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Liu J, Zheng W, Wang W, Yang X, Huang Y, Cui P, Ma Z, Zeng X, Zhai R, Weng X, Wu W, Zhang X. Identification of AGO2 and PLEC genes polymorphisms in Hu sheep and their relationship with body size traits. Anim Biotechnol 2024; 35:2295926. [PMID: 38149679 DOI: 10.1080/10495398.2023.2295926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
The body size traits are major traits in livestock, which intuitively displays the development of the animal's bones and muscles. This study used PCR amplification, Sanger sequencing, KASPar genotyping, and quantitative real-time reverse transcription PCR (qRT-PCR) to analyze the Single-nucleotide polymorphism and expression characteristics of Argonaute RISC catalytic component 2 (AGO2) and Plectin (PLEC) genes in Hu sheep. Two intron mutations were found in Hu sheep, which were AGO2 g.51700 A > C and PLEC g.23157 C > T, respectively. Through association analysis of two mutation sites and body size traits, it was found that AGO2 g.51700 A > C mainly affects the chest and cannon circumference of Hu sheep of while PLEC g.23157 C mainly affects body height and body length. The combined genotypes of AGO2 and PLEC genes with body size traits showed SNPs at the AGO2 g.51700 A > C and PLEC g.23157 C > T loci significantly improved the body size traits of Hu sheep. In addition, the AGO2 gene has the highest expression levels in the heart, rumen, and tail fat, and the PLEC gene is highly expressed in the heart. These two loci can provide new research ideas for improving the body size traits of Hu sheep.
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Affiliation(s)
- Jia Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Wenxin Zheng
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, China
| | - Weimin Wang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaobin Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yongliang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Panpan Cui
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiwen Zeng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Rui Zhai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiuxiu Weng
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Weiwei Wu
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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Leser JS, Frost JL, Wilson CJ, Rudy MJ, Clarke P, Tyler KL. VP1 is the primary determinant of neuropathogenesis in a mouse model of enterovirus D68 acute flaccid myelitis. J Virol 2024; 98:e0039724. [PMID: 38869283 PMCID: PMC11264684 DOI: 10.1128/jvi.00397-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 05/16/2024] [Indexed: 06/14/2024] Open
Abstract
Enterovirus D68 (EV-D68) is an emerging pathogen that can cause severe respiratory and neurologic disease [acute flaccid myelitis (AFM)]. Intramuscular (IM) injection of neonatal Swiss Webster (SW) mice with US/IL/14-18952 (IL52), a clinical isolate from the 2014 EV-D68 epidemic, results in many of the pathogenic features of human AFM, including viral infection of the spinal cord, death of motor neurons, and resultant progressive paralysis. In distinction, CA/14-4231 (CA4231), another clinical isolate from the 2014 EV-D68 outbreak, does not cause paralysis in mice, does not grow in the spinal cord, and does not cause motor neuron loss following IM injection. A panel of chimeric viruses containing sequences from IL52 and CA4231 was used to demonstrate that VP1 is the main determinant of EV-D68 neurovirulence following IM injection of neonatal SW mice. VP1 contains four amino acid differences between IL52 and CA4231. Mutations resulting in substituting these four amino acids (CA4231 residues into the IL52 polyprotein) completely abolished neurovirulence. Conversely, mutations resulting in substituting VP1 IL52 amino acid residues into the CA4231 polyprotein created a virus that induced paralysis to the same degree as IL52. Neurovirulence following infection of neonatal SW mice with parental and chimeric viruses was associated with viral growth in the spinal cord. IMPORTANCE Emerging viruses allow us to investigate mutations leading to increased disease severity. Enterovirus D68 (EV-D68), once the cause of rare cases of respiratory illness, recently acquired the ability to cause severe respiratory and neurologic disease. Chimeric viruses were used to demonstrate that viral structural protein VP1 determines growth in the spinal cord, motor neuron loss, and paralysis following intramuscular (IM) injection of neonatal Swiss Webster (SW) mice with EV-D68. These results have relevance for predicting the clinical outcome of future EV-D68 epidemics as well as targeting retrograde transport as a potential strategy for treating virus-induced neurologic disease.
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Affiliation(s)
- J. Smith Leser
- Department of Neurology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Joshua L. Frost
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Courtney J. Wilson
- Department of Neurology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Michael J. Rudy
- Department of Neurology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Penny Clarke
- Department of Neurology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Kenneth L. Tyler
- Department of Neurology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Division of Infectious Disease, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
- Neurology Service, Rocky Mountain VA Medical Center, Aurora, Colorado, USA
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Hossam Abdelmonem B, Abdelaal NM, Anwer EKE, Rashwan AA, Hussein MA, Ahmed YF, Khashana R, Hanna MM, Abdelnaser A. Decoding the Role of CYP450 Enzymes in Metabolism and Disease: A Comprehensive Review. Biomedicines 2024; 12:1467. [PMID: 39062040 PMCID: PMC11275228 DOI: 10.3390/biomedicines12071467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 07/28/2024] Open
Abstract
Cytochrome P450 (CYP450) is a group of enzymes that play an essential role in Phase I metabolism, with 57 functional genes classified into 18 families in the human genome, of which the CYP1, CYP2, and CYP3 families are prominent. Beyond drug metabolism, CYP enzymes metabolize endogenous compounds such as lipids, proteins, and hormones to maintain physiological homeostasis. Thus, dysregulation of CYP450 enzymes can lead to different endocrine disorders. Moreover, CYP450 enzymes significantly contribute to fatty acid metabolism, cholesterol synthesis, and bile acid biosynthesis, impacting cellular physiology and disease pathogenesis. Their diverse functions emphasize their therapeutic potential in managing hypercholesterolemia and neurodegenerative diseases. Additionally, CYP450 enzymes are implicated in the onset and development of illnesses such as cancer, influencing chemotherapy outcomes. Assessment of CYP450 enzyme expression and activity aids in evaluating liver health state and differentiating between liver diseases, guiding therapeutic decisions, and optimizing drug efficacy. Understanding the roles of CYP450 enzymes and the clinical effect of their genetic polymorphisms is crucial for developing personalized therapeutic strategies and enhancing drug responses in diverse patient populations.
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Affiliation(s)
- Basma Hossam Abdelmonem
- Institute of Global Health and Human Ecology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (B.H.A.); (M.A.H.); (Y.F.A.); (R.K.); (M.M.H.)
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences & Arts (MSA), Giza 12451, Egypt
| | - Noha M. Abdelaal
- Biotechnology Graduate Program, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (N.M.A.); (E.K.E.A.); (A.A.R.)
| | - Eman K. E. Anwer
- Biotechnology Graduate Program, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (N.M.A.); (E.K.E.A.); (A.A.R.)
- Department of Microbiology and Immunology, Faculty of Pharmacy, Modern University for Technology and Information, Cairo 4411601, Egypt
| | - Alaa A. Rashwan
- Biotechnology Graduate Program, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (N.M.A.); (E.K.E.A.); (A.A.R.)
| | - Mohamed Ali Hussein
- Institute of Global Health and Human Ecology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (B.H.A.); (M.A.H.); (Y.F.A.); (R.K.); (M.M.H.)
| | - Yasmin F. Ahmed
- Institute of Global Health and Human Ecology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (B.H.A.); (M.A.H.); (Y.F.A.); (R.K.); (M.M.H.)
| | - Rana Khashana
- Institute of Global Health and Human Ecology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (B.H.A.); (M.A.H.); (Y.F.A.); (R.K.); (M.M.H.)
| | - Mireille M. Hanna
- Institute of Global Health and Human Ecology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (B.H.A.); (M.A.H.); (Y.F.A.); (R.K.); (M.M.H.)
| | - Anwar Abdelnaser
- Institute of Global Health and Human Ecology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (B.H.A.); (M.A.H.); (Y.F.A.); (R.K.); (M.M.H.)
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Feng F, Yang G, Ma X, Zhang J, Huang C, Ma X, La Y, Yan P, Zhandui P, Liang C. Polymorphisms within the PRKG1 Gene of Gannan Yaks and Their Association with Milk Quality Characteristics. Foods 2024; 13:1913. [PMID: 38928854 PMCID: PMC11203268 DOI: 10.3390/foods13121913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Yak milk, known as the "liquid gold", is a nutritious food with extensive consumption. Compared with cow milk, yak milk contains higher levels of nutrients such as dry matter, milk fat, and milk protein, which demonstrates great potential for exploitation and utilization. Protein kinase cGMP-dependent 1 (PRKG1) is an important functional molecule in the cGMP signaling pathway, and its significant influence on milk fatty acids has been discovered. The aim of this study is to explore the correlation between single nucleotide polymorphisms (SNPs) in the PRKG1 gene and the quality traits of Gannan yak milk in order to identify candidate molecular markers for Gannan yak breeding. In this study, genotyping was performed on 172 healthy, 4-5-year-old lactating Gannan yaks with similar body types, naturally grazed, and two to three parity. Three SNPs (g.404195C>T, g.404213C>T, and g.760138T>C) were detected in the PRKG1 gene of Gannan yaks, which were uniformly distributed in the yak population. Linkage disequilibrium analysis was conducted, revealing complete linkage disequilibrium between g.404195C>T and g.404213C>T. After conducting a correlation analysis between SNPs in the PRKG1 gene and milk quality in Gannan yaks, we found that PRKG1 SNPs significantly increased the content of casein, protein, and SNFs in yak milk. Among them, the TT homozygous genotype at the PRKG1 g.404195C>T loci exhibited higher casein and protein contents compared to the CC and CT genotypes (p < 0.05). The SNP g.760138T>C locus was associated with casein, protein, SNFs, and TS traits (p < 0.05). The CC genotype had higher casein and protein contents than the TT and TA genotypes (p < 0.05). However, there were no significant differences in milk fat, lactose, and acidity among the three genotypes (p > 0.05). In summary, PRKG1 gene polymorphism can serve as a candidate molecular marker for improving milk quality in Gannan yaks.
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Affiliation(s)
- Fen Feng
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (F.F.); (G.Y.); (X.M.); (J.Z.); (C.H.); (X.M.); (Y.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Guowu Yang
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (F.F.); (G.Y.); (X.M.); (J.Z.); (C.H.); (X.M.); (Y.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xiaoyong Ma
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (F.F.); (G.Y.); (X.M.); (J.Z.); (C.H.); (X.M.); (Y.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Juanxiang Zhang
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (F.F.); (G.Y.); (X.M.); (J.Z.); (C.H.); (X.M.); (Y.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Chun Huang
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (F.F.); (G.Y.); (X.M.); (J.Z.); (C.H.); (X.M.); (Y.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xiaoming Ma
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (F.F.); (G.Y.); (X.M.); (J.Z.); (C.H.); (X.M.); (Y.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Yongfu La
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (F.F.); (G.Y.); (X.M.); (J.Z.); (C.H.); (X.M.); (Y.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Ping Yan
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (F.F.); (G.Y.); (X.M.); (J.Z.); (C.H.); (X.M.); (Y.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Pingcuo Zhandui
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lasa 850004, China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (F.F.); (G.Y.); (X.M.); (J.Z.); (C.H.); (X.M.); (Y.L.); (P.Y.)
- Plateau Agricultural Science and Technology Innovation Center, Lasa 850004, China
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Parsons BL, Beal MA, Dearfield KL, Douglas GR, Gi M, Gollapudi BB, Heflich RH, Horibata K, Kenyon M, Long AS, Lovell DP, Lynch AM, Myers MB, Pfuhler S, Vespa A, Zeller A, Johnson GE, White PA. Severity of effect considerations regarding the use of mutation as a toxicological endpoint for risk assessment: A report from the 8th International Workshop on Genotoxicity Testing (IWGT). ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024. [PMID: 38828778 DOI: 10.1002/em.22599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/13/2024] [Accepted: 04/15/2024] [Indexed: 06/05/2024]
Abstract
Exposure levels without appreciable human health risk may be determined by dividing a point of departure on a dose-response curve (e.g., benchmark dose) by a composite adjustment factor (AF). An "effect severity" AF (ESAF) is employed in some regulatory contexts. An ESAF of 10 may be incorporated in the derivation of a health-based guidance value (HBGV) when a "severe" toxicological endpoint, such as teratogenicity, irreversible reproductive effects, neurotoxicity, or cancer was observed in the reference study. Although mutation data have been used historically for hazard identification, this endpoint is suitable for quantitative dose-response modeling and risk assessment. As part of the 8th International Workshops on Genotoxicity Testing, a sub-group of the Quantitative Analysis Work Group (WG) explored how the concept of effect severity could be applied to mutation. To approach this question, the WG reviewed the prevailing regulatory guidance on how an ESAF is incorporated into risk assessments, evaluated current knowledge of associations between germline or somatic mutation and severe disease risk, and mined available data on the fraction of human germline mutations expected to cause severe disease. Based on this review and given that mutations are irreversible and some cause severe human disease, in regulatory settings where an ESAF is used, a majority of the WG recommends applying an ESAF value between 2 and 10 when deriving a HBGV from mutation data. This recommendation may need to be revisited in the future if direct measurement of disease-causing mutations by error-corrected next generation sequencing clarifies selection of ESAF values.
