Division of Biostatistics, Washington University in St. Louis, St. Louis, MO, United States
| | - Zachary A. Rodd
- Adial Pharmaceuticals, Inc., Charlottesville, VA, United States
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182
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Nour I, Blakey JR, Alvarez-Narvaez S, Mohanty SK. Whole Genome Sequencing of Infectious Bursal Disease Viruses Isolated from a Californian Outbreak Unravels the Underlying Virulence Markers and Highlights Positive Selection Incidence. Viruses 2023; 15:2044. [PMID: 37896821 PMCID: PMC10612053 DOI: 10.3390/v15102044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023] Open
Abstract
Outbreaks of the immunosuppressive infectious bursal disease (IBD) are frequently reported worldwide, despite the vaccination regimes. A 2009 Californian IBD outbreak caused by rA and rB isolates was described as very virulent (vv) IBD virus (IBDV); however, molecular factors beyond this virulence were not fully uncovered. Therefore, segments of both isolates were amplified, successfully cloned, whole genome sequenced by Next Generation Sequencing, genotyped, and the leading virulence factors were entirely investigated in terms of phylogenetic and amino acid analysis and protein modeling for positive selection orientation and interaction analysis. rA and rB isolates displayed the highest amino acid identity (97.84-100%) with Genotype 3 strains. Interestingly, rA and rB contained all virulence hallmarks of hypervariable (HVR), including 222A, 242I, 249Q, 256I, 284A, 286T, 294I, 299S, and 318G, as well as the serine-rich heptapeptide sequence. Moreover, we pinpointed the A3B2 genotype of rA and rB, predominant in non-reassortants, and we highlighted the absence of recombination events. Furthermore, gene-wise phylogenetic analysis showed the entire genes of rA and rB clustered with the vvIBDVs and emphasized their share in IBDV virulence. VP5 showed a virulence marker, MLSL (amino acid sequence). VP2 encountered three significant novel mutations apart from the HVR, including G163E in rA and Y173C and V178A in rB, all residing within interacting motifs. VP4 contained 168Y, 173N, 203S, and 239D characteristic for the vv phenotype. A235V mutation was detected at the dsRNA binding domain of VP3. In VP1, the TDN triplet and the mutation (V4I) were detected, characteristic of hypervirulence occurring at the N-terminus responsible for protein priming. Although selection analysis revealed seven sites, codon 222 was the only statistically significant selection site. The VP2 modeling of rA and rB highlighted great structure fitness, with 96.14% Ramachandran favored positioning including the 222A, i.e., not influencing the structure stability. The 222A was found to be non-interface surface residue, associated with no interaction with the attachment-mediated ligand motif. Our findings provide pivotal insights into the evolution and underlying virulence factors and will assist in the development of control strategies via sequence-based continuous monitoring for the early detection of novel vv strains.
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Affiliation(s)
| | | | | | - Sujit K. Mohanty
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), US National Poultry Research Center, Athens, GA 30605, USA; (I.N.); (J.R.B.); (S.A.-N.)
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183
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Fernandes da Silva C, Keeshan A, Cooper C. Hepatitis B virus genotypes influence clinical outcomes: A review. Can Liver J 2023; 6:347-352. [PMID: 38020195 PMCID: PMC10652982 DOI: 10.3138/canlivj-2023-0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/28/2023] [Indexed: 12/01/2023]
Abstract
Hepatitis B virus (HBV) is a hepatotropic virus that affects approximately 296 million people worldwide. A crucial step to HBV replication is the transcription of its infectious DNA from its viral RNA intermediate. The production of the RNA intermediate hinges on reverse transcription, and therefore the lack of proofreading in that process commonly yields mutants and has led to nine well-described genotypes (A-I) and over 30 known sub-genotypes of the virus. The influence of genotype on HBV infection outcomes, which include fibrosis progression, cirrhosis, and hepatocellular carcinoma (HCC), remain uncertain. This review aims to analyze the influence of HBV genotype on the risk of development of these outcomes. The response to current and future HBV therapies is considered. Further study of larger and more diverse samples will hopefully resolve outstanding uncertainties.
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Affiliation(s)
| | - Alexa Keeshan
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Curtis Cooper
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
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184
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Yang Y, Liang Q, Chen Y, Cao Y, Zhuo Q, Liu B, Wang S. Aldehyde dehydrogenase 2 gene rs671 G>A polymorphism is associated with an increased risk of digestive tract cancer. J Int Med Res 2023; 51:3000605231206257. [PMID: 37871625 PMCID: PMC10594971 DOI: 10.1177/03000605231206257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 09/21/2023] [Indexed: 10/25/2023] Open
Abstract
OBJECTIVE Acetaldehyde can accumulate in cells and form acetaldehyde-DNA adducts that result in digestive tract cancer development. Acetaldehyde dehydrogenase 2 (ALDH2) enzymatic activity is involved in this process. Here, we aimed to analyze the relationship between an ALDH2 gene polymorphism and the digestive tract cancer risk in the Hakka population in China. METHODS This was a retrospective study, with the ALDH2 rs671 genotype and medical record information collected from all subjects. The relationships between these factors, including various blood cell parameters, and digestive tract cancer susceptibility were analyzed. RESULTS Overall, 307 cancer patients and 317 controls were included. The cancer patients had significantly higher percentages with a history of smoking and drinking alcohol, as well as an increased platelet to lymphocyte ratio and lower lymphocyte to monocyte ratio, compared with the controls. The ALDH2 rs671 genotype and allele distributions were significantly different between the cancer patients and controls. Logistic regression analysis showed that the ALDH2 G/A genotype (G/A vs. G/G) and A/A genotype (A/A vs. G/G) in the co-dominant mode were risk factors for digestive tract cancer susceptibility. CONCLUSIONS ALDH2 rs671 G/A or A/A genotype carriers may have an increased risk of developing digestive tract cancers among the Hakka people.
