151
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Kariotis S, Jammeh E, Swietlik EM, Pickworth JA, Rhodes CJ, Otero P, Wharton J, Iremonger J, Dunning MJ, Pandya D, Mascarenhas TS, Errington N, Thompson AAR, Romanoski CE, Rischard F, Garcia JGN, Yuan JX, An TS, Desai AA, Coghlan G, Lordan J, Corris PA, Howard LS, Condliffe R, Kiely DG, Church C, Pepke-Zaba J, Toshner M, Wort S, Gräf S, Morrell NW, Wilkins MR, Lawrie A, Wang D; UK National PAH Cohort Study Consortium. Biological heterogeneity in idiopathic pulmonary arterial hypertension identified through unsupervised transcriptomic profiling of whole blood. Nat Commun 2021; 12:7104. [PMID: 34876579 DOI: 10.1038/s41467-021-27326-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 11/15/2021] [Indexed: 11/16/2022] Open
Abstract
Idiopathic pulmonary arterial hypertension (IPAH) is a rare but fatal disease diagnosed by right heart catheterisation and the exclusion of other forms of pulmonary arterial hypertension, producing a heterogeneous population with varied treatment response. Here we show unsupervised machine learning identification of three major patient subgroups that account for 92% of the cohort, each with unique whole blood transcriptomic and clinical feature signatures. These subgroups are associated with poor, moderate, and good prognosis. The poor prognosis subgroup is associated with upregulation of the ALAS2 and downregulation of several immunoglobulin genes, while the good prognosis subgroup is defined by upregulation of the bone morphogenetic protein signalling regulator NOG, and the C/C variant of HLA-DPA1/DPB1 (independently associated with survival). These findings independently validated provide evidence for the existence of 3 major subgroups (endophenotypes) within the IPAH classification, could improve risk stratification and provide molecular insights into the pathogenesis of IPAH.
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152
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Daniyarov A, Molkenov A, Rakhimova S, Akhmetova A, Yerezhepov D, Chingissova L, Bismilda V, Toksanbayeva B, Rakisheva A, Akilzhanova A, Kozhamkulov U, Kairov U. Genomic Analysis of Multidrug-Resistant Mycobacterium tuberculosis Strains From Patients in Kazakhstan. Front Genet 2021; 12:683515. [PMID: 34858467 PMCID: PMC8630622 DOI: 10.3389/fgene.2021.683515] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 10/15/2021] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) is an infectious disease that remains an essential public health problem in many countries. Despite decreasing numbers of new cases worldwide, the incidence of antibiotic-resistant forms (multidrug resistant and extensively drug-resistant) of TB is increasing. Next-generation sequencing technologies provide a high-throughput approach to identify known and novel potential genetic variants that are associated with drug resistance in Mycobacterium tuberculosis (Mtb). There are limited reports and data related to whole-genome characteristics of drug-resistant Mtb strains circulating in Kazakhstan. Here, we report whole-genome sequencing and analysis results of eight multidrug-resistant strains collected from TB patients in Kazakhstan. Genotyping and validation of all strains by MIRU-VNTR and spoligotyping methodologies revealed that these strains belong to the Beijing family. The spectrum of specific and potentially novel genomic variants (single-nucleotide polymorphisms, insertions, and deletions) related to drug resistance was identified and annotated. ResFinder, CARD, and CASTB antibiotic resistance databases were used for the characterization of genetic variants in genes associated with drug resistance. Our results provide reference data and genomic profiles of multidrug-resistant isolates for further comparative studies and investigations of genetic patterns in drug-resistant Mtb strains.