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Affiliation(s)
- Barbara L Parsons
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Marc A Beal
- Bureau of Chemical Safety, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Kerry L Dearfield
- U.S. Environmental Protection Agency and U.S. Department of Agriculture, Washington, DC, USA
| | - George R Douglas
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Min Gi
- Department of Environmental Risk Assessment, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | | | - Robert H Heflich
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | | | - Michelle Kenyon
- Portfolio and Regulatory Strategy, Drug Safety Research and Development, Pfizer, Groton, Connecticut, USA
| | - Alexandra S Long
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - David P Lovell
- Population Health Research Institute, St George's Medical School, University of London, London, UK
| | | | - Meagan B Myers
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | | | - Alisa Vespa
- Pharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Andreas Zeller
- Pharmaceutical Sciences, pRED Innovation Center Basel, Hoffmann-La Roche Ltd, Basel, Switzerland
| | - George E Johnson
- Swansea University Medical School, Swansea University, Swansea, Wales, UK
| | - Paul A White
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
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Gorlov IP, Gorlova OY, Tsavachidis S, Amos CI. Strength of selection in lung tumors correlates with clinical features better than tumor mutation burden. Sci Rep 2024; 14:12732. [PMID: 38831004 PMCID: PMC11148192 DOI: 10.1038/s41598-024-63468-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/29/2024] [Indexed: 06/05/2024] Open
Abstract
Single nucleotide substitutions are the most common type of somatic mutations in cancer genome. The goal of this study was to use publicly available somatic mutation data to quantify negative and positive selection in individual lung tumors and test how strength of directional and absolute selection is associated with clinical features. The analysis found a significant variation in strength of selection (both negative and positive) among tumors, with median selection tending to be negative even though tumors with strong positive selection also exist. Strength of selection estimated as the density of missense mutations relative to the density of silent mutations showed only a weak correlation with tumor mutation burden. In the "all histology together" analysis we found that absolute strength of selection was strongly correlated with all clinically relevant features analyzed. In histology-stratified analysis selection was strongest in small cell lung cancer. Selection in adenocarcinoma was somewhat higher compared to squamous cell carcinoma. The study suggests that somatic mutation- based quantifying of directional and absolute selection in individual tumors can be a useful biomarker of tumor aggressiveness.
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Affiliation(s)
- Ivan P Gorlov
- Institute for Clinical and Translational Research, Baylor College of Medicine, One Baylor Plaza, Mailstop: BCM451, Houston, TX, 77030, USA.
| | - Olga Y Gorlova
- Institute for Clinical and Translational Research, Baylor College of Medicine, One Baylor Plaza, Mailstop: BCM451, Houston, TX, 77030, USA
| | - Spyridon Tsavachidis
- Institute for Clinical and Translational Research, Baylor College of Medicine, One Baylor Plaza, Mailstop: BCM451, Houston, TX, 77030, USA
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, One Baylor Plaza, Mailstop: BCM451, Houston, TX, 77030, USA
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Rosca OC, Vele OE. Microsatellite Instability, Mismatch Repair, and Tumor Mutation Burden in Lung Cancer. Surg Pathol Clin 2024; 17:295-305. [PMID: 38692812 DOI: 10.1016/j.path.2023.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Since US Food and Drug Administration approval of programmed death ligand 1 (PD-L1) as the first companion diagnostic for immune checkpoint inhibitors (ICIs) in non-small cell lung cancer, many patients have experienced increased overall survival. To improve selection of ICI responders versus nonresponders, microsatellite instability/mismatch repair deficiency (MSI/MMR) and tumor mutation burden (TMB) came into play. Clinical data show PD-L1, MSI/MMR, and TMB are independent predictive immunotherapy biomarkers. Harmonization of testing methodologies, optimization of assay design, and results analysis are ongoing. Future algorithms to determine immunotherapy eligibility might involve complementary use of current and novel biomarkers. Artificial intelligence could facilitate algorithm implementation to convert complex genetic data into recommendations for specific ICIs.
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Affiliation(s)
- Oana C Rosca
- Molecular Pathologist/Cytopathologist, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell; Department of Pathology and Laboratory Medicine, 2200 Northern Boulevard, Suite 104, Greenvale, NY 11548, USA.
| | - Oana E Vele
- Molecular Pathologist/Cytopathologist, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell; Department of Pathology and Laboratory Medicine, Lenox Hill Hospital, New York, NY 10075, USA
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Tuffaha MZ, Castellano D, Colome CS, Gutenkunst RN, Wahl LM. Non-hypermutator cancers access driver mutations through reversals in germline mutational bias. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.591900. [PMID: 38746331 PMCID: PMC11092619 DOI: 10.1101/2024.04.30.591900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Cancer is an evolutionary disease driven by mutations in asexually-reproducing somatic cells. In asexual microbes, bias reversals in the mutation spectrum can speed adaptation by increasing access to previously undersampled beneficial mutations. By analyzing tumors from 20 tissues, along with normal tissue and the germline, we demonstrate this effect in cancer. Non-hypermutated tumors reverse the germline mutation bias and have consistent spectra across tissues. These spectra changes carry the signature of hypoxia, and they facilitate positive selection in cancer genes. Hypermutated and non-hypermutated tumors thus acquire driver mutations differently: hypermutated tumors by higher mutation rates and non-hypermutated tumors by changing the mutation spectrum to reverse the germline mutation bias.
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Affiliation(s)
- Marwa Z. Tuffaha
- Department of Mathematics, Western University, London, Ontario N6A 5B7, Canada
| | - David Castellano
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Claudia Serrano Colome
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Ryan N. Gutenkunst
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Lindi M. Wahl
- Department of Mathematics, Western University, London, Ontario N6A 5B7, Canada
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Xiao M, Ruan Y, Huang J, Dai L, Xu J, Xu H. Association analysis between Acetyl-Coenzyme A Acyltransferase-1 gene polymorphism and growth traits in Xiangsu pigs. Front Genet 2024; 15:1346903. [PMID: 38756449 PMCID: PMC11096523 DOI: 10.3389/fgene.2024.1346903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/15/2024] [Indexed: 05/18/2024] Open
Abstract
Introduction Acetyl-Coenzyme A Acyltransferase-1 (ACAA1) is a peroxisomal acyltransferase involved in fatty acid metabolism. Current evidence does not precisely reveal the effect of the ACAA1 gene on pig growth performance. Methods The present study assessed the mRNA expression levels of the ACAA1 gene in the heart, liver, spleen, lung, kidney of 6-month-old Xiangsu pigs and in the longissimus dorsi muscle at different growth stages (newborn, 6 months and 12 months of age) using RT-qPCR. The relationship between single-nucleotide polymorphisms (SNPs) of ACAA1 gene and growth traits in 6-month-old and 12-month-old Xiangsu pigs was investigated on 184 healthy Xiangsu pigs using Sanger sequencing. Results The ACAA1 gene was expressed in heart, liver, spleen, lung, kidney, and longissimus dorsi muscle of 6-month-old pigs, with the highest level of expression in the liver. ACAA1 gene expression in the longissimus dorsi muscle decreased with age (p < 0.01). In addition, four SNPs were identified in the ACAA1 gene, including exon g.48810 A>G (rs343060194), intron g.51546 T>C (rs319197012), exon g.55035 T>C (rs333279910), and exon g.55088 C>T (rs322138947). Hardy-Weinberg equilibrium (p > 0.05) was found for the four SNPs, and linkage disequilibrium (LD) analysis revealed a strong LD between g.55035 T>C (rs333279910) and g.55088 C>T (rs322138947) (r 2 = 1.000). Association analysis showed that g.48810 A>G (rs343060194), g.51546 T>C (rs319197012), g.55035 T>C (rs333279910), and g.55088 C>T (rs322138947) varied in body weight, body length, body height, abdominal circumference, leg and hip circumference and living backfat thickness between 6-month-old and 12-month-old Xiangsu pigs. Conclusion These findings strongly demonstrate that the ACAA1 gene can be exploited for marker-assisted selection to improve growth-related phenotypes in Xiangsu pigs and present new candidate genes for molecular pig breeding.
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Affiliation(s)
- Meimei Xiao
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, China
- College of Animal Science, Guizhou University, Guiyang, China
| | - Yong Ruan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, China
- College of Animal Science, Guizhou University, Guiyang, China
| | - Jiajin Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, China
- College of Animal Science, Guizhou University, Guiyang, China
| | - Lingang Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, China
- College of Animal Science, Guizhou University, Guiyang, China
| | - Jiali Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, China
- College of Animal Science, Guizhou University, Guiyang, China
| | - Houqiang Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, China
- College of Animal Science, Guizhou University, Guiyang, China
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10
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Alganmi N, Bashanfar A, Alotaibi R, Banjar H, Karim S, Mirza Z, Abusamra H, Al-Attas M, Turkistany S, Abuzenadah A. Uncovering hidden genetic risk factors for breast and ovarian cancers in BRCA-negative women: a machine learning approach in the Saudi population. PeerJ Comput Sci 2024; 10:e1942. [PMID: 38660159 PMCID: PMC11042021 DOI: 10.7717/peerj-cs.1942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/26/2024] [Indexed: 04/26/2024]
Abstract
Breast and ovarian cancers are prevalent worldwide, with genetic factors such as BRCA1 and BRCA2 mutations playing a significant role. However, not all patients carry these mutations, making it challenging to identify risk factors. Researchers have turned to whole exome sequencing (WES) as a tool to identify genetic risk factors in BRCA-negative women. WES allows the sequencing of all protein-coding regions of an individual's genome, providing a comprehensive analysis that surpasses traditional gene-by-gene sequencing methods. This technology offers efficiency, cost-effectiveness and the potential to identify new genetic variants contributing to the susceptibility to the diseases. Interpreting WES data for disease-causing variants is challenging due to its complex nature. Machine learning techniques can uncover hidden genetic-variant patterns associated with cancer susceptibility. In this study, we used the extreme gradient boosting (XGBoost) and random forest (RF) algorithms to identify BRCA-related cancer high-risk genes specifically in the Saudi population. The experimental results exposed that the RF method scored superior performance with an accuracy of 88.16% and an area under the receiver-operator characteristic curve of 0.95. Using bioinformatics analysis tools, we explored the top features of the high-accuracy machine learning model that we built to enhance our knowledge of genetic interactions and find complex genetic patterns connected to the development of BRCA-related cancers. We were able to identify the significance of HLA gene variations in these WES datasets for BRCA-related patients. We find that immune response mechanisms play a major role in the development of BRCA-related cancer. It specifically highlights genes associated with antigen processing and presentation, such as HLA-B, HLA-A and HLA-DRB1 and their possible effects on tumour progression and immune evasion. In summary, by utilizing machine learning approaches, we have the potential to aid in the development of precision medicine approaches for early detection and personalized treatment strategies.
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Affiliation(s)
- Nofe Alganmi
- Computer Science, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Arwa Bashanfar
- Information Technology, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Reem Alotaibi
- Information Technology, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Haneen Banjar
- Computer Science, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sajjad Karim
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Lab Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Zeenat Mirza
- Department of Medical Lab Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- King Fahd Medical Research Center, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Heba Abusamra
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Manal Al-Attas
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Shereen Turkistany
- Center of Innovation Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Adel Abuzenadah
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Lab Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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11
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Chen S, Navickas A, Goodarzi H. Translational adaptation in breast cancer metastasis and emerging therapeutic opportunities. Trends Pharmacol Sci 2024; 45:304-318. [PMID: 38453522 DOI: 10.1016/j.tips.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 03/09/2024]
Abstract
Breast cancer's tendency to metastasize poses a critical barrier to effective treatment, making it a leading cause of mortality among women worldwide. A growing body of evidence is showing that translational adaptation is emerging as a key mechanism enabling cancer cells to thrive in the dynamic tumor microenvironment (TME). Here, we systematically summarize how breast cancer cells utilize translational adaptation to drive metastasis, highlighting the intricate regulation by specific translation machinery and mRNA attributes such as sequences and structures, along with the involvement of tRNAs and other trans-acting RNAs. We provide an overview of the latest findings and emerging concepts in this area, discussing their potential implications for therapeutic strategies in breast cancer.
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Affiliation(s)
- Siyu Chen
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Albertas Navickas
- Institut Curie, PSL Research University, CNRS UMR3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR3348, INSERM U1278, Orsay, France.
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA.
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12
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Chen Z, Zhao F, He Z, Sun H, Xi Q, Yu X, Ding Y, An Z, Wang J, Liu X, Li M, Hao Z, Li S. Expression Localization of the KRT32 Gene and Its Association of Genetic Variation with Wool Traits. Curr Issues Mol Biol 2024; 46:2961-2974. [PMID: 38666915 PMCID: PMC11049001 DOI: 10.3390/cimb46040185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 04/28/2024] Open
Abstract
Changes in keratin gene expression and spatiotemporal regulation determine the compositional content and cellular localization of wool keratin, thereby affecting wool traits. Therefore, keratin gene family member 32 (KRT32) was selected for a study using RT-qPCR, immunofluorescence, and penta-primer amplification refractory mutation system (PARMS) techniques. The results showed that KRT32 mRNA was highly expressed in the skin and localized to the inner root sheath (IRS), outer root sheath (ORS) and dermal papilla (DP). Sequencing results identified eight SNPs in KRT32, and association analyses revealed that the variations were significantly associated with multiple traits in wool (p < 0.05), including MFD, CF and MFC. The constructed haplotype combination H2H3 has higher CF and smaller MFD than other haplotype combination (p < 0.05). In conclusion, KRT32 can be used as a candidate gene for molecular genetic improvement of wool in Gansu Alpine Fine-wool sheep.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.C.); (F.Z.); (Z.H.); (H.S.); (Q.X.); (X.Y.); (Y.D.); (Z.A.); (J.W.); (X.L.); (M.L.); (Z.H.)