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Affiliation(s)
- Yang Yang
- Department of Gastroenterology, Meizhou People's Hospital, Meizhou, China
| | - Qun Liang
- Department of Gastroenterology, Meizhou People's Hospital, Meizhou, China
| | - Yijin Chen
- Department of Gastroenterology, Meizhou People's Hospital, Meizhou, China
| | - Yu Cao
- Department of Gastrointestinal Surgery, Meizhou People's Hospital, Meizhou, China
| | - Qingqing Zhuo
- Department of Gastroenterology, Meizhou People's Hospital, Meizhou, China
| | - Boying Liu
- Department of Gastroenterology, Meizhou People's Hospital, Meizhou, China
| | - Shengbing Wang
- Department of Gastroenterology, Meizhou People's Hospital, Meizhou, China
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185
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Yi J, Li X, Zhang R, Kong L, Wang Z, Yu Q, Zhang H, Chen B, Li S, Xu Y, Chen Y. The impact of the COVID-19 pandemic on the prevalence and genotype distribution of HPV infection in Beijing, China. J Med Virol 2023; 95:e29155. [PMID: 37815056 DOI: 10.1002/jmv.29155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/11/2023]
Abstract
Human papillomavirus (HPV) is one of the most common sexually transmitted infections nationwide. The COVID-19 pandemic has greatly influenced on the HPV prevention project. The objective of this study was to examine the influence of the pandemic on HPV prevalence and genotype distribution in Beijing, China. A total of 44 401 genital swabs were obtained from outpatients at Peking Union Medical College Hospital during two distinct periods: the prepandemic stage from January 2017 to December 2019 and the pandemic stage from January 2020 to December 2022. During the prepandemic and pandemic stages, a total of 33 531 and 10 870 swabs were respectively collected. Fifteen high-risk HPV (HR-HPV) DNA type and a combination of two low-risk (LR-HPV) types (6/11) of genital swabs were detected to compare the HPV infection rates and genotype distributions in two stages. The results showed that the pandemic period witnessed a decrease in the overall HPV infection rate from 33.43% (11 245/33 531) to 29.43% (5527/18 780) compared to the prepandemic. There were statistically significant differences in infection rates between females and males (p < 0.05). Single infection was the predominant type while multiple infection was more prevalent in males than females in both prepandemic and pandemic periods. HR-HPV infection constituted the majority of infections and cannot be disregarded. The distribution of HR-HPV genotypes exhibited little variation before and after the outbreak, but there were some differences between females and males. HPV 16, 52, 58, 56, and 66 were the most commonly detected genotypes in females, whereas HPV 16, 52, 51, 58, and 18 were frequently detected in males. Additionally, HPV 6/11 exhibited a higher prevalence in males than in females. Notably, the age group of 31-40 years old exhibited the highest prevalence of HPV and the lowest infection rate was detected among individuals aged ≤20 years (p < 0.05), which remained relatively consistent before and during the pandemic. These findings underscore the importance of monitoring the trend of HPV epidemic and offer valuable insights for the prevention, treatment, and scientific investigation of HPV in the post-COVID-19 era.
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Affiliation(s)
- Jie Yi
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xu Li
- Coyote Bioscience Co., Ltd., Beijing, China
| | - Rui Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lingjun Kong
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ziyi Wang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qi Yu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Han Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | | | - Sabrina Li
- Coyote Bioscience Co., Ltd., Beijing, China
| | - Yingchun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yu Chen
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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186
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Li J, Xu H, Hung A, Javed MJ, Upchurch GR, Jiang Z. Commonly Used Myh11-CreERT2Strain Carries a Y-Linked Functional Wild-Type Tlr7 Allele. Arterioscler Thromb Vasc Biol 2023; 43:2068-2070. [PMID: 37317852 PMCID: PMC10538427 DOI: 10.1161/atvbaha.122.318919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Affiliation(s)
- Jie Li
- Division of Vascular Surgery and Endovascular Therapy, University of Florida College of Medicine, Gainesville
| | - Haiyan Xu
- Division of Vascular Surgery and Endovascular Therapy, University of Florida College of Medicine, Gainesville
| | - Alex Hung
- Division of Vascular Surgery and Endovascular Therapy, University of Florida College of Medicine, Gainesville
| | - Muhammad Javad Javed
- Division of Vascular Surgery and Endovascular Therapy, University of Florida College of Medicine, Gainesville
| | - Gilbert R Upchurch
- Division of Vascular Surgery and Endovascular Therapy, University of Florida College of Medicine, Gainesville
| | - Zhihua Jiang
- Division of Vascular Surgery and Endovascular Therapy, University of Florida College of Medicine, Gainesville
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Ilardi P, Valdes S, Rivera J, Irgang R, Avendaño-Herrera R. Co-occurrence of heterogeneous Flavobacterium psychrophilum isolates within the same Chilean farm and during the same infectious outbreak. J Fish Dis 2023; 46:1085-1096. [PMID: 37357563 DOI: 10.1111/jfd.13828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/27/2023]
Abstract
Flavobacterium psychrophilum is a pathogenic bacterium affecting Chilean salmonid farms. High antigenic and genetic diversity exists among Chilean F. psychrophilum isolates, but the distribution thereof among farms is poorly understood. These epidemiological data are key for developing isolate-specific vaccines. The present study isolated F. psychrophilum in diseased Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) from five freshwater farms between 2018 and 2019. Each farm only raised one salmonid species and was geographically separated from and did not share culturing water with the other farms. Antigenic and genetic analyses were conducted to shed light on the possibility of isolates coexisting within the same farm during outbreaks. A total of 68 Chilean F. psychrophilum isolates were recovered from skin lesions, gills, fins, kidney and spleen of moribund and live fish. Among the 68 Chilean isolates, mPCR-serotyping indicated three major serotypes (i.e. 23.5% type 0; 47.1% type 2; and 26.5% type 4) and, to a lesser degree, serotype 1 (2.9%). Sixteen antigenic groups were detected by slide agglutination. Genetic characterizations by 16S rRNA alleles identified 71% of the isolates as the virulent genogroup CSF259-93 allele. A predominant serotype was associated with each farm, with types 0 and 4 related to Atlantic salmon and types 1 and 2 to rainbow trout. Notwithstanding, several antigenic groups coexisted within some farms. Likewise, the experimental intramuscular challenges (n = 20) demonstrated that the type-2 isolates from rainbow trout were the most pathogenic among isolates recovered from infectious outbreaks in Atlantic salmon, especially as compared to those from types-0 and -4. These results allow us to suggest that prevention measures, specifically vaccines, should be developed according to dominant isolates and with specificity to each farm, that is the use of autogenous or site-specific vaccines.