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Affiliation(s)
- Asset Daniyarov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Askhat Molkenov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Saule Rakhimova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ainur Akhmetova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Dauren Yerezhepov
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Lyailya Chingissova
- National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty, Kazakhstan
| | - Venera Bismilda
- National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty, Kazakhstan
| | - Bekzat Toksanbayeva
- National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty, Kazakhstan
| | - Anar Rakisheva
- Department of Phthisiopulmonology, School of General Medicine, Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan
| | - Ainur Akilzhanova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ulan Kozhamkulov
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ulykbek Kairov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
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153
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Hakim A, Moll M, Brancale J, Liu J, Lasky-Su JA, Silverman EK, Vilarinho S, Jiang ZG, Pita-Juárez YH, Vlachos IS, Zhang X, Åberg F, Afdhal NH, Hobbs BD, Cho MH. Genetic Variation in the Mitochondrial Glycerol-3-Phosphate Acyltransferase Is Associated With Liver Injury. Hepatology 2021; 74:3394-3408. [PMID: 34216018 PMCID: PMC8639615 DOI: 10.1002/hep.32038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/17/2021] [Accepted: 06/28/2021] [Indexed: 12/26/2022]
Abstract
BACKGROUND AND AIMS Most of the genetic basis of chronic liver disease remains undiscovered. APPROACH AND RESULTS To identify genetic loci that modulate the risk of liver injury, we performed genome-wide association studies on circulating levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), and total bilirubin across 312,671 White British participants in the UK Biobank. We focused on variants associated with elevations in all four liver biochemistries at genome-wide significance (P < 5 × 10-8 ) and that replicated using Mass General Brigham Biobank in 19,323 European ancestry individuals. We identified a genetic locus in mitochondrial glycerol-3-phosphate acyltransferase (GPAM rs10787429) associated with increased levels of ALT (P = 1.4 × 10-30 ), AST (P = 3.6 × 10-10 ), ALP (P = 9.5 × 10-30 ), and total bilirubin (P = 2.9 × 10-12 ). This common genetic variant was also associated with an allele dose-dependent risk of alcohol-associated liver disease (odd ratio [OR] = 1.34, P = 2.6 × 10-5 ) and fatty liver disease (OR = 1.18, P = 5.8 × 10-4 ) by International Classification of Diseases, 10th Revision codes. We identified significant interactions between GPAM rs10787429 and elevated body mass index in association with ALT and AST (P = 7.1 × 10-9 and 3.95 × 10-8 , respectively), as well as between GPAM rs10787429 and weekly alcohol consumption in association with ALT, AST, and alcohol-associated liver disease (P = 4.0 × 10-2 , 1.6 × 10-2 , and 1.3 × 10-2 , respectively). Unlike previously described genetic variants that are associated with an increased risk of liver injury but confer a protective effect on circulating lipids, GPAM rs10787429 was associated with an increase in total cholesterol (P = 2.0 × 10-17 ), LDL cholesterol (P = 2.0 × 10-10 ), and HDL cholesterol (P = 6.6 × 10-37 ). Single-cell RNA-sequencing data demonstrated hepatocyte-predominant expression of GPAM in cells that co-express genes related to VLDL production (P = 9.4 × 10-103 ). CONCLUSIONS Genetic variation in GPAM is associated with susceptibility to liver injury. GPAM may represent a therapeutic target in chronic liver disease.