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13
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Yeyeodu S, Hanafi D, Webb K, Laurie NA, Kimbro KS. Population-enriched innate immune variants may identify candidate gene targets at the intersection of cancer and cardio-metabolic disease. Front Endocrinol (Lausanne) 2024; 14:1286979. [PMID: 38577257 PMCID: PMC10991756 DOI: 10.3389/fendo.2023.1286979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 12/07/2023] [Indexed: 04/06/2024] Open
Abstract
Both cancer and cardio-metabolic disease disparities exist among specific populations in the US. For example, African Americans experience the highest rates of breast and prostate cancer mortality and the highest incidence of obesity. Native and Hispanic Americans experience the highest rates of liver cancer mortality. At the same time, Pacific Islanders have the highest death rate attributed to type 2 diabetes (T2D), and Asian Americans experience the highest incidence of non-alcoholic fatty liver disease (NAFLD) and cancers induced by infectious agents. Notably, the pathologic progression of both cancer and cardio-metabolic diseases involves innate immunity and mechanisms of inflammation. Innate immunity in individuals is established through genetic inheritance and external stimuli to respond to environmental threats and stresses such as pathogen exposure. Further, individual genomes contain characteristic genetic markers associated with one or more geographic ancestries (ethnic groups), including protective innate immune genetic programming optimized for survival in their corresponding ancestral environment(s). This perspective explores evidence related to our working hypothesis that genetic variations in innate immune genes, particularly those that are commonly found but unevenly distributed between populations, are associated with disparities between populations in both cancer and cardio-metabolic diseases. Identifying conventional and unconventional innate immune genes that fit this profile may provide critical insights into the underlying mechanisms that connect these two families of complex diseases and offer novel targets for precision-based treatment of cancer and/or cardio-metabolic disease.
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Affiliation(s)
- Susan Yeyeodu
- Julius L Chambers Biomedical/Biotechnology Institute (JLC-BBRI), North Carolina Central University, Durham, NC, United States
- Charles River Discovery Services, Morrisville, NC, United States
| | - Donia Hanafi
- Julius L Chambers Biomedical/Biotechnology Institute (JLC-BBRI), North Carolina Central University, Durham, NC, United States
| | - Kenisha Webb
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, United States
| | - Nikia A. Laurie
- Julius L Chambers Biomedical/Biotechnology Institute (JLC-BBRI), North Carolina Central University, Durham, NC, United States
| | - K. Sean Kimbro
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, United States
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14
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Khandia R, Gurjar P, Kamal MA, Greig NH. Relative synonymous codon usage and codon pair analysis of depression associated genes. Sci Rep 2024; 14:3502. [PMID: 38346990 PMCID: PMC10861588 DOI: 10.1038/s41598-024-51909-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/11/2024] [Indexed: 02/15/2024] Open
Abstract
Depression negatively impacts mood, behavior, and mental and physical health. It is the third leading cause of suicides worldwide and leads to decreased quality of life. We examined 18 genes available at the genetic testing registry (GTR) from the National Center for Biotechnological Information to investigate molecular patterns present in depression-associated genes. Different genotypes and differential expression of the genes are responsible for ensuing depression. The present study, investigated codon pattern analysis, which might play imperative roles in modulating gene expression of depression-associated genes. Of the 18 genes, seven and two genes tended to up- and down-regulate, respectively, and, for the remaining genes, different genotypes, an outcome of SNPs were responsible alone or in combination with differential expression for different conditions associated with depression. Codon context analysis revealed the abundance of identical GTG-GTG and CTG-CTG pairs, and the rarity of methionine-initiated codon pairs. Information based on codon usage, preferred codons, rare, and codon context might be used in constructing a deliverable synthetic construct to correct the gene expression level of the human body, which is altered in the depressive state. Other molecular signatures also revealed the role of evolutionary forces in shaping codon usage.
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Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, 462026, MP, India.
| | - Pankaj Gurjar
- Centre for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamilnadu, India
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Mohammad Amjad Kamal
- Joint Laboratory of Artificial Intelligence in Healthcare, Institutes for Systems Genetics and West China School of Nursing, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, 1207, Bangladesh
- Enzymoics, Novel Global Community Educational Foundation, 7 Peterlee place, Hebersham, NSW, 2770, Australia
| | - Nigel H Greig
- Translational Gerontology Branch, Intramural Research Program, National Institute on Aging, NIH, Baltimore, MD, 21224, USA.
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15
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Chen H, Fang X, Shao J, Zhang Q, Xu L, Chen J, Mei Y, Jiang M, Wang Y, Li Z, Chen Z, Chen Y, Yu C, Ma L, Zhang P, Zhang T, Liao Y, Lv Y, Wang X, Yang L, Fu Y, Chen D, Jiang L, Yan F, Lu W, Chen G, Shen H, Wang J, Wang C, Liang T, Han X, Wang Y, Guo G. Pan-Cancer Single-Nucleus Total RNA Sequencing Using snHH-Seq. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2304755. [PMID: 38010945 PMCID: PMC10837386 DOI: 10.1002/advs.202304755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/11/2023] [Indexed: 11/29/2023]
Abstract
Tumor heterogeneity and its drivers impair tumor progression and cancer therapy. Single-cell RNA sequencing is used to investigate the heterogeneity of tumor ecosystems. However, most methods of scRNA-seq amplify the termini of polyadenylated transcripts, making it challenging to perform total RNA analysis and somatic mutation analysis.Therefore, a high-throughput and high-sensitivity method called snHH-seq is developed, which combines random primers and a preindex strategy in the droplet microfluidic platform. This innovative method allows for the detection of total RNA in single nuclei from clinically frozen samples. A robust pipeline to facilitate the analysis of full-length RNA-seq data is also established. snHH-seq is applied to more than 730 000 single nuclei from 32 patients with various tumor types. The pan-cancer study enables it to comprehensively profile data on the tumor transcriptome, including expression levels, mutations, splicing patterns, clone dynamics, etc. New malignant cell subclusters and exploring their specific function across cancers are identified. Furthermore, the malignant status of epithelial cells is investigated among different cancer types with respect to mutation and splicing patterns. The ability to detect full-length RNA at the single-nucleus level provides a powerful tool for studying complex biological systems and has broad implications for understanding tumor pathology.
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Affiliation(s)
- Haide Chen
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
- M20 Genomics, Hangzhou, 311121, China
| | - Xiunan Fang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, 999077, China
| | - Jikai Shao
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
| | - Qi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, 310006, China
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, 310006, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Liwei Xu
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, China
| | | | - Yuqing Mei
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Mengmeng Jiang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
| | - Yuting Wang
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Zhouyang Li
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Zihang Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, 310009, China
| | - Yang Chen
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology, Hangzhou, 310022, China
- The Second Clinical Medical College of Zhejiang Chinese Medical University Hangzhou, Hangzhou, 310053, China
| | - Chengxuan Yu
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Zhejiang Provincial Clinical Research Center for Cancer, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Lifeng Ma
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Peijing Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, 310058, China
| | | | - Yuan Liao
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- M20 Genomics, Hangzhou, 311121, China
| | | | - Xueyi Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Lei Yang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yuting Fu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Daobao Chen
- Department of Breast Surgery, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Liming Jiang
- Department of Radiology, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Feng Yan
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, 310009, China
| | - Wei Lu
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Zhejiang Provincial Clinical Research Center for Cancer, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Gao Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, 310009, China
| | - Huahao Shen
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- State Key Laboratory of Respiratory Disease, Guangzhou, 510120, China
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
| | - Changchun Wang
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, China
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology, Hangzhou, 310022, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, 310006, China
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, 310006, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoping Han
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yongcheng Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, 310058, China
- Institute of Hematology, Zhejiang University, Hangzhou, 310006, China
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16
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Cheng N, Bi C, Shi Y, Liu M, Cao A, Ren M, Xia J, Liang Z. Effect Predictor of Driver Synonymous Mutations Based on Multi-Feature Fusion and Iterative Feature Representation Learning. IEEE J Biomed Health Inform 2024; 28:1144-1151. [PMID: 38096097 DOI: 10.1109/jbhi.2023.3343075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Accurate identification of driver mutations is crucial in genetic studies of human cancers. While numerous cancer driver missense mutations have been identified, research into potential cancer drivers for synonymous mutations has shown limited success to date. Here, we developed a novel machine learning framework, epSMic, for predicting cancer driver synonymous mutations. epSMic employs an iterative feature representation scheme that facilitates the learning of discriminative features from various sequential models in a supervised iterative mode. We constructed the benchmark datasets and encoded the embedding sequence, physicochemical property, and basic information such as conservation and splicing feature. The evaluation results on benchmark test datasets demonstrate that epSMic outperforms existing methods, making it a valuable tool for researchers in identifying functional synonymous mutations in cancer. We hope epSMic can enable researchers to concentrate on synonymous mutations that have a functional impact on cancer.
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17
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Sun H, He Z, Zhao F, Hu J, Wang J, Liu X, Zhao Z, Li M, Luo Y, Li S. Molecular Genetic Characteristics of the Hoxc13 Gene and Association Analysis of Wool Traits. Int J Mol Sci 2024; 25:1594. [PMID: 38338874 PMCID: PMC10855228 DOI: 10.3390/ijms25031594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Homobox C13 (Hoxc13) is an important transcription factor in hair follicle cycle development, and its deletion had been found in a variety of animals leading to abnormal hair growth and disruption of the hair follicle system. In this study, we used immunofluorescence, immunohistochemistry, real-time fluorescence quantitative PCR (RT-qPCR), and Kompetitive Allele-Specific PCR (KASP) genotyping to investigate molecular genetic characteristics of the Hoxc13 gene in Gansu alpine fine-wool sheep. The results revealed that Hoxc13 was significantly expressed during both the anagen and catagen phases (p < 0.05). It was found to be highly expressed predominantly in the dermal papillae and the inner and outer root sheaths, showing a distinct spatiotemporal expression pattern. Two single nucleotide polymorphisms (SNPs) in the exon 1 of Hoxc13, both the individual locus genotypes and the combined haplotypes were found to be correlated with wool length (p < 0.05). It was determined the mutations led to changes in mRNA expression, in which higher expression of this gene was related with longer wool length. In summary, this unique spatiotemporal expression pattern of the Hoxc13 gene may regulate the wool length of Gansu alpine fine-wool sheep, which can be used as a molecular genetic marker for wool traits and thus improve the breed.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, International Wool Research Institute, Gansu Agricultural University, Lanzhou 730070, China; (H.S.); (Z.H.); (F.Z.); (J.H.); (J.W.); (X.L.); (Z.Z.); (M.L.); (Y.L.)
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18
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Ali U, Vungarala S, Tiriveedhi V. Genomic Features of Homologous Recombination Deficiency in Breast Cancer: Impact on Testing and Immunotherapy. Genes (Basel) 2024; 15:162. [PMID: 38397152 PMCID: PMC10887603 DOI: 10.3390/genes15020162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/21/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Genomic instability is one of the well-established hallmarks of cancer. The homologous recombination repair (HRR) pathway plays a critical role in correcting the double-stranded breaks (DSB) due to DNA damage in human cells. Traditionally, the BRCA1/2 genes in the HRR pathway have been tested for their association with breast cancer. However, defects in the HRR pathway (HRD, also termed 'BRCAness'), which has up to 50 genes, have been shown to be involved in tumorigenesis and treatment susceptibility to poly-ADP ribose polymerase inhibitors (PARPis), platinum-based chemotherapy, and immune checkpoint inhibitors (ICIs). A reliable consensus on HRD scores is yet to be established. Emerging evidence suggests that only a subset of breast cancer patients benefit from ICI-based immunotherapy. Currently, albeit with limitations, the expression of programmed death-ligand 1 (PDL1) and tumor mutational burden (TMB) are utilized as biomarkers to predict the favorable outcomes of ICI therapy in breast cancer patients. Preclinical studies demonstrate an interplay between the HRR pathway and PDL1 expression. In this review, we outline the current understanding of the role of HRD in genomic instability leading to breast tumorigenesis and delineate outcomes from various clinical trials. Furthermore, we discuss potential strategies for combining HRD-targeted therapy with immunotherapy to achieve the best healthcare outcomes in breast cancer patients.