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Affiliation(s)
- Pedro Ilardi
- Farmacología en Aquacultura Veterinaria FAV S.A., Investigación y Desarrollo, Santiago, Chile
| | - Sara Valdes
- Farmacología en Aquacultura Veterinaria FAV S.A., Laboratorio de Investigación y Desarrollo, Puerto Varas, Chile
| | - Javier Rivera
- Centro Experimental Farmacología en Aquacultura Veterinaria FAV S.A. Abbott (CEFA), Puerto Varas, Chile
| | - Rute Irgang
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile
- Centro FONDAP Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile
| | - Ruben Avendaño-Herrera
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile
- Centro FONDAP Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile
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Bimouhen A, Regragui Z, El Falaki F, Ihazmade H, Benkerroum S, Barakat A, Rguig A, Benamar T, Triki S, Bakri Y, Oumzil H. Circulation patterns and molecular epidemiology of human respiratory syncytial virus over five consecutive seasons in Morocco. Influenza Other Respir Viruses 2023; 17:e13203. [PMID: 37859975 PMCID: PMC10582604 DOI: 10.1111/irv.13203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/05/2023] [Accepted: 09/10/2023] [Indexed: 10/21/2023] Open
Abstract
Background Respiratory syncytial virus (HRSV) is the leading cause of respiratory tract infections in infants and young children. we investigated the prevalence and characteristics of HRSV in Morocco and explored trends in circulating genotypes through partial G gene analysis of HRSV strains prevalent from 2012 to 2017. Methods Respiratory samples were gathered from both outpatients and inpatients meeting ILI or SARI case definitions. The patients' ages varied from 1 month to 99 years old. Nucleic acids were extracted and HRSV type/subtype was detected by RT-qPCR. A subset of positive samples was randomly selected in each epidemic year, the complete viral genome was sequenced, phylogenetic analysis was performed using the MEGA7 program and the genotypes were confirmed. Results The 3679 specimens were collected from 2012 to 2017, of which 726 (19.7%) were positive for HRSV. The 35% (257/726) of HRSV-positives were of the HRSV-A subtype, while the HRSV-B subtype accounted for 61% (442/726). The co-infection rate was 3.7% (27/726). The virus circulates in a periodic pattern, where epidemics occur during the fall months through early spring. HRSV genotype was confirmed in 127 specimens (56 HRSV-A and 71 HRSV-B). Based on phylogenetic analysis, all HRSV-A were ON1 genotype, and HRSV-B were mostly BA9 genotype. HRSV-B belonging to the BA10 genotype was detected in 2012 exclusively. Conclusions BA9, BA10, and ON1 were the only HRSV genotypes detected between 2012 and 2017. Variations in the G gene amino acid chain were identified in local strains, which suggests an increased need for continuous genomic surveillance.
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Affiliation(s)
- Abderrahman Bimouhen
- Laboratory of Human Pathologies Biology, Faculty of SciencesMohammed V University in RabatRabatMorocco
- National Influenza Center, Virology DepartmentNational Institute of Hygiene, Ministry of HealthRabatMorocco
| | - Zakia Regragui
- National Influenza Center, Virology DepartmentNational Institute of Hygiene, Ministry of HealthRabatMorocco
| | - Fatima El Falaki
- National Influenza Center, Virology DepartmentNational Institute of Hygiene, Ministry of HealthRabatMorocco
| | - Hassan Ihazmade
- National Influenza Center, Virology DepartmentNational Institute of Hygiene, Ministry of HealthRabatMorocco
| | - Samira Benkerroum
- National Influenza Center, Virology DepartmentNational Institute of Hygiene, Ministry of HealthRabatMorocco
| | - Amal Barakat
- World Health Organization Regional Office for the Eastern MediterraneanCairoEgypt
| | - Ahmed Rguig
- Directorate of Epidemiology and Disease ControlMinistry of HealthRabatMorocco
| | - Touria Benamar
- Directorate of Epidemiology and Disease ControlMinistry of HealthRabatMorocco
| | - Soumia Triki
- World Health Organization Country Office of MoroccoRabatMorocco
| | - Youssef Bakri
- Laboratory of Human Pathologies Biology, Faculty of SciencesMohammed V University in RabatRabatMorocco
- Center of human pathologies genomic, faculty of Medicine and PharmacyMohammed V university in RabatRabatMorocco
| | - Hicham Oumzil
- National Influenza Center, Virology DepartmentNational Institute of Hygiene, Ministry of HealthRabatMorocco
- Pedagogy and Research Unit of Microbiology, School of Medicine and PharmacyMohammed V University in RabatRabatMorocco
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Zhao B, Jiang Q, Lin J, Wei Q, Li C, Hou Y, Cao B, Zhang L, Ou R, Liu K, Yang T, Xiao Y, Shang H. TBK1 variants in Chinese patients with amyotrophic lateral sclerosis: Genetic analysis and clinical features. Eur J Neurol 2023; 30:3079-3089. [PMID: 37422901 DOI: 10.1111/ene.15973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 03/09/2023] [Accepted: 07/04/2023] [Indexed: 07/11/2023]
Abstract
BACKGROUND AND PURPOSE Haploinsufficiency of TANK-binding kinase 1 (TBK1) loss-of-function (LoF) variants has been shown to be pathogenic in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). However, the genetic spectrum of TBK1 and clinical features of ALS patients with TBK1 variants remain largely unknown in Asians. METHODS Genetic analysis was performed on 2011 Chinese ALS patients. Software was used to predict the deleteriousness of missense variants in TBK1. In addition, PubMed, Embase and Web of Science were searched for related literature. RESULTS Twenty-six TBK1 variants were identified in 33 of 2011 ALS patients, including six novel LoF variants (0.3%) and 20 rare missense variants, 12 of which were predicted to be deleterious (0.6%). In addition to TBK1 variants, 11 patients had other ALS-related gene variants. Forty-two previous studies found that the frequency of TBK1 variants was 1.81% in ALS/FTD patients. The frequency of TBK1 LoF variants in ALS was 0.5% (Asians 0.4%; Caucasian 0.6%) and that of missense variants was 0.8% (Asians 1.0%; Caucasian 0.8%). ALS patients with TBK1 LoF variants affecting the kinase domain had a significantly younger age of onset than patients carrying LoF variants affecting the coiled coil domains CCD1 and CCD2. FTD has a frequency of 10% in Caucasian ALS patients with TBK1 LoF variants, which was not found in our cohort. CONCLUSION Our study expanded the genotypic spectrum of ALS patients with TBK1 variants and found that the clinical manifestations of TBK1 carriers are diverse.