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Affiliation(s)
- Aaron Hakim
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA
- Division of Gastroenterology and Hepatology, Beth Israel Deaconess Medical Center, Boston, MA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Matthew Moll
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA
| | - Joseph Brancale
- Departments of Internal Medicine, Section of Digestive Diseases, and of Pathology, Yale School of Medicine, New Haven, CT
| | - Jiangyuan Liu
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Jessica A. Lasky-Su
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA
| | - Silvia Vilarinho
- Departments of Internal Medicine, Section of Digestive Diseases, and of Pathology, Yale School of Medicine, New Haven, CT
| | - Z. Gordon Jiang
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA
- Division of Gastroenterology and Hepatology, Beth Israel Deaconess Medical Center, Boston, MA
| | | | - Ioannis S. Vlachos
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA
| | - Xuehong Zhang
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Fredrik Åberg
- Transplantation and Liver Surgery Clinic, Helsinki University Hospital, Helsinki, Finland
| | - Nezam H. Afdhal
- Division of Gastroenterology and Hepatology, Beth Israel Deaconess Medical Center, Boston, MA
| | - Brian D. Hobbs
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA
| | - Michael H. Cho
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA
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154
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Kadyrov ZA, Stepanov VS, Aldyrakov EM, Machinashvili SG. [Urethral microbiota in healthy men and patients with urethritis]. Urologiia 2021:136-140. [PMID: 34967176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Non-gonococcal urethritis (NGU) is a common disease in men. The main cause of NGU is sexually transmitted infections, which can cause various complications, including reproductive ones. Chlamydia trachomatis and Mycoplasma genitalium are the most common causes of NGU, but no known viral or bacterial pathogens are detected in 28-50% of cases. Traditional research methods revealed a higher load of specific pathogens in patients with urethritis compared to the control, but these studies do not allow us to determine the total bacterial load in the urethra. Using the 16S rRNA sequencing method to characterize the urine and urethral microbiota reveals a diverse bacterial microbiota in both asymptomatic men and patients with NGU, which has a high diversity. The revealed microbiota in both healthy and patients with urethritis still has an ambiguous interpretation and requires further study.
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Affiliation(s)
- Z A Kadyrov
- Peoples Friendship University of Russia, Department of professional Development of the Medical Men, Endoscopic Urology clinic, Moscow, Russia
| | - V S Stepanov
- Peoples Friendship University of Russia, Department of professional Development of the Medical Men, Endoscopic Urology clinic, Moscow, Russia
| | - E M Aldyrakov
- Peoples Friendship University of Russia, Department of professional Development of the Medical Men, Endoscopic Urology clinic, Moscow, Russia
| | - Sh G Machinashvili
- Peoples Friendship University of Russia, Department of professional Development of the Medical Men, Endoscopic Urology clinic, Moscow, Russia
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155
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Rimini M, Puzzoni M, Pedica F, Silvestris N, Fornaro L, Aprile G, Loi E, Brunetti O, Vivaldi C, Simionato F, Zavattari P, Scartozzi M, Burgio V, Ratti F, Aldrighetti L, Cascinu S, Casadei-Gardini A. Cholangiocarcinoma: new perspectives for new horizons. Expert Rev Gastroenterol Hepatol 2021; 15:1367-1383. [PMID: 34669536 DOI: 10.1080/17474124.2021.1991313] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Biliary tract cancer represents a heterogeneous group of malignancies characterized by dismal prognosis and scarce therapeutic options. AREA COVERED In the last years, a growing interest in BTC pathology has emerged, thus highlighting a significant heterogeneity of the pathways underlying the carcinogenesis process, from both a molecular and genomic point of view. A better understanding of these differences is mandatory to deepen the behavior of this complex disease, as well as to identify new targetable target mutations, with the aim to improve the survival outcomes. The authors decided to provide a comprehensive overview of the recent highlights on BTCs, with a special focus on the genetic, epigenetic and molecular alterations, which may have an interesting clinical application in the next future. EXPERT OPINION In the last years, the efforts resulted from international collaborations have led to the identification of new promising targets for precision medicine approaches in the BTC setting. Further investigations and prospective trials are needed, but the hope is that these new knowledge in cooperation with the new technologies and procedures, including bio-molecular and genomic analysis as well radiomic studies, will enrich the therapeutic armamentarium thus improving the survival outcomes in a such lethal and complex disease.