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Affiliation(s)
- Umer Ali
- Department of Biological Sciences, Tennessee State University, Nashville, TN 37209, USA;
| | - Sunitha Vungarala
- Meharry-Vanderbilt Alliance, Vanderbilt University Medical Center, Nashville, TN 37209, USA;
| | - Venkataswarup Tiriveedhi
- Department of Biological Sciences, Tennessee State University, Nashville, TN 37209, USA;
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37209, USA
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Karakostis K, Malbert-Colas L, Thermou A, Vojtesek B, Fåhraeus R. The DNA damage sensor ATM kinase interacts with the p53 mRNA and guides the DNA damage response pathway. Mol Cancer 2024; 23:21. [PMID: 38263180 PMCID: PMC10804554 DOI: 10.1186/s12943-024-01933-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND The ATM kinase constitutes a master regulatory hub of DNA damage and activates the p53 response pathway by phosphorylating the MDM2 protein, which develops an affinity for the p53 mRNA secondary structure. Disruption of this interaction prevents the activation of the nascent p53. The link of the MDM2 protein-p53 mRNA interaction with the upstream DNA damage sensor ATM kinase and the role of the p53 mRNA in the DNA damage sensing mechanism, are still highly anticipated. METHODS The proximity ligation assay (PLA) has been extensively used to reveal the sub-cellular localisation of the protein-mRNA and protein-protein interactions. ELISA and co-immunoprecipitation confirmed the interactions in vitro and in cells. RESULTS This study provides a novel mechanism whereby the p53 mRNA interacts with the ATM kinase enzyme and shows that the L22L synonymous mutant, known to alter the secondary structure of the p53 mRNA, prevents the interaction. The relevant mechanistic roles in the DNA Damage Sensing pathway, which is linked to downstream DNA damage response, are explored. Following DNA damage (double-stranded DNA breaks activating ATM), activated MDMX protein competes the ATM-p53 mRNA interaction and prevents the association of the p53 mRNA with NBS1 (MRN complex). These data also reveal the binding domains and the phosphorylation events on ATM that regulate the interaction and the trafficking of the complex to the cytoplasm. CONCLUSION The presented model shows a novel interaction of ATM with the p53 mRNA and describes the link between DNA Damage Sensing with the downstream p53 activation pathways; supporting the rising functional implications of synonymous mutations altering secondary mRNA structures.
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Affiliation(s)
- Konstantinos Karakostis
- Inserm UMRS1131, Institut de Génétique Moléculaire, Paris Cité Université, Hôpital St. Louis, Paris, France.
- Institut de Biotecnologia I de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain.
| | - Laurence Malbert-Colas
- Inserm UMRS1131, Institut de Génétique Moléculaire, Paris Cité Université, Hôpital St. Louis, Paris, France
| | - Aikaterini Thermou
- Inserm UMRS1131, Institut de Génétique Moléculaire, Paris Cité Université, Hôpital St. Louis, Paris, France
| | - Borek Vojtesek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Robin Fåhraeus
- Inserm UMRS1131, Institut de Génétique Moléculaire, Paris Cité Université, Hôpital St. Louis, Paris, France.
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, Brno, Czech Republic.
- Department of Medical Biosciences, Umeå University, Umeå, 90185, Sweden.
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20
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Wei L, Xiao W, Chen B, Zou Z, Zhu J, Li D, Yu J, Yang H. Single nucleotide polymorphisms in the MRFs gene family associated with growth in Nile tilapia. Mol Biol Rep 2024; 51:128. [PMID: 38236311 DOI: 10.1007/s11033-023-08955-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/17/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND Muscle occupies most of the fish body, promoting the proliferation of fish muscle fibers can facilitate rapid growth and increase the body weight of fish. Some studiesSeveral previous suggest that Myogenic regulatory factors (MRFs) play an important role in the growth of fish. OBJECTIVE To investigate the association between the polymorphism of MRFs gene family and growth traits in Nile tilapia (Oreochromis niloticus), get more molecular markers for growth. METHODS Amplified the Nile tilapia MRFs family gene, including Myogenic determination 1 (Myod1), Myogenic determination 2 (Myod2), Myogenin (Myog), Myogenic factor 5 (Myf5), and Myogenic factor 6 (Myf6), single nucleotide polymorphism (SNP) were screened by Sanger sequencing. RESULTS A total of 16 SNP loci were screened, including six for Myf5, six for Myf6, one for Myog, one for Myod1 and two for Myod2. The growth traits were analyzed in relation to these 16 SNP loci, and the results indicated significant associations between all 16 SNP loci and the growth traits (P < 0.05). The linkage disequilibrium analysis revealed that D1 and D2 diplotypes of Myf5 gene, E1, E2, E3 and E4 of Myf6 gene, and F1 diplotype of Myod2 gene were significantly associated with superior growth traits. CONCLUSION There were 6, 6, 1, 1 and 2 growth-related molecular markers in Myf5, Myf6, Myog, Myod1 and Myod2 genes, respectively, which could be applied to the breeding of Nile tilapia.
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Affiliation(s)
- Longjie Wei
- Wuxi Fisheries College, Nanjing Agricultural University, 214081, Wuxi, China
| | - Wei Xiao
- Wuxi Fisheries College, Nanjing Agricultural University, 214081, Wuxi, China.
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, 214081, Wuxi, China.
| | - Binglin Chen
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, 214081, Wuxi, China
| | - Zhiying Zou
- Wuxi Fisheries College, Nanjing Agricultural University, 214081, Wuxi, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, 214081, Wuxi, China
| | - Jinglin Zhu
- Wuxi Fisheries College, Nanjing Agricultural University, 214081, Wuxi, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, 214081, Wuxi, China
| | - Dayu Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, 214081, Wuxi, China
| | - Jie Yu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, 214081, Wuxi, China
| | - Hong Yang
- Wuxi Fisheries College, Nanjing Agricultural University, 214081, Wuxi, China.
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, 214081, Wuxi, China.
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21
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Corzo G, Seeling-Branscomb CE, Seeling JM. Differential Synonymous Codon Selection in the B56 Gene Family of PP2A Regulatory Subunits. Int J Mol Sci 2023; 25:392. [PMID: 38203563 PMCID: PMC10778929 DOI: 10.3390/ijms25010392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/18/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
Protein phosphatase 2A (PP2A) functions as a tumor suppressor and consists of a scaffolding, catalytic, and regulatory subunit. The B56 gene family of regulatory subunits impart distinct functions onto PP2A. Codon usage bias (CUB) involves the selection of synonymous codons, which can affect gene expression by modulating processes such as transcription and translation. CUB can vary along the length of a gene, and differential use of synonymous codons can be important in the divergence of gene families. The N-termini of the gene product encoded by B56α possessed high CUB, high GC content at the third codon position (GC3), and high rare codon content. In addition, differential CUB was found in the sequence encoding two B56γ N-terminal splice forms. The sequence encoding the N-termini of B56γ/γ, relative to B56δ/γ, displayed CUB, utilized more frequent codons, and had higher GC3 content. B56α mRNA had stronger than predicted secondary structure at their 5' end, and the B56δ/γ splice variants had long regions of weaker than predicted secondary structure at their 5' end. The data suggest that B56α is expressed at relatively low levels as compared to the other B56 isoforms and that the B56δ/γ splice variant is expressed more highly than B56γ/γ.
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Affiliation(s)
- Gabriel Corzo
- Department of Biology, Hofstra University, Hempstead, NY 11549, USA;
| | | | - Joni M. Seeling
- Department of Biology, Hofstra University, Hempstead, NY 11549, USA;
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22
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Malekian N, Sainath S, Al-Fatlawi A, Schroeder M. Word-based GWAS harnesses the rich potential of genomic data for E. coli quinolone resistance. Front Microbiol 2023; 14:1276332. [PMID: 38152371 PMCID: PMC10751334 DOI: 10.3389/fmicb.2023.1276332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/16/2023] [Indexed: 12/29/2023] Open
Abstract
Quinolone resistance presents a growing global health threat. We employed word-based GWAS to explore genomic data, aiming to enhance our understanding of this phenomenon. Unlike traditional variant-based GWAS analyses, this approach simultaneously captures multiple genomic factors, including single and interacting resistance mutations and genes. Analyzing a dataset of 92 genomic E. coli samples from a wastewater treatment plant in Dresden, we identified 54 DNA unitigs significantly associated with quinolone resistance. Remarkably, our analysis not only validated known mutations in gyrA and parC genes and the results of our variant-based GWAS but also revealed new (mutated) genes such as mdfA, the AcrEF-TolC multidrug efflux system, ptrB, and hisI, implicated in antibiotic resistance. Furthermore, our study identified joint mutations in 14 genes including the known gyrA gene, providing insights into potential synergistic effects contributing to quinolone resistance. These findings showcase the exceptional capabilities of word-based GWAS in unraveling the intricate genomic foundations of quinolone resistance.
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Affiliation(s)
- Negin Malekian
- Biotechnology Center (BIOTEC), Technische Universität Dresden, Dresden, Germany
| | - Srividhya Sainath
- Biotechnology Center (BIOTEC), Technische Universität Dresden, Dresden, Germany
| | - Ali Al-Fatlawi
- Biotechnology Center (BIOTEC), Technische Universität Dresden, Dresden, Germany
- ITRDC, University of Kufa, Najaf, Iraq
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), Technische Universität Dresden, Dresden, Germany
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), TU Dresden, Dresden, Germany
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23
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Rao Y, Ahmed N, Pritchard J, O'Brien EP. Incorporating mutational heterogeneity to identify genes that are enriched for synonymous mutations in cancer. BMC Bioinformatics 2023; 24:462. [PMID: 38062391 PMCID: PMC10704839 DOI: 10.1186/s12859-023-05521-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 10/05/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Synonymous mutations, which change the DNA sequence but not the encoded protein sequence, can affect protein structure and function, mRNA maturation, and mRNA half-lives. The possibility that synonymous mutations might be enriched in cancer has been explored in several recent studies. However, none of these studies control for all three types of mutational heterogeneity (patient, histology, and gene) that are known to affect the accurate identification of non-synonymous cancer-associated genes. Our goal is to adopt the current standard for non-synonymous mutations in an investigation of synonymous mutations. RESULTS Here, we create an algorithm, MutSigCVsyn, an adaptation of MutSigCV, to identify cancer-associated genes that are enriched for synonymous mutations based on a non-coding background model that takes into account the mutational heterogeneity across these levels. Using MutSigCVsyn, we first analyzed 2572 cancer whole-genome samples from the Pan-cancer Analysis of Whole Genomes (PCAWG) to identify non-synonymous cancer drivers as a quality control. Indicative of the algorithm accuracy we find that 58.6% of these candidate genes were also found in Cancer Census Gene (CGC) list, and 66.2% were found within the PCAWG cancer driver list. We then applied it to identify 30 putative cancer-associated genes that are enriched for synonymous mutations within the same samples. One of the promising gene candidates is the B cell lymphoma 2 (BCL-2) gene. BCL-2 regulates apoptosis by antagonizing the action of proapoptotic BCL-2 family member proteins. The synonymous mutations in BCL2 are enriched in its anti-apoptotic domain and likely play a role in cancer cell proliferation. CONCLUSION Our study introduces MutSigCVsyn, an algorithm that accounts for mutational heterogeneity at patient, histology, and gene levels, to identify cancer-associated genes that are enriched for synonymous mutations using whole genome sequencing data. We identified 30 putative candidate genes that will benefit from future experimental studies on the role of synonymous mutations in cancer biology.
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Affiliation(s)
- Yiyun Rao
- Huck Institute of the Life Sciences, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Nabeel Ahmed
- Huck Institute of the Life Sciences, Pennsylvania State University, University Park, State College, PA, 16802, USA
- Moderna, Inc., Cambridge, USA
| | - Justin Pritchard
- Department of Biomedical Engineering, Pennsylvania State University, University Park, State College, PA, 16802, USA.
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, State College, PA, 16802, USA.
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, State College, PA, 16802, USA.
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24
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Yang X, Wang W, Wang X, Zhang D, Li X, Zhang Y, Zhao Y, Zhao L, Wang J, Xu D, Cheng J, Li W, Zhou B, Lin C, Zeng X, Zhai R, Ma Z, Liu J, Cui P, Zhang X. Polymorphism in ovine ADCY8 gene and its association with residual feed intake in Hu sheep. Anim Biotechnol 2023; 34:3355-3362. [PMID: 36384395 DOI: 10.1080/10495398.2022.2145294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Feed efficiency makes up a large part of sheep production, which also has a crucial impact on the economic benefits of producers. This study explores the polymorphism of Adenylyl cyclase 8 gene associated with feed efficiency and detects the expression characteristics of ADCY8 in ten tissues of Hu sheep. The polymorphism of ADCY8 was recognized by using PCR amplification and Sanger sequencing, KASPar technology was used for genotyping subsequently, and the relationship between SNP and RFI is also studied. The results indicated that an intronic mutation g.24799148 C > T (rs 423395741) was identified in ADCY8, and association analysis showed that the SNP g.24799148 C > T (rs 423395741) was significantly associated with RFI at 100-120, 100-140, 100-160, and 100-180 days (p < 0.05). The quantitative real-time PCR (qRT-PCR) result showed that ADCY8 was expressed in ten tissues, and the expression of ADCY8 gene in rumen tissue was significantly higher than in the other tested tissues. Therefore, these results indicated that the ADCY8 mutation locus may be used as a candidate molecular marker for evaluating the feed efficiency of Hu sheep.