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Affiliation(s)
- Bi Zhao
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
| | - Qirui Jiang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
| | - Junyu Lin
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
| | - Qianqian Wei
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
| | - Chunyu Li
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
| | - Yanbing Hou
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
| | - Bei Cao
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
| | - Lingyu Zhang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
| | - Ruwei Ou
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
| | - Kuncheng Liu
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
| | - Tianmi Yang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
| | - Yi Xiao
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
| | - Huifang Shang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
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Wang Y, Gao Z, Lu Q, Liu B, Jia L, Shen L, Tian Y, Li W, Yan H, Zhang D, Yang P, Fang L, Wang Q, Cui F. Transmissibility quantification of norovirus outbreaks in 2016-2021 in Beijing, China. J Med Virol 2023; 95:e29153. [PMID: 37804388 DOI: 10.1002/jmv.29153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/08/2023] [Accepted: 09/25/2023] [Indexed: 10/09/2023]
Abstract
The transmissibility is a crucial feature for norovirus, yet its quantitative estimation has been limited. Our objective was to estimate the basic reproduction number (R0 ) of norovirus and investigate its variation characteristics. Norovirus outbreaks reported from September 2016 to August 2021 in Beijing were analyzed. The susceptible-infected-removed compartment model was established to estimate R0 . Linear regression models and logistic regression models were used to explore the factors affecting the transmissibility of norovirus. The overall median R0 of norovirus was estimated as 2.1 (interquartile range [IQR] 1.8-2.5), with 650 norovirus outbreaks. The transmissibility of norovirus varied by year, outbreak setting and genotype. The R0 of norovirus during September 2019 to August 2020 (median 2.1, IQR 1.8-2.4) and September 2020 to August 2021 (median 2.0, IQR 1.7-2.3) was lower than that of September 2016 to August 2017 (median 2.3, IQR 1.8-2.7) (β = 0.94, p = 0.05; β = 0.93, p = 0.008). The R0 of norovirus for all other settings was lower than that for kindergarten (median 2.4, IQR 2.0-2.9) (primary school: median 2.0, IQR 1.7-2.4, β = 0.94, p = 0.001; secondary school: median 1.7, IQR 1.5-2.0, β = 0.87, p < 0.001; college: median 1.7, IQR 1.5-1.8, β = 0.89, p = 0.03; other closed settings: median 1.8, IQR 1.5-2.0, β = 0.90, p = 0.004). GⅡ.2[P16] outbreaks had a median R0 of 2.2 (IQR 1.8-2.7), which was higher than that for GⅡ.6[P7] outbreaks (median 1.8, IQR: 1.8-2.0, odds ratio = 0.19, p = 0.03; GⅡ.2[P16] as reference) and mixed-genotype outbreaks (median 1.7, IQR: 1.5-1.8, β = 0.92, p = 0.02; mixed-genotype as reference). In kindergartens and primary schools, norovirus shows increased transmissibility, emphasizing the vulnerable population and high-risk settings. Furthermore, the transmissibility of norovirus may change over time and with virus evolution, necessitating additional research to uncover the underlying mechanisms.
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Affiliation(s)
- Yu Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Zhiyong Gao
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Qingbin Lu
- Department of Laboratory Science and Technology & Vaccine Research Center, School of Public Health, Peking University, Beijing, China
| | - Baiwei Liu
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Lei Jia
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Lingyu Shen
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Yi Tian
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Weihong Li
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Hanqiu Yan
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Daitao Zhang
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Peng Yang
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Liqun Fang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Quanyi Wang
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Fuqiang Cui
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Department of Laboratory Science and Technology & Vaccine Research Center, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing, China
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Xu C, Tang Y, Dong L, Shen Y. Clinical and genetic characteristics of children with cystic fibrosis in Henan China: A single-center retrospective analysis. Pediatr Pulmonol 2023; 58:2865-2870. [PMID: 37477516 DOI: 10.1002/ppul.26601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/19/2023] [Accepted: 07/03/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND Despite the growing awareness of cystic fibrosis (CF) in China, few cases have been reported in Henan, which is the most populous province in the country. This study aimed to describe the clinical phenotype and genotype of children with CF in Henan. METHODS We retrospectively recruited 18 Chinese children with CF who presented to Children's Hospital affiliated to Zhengzhou University from January 2019 to June 2023. The demographic data, imaging examinations, and laboratory tests of the patients were reviewed to clarify the clinical phenotype. Whole exome sequencing was conducted to identify the genotype. RESULTS Respiratory diseases were the main clinical manifestation, including recurrent/persistent pneumonia (88.9%), sinusitis (77.8%), bronchiectasis (77.8%). CF-related liver disease and pancreatic insufficiency were less common. Infant cases had high frequency of pseudo-Bartter Syndrome (80.0%). Chest computed tomography showed bronchiectasis in older children and air trapping in infant cases. The most common pathogens in the airway were Pseudomonas aeruginosa (72.2%) and Staphylococcus aureus (66.7%). Twenty-five different cystic fibrosis transmembrane conductance regulator (CFTR) gene variants were detected, including five novel observations (c.1064C>G[p. Pro355Arg], c.1209+1G>C, c.1925C>G[p. Ser642X], c.2810T>G[p. Leu937Arg], and c.3792delA[p. Gly1265GlufsX13]). The most common variant was c.2909G>A(p. Gly970Asp), with a detected rate of 21.9%. CONCLUSION Children with CF in Henan had varied clinical phenotypes by age, with respiratory disease being predominant. The most frequent CFTR gene variant was c.2909G>A(p. Gly970Asp). This study is the first and most comprehensive one on the clinical phenotype and genotype of children with CF in Henan, China. We also reported the first CF case of Mycobacterium abscessus infection in China.
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Affiliation(s)
- Chunna Xu
- Respiratory Department, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Yu Tang
- Respiratory Department, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Lili Dong
- Respiratory Department, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Yuelin Shen
- Respiratory Department II, National Clinical Research Center for Respiratory Diseases, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
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Møller PL, Rohde PD, Dahl JN, Rasmussen LD, Schmidt SE, Nissen L, McGilligan V, Bentzon JF, Gudbjartsson DF, Stefansson K, Holm H, Winther S, Bøttcher M, Nyegaard M. Combining Polygenic and Proteomic Risk Scores With Clinical Risk Factors to Improve Performance for Diagnosing Absence of Coronary Artery Disease in Patients With de novo Chest Pain. Circ Genom Precis Med 2023; 16:442-451. [PMID: 37753640 DOI: 10.1161/circgen.123.004053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/11/2023] [Indexed: 09/28/2023]
Abstract
BACKGROUND Patients with de novo chest pain, referred for evaluation of possible coronary artery disease (CAD), frequently have an absence of CAD resulting in millions of tests not having any clinical impact. The objective of this study was to investigate whether polygenic risk scores and targeted proteomics improve the prediction of absence of CAD in patients with suspected CAD, when added to the PROMISE (Prospective Multicenter Imaging Study for Evaluation of Chest Pain) minimal risk score (PMRS). METHODS Genotyping and targeted plasma proteomics (N=368 proteins) were performed in 1440 patients with symptoms suspected to be caused by CAD undergoing coronary computed tomography angiography. Based on individual genotypes, a polygenic risk score for CAD (PRSCAD) was calculated. The prediction was performed using combinations of PRSCAD, proteins, and PMRS as features in models using stability selection and machine learning. RESULTS Prediction of absence of CAD yielded an area under the curve of PRSCAD-model, 0.64±0.03; proteomic-model, 0.58±0.03; and PMRS model, 0.76±0.02. No significant correlation was found between the genetic and proteomic risk scores (Pearson correlation coefficient, -0.04; P=0.13). Optimal predictive ability was achieved by the full model (PRSCAD+protein+PMRS) yielding an area under the curve of 0.80±0.02 for absence of CAD, significantly better than the PMRS model alone (P<0.001). For reclassification purpose, the full model enabled down-classification of 49% (324 of 661) of the 5% to 15% pretest probability patients and 18% (113 of 611) of >15% pretest probability patients. CONCLUSIONS For patients with chest pain and low-intermediate CAD risk, incorporating targeted proteomics and polygenic risk scores into the risk assessment substantially improved the ability to predict the absence of CAD. Genetics and proteomics seem to add complementary information to the clinical risk factors and improve risk stratification in this large patient group. REGISTRATION URL: https://www. CLINICALTRIALS gov; Unique identifier: NCT02264717.