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Affiliation(s)
- Margherita Rimini
- Department of Oncology and Hematology, Division of Oncology, University of Modena and Reggio Emilia, Modena, Italy
| | - Marco Puzzoni
- Medical Oncology, University and University Hospital of Cagliari, Italy
| | - Federica Pedica
- Department of Pathology, San Raffaele Scientific Institute, Milan, Italy
| | - Nicola Silvestris
- Department of oncology, Instituto Di Ricovero E Cura a Carattere Scientifico (IRCCS) Istituto Tumori "Giovanni Paolo Ii" of Bari, Bari, Italy.,Department of Biomedical Sciences and Human Oncology, Aldo Moro University of Bari, Bari, Italy
| | - Lorenzo Fornaro
- Department of medical oncology, U.O. Oncologia Medica 2 Universitaria, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Giuseppe Aprile
- Department of Oncology, San Bortolo General Hospital, Azienda ULSS8 Berica, Vicenza, Italy
| | - Eleonora Loi
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, Cagliari, Italy
| | - Oronzo Brunetti
- Department of oncology, Instituto Di Ricovero E Cura a Carattere Scientifico (IRCCS) Istituto Tumori "Giovanni Paolo Ii" of Bari, Bari, Italy
| | - Caterina Vivaldi
- Department of medical oncology, U.O. Oncologia Medica 2 Universitaria, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Francesca Simionato
- Department of Oncology, San Bortolo General Hospital, Azienda ULSS8 Berica, Vicenza, Italy
| | - Patrizia Zavattari
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, Cagliari, Italy
| | - Mario Scartozzi
- Medical Oncology, University and University Hospital of Cagliari, Italy
| | - Valentina Burgio
- Department of Oncology, IRCCS San Raffaele Scientific Institute Hospital, Milan, Italy
| | - Francesca Ratti
- Hepatobiliary Surgery Division, IRCCS San Raffaele and Vita-Salute University, Italy
| | - Luca Aldrighetti
- Hepatobiliary Surgery Division, IRCCS San Raffaele and Vita-Salute University, Italy
| | - Stefano Cascinu
- Department of Oncology, IRCCS San Raffaele Scientific Institute Hospital, Milan, Italy
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156
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Brancaccio M, Mennitti C, Cesaro A, Monda E, D’Argenio V, Casaburi G, Mazzaccara C, Ranieri A, Fimiani F, Barretta F, Uomo F, Caiazza M, Lioncino M, D’Alicandro G, Limongelli G, Calabrò P, Terracciano D, Lombardo B, Frisso G, Scudiero O. Multidisciplinary In-Depth Investigation in a Young Athlete Suffering from Syncope Caused by Myocardial Bridge. Diagnostics (Basel) 2021; 11:diagnostics11112144. [PMID: 34829491 PMCID: PMC8618222 DOI: 10.3390/diagnostics11112144] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 12/20/2022] Open
Abstract
Laboratory medicine, along with genetic investigations in sports medicine, is taking on an increasingly important role in monitoring athletes’ health conditions. Acute or intense exercise can result in metabolic imbalances, muscle injuries or reveal cardiovascular disorders. This study aimed to monitor the health status of a basketball player with an integrated approach, including biochemical and genetic investigations and advanced imaging techniques, to shed light on the causes of recurrent syncope he experienced during exercise. Biochemical analyses showed that the athlete had abnormal iron, ferritin and bilirubin levels. Coronary Computed Tomographic Angiography highlighted the presence of an intramyocardial bridge, suggesting this may be the cause of the observed syncopes. The athlete was excluded from competitive activity. In order to understand if this cardiac malformation could be caused by an inherited genetic condition, both array-CGH and whole exome sequencing were performed. Array-CGH showed two intronic deletions involving MACROD2 and COMMD10 genes, which could be related to a congenital heart defect; whole exome sequencing highlighted the genotype compatible with Gilbert syndrome. However, no clear pathogenic mutations related to the patient’s cardiological phenotype were detected, even after applying machine learning methods. This case report highlights the importance and the need to provide exhaustive personalized diagnostic work up for the athletes in order to cover the cause of their malaise and for safeguarding their health. This multidisciplinary approach can be useful to create ad personam training and treatments, thus avoiding the appearance of diseases and injuries which, if underestimated, can become irreversible disorders and sometimes can result in the death of the athlete.