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Affiliation(s)
- Xiaobin Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Xiaojuan Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Bubo Zhou
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Xiwen Zeng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Rui Zhai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Jia Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Panpan Cui
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
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25
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Lali FA, Anilkumar K, Potu H, Naicy T, Aravindakshan TV. Two novel SNPs identified in STAT1 gene adjoining a QTL for milk production in Holstein Friesian crossbreds of Kerala. Anim Biotechnol 2023; 34:3837-3846. [PMID: 37428559 DOI: 10.1080/10495398.2023.2232662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
We analyzed the effect of a single nucleotide polymorphism, g. C3141T in the 3' UTR of Signal transducer and activator of transcription-1 gene (STAT1) on milk production traits in the Holstein Friesian crossbred cattle of Kerala (n = 144) by association analysis and expression study. The population was genotyped by restriction fragment length polymorphism using Pag1. Association study using the General Linear Model-Analysis of Variance revealed that none of the yield or composition traits analyzed were significantly differed. The expression profile of STAT1 gene in leucocytes of animals bearing homozygous genotypes was compared by quantitative real time PCR using SYBR green chemistry with and relative expression was not found to be significantly differed. The second stage of the study, the STAT1 mRNA spanning 3213 bp was amplified from leucocytes and sequenced (GenBank: MT459802.1). Two novel SNPs were identified; one synonymous mutation in the coding region (g.A1212G) and the other in the 3'UTR (g.T3042C). The novel SNPs might contribute to STAT1 gene regulation mediated by alternate spicing or binding sites for regulatory molecules. The results reiterate the importance of extensive studies of STAT1 gene variants to substantiate the presence of a quantitative trait loci for dairy traits in the vicinity of STAT1 gene.
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Affiliation(s)
- F A Lali
- Department of Animal Genetics and Breeding, College of Veterinary and Animal Sciences, Kerala Veterinary and Animal Sciences University, Thrissur, Kerala, India
| | - K Anilkumar
- Department of Animal Genetics and Breeding, College of Veterinary and Animal Sciences, Kerala Veterinary and Animal Sciences University, Thrissur, Kerala, India
| | - Hemanth Potu
- Department of Animal Genetics and Breeding, College of Veterinary and Animal Sciences, Kerala Veterinary and Animal Sciences University, Thrissur, Kerala, India
| | - Thomas Naicy
- Base Farm, Kolahalamedu, Kerala Veterinary and Animal Sciences University, Idukki, Kerala, India
| | - T V Aravindakshan
- Centre for Advanced Studies in Animal Genetics and Breeding, Kerala Veterinary and Animal Sciences University, Thrissur, Kerala, India
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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] [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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27
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Ormandjieva A, Yordanov S, Stoyanov H, Deliverska E, Shivarov V, Ivanova M. The role of non-classical and chain-related human leukocyte antigen polymorphisms in laryngeal squamous cell carcinoma. Mol Biol Rep 2023; 50:7245-7252. [PMID: 37418079 DOI: 10.1007/s11033-023-08629-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/23/2023] [Indexed: 07/08/2023]
Abstract
BACKGROUND Laryngeal squamous cell carcinoma (LSCC) is the major pathological subtype of laryngeal cancer. It has been shown that alterations of the expression of non-classical human leukocyte antigens (HLA) and the chain-related MIC molecules by malignant cells can lead to escape from the immune system control and certain allele variants may participate in immune editing and therefore be associated with modulation of cancer risk. The aim of the present study was to investigate the role of non-classical HLA class Ib and chain-related MIC polymorphisms, determined at the allelic level by next-generation sequencing (NGS), in patients from the Bulgarian population, diagnosed with LSCC. MATERIALS AND METHODS In the present study DNA samples from 48 patients with LSCC were used. Data was compared to 63 healthy controls analysed in previous studies. HLA genotyping was performed by using the AlloSeq Tx17 early pooling protocol and the library preparation AlloSeq Tx17 kit (CareDx). Sequencing was performed on MiniSeq sequencing platform (Illumina) and HLA genotypes were assigned with the AlloSeq Assign analysis software v1.0.3 (CareDx) and the IPD-IMGT/HLA database 3.45.1.2. RESULTS The HLA disease association tests revealed a statistically significant predisposing association of HLA-F*01:01:02 (Pc = 0.0103, OR = 24.0194) with LSCC, while HLA-F*01:01:01 (Pc = 8.21e-04, OR = 0.0485) has a possible protective association. Additionally we observed several haplotypes with statistically significant protective and predisposing associations. The strongest association was observed for F*01:01:01-H*01:01:01 (P = 0.0054, haplotype score=-2.7801). CONCLUSION Our preliminary study suggests the involvement of HLA class Ib in cancer development and the possible role of the shown alleles as biomarkers of LSCC.
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Affiliation(s)
- Anastasia Ormandjieva
- Department of Clinical Immunology, Medical Faculty, Medical University, Sofia, Bulgaria.
| | | | - Hristo Stoyanov
- Department of Dental, Oral and Maxillofacial surgery, FDM, Medical University - Sofia, Sofia, Bulgaria
| | - Elitsa Deliverska
- Department of Dental, Oral and Maxillofacial surgery, FDM, Medical University - Sofia, Sofia, Bulgaria
| | - Velizar Shivarov
- Department of Experimental Research, Medical University Pleven, Pleven, Bulgaria
| | - Milena Ivanova
- Department of Clinical Immunology, Medical Faculty, Medical University, Sofia, Bulgaria
- Clinic of Clinical Immunology with Stem Cell Bank, University Hospital ''Alexandrovska'', Sofia, Bulgaria
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Giovanetti M, Vazquez C, Lima M, Castro E, Rojas A, Gomez de la Fuente A, Aquino C, Cantero C, Fleitas F, Torales J, Barrios J, Ortega MJ, Gamarra ML, Villalba S, Alfonzo T, Xavier J, Adelino T, Fritsch H, Iani FC, Pereira GC, de Oliveira C, Schuab G, Rodrigues ES, Kashima S, Leite J, Gresh L, Franco L, Tegally H, Van Voorhis WC, Lessels R, de Filippis AMB, Ojeda A, Sequera G, Montoya R, Holmes EC, de Oliveira T, Rico JM, Lourenço J, Fonseca V, Alcantara LC. Rapid Epidemic Expansion of Chikungunya Virus East/Central/South African Lineage, Paraguay. Emerg Infect Dis 2023; 29:1859-1863. [PMID: 37488810 PMCID: PMC10461647 DOI: 10.3201/eid2909.230523] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023] Open
Abstract
The spread of Chikungunya virus is a major public health concern in the Americas. There were >120,000 cases and 51 deaths in 2023, of which 46 occurred in Paraguay. Using a suite of genomic, phylodynamic, and epidemiologic techniques, we characterized the ongoing large chikungunya epidemic in Paraguay.
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Affiliation(s)
| | | | | | | | - Analia Rojas
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Andrea Gomez de la Fuente
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Carolina Aquino
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Cesar Cantero
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Fatima Fleitas
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Juan Torales
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Julio Barrios
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Maria J. Ortega
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Maria L. Gamarra
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Shirley Villalba
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Tania Alfonzo
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Joilson Xavier
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Talita Adelino
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Hegger Fritsch
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Felipe C.M. Iani
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Glauco C. Pereira
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Carla de Oliveira
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Gabriel Schuab
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Evandra S. Rodrigues
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Simone Kashima
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Juliana Leite
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Lionel Gresh
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Leticia Franco
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Houriiyah Tegally
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Wesley C. Van Voorhis
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Richard Lessels
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Ana Maria Bispo de Filippis
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Andrea Ojeda
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Guillermo Sequera
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Romeo Montoya
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Edward C. Holmes
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Tulio de Oliveira
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Jairo M. Rico
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - José Lourenço
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Vagner Fonseca
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
| | - Luiz C.J. Alcantara
- Università Campus Bio-Medico di Roma, Italy (M. Giovanetti)
- Instituto Oswaldo Cruz, Belo Horizonte, Brazil (M. Giovanetti, M. Lima, E. Castro, J. Xavier, H. Fritsch, L.C.J. Alcantara)
- Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Rojas, A. Gomez de la Fuente, C. Aquino, C. Cantero, F. Fleitas, J. Torales, J. Barrios, M.J. Ortega, M.L. Gamarra, S. Villalba, T. Alfonzo)
- Central de Saúde Pública do Estado de Minas Gerais, Ezequiel Dias, Brazil (M. Lima, E. Castro, T. Adelino, F.C.M. Iani, G.C. Pereira)
- Universidade Federal de Minas Gerais, Belo Horizonte (J. Xavier, H. Fritsch)
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil (C. de Oliveira, G. Schuab, A.M.B. de Filippis)
- University of São Paulo, São Paulo, Brazil (E.S. Rodrigues, S. Kashima)
- Pan American Health Organization/World Health Organization, Washington, DC, USA (J. Leite, L. Gresh, L. Franco, J.M. Rico)
- Stellenbosch University, Stellenbosch, South Africa (H. Tegally, T. de Oliveira)
- University of KwaZulu-Natal, Durban, South Africa (H. Tegally, R. Lessels, T. de Oliveira)
- National Institutes of Health, Bethesda, Maryland, USA (W.C. Van Voorhis)
- Dirección General de Vigilancia de la Salud, Asunción (A. Ojeda, G. Sequera)
- Organización Panamericana de la Salud/Organización Mundial de la Salud Asuncion (R. Montoya)
- University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)
- University of Lisbon, Lisbon, Portugal (J. Lourenço)
- Organização Pan-Americana da Saúde/Organização/Mundial da Saúde, Brasilia, Brazil. (V. Fonseca)
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29
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Maitre E, Macro M, Troussard X. Hairy cell leukaemia with unusual BRAF mutations. J Cell Mol Med 2023; 27:2626-2630. [PMID: 37530550 PMCID: PMC10468650 DOI: 10.1111/jcmm.17890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/06/2023] [Accepted: 07/22/2023] [Indexed: 08/03/2023] Open
Abstract
Hairy cell leukaemia (HCL) diagnosis is based on the morphologic detection of circulating abnormal hairy cells in the peripheral blood and/or bone marrow, an HCL immunological score of 3 or 4 based on the expression of the CD11c, CD25, CD103 and CD123 and also the presence of a BRAF V600E activating mutation in the B-raf proto-oncogene (BRAF gene) (7q34). When using new generation sequencing of 21 targeted genes in 124 HCL patients, we identified a cohort of 6/124 (2%) patients with unusual BRAF mutations: two patients presented non-V600 mutations (BRAF F595L, BRAF W604L respectively) and four other patients silent BRAF mutations. When using droplet digital PCR (ddPCR) three of the four patients with concomitant BRAF V600E and silent mutation were negative. The respective role of these mutations in the occurrence of HCL or its progression remains to be clarified, but BRAF sequencing is necessary in case of negative BRAF V600E by ddPCR.
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Affiliation(s)
- Elsa Maitre
- Laboratoire d'HématologieCHU Caen NormandieCaenFrance
| | - Margaret Macro
- Institut bas Normand d'HématologieCHU Caen NormandieCaenFrance
| | - Xavier Troussard
- Laboratoire d'HématologieCHU Caen NormandieCaenFrance
- Institut bas Normand d'HématologieCHU Caen NormandieCaenFrance
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30
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Liu Y, Qu HQ, Chang X, Mentch FD, Qiu H, Wang X, Saeidian AH, Watson D, Glessner J, Hakonarson H. Genomic variants exclusively identified in children with birth defects and concurrent malignant tumors predispose to cancer development. Mol Cancer 2023; 22:126. [PMID: 37543594 PMCID: PMC10403830 DOI: 10.1186/s12943-023-01828-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/18/2023] [Indexed: 08/07/2023] Open
Abstract
Children with birth defects (BD) express distinct clinical features that often have various medical consequences, one of which is predisposition to the development of cancers. Identification of the underlying genetic mechanisms related to the development of cancer in BD patients would allow for preventive measures. We performed a whole genome sequencing (WGS) study on blood-derived DNA samples from 1566 individuals without chromosomal anomalies, including 454 BD probands with at least one type of malignant tumors, 767 cancer-free BD probands, and 345 healthy individuals. Exclusive recurrent variants were identified in BD-cancer and BD-only patients and mapped to their corresponding genomic regions. We observed statistically significant overlaps for protein-coding/ncRNA with exclusive variants in exons, introns, ncRNAs, and 3'UTR regions. Exclusive exonic variants, especially synonymous variants, tend to occur in prior exons locus in BD-cancer children. Intronic variants close to splicing site (< 500 bp from exon) have little overlaps in BD-cancer and BD-only patients. Exonic variants in non-coding RNA (ncRNA) tend to occur in different ncRNAs exons regardless of the overlaps. Notably, genes with 5' UTR variants are almost mutually exclusive between the two phenotypes. In conclusion, we conducted the first genomic study to explore the impact of recurrent variants exclusive to the two distinguished clinical phenotypes under study, BD with or without cancer, demonstrating enrichment of selective protein-coding/ncRNAs differentially expressed between these two phenotypes, suggesting that selective genetic factors may underlie the molecular processes of pediatric cancer development in BD children.
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Affiliation(s)
- Yichuan Liu
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, 3615 Civic Center Blvd Abramson Building, Philadelphia, PA, 19104, USA.
| | - Hui-Qi Qu
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, 3615 Civic Center Blvd Abramson Building, Philadelphia, PA, 19104, USA
| | - Xiao Chang
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, 3615 Civic Center Blvd Abramson Building, Philadelphia, PA, 19104, USA
| | - Frank D Mentch
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, 3615 Civic Center Blvd Abramson Building, Philadelphia, PA, 19104, USA
| | - Haijun Qiu
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, 3615 Civic Center Blvd Abramson Building, Philadelphia, PA, 19104, USA
| | - Xiang Wang
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, 3615 Civic Center Blvd Abramson Building, Philadelphia, PA, 19104, USA
| | - Amir Hossein Saeidian
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, 3615 Civic Center Blvd Abramson Building, Philadelphia, PA, 19104, USA
| | - Deborah Watson
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, 3615 Civic Center Blvd Abramson Building, Philadelphia, PA, 19104, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Joseph Glessner
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, 3615 Civic Center Blvd Abramson Building, Philadelphia, PA, 19104, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hakon Hakonarson
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, 3615 Civic Center Blvd Abramson Building, Philadelphia, PA, 19104, USA.