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Affiliation(s)
- Peter Loof Møller
- Department of Biomedicine (P.L.M., M.N.), Aarhus University
- Department of Health Science and Technology, Aalborg University (P.L.M., P.D.R., S.E.S., M.N.)
| | - Palle Duun Rohde
- Department of Health Science and Technology, Aalborg University (P.L.M., P.D.R., S.E.S., M.N.)
| | - Jonathan Nørtoft Dahl
- Department of Clinical Medicine (J.N.D., L.D.R., L.N., J.F.B., S.W., M.B.), Aarhus University
- Department of Cardiology, Gødstrup Hospital, Herning, Denmark (J.N.D., L.D.R., L.N., S.W., M.B.)
| | - Laust Dupont Rasmussen
- Department of Clinical Medicine (J.N.D., L.D.R., L.N., J.F.B., S.W., M.B.), Aarhus University
- Department of Cardiology, Gødstrup Hospital, Herning, Denmark (J.N.D., L.D.R., L.N., S.W., M.B.)
| | - Samuel Emil Schmidt
- Department of Health Science and Technology, Aalborg University (P.L.M., P.D.R., S.E.S., M.N.)
| | - Louise Nissen
- Department of Clinical Medicine (J.N.D., L.D.R., L.N., J.F.B., S.W., M.B.), Aarhus University
- Department of Cardiology, Gødstrup Hospital, Herning, Denmark (J.N.D., L.D.R., L.N., S.W., M.B.)
| | - Victoria McGilligan
- Personalized Medicine Centre, Ulster University, Derry, Northern Ireland (V.M.)
| | - Jacob F Bentzon
- Department of Clinical Medicine (J.N.D., L.D.R., L.N., J.F.B., S.W., M.B.), Aarhus University
- Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (J.F.B.)
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Inc. (D.F.G., K.S., H.H.)
- School of Engineering and Natural Sciences (D.F.G.)
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc. (D.F.G., K.S., H.H.)
- Faculty of Medicine, University of Iceland, Reykjavik (K.S.)
| | - Hilma Holm
- deCODE genetics/Amgen, Inc. (D.F.G., K.S., H.H.)
| | - Simon Winther
- Department of Clinical Medicine (J.N.D., L.D.R., L.N., J.F.B., S.W., M.B.), Aarhus University
- Department of Cardiology, Gødstrup Hospital, Herning, Denmark (J.N.D., L.D.R., L.N., S.W., M.B.)
| | - Morten Bøttcher
- Department of Clinical Medicine (J.N.D., L.D.R., L.N., J.F.B., S.W., M.B.), Aarhus University
- Department of Cardiology, Gødstrup Hospital, Herning, Denmark (J.N.D., L.D.R., L.N., S.W., M.B.)
| | - Mette Nyegaard
- Department of Biomedicine (P.L.M., M.N.), Aarhus University
- Department of Health Science and Technology, Aalborg University (P.L.M., P.D.R., S.E.S., M.N.)
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Izhari MA. Molecular Mechanisms of Resistance to Direct-Acting Antiviral (DAA) Drugs for the Treatment of Hepatitis C Virus Infections. Diagnostics (Basel) 2023; 13:3102. [PMID: 37835845 PMCID: PMC10572573 DOI: 10.3390/diagnostics13193102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/23/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Hepatitis C virus (HCV) is a hepatotropic virus that affects millions of human lives worldwide. Direct-acting antiviral (DAA) regimens are the most effective HCV treatment option. However, amino acid substitution-dependent resistance to DAAs has been a major challenge. This study aimed to determine the increasing risk of DAA resistance due to substitutions in DAA target non-structural proteins (NS3/4A, NS5A, and NS5B). Using a Sequence Retrieval System (SRS) at the virus pathogen resource (ViPR/BV-BRC), n = 32763 target protein sequences were retrieved and analyzed for resistance-associated amino acid substitutions (RAASs) by the Sequence Feature Variant Type (SFVT) antiviral-resistance assessment modeling tool. Reference target protein sequences with 100% identity were retried from UniProt following NCBI BLAST. The types and locations of RAASs were identified and visualized by AlphaFold and PyMol. Linux-r-base/R-studio was used for the data presentation. Multi-drug-resistant variants of NS3/4A in genotype 1 (n = 9) and genotype 5 (n = 5) along with DAA-specific NS3/4A, NS5A, and NS5B variants were identified pan-genotypically. A total of 27 variants (RAASs) of all the targets were identified. Fourteen genotype 1-specific substitutions: V1196A, V1158I, D1194A/T/G, R1181K, T1080S, Q1106R, V1062A, S1148G, A1182V, Y2065N, M2000T, and L2003V were identified. The most frequent substitutions were V1062L and L2003M, followed by Q2002H. L2003V, Q2002H, M2000T, Y2065N, and NL2003M of NS5A and L2003M of NS5B conferred resistance to daclatasvir. S2702T NS5B was the sofosbuvir-resistant variant. D1194A NS3/4A was triple DAA (simeprevir, faldaprevir, and asunaprevir) resistant. The double-drug resistant variants R1181K (faldaprevir and asunaprevir), A1182V and Q1106K/R (faldaprevir and simeprevir), T1080S (faldaprevir and telaprevir), and single drug-resistant variants V1062L (telaprevir), D1194E/T (simeprevir), D1194G (asunaprevir), S1148A/G (simeprevir), and Q1106L (Boceprevir) of NS3/4A were determined. The molecular phenomenon of DAA resistance is paramount in the development of HCV drug candidates. RAASs in NS3, NS5A, and NS5B reduce the susceptibility to DAAs; therefore, continuous RAAS-dependent resistance profiling in HCV is recommended to minimize the probability of DAA therapeutic failure.