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Affiliation(s)
- Mariarita Brancaccio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (M.B.); (C.M.); (C.M.); (F.B.); (F.U.); (B.L.)
| | - Cristina Mennitti
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (M.B.); (C.M.); (C.M.); (F.B.); (F.U.); (B.L.)
| | - Arturo Cesaro
- Department of Translational Medical Sciences, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.C.); (E.M.); (M.L.); (G.L.); (P.C.)
- Division of Clinical Cardiology, A.O.R.N. “Sant’Anna e San Sebastiano”, 81100 Caserta, Italy
| | - Emanuele Monda
- Department of Translational Medical Sciences, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.C.); (E.M.); (M.L.); (G.L.); (P.C.)
| | - Valeria D’Argenio
- Ceinge Biotecnologie Avanzate S. C. a R. L., 80131 Naples, Italy; (V.D.); (A.R.)
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, Via di val Cannuta 247, 00166 Roma, Italy
| | - Giorgio Casaburi
- Prescient Metabiomics, 1600 Faraday Ave, Carlsbad, CA 9200, USA;
| | - Cristina Mazzaccara
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (M.B.); (C.M.); (C.M.); (F.B.); (F.U.); (B.L.)
- Ceinge Biotecnologie Avanzate S. C. a R. L., 80131 Naples, Italy; (V.D.); (A.R.)
| | - Annaluisa Ranieri
- Ceinge Biotecnologie Avanzate S. C. a R. L., 80131 Naples, Italy; (V.D.); (A.R.)
| | - Fabio Fimiani
- Unit of Inherited and Rare Cardiovascular Diseases, Azienda Ospedaliera di Rilievo Nazionale AORN Dei Colli, “V. Monaldi”, 80122 Naples, Italy;
| | - Ferdinando Barretta
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (M.B.); (C.M.); (C.M.); (F.B.); (F.U.); (B.L.)
- Ceinge Biotecnologie Avanzate S. C. a R. L., 80131 Naples, Italy; (V.D.); (A.R.)
| | - Fabiana Uomo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (M.B.); (C.M.); (C.M.); (F.B.); (F.U.); (B.L.)
- Ceinge Biotecnologie Avanzate S. C. a R. L., 80131 Naples, Italy; (V.D.); (A.R.)
| | - Martina Caiazza
- Inherited and Rare Cardiovascular Diseases, Department of Translational Medical Sciences, University of Campania “Luigi Vanvitelli”, Monaldi Hospital, 81100 Naples, Italy;
| | - Michele Lioncino
- Department of Translational Medical Sciences, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.C.); (E.M.); (M.L.); (G.L.); (P.C.)
| | - Giovanni D’Alicandro
- Department of Neuroscience and Rehabilitation, Center of Sports Medicine and Disability, AORN, Santobono-Pausillipon, 80122 Naples, Italy;
| | - Giuseppe Limongelli
- Department of Translational Medical Sciences, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.C.); (E.M.); (M.L.); (G.L.); (P.C.)
| | - Paolo Calabrò
- Department of Translational Medical Sciences, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.C.); (E.M.); (M.L.); (G.L.); (P.C.)
- Division of Clinical Cardiology, A.O.R.N. “Sant’Anna e San Sebastiano”, 81100 Caserta, Italy
| | - Daniela Terracciano
- Department of Translational Medical Sciences, University of Naples Federico II, 80131 Naples, Italy;
| | - Barbara Lombardo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (M.B.); (C.M.); (C.M.); (F.B.); (F.U.); (B.L.)
- Ceinge Biotecnologie Avanzate S. C. a R. L., 80131 Naples, Italy; (V.D.); (A.R.)
| | - Giulia Frisso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (M.B.); (C.M.); (C.M.); (F.B.); (F.U.); (B.L.)