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland.
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31
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Majic P, Payne JL. Developmental Selection and the Perception of Mutation Bias. Mol Biol Evol 2023; 40:msad179. [PMID: 37556606 PMCID: PMC10443735 DOI: 10.1093/molbev/msad179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/22/2023] [Accepted: 07/26/2023] [Indexed: 08/11/2023] Open
Abstract
The notion that mutations are random relative to their fitness effects is central to the Neo-Darwinian view of evolution. However, a recent interpretation of the patterns of mutation accumulation in the genome of Arabidopsis thaliana has challenged this notion, arguing for the presence of a targeted DNA repair mechanism that causes a nonrandom association of mutation rates and fitness effects. Specifically, this mechanism was suggested to cause a reduction in the rates of mutations on essential genes, thus lowering the rates of deleterious mutations. Central to this argument were attempts to rule out selection at the population level. Here, we offer an alternative and parsimonious interpretation of the patterns of mutation accumulation previously attributed to mutation bias, showing how they can instead or additionally be caused by developmental selection, that is selection occurring at the cellular level during the development of a multicellular organism. Thus, the depletion of deleterious mutations in A. thaliana may indeed be the result of a selective process, rather than a bias in mutation. More broadly, our work highlights the importance of considering development in the interpretation of population-genetic analyses of multicellular organisms, and it emphasizes that efforts to identify mechanisms involved in mutational biases should explicitly account for developmental selection.
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Affiliation(s)
- Paco Majic
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joshua L Payne
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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32
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Vihinen M. Nonsynonymous Synonymous Variants Demand for a Paradigm Shift in Genetics. Curr Genomics 2023; 24:18-23. [PMID: 37920730 PMCID: PMC10334700 DOI: 10.2174/1389202924666230417101020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/20/2023] [Accepted: 03/01/2023] [Indexed: 11/04/2023] Open
Abstract
Synonymous (also known as silent) variations are by definition not considered to change the coded protein. Still many variations in this category affect either protein abundance or properties. As this situation is confusing, we have recently introduced systematics for synonymous variations and those that may on the surface look like synonymous, but these may affect the coded protein in various ways. A new category, unsense variation, was introduced to describe variants that do not introduce a stop codon into the variation site, but which lead to different types of changes in the coded protein. Many of these variations lead to mRNA degradation and missing protein. Here, consequences of the systematics are discussed from the perspectives of variation annotation and interpretation, evolutionary calculations, nonsynonymous-to-synonymous substitution rates, phylogenetics and other evolutionary inferences that are based on the principle of (nearly) neutral synonymous variations. It may be necessary to reassess published results. Further, databases for synonymous variations and prediction methods for such variations should consider unsense variations. Thus, there is a need to evaluate and reflect principles of numerous aspects in genetics, ranging from variation naming and classification to evolutionary calculations.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, Lund University, Lund, BMC B13, Sweden
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Alfieri F, Caravagna G, Schaefer MH. Cancer genomes tolerate deleterious coding mutations through somatic copy number amplifications of wild-type regions. Nat Commun 2023; 14:3594. [PMID: 37328455 PMCID: PMC10276008 DOI: 10.1038/s41467-023-39313-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 06/01/2023] [Indexed: 06/18/2023] Open
Abstract
Cancers evolve under the accumulation of thousands of somatic mutations and chromosomal aberrations. While most coding mutations are deleterious, almost all protein-coding genes lack detectable signals of negative selection. This raises the question of how tumors tolerate such large amounts of deleterious mutations. Using 8,690 tumor samples from The Cancer Genome Atlas, we demonstrate that copy number amplifications frequently cover haploinsufficient genes in mutation-prone regions. This could increase tolerance towards the deleterious impact of mutations by creating safe copies of wild-type regions and, hence, protecting the genes therein. Our findings demonstrate that these potential buffering events are highly influenced by gene functions, essentiality, and mutation impact and that they occur early during tumor evolution. We show how cancer type-specific mutation landscapes drive copy number alteration patterns across cancer types. Ultimately, our work paves the way for the detection of novel cancer vulnerabilities by revealing genes that fall within amplifications likely selected during evolution to mitigate the effect of mutations.
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Affiliation(s)
- Fabio Alfieri
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, 20139, Italy
| | - Giulio Caravagna
- Department of Mathematics and Geosciences, University of Trieste, Trieste, 34127, Italy
| | - Martin H Schaefer
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, 20139, Italy.
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Lin BC, Katneni U, Jankowska KI, Meyer D, Kimchi-Sarfaty C. In silico methods for predicting functional synonymous variants. Genome Biol 2023; 24:126. [PMID: 37217943 PMCID: PMC10204308 DOI: 10.1186/s13059-023-02966-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 05/10/2023] [Indexed: 05/24/2023] Open
Abstract
Single nucleotide variants (SNVs) contribute to human genomic diversity. Synonymous SNVs are previously considered to be "silent," but mounting evidence has revealed that these variants can cause RNA and protein changes and are implicated in over 85 human diseases and cancers. Recent improvements in computational platforms have led to the development of numerous machine-learning tools, which can be used to advance synonymous SNV research. In this review, we discuss tools that should be used to investigate synonymous variants. We provide supportive examples from seminal studies that demonstrate how these tools have driven new discoveries of functional synonymous SNVs.
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Affiliation(s)
- Brian C Lin
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
| | - Upendra Katneni
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
| | - Katarzyna I Jankowska
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
| | - Douglas Meyer
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
| | - Chava Kimchi-Sarfaty
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA.
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Kikutake C, Suyama M. Possible involvement of silent mutations in cancer pathogenesis and evolution. Sci Rep 2023; 13:7593. [PMID: 37165041 PMCID: PMC10172315 DOI: 10.1038/s41598-023-34452-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/30/2023] [Indexed: 05/12/2023] Open
Abstract
Recent studies have shown that some silent mutations can be harmful to various processes. In this study, we performed a comprehensive in silico analysis to elucidate the effects of silent mutations on cancer pathogenesis using exome sequencing data derived from the Cancer Genome Atlas. We focused on the codon optimality scores of silent mutations, which were defined as the difference between the optimality of synonymous codons, calculated using the codon usage table. The relationship between cancer evolution and silent mutations showed that the codon optimality score of the mutations that occurred later in carcinogenesis was significantly higher than of those that occurred earlier. In addition, mutations with higher scores were enriched in genes involved in the cell cycle and cell division, while those with lower scores were enriched in genes involved in apoptosis and cellular senescence. Our results demonstrate that some silent mutations can be involved in cancer pathogenesis.
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Affiliation(s)
- Chie Kikutake
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Mikita Suyama
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
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Giovanetti M, Vazquez C, Lima M, Castro E, Rojas A, de la Fuente AG, Aquino C, Cantero C, Fleitas F, Torales J, Barrios J, Ortega MJ, Gamarra ML, Villalba S, Alfonzo T, Xavier J, Adelino T, Fritsch H, Iani FCM, Pereira GC, de Oliveira C, Schuab G, Rodrigues ES, Kashima S, Leite J, Gresh L, Franco L, Tegally H, Van Voorhis WC, Lessels R, de Filippis AMB, Ojeda A, Sequera G, Montoya R, Holmes EC, de Oliveira T, Rico JM, Lourenço J, Fonseca V, Alcantara LCJ. Rapid epidemic expansion of chikungunya virus-ECSA lineage in Paraguay. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.16.23288635. [PMID: 37131602 PMCID: PMC10153315 DOI: 10.1101/2023.04.16.23288635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The spread of vector-borne viruses, such as CHIKV, is a significant public health concern in the Americas, with over 120,000 cases and 51 deaths in 2023, of which 46 occurred in Paraguay. Using a suite of genomic, phylodynamic, and epidemiological techniques, we characterized the ongoing large CHIKV epidemic in Paraguay. Article Summary Line Genomic and epidemiological characterization of the ongoing Chikungunya virus epidemic in Paraguay.
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Affiliation(s)
- Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
- Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico,Rome, Italy
| | | | - Mauricio Lima
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Brazil
| | - Emerson Castro
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Brazil
| | - Analia Rojas
- Laboratorio Central de Salud Pública, Asunción, Paraguay
| | | | | | - Cesar Cantero
- Laboratorio Central de Salud Pública, Asunción, Paraguay
| | - Fatima Fleitas
- Laboratorio Central de Salud Pública, Asunción, Paraguay
| | - Juan Torales
- Laboratorio Central de Salud Pública, Asunción, Paraguay
| | - Julio Barrios
- Laboratorio Central de Salud Pública, Asunción, Paraguay
| | | | | | | | - Tania Alfonzo
- Laboratorio Central de Salud Pública, Asunción, Paraguay
| | - Joilson Xavier
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Talita Adelino
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Brazil
| | - Hegger Fritsch
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Felipe C. M. Iani
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Brazil
| | - Glauco Carvalho Pereira
- Laboratorio Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Brazil
| | - Carla de Oliveira
- Laboratório de Arbovírus e Vírus Hemorrágicos (LARBOH), Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Gabriel Schuab
- Laboratório de Arbovírus e Vírus Hemorrágicos (LARBOH), Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Evandra Strazza Rodrigues
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Simone Kashima
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Juliana Leite
- Infectious Hazards Management, Health Emergencies Department (PHE), Pan American Health Organization / World Health Organization (PAHO/WHO), Washington DC, USA
| | - Lionel Gresh
- Infectious Hazards Management, Health Emergencies Department (PHE), Pan American Health Organization / World Health Organization (PAHO/WHO), Washington DC, USA
| | - Leticia Franco
- Infectious Hazards Management, Health Emergencies Department (PHE), Pan American Health Organization / World Health Organization (PAHO/WHO), Washington DC, USA
| | - Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Wesley C. Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, USA
| | - Richard Lessels
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Ana Maria Bispo de Filippis
- Laboratório de Arbovírus e Vírus Hemorrágicos (LARBOH), Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Andrea Ojeda
- Dirección General de Vigilancia de la Salud, Asunción, Paraguay
| | | | - Romeo Montoya
- Enfermedades Trasmisibles y Determinantes Ambientales de la Salud CDE/HA/PHE, Organización Panamericana de la Salud / Organización Mundial de la Salud (OPS/OMS), Asuncion, Paraguay
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Jairo Mendez Rico
- Infectious Hazards Management, Health Emergencies Department (PHE), Pan American Health Organization / World Health Organization (PAHO/WHO), Washington DC, USA
| | - José Lourenço
- Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, 1749-016, Portugal
| | - Vagner Fonseca
- Coordenação de Vigilância, Preparação e Resposta à Emergências e Desastres (PHE), Organização Pan-Americana da Saúde / Organização Mundial da Saúde (OPAS/OMS), Brasilia DF, Brazil
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Jena NR, Das P, Shukla PK. Complementary base pair interactions between different rare tautomers of the second-generation artificial genetic alphabets. J Mol Model 2023; 29:125. [PMID: 37014428 DOI: 10.1007/s00894-023-05537-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 03/29/2023] [Indexed: 04/05/2023]
Abstract
The functionality of a semisynthetic DNA in the biological environment will depend on the base pair nature of its complementary base pairs. To understand this, base pair interactions between complementary bases of recently proposed eight second-generation artificial nucleobases are studied herein by considering their rare tautomeric conformations and a dispersion-corrected density functional theoretic method. It is found that the binding energies of two hydrogen-bonded complementary base pairs are more negative than those of the three hydrogen-bonded base pairs. However, as the former base pairs are endothermic, the semisynthetic duplex DNA would involve the latter base pairs.
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Affiliation(s)
- N R Jena
- Discipline of Natural Sciences, Indian Institute of Information Technology, Design, and Manufacturing, Jabalpur, 482005, India.
| | - P Das
- Discipline of Natural Sciences, Indian Institute of Information Technology, Design, and Manufacturing, Jabalpur, 482005, India
| | - P K Shukla
- Department of Physics, Assam University, Silchar, 788011, India
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Rogalska ME, Vivori C, Valcárcel J. Regulation of pre-mRNA splicing: roles in physiology and disease, and therapeutic prospects. Nat Rev Genet 2023; 24:251-269. [PMID: 36526860 DOI: 10.1038/s41576-022-00556-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2022] [Indexed: 12/23/2022]
Abstract
The removal of introns from mRNA precursors and its regulation by alternative splicing are key for eukaryotic gene expression and cellular function, as evidenced by the numerous pathologies induced or modified by splicing alterations. Major recent advances have been made in understanding the structures and functions of the splicing machinery, in the description and classification of physiological and pathological isoforms and in the development of the first therapies for genetic diseases based on modulation of splicing. Here, we review this progress and discuss important remaining challenges, including predicting splice sites from genomic sequences, understanding the variety of molecular mechanisms and logic of splicing regulation, and harnessing this knowledge for probing gene function and disease aetiology and for the design of novel therapeutic approaches.