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Affiliation(s)
- Mohammad Asrar Izhari
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha 65522, Saudi Arabia
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Zhao XJ, Bai CY, Li XY, Wang L, Wang RP, Xia Y, Liu G, Zhao HL, Xu HZ. A Novel Variant in the Desmoplakin Gene in One Case of the Rare Carvajal Syndrome with Dilated Cardiomyopathy: A Case Report and Literature Review. Clin Cosmet Investig Dermatol 2023; 16:2737-2748. [PMID: 37799505 PMCID: PMC10547600 DOI: 10.2147/ccid.s429030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/14/2023] [Indexed: 10/07/2023]
Abstract
Carvajal syndrome is a rare hereditary cardiocutaneous syndrome caused by the variants of the desmoplakin (DSP) gene. In this study, we report a patient of Carvajal syndrome with a novel homozygous missense variant of DSP gene. We diagnosed a 7-year-old female patient with Carvajal syndrome characterized by dilated cardiomyopathy, palmoplantar keratoderma, woolly hair, and dental dysplasia, who disclosed a novel homozygous missense variant c.4597C > T (p.Q1533X) in exon 6 of the DSP gene found for the first time. Both her parents were heterozygous for the identified nonsense variant c.4597C > T (p.Q1533X) in DSP gene but neither showed evidence of Carvajal syndrome, indicating that this novel variant causes the disease in an autosomal recessive manner. Genotypes of Carvajal syndrome are even broader than so far anticipated. When patients with dilated cardiomyopathy, palmoplantar keratoderma, woolly hair, and dental dysplasia are found in clinical practice, Carvajal syndrome should be highly suspected, and family gene sequencing should be actively carried out.
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Affiliation(s)
- Xiu-Jie Zhao
- Department of Cardiology, The First Hospital of Hebei Medical University, Shijiazhuang, 050031, People’s Republic of China
| | - Chun-Yu Bai
- Department of Cardiology, Shijiazhuang Great Wall Cardiovascular Hospital, Shijiazhuang, 050035, People’s Republic of China
| | - Xiao-Yan Li
- Department of Cardiology, The First Hospital of Hebei Medical University, Shijiazhuang, 050031, People’s Republic of China
| | - Lei Wang
- Department of Cardiology, Shijiazhuang Great Wall Cardiovascular Hospital, Shijiazhuang, 050035, People’s Republic of China
| | - Ren-Ping Wang
- Department of Cardiology, Shijiazhuang Great Wall Cardiovascular Hospital, Shijiazhuang, 050035, People’s Republic of China
| | - Yue Xia
- Department of Cardiology, The First Hospital of Hebei Medical University, Shijiazhuang, 050031, People’s Republic of China
- Department of Cardiology, Shijiazhuang Great Wall Cardiovascular Hospital, Shijiazhuang, 050035, People’s Republic of China
| | - Gang Liu
- Department of Cardiology, The First Hospital of Hebei Medical University, Shijiazhuang, 050031, People’s Republic of China
| | - Hong-Liang Zhao
- Department of Cardiology, The First Hospital of Hebei Medical University, Shijiazhuang, 050031, People’s Republic of China
| | - Hong-Zun Xu
- Department of Cardiology, Shijiazhuang Great Wall Cardiovascular Hospital, Shijiazhuang, 050035, People’s Republic of China
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Weng YH, Yu WT, Luo YP, Liu C, Gu XX, Chen HY, Liu HB. Association between miR-365 polymorphism and ischemic stroke in a Chinese population. Front Neurol 2023; 14:1260230. [PMID: 37840919 PMCID: PMC10569467 DOI: 10.3389/fneur.2023.1260230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 08/30/2023] [Indexed: 10/17/2023] Open
Abstract
Background Ischemic stroke (IS) represents a major cause of morbidity and mortality across the globe. The aberrant expression of miR-365 has been found to be implicated in a wide array of human diseases, including atherosclerosis and cancer. Studies on single-nucleotide polymorphisms (SNPs) in miRNA genes can help gain insight into the susceptibility to the condition. This study aimed to examine the relationship between miR-365 SNPs and the risk of IS. Methods The study recruited 215 IS patients and 220 controls. The SNPscans genotyping was employed to genotype three polymorphic loci (rs121224, rs30230, and rs178553) of miR-365. The relative expression of miR-365 in peripheral blood mononuclear cells of the patients and controls was determined by using real-time quantitative PCR. Results The miR-365 rs30230 polymorphism exhibited a significant association with the risk of developing IS (TC vs. CC: adjusted OR = 0.55, 95% CI: 0.33-0.92, P = 0.022; TT vs. CC: adjusted OR = 0.34, 95% CI: 0.14-0.85, P = 0.021; TC +TT vs. CC: adjusted OR = 0.51, 95% CI: 0.31-0.83, P = 0.007; T vs. C: adjusted OR = 0.57, 95% CI: 0.39-0.83, P = 0.004). Haplotype analysis revealed that the C-T-G haplotype was associated with a decreased risk of IS (OR = 0.68, 95% CI: 0.46-1.00, P = 0.047). Furthermore, miR-365 expression was significantly higher in IS patients than in controls (P < 0.001). Interestingly, patients with rs30230 TC or TT genotypes had lower miR-365 levels compared to their counterparts with CC genotypes (P < 0.001). Conclusions The miR-365 rs30230 polymorphism might bear an association with IS susceptibility in the Chinese population, and the rs30230 TC/TT genotype might be a protective factor against IS.