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Affiliation(s)
- Malgorzata Ewa Rogalska
- Genome Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Claudia Vivori
- Genome Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- The Francis Crick Institute, London, UK
| | - Juan Valcárcel
- Genome Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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Most synonymous allelic variants in HIV tat are not silent. Genomics 2023; 115:110603. [PMID: 36893872 DOI: 10.1016/j.ygeno.2023.110603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/12/2023] [Accepted: 03/03/2023] [Indexed: 03/09/2023]
Abstract
The genetic code has degenerate codons that produce no change in the translated protein sequence and are generally thought to be silent. However, some synonymous variants are clearly not silent. Herein, we questioned the frequency of non-silent synonymous variants. We tested how random synonymous variants in the HIV Tat transcription factor effect transcription of an LTR-GFP reporter. Our model system has the advantage of directly measuring the function of the gene in human cells. Approximately, 67% of synonymous variants in Tat were non-silent, either having reduced activity or were full loss-of-function alleles. Eight mutant codons had higher codon usage than wild type, accompanied by reduced transcriptional activity. These were clustered on a loop in the Tat structure. We conclude that most synonymous Tat variants are not silent in human cells, and 25% are associated with changes in codon usage, likely effecting protein folding.
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40
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Identification and in silico characterization of CSRP3 synonymous variants in dilated cardiomyopathy. Mol Biol Rep 2023; 50:4105-4117. [PMID: 36877346 DOI: 10.1007/s11033-023-08314-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/31/2023] [Indexed: 03/07/2023]
Abstract
BACKGROUND Synonymous variations have always been ignored while studying the underlying genetic mechanisms for most of the human diseases. However, recent studies have suggested that these silent changes in the genome can alter the protein expression and folding. METHODS AND RESULTS CSRP3, which is a well-known candidate gene associated with dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM), was screened for 100 idiopathic DCM cases and 100 controls. Three synonymous variations were identified viz., c.96G > A, p.K32=; c.336G > A, p.A112=; c.354G > A, p.E118=. A comprehensive in silico analysis was performed using various web based widely accepted tools, Mfold, Codon Usage, HSF3.1 and RNA22. Mfold predicted structural changes in all the variants except c.96 G > A (p.K32=), however it predicted changes in the stability of mRNA due to all the synonymous variants. Codon bias was observed as evident by the Relative Synonymous Codon Usage and Log Ratio of Codon Usage Frequencies. The Human Splicing Finder also predicted remarkable changes in the regulatory elements in the variants c.336G > A and c.354 G > A. The miRNA target prediction using varied modes available in RNA22 revealed that 70.6% of the target sites of miRNAs in CSRP3 were altered due to variant c.336G > A while 29.41% sites were completely lost. CONCLUSION Findings of the present study suggest that synonymous variants revealed striking deviations in the structural conformation of mRNA, stability of mRNA, relative synonymous codon usage, splicing and miRNA binding sites from the wild type suggesting their possible role in the pathogenesis of DCM, either by destabilizing the mRNA structure, or codon usage bias or else altering the cis-acting regulatory elements during splicing.
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Mortazavi M, Torkzadeh-Mahani M, Rahimi M, Maleki M, Lotfi S, Riahi-Madvar A. Effects of synonymous mutations on kinetic properties and structure of firefly luciferase: Molecular dynamics simulation, molecular docking, RNA folding, and experimental study. Int J Biol Macromol 2023; 235:123835. [PMID: 36870640 DOI: 10.1016/j.ijbiomac.2023.123835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/19/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023]
Abstract
Although synonymous mutations have long been thought to lack striking results, a growing body of research shows these mutations have highly variable effects. In this study, the impact of synonymous mutations in the development of thermostable luciferase was investigated using a combination of experimental and theoretical approaches. Using bioinformatics analysis, the codon usage features in the Lampyridae family's luciferases were studied and four synonymous mutations of Arg in luciferase were created. An exciting result was that the analysis of kinetic parameters showed a slight increase in the thermal stability of the mutant luciferase. AutoDock Vina, %MinMax algorithm, and UNAFold Server were used to perform molecular docking, folding rate, and RNA folding, respectively. Here, it was assumed that in the region (Arg337) with a moderate propensity for coil, synonymous mutation altered the rate of translation, which in turn may lead to a slight change in the structure of the enzyme. According to the molecular dynamics simulation data, local minor global flexibility is observed in the context of the protein conformation. A plausible explanation is that this flexibility may strengthen hydrophobic interactions due to its sensitivity to a molecular collision. Accordingly, thermostability originated mainly from hydrophobic interaction.
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Affiliation(s)
- Mojtaba Mortazavi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman 7631885356, Iran.
| | - Masoud Torkzadeh-Mahani
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman 7631885356, Iran
| | - Mehdi Rahimi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman 7631885356, Iran
| | - Mahmood Maleki
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman 7631885356, Iran
| | - Safa Lotfi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman 7631885356, Iran
| | - Ali Riahi-Madvar
- Department of Molecular and Cell Biology, Faculty of Basic Sciences, Kosar University of Bojnord, Bojnord, Iran
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Benisty H, Hernandez-Alias X, Weber M, Anglada-Girotto M, Mantica F, Radusky L, Senger G, Calvet F, Weghorn D, Irimia M, Schaefer MH, Serrano L. Genes enriched in A/T-ending codons are co-regulated and conserved across mammals. Cell Syst 2023; 14:312-323.e3. [PMID: 36889307 DOI: 10.1016/j.cels.2023.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 07/11/2022] [Accepted: 02/09/2023] [Indexed: 03/09/2023]
Abstract
Codon usage influences gene expression distinctly depending on the cell context. Yet, the importance of codon bias in the simultaneous turnover of specific groups of protein-coding genes remains to be investigated. Here, we find that genes enriched in A/T-ending codons are expressed more coordinately in general and across tissues and development than those enriched in G/C-ending codons. tRNA abundance measurements indicate that this coordination is linked to the expression changes of tRNA isoacceptors reading A/T-ending codons. Genes with similar codon composition are more likely to be part of the same protein complex, especially for genes with A/T-ending codons. The codon preferences of genes with A/T-ending codons are conserved among mammals and other vertebrates. We suggest that this orchestration contributes to tissue-specific and ontogenetic-specific expression, which can facilitate, for instance, timely protein complex formation.
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Affiliation(s)
- Hannah Benisty
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.
| | - Xavier Hernandez-Alias
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Marc Weber
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Miquel Anglada-Girotto
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Federica Mantica
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Leandro Radusky
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Gökçe Senger
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, Milan 20139, Italy
| | - Ferriol Calvet
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Donate Weghorn
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain
| | - Martin H Schaefer
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, Milan 20139, Italy
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain; ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain.
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Wang Z, Wang C, Zhang Y, Liu S, Cheng Y, Wang S, Xia P, Hao L. Porcine IGF-1R synonymous mutations in the extracellular domain affect proliferation and differentiation of skeletal muscle cells. Gene 2023; 854:147098. [PMID: 36496177 DOI: 10.1016/j.gene.2022.147098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Miniature pigs are considered ideal organ donors for xenotransplantation in humans, but the mechanism underlying their dwarfism remains to be elucidated. IGF-1R is a crucial factor in body size formation in mammals, including skeletal muscle formation and development. The extracellular domain (ECD) binds to the ligand, a phenomenon that results in the activation of downstream pathways. METHODS In this study, the coding sequences of two IGF-1R ECD haplotypes of the large Landrace (LP) pig and the small Bama Xiang (BM) pig were cloned into pcDNA3.1 vectors to generate pcDNA3.1-LP and pcDNA3.1-BM. The two recombinant vectors were then transfected into skeletal muscle cells. RESULTS IGF-1R transcript was found to be expressed at higher levels in the pcDNA3.1-LP group than in the pcDNA3.1-BM group. The IGF-1R ECD from LP promoted cell proliferation and CyclinD1 expression, and promoted the phosphorylation of protein kinase B (to yield p-AKT). Moreover, the IGF-1R ECD from LP increased cell differentiation and the expression of myogenic determination factor (MyoD). CONCLUSION Our data indicated that the IGF-1R ECD haplotypes between pig breeds with different body sizes affect IGF-1R expression, in turn affecting the proliferation and differentiation of skeletal muscle cells by activating downstream signalling pathways.
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Affiliation(s)
- Zhaoguo Wang
- College of Animal Science, Jilin University, Changchun, Jilin 130061, China
| | - Chunli Wang
- College of Animal Science, Jilin University, Changchun, Jilin 130061, China
| | - Ying Zhang
- College of Animal Science, Jilin University, Changchun, Jilin 130061, China
| | - Songcai Liu
- College of Animal Science, Jilin University, Changchun, Jilin 130061, China.
| | - Yunyun Cheng
- Ministry of Health Key Laboratory of Radiobiology, College of Public Health, Jilin University, Changchun, Jilin 130061, China
| | - Siyao Wang
- College of Animal Science, Jilin University, Changchun, Jilin 130061, China
| | - Peijun Xia
- College of Animal Science, Jilin University, Changchun, Jilin 130061, China
| | - Linlin Hao
- College of Animal Science, Jilin University, Changchun, Jilin 130061, China.
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Lee SHT, Kim JY, Kim P, Dong Z, Su CY, Ahn EH. Changes of Mutations and Copy-Number and Enhanced Cell Migration during Breast Tumorigenesis. Adv Biol (Weinh) 2023; 7:e2200072. [PMID: 36449747 PMCID: PMC10836759 DOI: 10.1002/adbi.202200072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 11/14/2022] [Indexed: 12/02/2022]
Abstract
Although cancer stem cells (CSCs) play a major role in tumorigenesis and metastasis, the role of genetic alterations in invasiveness of CSCs is still unclear. Tumor microenvironment signals, such as extracellular matrix (ECM) composition, significantly influence cell behaviors. Unfortunately, these signals are often lost in in vitro cell culture. This study determines putative CSC populations, examines genetic changes during tumorigenesis of human breast epithelial stem cells, and investigates single-cell migration properties on ECM-mimetic platforms. Whole exome sequencing data indicate that tumorigenic cells have a higher somatic mutation burden than non-tumorigenic cells, and that mutations exclusive to tumorigenic cells exhibit higher predictive deleterious scores. Tumorigenic cells exhibit distinct somatic copy number variations (CNVs) including gain of duplications in chromosomes 5 and 8. ECM-mimetic topography selectively enhances migration speed of tumorigenic cells, but not of non-tumorigenic cells, and results in a wide distribution of tumorigenic single-cell migration speeds, suggesting heterogeneity in cellular sensing of contact guidance cues. This study identifies mutations and CNVs acquired during breast tumorigenesis, which can be associated with enhanced migration of breast tumorigenic cells, and demonstrates that a nanotopographically-defined platform can be applied to recapitulate an ECM structure for investigating cellular migration in the simulated tumor microenvironment.
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Affiliation(s)
- Seung Hyuk T. Lee
- Department of Pathology, University of Washington, Seattle,
WA 98195, USA
| | - Joon Yup Kim
- Department of Pathology, University of Washington, Seattle,
WA 98195, USA
| | - Peter Kim
- Department of Bioengineering, University of Washington,
Seattle, WA 98195, USA
| | - Zhipeng Dong
- Department of Biomedical Engineering, Johns Hopkins
University, Baltimore, MD 21205, USA
| | - Chia-Yi Su
- Department of Biomedical Engineering, Johns Hopkins
University, Baltimore, MD 21205, USA
| | - Eun Hyun Ahn
- Department of Biomedical Engineering, Johns Hopkins
University, Baltimore, MD 21205, USA
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Lin C, Wang W, Zhang D, Huang K, Li X, Zhang Y, Zhao Y, Wang J, Zhou B, Cheng J, Xu D, Li W, Zhao L, Ma Z, Yang X, Huang Y, Cui P, Liu J, Zeng X, Zhai R, Sun L, Weng X, Wu W, Zhang X, Zheng W. Polymorphisms in SHISA3 and RFC3 genes and their association with feed conversion ratio in Hu sheep. Front Vet Sci 2023; 9:1010045. [PMID: 36686193 PMCID: PMC9850526 DOI: 10.3389/fvets.2022.1010045] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/05/2022] [Indexed: 01/07/2023] Open
Abstract
In animal husbandry, feed efficiency is a crucial economic trait. In this study, the general linear model was used to perform association analysis for various genotypes and feed conversion ratio (FCR)-related traits. Reverse transcription-quantitative PCR (RT-qPCR) was used to detect the expression of SHISA3 and RFC3 mRNA levels in 10 tissues from 6 sheep. The results showed that SNPs in the NC_040257.1:c.625 T > C and NC_040261.1:g.9905 T > C were analyzed whether they were associated to feed efficiency parameters in Hu sheep (body weight, feed intake, average daily growth, and feed conversion ratio). NC_040257.1:c.625 T > C was shown to be significantly associated with body weight at 80, 100, and 120 days as well as feed conversion ratio (P < 0.05), whereas NC_040261.1:g.9905 T > C was found to be significantly associated with average daily weight gain from 80-140 days (ADG80-140) and FCR (P < 0.05). In Hu sheep, the CC genotypes of SHISA3 and RFC3 were the most common genotypes related to feed efficiency traits. Furthermore, the feed conversion ratio of the combined genotypes TT SHISA3-CC RFC3, TT SHISA3-CT RFC3, TT SHISA3-TT RFC3, CT SHISA3-CC RFC3 and CT SHISA3-CT RFC3 was significantly better than the FCR of CC SHISA3-TT RFC3. RT-qPCR results showed that the expression levels of SHISA3 were lower in the lung than in spleen, kidney, muscle and lymph (P < 0.05), and RFC3 was the lung had a highly significant higher expression level than the heart, liver, spleen, and muscle (P < 0.01). In conclusion, SHISA3 and RFC3 polymorphisms can be used as genetic markers for improving feed conversion efficiency in Hu sheep.