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Affiliation(s)
- Yin-Hua Weng
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin, China
- College of Medical Laboratory Science, Guilin Medical University, Guilin, China
- School of Clinical Medicine, Guilin Medical University, Guilin, China
| | - Wen-Tao Yu
- School of Clinical Medicine, Guilin Medical University, Guilin, China
| | - Yan-Ping Luo
- School of Clinical Medicine, Guilin Medical University, Guilin, China
| | - Chao Liu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin, China
- College of Medical Laboratory Science, Guilin Medical University, Guilin, China
- School of Clinical Medicine, Guilin Medical University, Guilin, China
| | - Xi-Xi Gu
- School of Clinical Medicine, Guilin Medical University, Guilin, China
| | - Huo-Ying Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin, China
- College of Medical Laboratory Science, Guilin Medical University, Guilin, China
- Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, Guangxi Key Laboratory of Metabolic Reprogramming and Intelligent Medical Engineering for Chronic Diseases, The Second Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Hong-Bo Liu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin, China
- College of Medical Laboratory Science, Guilin Medical University, Guilin, China
- Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, Guangxi Key Laboratory of Metabolic Reprogramming and Intelligent Medical Engineering for Chronic Diseases, The Second Affiliated Hospital of Guilin Medical University, Guilin, China
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196
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Babigumira BM, Sölkner J, Mészáros G, Wurzinger M, Pfeiffer C, Lewis CRG, Lukuyu B, Ouma E, Marshall K. The effect of the proportion of Modern European ancestry on grower and sow performance of pigs in smallholder systems in Uganda. Front Genet 2023; 14:1123826. [PMID: 37818103 PMCID: PMC10561553 DOI: 10.3389/fgene.2023.1123826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 08/21/2023] [Indexed: 10/12/2023] Open
Abstract
Several factors, including breed, lead to divergent performance of pigs for production and reproduction traits in different environments. A recent genomics study showed that Modern European (ME) pig breeds contribute to the ancestry of smallholder pigs in the Hoima and Kamuli districts, Uganda. These pigs were also involved in a longitudinal study with several traits recorded, including 540 body weights (WT) of 374 growing pigs, 195 records of total number of piglets born alive (TBA) of 157 sows, and 110 total number weaned (TNW) records of 94 sows. Linear mixed-effects models were used to test for the significance of environmental effects, including housing system, geographic location, and the season when the events occurred as well as animal-specific effects like age, sex, parity, and farrow-to-weaning interval. Stepwise model reduction starting from models with all main effects and pairwise interactions was applied. The final models were then expanded to include proportions of Modern European (ME) ancestry for the subset of animals genotyped, following genomic ancestry analysis based on a Porcine 50K SNP Chip. ME ancestry proportions ranged from 0.02 to 0.50 and were categorized into three classes (low/medium/high ME) based on 33.3% quantiles. The effects of ME classes on WT and TBA were not significant. ME showed a significant effect on TNW. Sows with a high proportion of ME weaned 2.4 piglets more than the low group, the medium ME group being intermediate. This study used genomic data to investigate the effects of genetic ancestry on the performance of smallholder pigs in Uganda. The proportion of Modern European ancestry did not exceed 0.50, therefore not allowing for the comparison of local versus pure "exotic" types of pigs. For the range of ancestries observed, which is the relevant one for current smallholder systems in Uganda, differences were small for the body weight of growing pigs and the number of piglets born alive, while higher proportions of ME ancestry resulted in significantly more piglets weaned. The availability of genotypes of a higher number of growing pigs would have been beneficial for drawing conclusions on the effect of ME ancestry on the growth rates of smallholder pigs in Uganda.
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Affiliation(s)
- Brian Martin Babigumira
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
- International Livestock Research Institute, Kampala, Uganda
| | - Johann Sölkner
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Gábor Mészáros
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Maria Wurzinger
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christina Pfeiffer
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
- PIG Austria GmbH, Steinhaus, Austria
| | | | - Ben Lukuyu
- International Livestock Research Institute, Kampala, Uganda
| | - Emily Ouma
- International Livestock Research Institute, Kampala, Uganda
| | - Karen Marshall
- International Livestock Research Institute, Nairobi, Kenya
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197
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Dratwa M, Łacina P, Butrym A, Porzuczek D, Mazur G, Bogunia-Kubik K. Telomere length and hTERT genetic variants as potential prognostic markers in multiple myeloma. Sci Rep 2023; 13:15792. [PMID: 37737335 PMCID: PMC10517131 DOI: 10.1038/s41598-023-43141-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/20/2023] [Indexed: 09/23/2023] Open
Abstract
Telomere dysfunction is a notable event observed in many cancers contributing to their genomic instability. A major factor controlling telomere stability is the human telomerase reverse transcriptase catalytic subunit (hTERT). Telomere shortening has been observed in multiple myeloma (MM), a plasma cell malignancy with a complex and heterogeneous genetic background. In the present study, we aimed to analyse telomere length and hTERT genetic variants as potential markers of risk and survival in 251 MM patients. We found that telomere length was significantly shorter in MM patients than in healthy individuals, and patients with more advanced disease (stage III according to the International Staging System) had shorter telomeres than patients with less advanced disease. MM patients with hTERT allele rs2736100 T were characterized with significantly shorter progression-free survival (PFS). Moreover, allele rs2736100 T was also found to be less common in patients with disease progression in response to treatment. hTERT rs2853690 T was associated with higher haemoglobin blood levels and lower C-reactive protein. In conclusion, our results suggest that telomere length and hTERT genetic variability may affect MM development and can be potential prognostic markers in this disease.
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Affiliation(s)
- Marta Dratwa
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Piotr Łacina
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Aleksandra Butrym
- Department of Cancer Prevention and Therapy, Wroclaw Medical University, Wrocław, Poland
| | - Diana Porzuczek
- Department of Internal, Occupational Diseases, Hypertension and Clinical Oncology, Wroclaw Medical University, Wrocław, Poland
| | - Grzegorz Mazur
- Department of Internal, Occupational Diseases, Hypertension and Clinical Oncology, Wroclaw Medical University, Wrocław, Poland
| | - Katarzyna Bogunia-Kubik
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland.