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Affiliation(s)
- Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Weimin Wang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Kai Huang
- 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
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yuan Zhao
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou 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
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaobin Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yongliang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Panpan Cui
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jia Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiwen Zeng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Rui Zhai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Landi Sun
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiuxiu Weng
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Weiwei Wu
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Ürümqi, Xinjiang, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China,*Correspondence: Xiaoxue Zhang ✉
| | - Wenxin Zheng
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Ürümqi, Xinjiang, China,Wenxin Zheng ✉
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Kaur G, Bhadada SK, Santra M, Pal R, Sarma P, Sachdeva N, Dhiman V, Dahiya D, Saikia UN, Chakraborty A, Sood A, Prakash M, Behera A, Rao SD. Multilevel Annotation of Germline MEN1 Variants of Synonymous, Nonsynonymous, and Uncertain Significance in Indian Patients With Sporadic Primary Hyperparathyroidism. J Bone Miner Res 2022; 37:1860-1875. [PMID: 35856247 DOI: 10.1002/jbmr.4653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 07/12/2022] [Accepted: 07/16/2022] [Indexed: 11/08/2022]
Abstract
Primary hyperparathyroidism (PHPT) is third most common endocrine disorder characterized by hypercalcemia with elevated or nonsuppressed parathyroid hormone levels by parathyroid tumors. Familial PHPT, as part of multiple endocrine type-1, occurs due to the germline mutation in the MEN1 gene. The involvement and the role of germline MEN1 variations in sporadic PHPT of Indian PHPT patients are unknown. Precise classifications of different types of MEN1 variations are fundamental for determining clinical relevance and diagnostic role. This prospective cohort study was performed on 82 patients with PHPT (with no clinical or history of MEN1) who underwent screening for MEN1 variations through Sanger sequencing. Multilevel computational analysis was performed to determine the structure-function relationship of synonymous, nonsynonymous, and variants of uncertain significance (VUS). Of the 82 PHPT patients, 42 (51%) had 26 germline MEN1 variants, including eight nonsynonymous, seven synonymous, nine VUS, one splice site, and one regulatory variation. Five most common germline variations (c.1838A>G, c.1817C>T, c.1525C>A, c.-35A>T, and c.250T>C) were observed in this study. c.-35A>T (5' untranslated region [UTR]) was associated with recurrence of PHPT (odds ratio [OR] = 5.4; p = 0.04) and subsequent detection of other endocrine tumors (OR = 13.6, p = 0.035). c.1525C>A was associated with multi glandular parathyroid tumor (OR = 13.6, p = 0.035). Align-Grantham variation and Grantham deviation (Align-GVGD), functional analysis through hidden Markov MODEL (FATHMM), and MutationTaster analysis reported the disease-specific potential of VUS and synonymous variations. Significant linkage disequilibrium was observed in c.1785G>A and c.1817C>T (r2 = 0.3859, p = 0.0001), c.1475C>G and c.1525C>A (r2 = 0.385, p = 0.0004), and c.1569T>C and c.1838A>G (r2 = 0.488, p = 0.0001). The detection of MEN1 variations, especially those with disease-specific potential, can prompt early screening for other MEN1-related tumors and disease recurrence. © 2022 American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Gurjeet Kaur
- Department of Endocrinology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Sanjay Kumar Bhadada
- Department of Endocrinology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Mithun Santra
- Department of Endocrinology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Rimesh Pal
- Department of Endocrinology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Phulen Sarma
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Naresh Sachdeva
- Department of Endocrinology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Vandana Dhiman
- Department of Endocrinology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Divya Dahiya
- Department of General Surgery, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Uma Nahar Saikia
- Department of Histopathology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Anuradha Chakraborty
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Ashwani Sood
- Department of Nuclear Medicine, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Mahesh Prakash
- Department of Radiodiagnosis, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Arunanshu Behera
- Department of General Surgery, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Sudhaker D Rao
- Bone and Mineral Research Laboratory, Henry Ford Hospital, Detroit, MI, USA
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Chen XY, Zhu XJ, Chen M, Lu MP, Wang ML, Yin M, Chen RX, Wu ZF, Bu DY, Zhang ZD, Cheng L. GARP Polymorphisms Associated with Susceptibility to House Dust Mite-Sensitized Persistent Allergic Rhinitis in a Chinese Population. J Asthma Allergy 2022; 15:1369-1381. [PMID: 36196093 PMCID: PMC9527031 DOI: 10.2147/jaa.s366815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 08/27/2022] [Indexed: 11/23/2022] Open
Abstract
Background Genetic variants in GARP (also known as LRRC32) have been reported to have significant associations with asthma and eczema in special populations, but little is known about allergic rhinitis. This study purposes to evaluate the association of single nucleotide polymorphisms (SNPs) in GARP with house dust mite (HDM)-sensitized persistent allergic rhinitis (PER) in a population of Han Chinese. Methods In this hospital-based case–control study, 534 HDM-sensitized PER patients and 451 healthy controls were recruited from East China. In this population, six SNPs in GARP were identified. Serum total and specific IgE levels were measured with ImmunoCAP. Secondary structure and minimum free energy were predicted by RNAfold. Results rs79525962 was associated with the risk of HDM-sensitized PER (P < 0.05). The individuals with CT+TT genotype demonstrated a higher risk of HDM-sensitized PER than those with CC genotype (adjusted OR = 1.393, 95% CI = 1.019–1.904). The homozygous genotype CC of rs3781699 rendered a lower risk of HDM-sensitized PER than the wild-type genotype AA (adjusted OR = 0.646, 95% CI = 0.427–0.976); however, the genotype and allele frequencies of rs3781699 demonstrated no associations with HDM-sensitized PER (P > 0.05). rs79525962 increased the risk of HDM-sensitized PER in the subgroup aged ≥16 years (adjusted OR = 1.745, 95% CI = 1.103–2.760), and this high risk was also found in the females (adjusted OR = 1.708, 95% CI = 1.021–2.856). The G-C haplotype of rs1320646-rs3781699 rendered a lower risk of HDM-sensitized PER than the common haplotype G-A (adjusted OR = 0.819, 95% CI = 0.676–0.993). The secondary structure of GARP altered in response to different genotypes of rs79525962 and rs3781699. Conclusion SNP rs79525962 in the GARP gene marks a risk locus of HDM-sensitized PER in Chinese Hans.
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Affiliation(s)
- Xin-Yuan Chen
- Department of Otorhinolaryngology & Clinical Allergy Center, The First Affiliated Hospital, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Xin-Jie Zhu
- Department of Otorhinolaryngology & Clinical Allergy Center, The First Affiliated Hospital, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Min Chen
- Department of Otorhinolaryngology & Clinical Allergy Center, The First Affiliated Hospital, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Mei-Ping Lu
- Department of Otorhinolaryngology & Clinical Allergy Center, The First Affiliated Hospital, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Mei-Lin Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People’s Republic of China
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Min Yin
- Department of Otorhinolaryngology & Clinical Allergy Center, The First Affiliated Hospital, Nanjing Medical University, Nanjing, People’s Republic of China
- International Centre for Allergy Research, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Ruo-Xi Chen
- Department of Otorhinolaryngology & Clinical Allergy Center, The First Affiliated Hospital, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Zhong-Fei Wu
- Department of Otorhinolaryngology & Clinical Allergy Center, The First Affiliated Hospital, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Dong-Yun Bu
- Department of Otorhinolaryngology & Clinical Allergy Center, The First Affiliated Hospital, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Zheng-Dong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People’s Republic of China
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, People’s Republic of China
- Zheng-Dong Zhang, Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, People’s Republic of China, Email
| | - Lei Cheng
- Department of Otorhinolaryngology & Clinical Allergy Center, The First Affiliated Hospital, Nanjing Medical University, Nanjing, People’s Republic of China
- International Centre for Allergy Research, Nanjing Medical University, Nanjing, People’s Republic of China
- Correspondence: Lei Cheng, Department of Otorhinolaryngology & Clinical Allergy Center, The First Affiliated Hospital, Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, People’s Republic of China, Email
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Molecular Characterization, Expression Profiles of SMAD4, SMAD5 and SMAD7 Genes and Lack of Association with Litter Size in Tibetan Sheep. Animals (Basel) 2022; 12:ani12172232. [PMID: 36077952 PMCID: PMC9455033 DOI: 10.3390/ani12172232] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
SMAD4, SMAD5 and SMAD7 belonging to the transforming growth factor β (TGF-β) superfamily are indispensable for oocyte formation and development, ovarian organogenesis and folliculogenesis. However, only a few studies have investigated the characteristics of SMAD4, SMAD5 and SMAD7 in Tibetan sheep and the effect of their polymorphism on litter size. In this study, we examined the expression of SMAD4, SMAD5 and SMAD7 in 13 tissues of Tibetan sheep by reverse transcription-quantitative polymerase chain reaction. Further, cDNA of these genes was cloned, sequenced and subjected to bioinformatics analysis. DNA sequencing was also used to detect single nucleotide polymorphisms (SNPs). However, iM-LDRTM technology was used for SNP genotyping. Associations between polymorphisms and litter size were analyzed using data from genotyping of 433 Tibetan sheep. The results showed that the expression of SMAD4, SMAD5 and SMAD7 genes was ubiquitous in the tissues of Tibetan sheep, such as the ovary, uterus and oviduct, hypothalamus, hypophysis, heart, liver, spleen, lung, kidney, rumen, duodenum and longissimus dorsi. However, the expression was unbalanced and upregulated in the spleen, lung, ovary and uterus and downregulated in the longissimus dorsi. The bioinformatics analysis showed that SMAD4, SMAD5 and SMAD7 in Tibetan sheep encoded proteins of 533, 465 and 427 amino acids, respectively. Sequence homology analysis of the three proteins among other animals showed that the sequences of SMAD4, SMAD5 and SMAD7 of Tibetan sheep were similar to those in sheep, yak, cattle, dog, human, pig, chimpanzee, rhesus monkey and house mouse. Two synonymous mutations, g.51537A>G and g.319C>T, were detected in SMAD5 and SMAD7, respectively. The associations of these SNPs and litter size were determined, and it was found that both g.51537A>G and g.319C>T have no significant effect on the litter size of Tibetan sheep. The results provided novel insights into the molecular characterization, expression profiles and polymorphisms of SMAD4, SMAD5 and SMAD7 in Tibetan sheep, but our results do not support associations between these genes and the litter size of Tibetan sheep.
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When a Synonymous Variant Is Nonsynonymous. Genes (Basel) 2022; 13:genes13081485. [PMID: 36011397 PMCID: PMC9408308 DOI: 10.3390/genes13081485] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/17/2022] [Accepted: 08/17/2022] [Indexed: 12/27/2022] Open
Abstract
Term synonymous variation is widely used, but frequently in a wrong or misleading meaning and context. Twenty three point eight % of possible nucleotide substitution types in the universal genetic code are for synonymous amino acid changes, but when these variants have a phenotype and functional effect, they are very seldom synonymous. Such variants may manifest changes at DNA, RNA and/or protein levels. Large numbers of variations are erroneously annotated as synonymous, which causes problems e.g., in clinical genetics and diagnosis of diseases. To facilitate precise communication, novel systematics and nomenclature are introduced for variants that when looking only at the genetic code seem like synonymous, but which have phenotypes. A new term, unsense variant is defined as a substitution in the mRNA coding region that affects gene expression and protein production without introducing a stop codon in the variation site. Such variants are common and need to be correctly annotated. Proper naming and annotation are important also to increase awareness of these variants and their consequences.
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50
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Brunet MA, Leblanc S, Roucou X. OpenVar: functional annotation of variants in non-canonical open reading frames. Cell Biosci 2022; 12:130. [PMID: 35965322 PMCID: PMC9375913 DOI: 10.1186/s13578-022-00871-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/03/2022] [Indexed: 11/12/2022] Open
Abstract
Background Recent technological advances have revealed thousands of functional open reading frames (ORF) that have eluded reference genome annotations. These overlooked ORFs are found throughout the genome, in any reading frame of transcripts, mature or non-coding, and can overlap annotated ORFs in a different reading frame. The exploration of these novel ORFs in genomic datasets and of their role in genetic traits is hindered by a lack of software. Results Here, we present OpenVar, a genomic variant annotator that mends that gap and fosters meaningful discoveries. To illustrate the potential of OpenVar, we analysed all variants within SynMicDB, a database of cancer-associated synonymous mutations. By including non-canonical ORFs in the analysis, OpenVar yields a 33.6-fold, 13.8-fold and 8.3-fold increase in high impact variants over Annovar, SnpEff and VEP respectively. We highlighted an overlapping non-canonical ORF in the HEY2 gene where variants significantly clustered. Conclusions OpenVar integrates non-canonical ORFs in the analysis of genomic variants, unveiling new research avenues to better understand the genotype–phenotype relationships.
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