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198
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Chang SC, Kao CY, Lin LC, Hidrosollo JH, Lu JJ. Lugdunin production and activity in Staphylococcus lugdunensis isolates are associated with its genotypes. Microbiol Spectr 2023; 11:e0129823. [PMID: 37732790 PMCID: PMC10580833 DOI: 10.1128/spectrum.01298-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/20/2023] [Indexed: 09/22/2023] Open
Abstract
Lugdunin produced by Staphylococcus lugdunensis has been shown to have broad inhibitory activity against Gram-positive bacteria; however, lugdunin activity among S. lugdunensis isolates and its association with different agr, SCCmec, and sequence types remain unclear. We used matrix-assisted laser desorption ionization-time-of-flight mass spectrometry to identify S. lugdunensis and collected 202 S. lugdunensis samples for further assays. Agar spot tests were performed to characterize S. lugdunensis lugdunin production and activity. Multilocus sequence typing, SCCmec, and agr genotyping were performed on S. lugdunensis. In all, 91 Staphylococcus aureus strains with varying vancomycin susceptibilities were used to examine lugdunin activity in S. lugdunensis. In total, 48 S. lugdunensis strains (23.8%) were found to be oxacillin-resistant S. lugdunensis (ORSL), whereas 154 (76.2%) were classified as oxacillin-sensitive S. lugdunensis (OSSL). Moreover, 16 (33.3%) ORSL and 35 (22.7%) OSSL strains showed antibacterial activity against S. aureus. Our data showed that most lugdunin-producing ORSL strains (14/48, 29.2%) were of ST3-SCCmec V-agr II genotypes, whereas most lugdunin-producing OSSL strains (15/154, 9.7%) were of ST3-agr II, followed by ST1-agr I (10/154, 6.5%). Our data also revealed that lugdunin exhibited weak inhibitory activity against the VISA ST239 isolate. In addition, we observed that ST239 VSSA was more resistant to lugdunin than ST5, ST59, and ST45 VSSA. Taken together, our data pioneered the epidemiology of lugdunin production in S. lugdunensis isolates and revealed its association with genotypes. However, further molecular and bioinformatics investigations are needed to elucidate the regulatory mechanisms of lugdunin production and activity. IMPORTANCE Lugdunin is active against both methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci by dissipating their membrane potential. However, the association of lugdunin activity with the genotypes of Staphylococcus lugdunensis has not been addressed. Here, we show the high prevalence of lugdunin-producing strains among ST1 (83.3%), ST2 (66.7%), and ST3 (53.3%) S. lugdunensis. Moreover, we identified the antibacterial activity of lugdunin-producing strains against VISA and hVISA. These results shed light on the potential application of lugdunin for the treatment of drug-resistant pathogens.
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Affiliation(s)
- Shih-Cheng Chang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Cheng-Yen Kao
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Lee-Chung Lin
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Jazon Harl Hidrosollo
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Jang-Jih Lu
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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Amin AB, Cates JE, Liu Z, Wu J, Ali I, Rodriguez A, Panjwani J, Tate JE, Lopman BA, Parashar UD. Rotavirus genotypes in the post-vaccine era: A systematic review and meta-analysis of global, regional, and temporal trends in settings with and without rotavirus vaccine introduction. J Infect Dis 2023:jiad403. [PMID: 37738554 DOI: 10.1093/infdis/jiad403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/31/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND Even moderate differences in rotavirus vaccine effectiveness against non-vaccine genotypes may exert selective pressures on circulating rotaviruses. Whether this vaccine effect or natural temporal fluctuations underlie observed changes in genotype distributions is unclear. METHODS We systematically reviewed studies reporting rotavirus genotypes from children <5 years of age globally between 2005 and 2023. We compared rotavirus genotypes between vaccine-introducing and non-introducing settings globally and by World Health Organization (WHO) region, calendar time, and time since vaccine introduction. RESULTS Crude pooling of genotype data from 361 studies indicated higher G2P[4], a non-vaccine genotype, prevalence in vaccine-introducing settings, both globally and by WHO region. This difference did not emerge when examining genotypes over time in the Americas, the only region with robust longitudinal data. Relative to non-introducing settings, G2P[4] detections were more likely in settings with recent introduction (e.g. 1-2 years post-introduction aOR: 4.39 (95% CI: 2.87-6.72)) but were similarly likely in settings with more time elapsed since introduction, (e.g. 7 or more years aOR (1.62 95% CI: 0.49-5.37)). CONCLUSIONS When accounting for both regional and temporal trends, there was no substantial evidence of long-term vaccine-related selective pressures on circulating genotypes. Increased prevalence of G2P[4] may be transient after rotavirus vaccine introduction.
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Affiliation(s)
- Avnika B Amin
- Rollins School of Public Health, Emory University, Atlanta, Georgia, United States
| | - Jordan E Cates
- Viral Gastroenteritis Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Zihao Liu
- Rollins School of Public Health, Emory University, Atlanta, Georgia, United States
| | - Joanne Wu
- Rollins School of Public Health, Emory University, Atlanta, Georgia, United States
| | - Iman Ali
- CDC Foundation, Atlanta, Georgia, United States
| | - Alexia Rodriguez
- Rollins School of Public Health, Emory University, Atlanta, Georgia, United States
| | - Junaid Panjwani
- Viral Gastroenteritis Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Jacqueline E Tate
- Viral Gastroenteritis Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Benjamin A Lopman
- Rollins School of Public Health, Emory University, Atlanta, Georgia, United States
| | - Umesh D Parashar
- Viral Gastroenteritis Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
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200
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Reuter G, Boros Á, Pankovics P. Molecular epidemiology and characterization of endemic, epidemic and imported hepatitis A virus (HAV) strains in Hungary (2003-2022). Acta Microbiol Immunol Hung 2023; 70:246-251. [PMID: 37490367 DOI: 10.1556/030.2023.02099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 07/12/2023] [Indexed: 07/27/2023]
Abstract
Hepatitis A virus (HAV) is one of the most important etiological agents of acute viral hepatitis but comprehensive molecular epidemiological study with chrono-phylogeographical data are not available from Hungary.Between 2003 and 2022, a total of 8,307 HAV infections were registered officially in Hungary of which 400 (4.8%) HAV IgM antibody-positive serum samples were collected countrywide. HAV genomic RNA was successfully detected in 216/400 (54%) sera by RT-PCR subsequently confirmed by sequencing. The complete nucleotide sequences of VP1 region were determined in 32 representative HAV strains. Based on the sequence analysis, 150 (69.4%) strains were characterized as HAV sub-genotype IA and 66 (30.6%) as sub-genotype IB, respectively. Based on the combined epidemiological and molecular data, epidemic, endemic, and imported HAV strains were also characterized. The first two registered countrywide outbreaks started among men-sex-with men (MSM) in 2011 (sub-genotype IA) and 2021 (sub-genotype IB), the continuously circulating endemic/domestic HAV strain (sub-genotype IA) in East Hungary and the travel-related sub-genotype IB strains from Egypt should be highlighted. All HAV strains are deposited in the HAVNET database (https://www.rivm.nl/en/havnet).In this 20-year-long comprehensive molecular epidemiological study, we report the genetic characterization and geographic distribution of endemic, epidemic and imported HAV strains for the first time in Hungary with continuous co-circulation of sub-genotypes IA and IB HAV strains since 2003. These data provide basic information about the HAV situation in the country in an international context and can promote more effective national public health intervention strategies for the prevention of HAV transmissions and infections.
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Affiliation(s)
- Gábor Reuter
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Ákos Boros
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Péter Pankovics
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
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