- Ceinge Biotecnologie Avanzate S. C. a R. L., 80131 Naples, Italy; (V.D.); (A.R.)
- Correspondence: (G.F.); (O.S.); Tel.: +39-3472409595 (G.F.); +39-3396139908 (O.S.)
| | - Olga Scudiero
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (M.B.); (C.M.); (C.M.); (F.B.); (F.U.); (B.L.)
- Ceinge Biotecnologie Avanzate S. C. a R. L., 80131 Naples, Italy; (V.D.); (A.R.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80100 Naples, Italy
- Correspondence: (G.F.); (O.S.); Tel.: +39-3472409595 (G.F.); +39-3396139908 (O.S.)
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157
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Singh UB, Rophina M, Chaudhry R, Senthivel V, Bala K, Bhoyar RC, Jolly B, Jamshed N, Imran M, Gupta R, Aggarwal P, Divakar MK, Sinha S, Arvinden VR, Bajaj A, Shamnath A, Jain A, Scaria V, Sivasubbu S, Guleria R. Variants of concern responsible for SARS-CoV-2 vaccine breakthrough infections from India. J Med Virol 2021; 94:1696-1700. [PMID: 34786733 PMCID: PMC8662202 DOI: 10.1002/jmv.27461] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/11/2021] [Accepted: 11/13/2021] [Indexed: 11/08/2022]
Abstract
Emerging reports of SARS‐CoV‐2 breakthrough infections entail methodical genomic surveillance for determining the efficacy of vaccines. This study elaborates genomic analysis of isolates from breakthrough infections following vaccination with AZD1222/Covishield and BBV152/Covaxin. Variants of concern B.1.617.2 and B.1.1.7 responsible for cases surge in April–May 2021 in Delhi, were the predominant lineages among breakthrough infections.
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Affiliation(s)
- Urvashi B Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Mercy Rophina
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.,Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, India
| | - Rama Chaudhry
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Vigneshwar Senthivel
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.,Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, India
| | - Kiran Bala
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Rahul C Bhoyar
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Bani Jolly
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.,Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, India
| | - Nayer Jamshed
- Department of Emergency Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Mohamed Imran
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.,Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, India
| | - Ritu Gupta
- Department of Laboratory Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Praveen Aggarwal
- Department of Emergency Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Mohit K Divakar
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.,Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, India
| | - Subrata Sinha
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - V R Arvinden
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.,Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, India
| | - Anjali Bajaj
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.,Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, India
| | - Afra Shamnath
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Abhinav Jain
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.,Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, India
| | | | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.,Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, India
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.,Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, India
| | - Randeep Guleria
- Department of Pulmonary Critical Care & Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
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158
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Ji C, Zhang M, Kong Z, Chen X, Wang X, Ding W, Lai H, Guo Q. Genomic Analysis Reveals Potential Mechanisms Underlying Promotion of Tomato Plant Growth and Antagonism of Soilborne Pathogens by Bacillus amyloliquefaciens Ba13. Microbiol Spectr 2021;:e0161521. [PMID: 34756081 DOI: 10.1128/Spectrum.01615-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus amyloliquefaciens Ba13 is a plant beneficial bacterium isolated from loessial soil with notable biological activity. This study clarified potential mechanisms underlying the plant growth-promoting and antipathogenic effects of strain Ba13. A pot experiment was used to verify the plant growth-promoting effects of strain Ba13 on tomato, and the antipathogenic activity was tested in petri dishes. The underlying mechanisms were explored based on whole-genome sequencing of strain Ba13 and liquid chromatography-tandem mass spectrometry (LC-MS/MS) detection of plant hormones and biosynthetic intermediates. The results showed that exposure to strain Ba13 promoted tomato plant growth significantly. Compared with control treatment, bacterial treatment increased plant height and fresh weight by 10.98% and 20.15%, respectively, at 28 days after inoculation. Strain Ba13 exhibited antagonistic activity against all eight plant pathogens tested. The 3,861,210-bp genome of strain Ba13 was predicted to encode antibiotics (e.g., surfactin, bacillaene, bacillomycin D, bacilysin, and bacillibactin) and volatile gaseous compounds (e.g., 2,3-butanediol and acetoin). Genes were also predicted to encode extracellular phytase and β-glucanase that are secreted through the secretory (Sec) system. Strain Ba13 could synthesize indole-3-acetic acid through the indole-3-pyruvic acid pathway. The results of this study indicate that B. amyloliquefaciens Ba13 has multiple effects on tomato plants and associated microorganisms, directly or indirectly promoting plant growth and controlling plant diseases. IMPORTANCE Microbial agents are considered the optimal alternative for chemical agents. Exploring the mechanisms underlying the beneficial effects of microbial agents is essential for rational applications in the field. In this study, we report a functional bacterial strain, Bacillus amyloliquefaciens Ba13, which exhibited plant growth-promoting and antipathogenic effects. The whole genome of strain Ba13 was sequenced, and functional genes of interest were predicted. Strain Ba13 could synthesize indole-3-acetic acid through the indole-3-pyruvic acid pathway.
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159
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Yu J, Hulse-Kemp AM, Babiker E, Staton M. High-quality reference genome and annotation aids understanding of berry development for evergreen blueberry (Vaccinium darrowii). Hortic Res 2021; 8:228. [PMID: 34719668 PMCID: PMC8558335 DOI: 10.1038/s41438-021-00641-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/22/2021] [Accepted: 07/13/2021] [Indexed: 05/07/2023]
Abstract
Vaccinium darrowii Camp (2n = 2x = 24) is a native North American blueberry species and an important source of traits such as low chill requirement in commercial southern highbush blueberry breeding (Vaccinium corymbosum, 2n = 4x = 48). We present a chromosomal-scale genome of V. darrowii generated by the combination of PacBio sequencing and high throughput chromatin conformation capture (Hi-C) scaffolding technologies, yielding a total length of 1.06 Gigabases (Gb). Over 97.8% of the genome sequences are scaffolded into 24 chromosomes representing the two haplotypes. The primary haplotype assembly of V. darrowii contains 34,809 protein-coding genes. Comparison to a V. corymbosum haplotype assembly reveals high collinearity between the two genomes with small intrachromosomal rearrangements in eight chromosome pairs. With small RNA sequencing, the annotation was further expanded to include more than 200,000 small RNA loci and 638 microRNAs expressed in berry tissues. Transcriptome analysis across fruit development stages indicates that genes involved in photosynthesis are downregulated, while genes involved in flavonoid and anthocyanin biosynthesis are significantly increased at the late stage of berry ripening. A high-quality reference genome and accompanying annotation of V. darrowii is a significant new resource for assessing the evergreen blueberry contribution to the breeding of southern highbush blueberries.
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Affiliation(s)
- Jiali Yu
- Genome Science and Technology Program, University of Tennessee, Knoxville, TN, 37996, USA
| | - Amanda M Hulse-Kemp
- USDA-ARS Genomics and Bioinformatics Research Unit, Raleigh, NC, USA
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, USA
| | - Ebrahiem Babiker
- USDA-ARS Thad Cochran Southern Horticultural Laboratory, Poplarville, MS, USA.
| | - Margaret Staton
- Genome Science and Technology Program, University of Tennessee, Knoxville, TN, 37996, USA.
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA.
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160
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Marques AT, Tanoeiro L, Duarte A, Gonçalves L, Vítor JMB, Vale FF. Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates. Microorganisms 2021; 9:2252. [PMID: 34835377 PMCID: PMC8617712 DOI: 10.3390/microorganisms9112252] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/15/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022] Open
Abstract
Klebsiella pneumoniae is an increasing threat to public health and represents one of the most concerning pathogens involved in life-threatening infections. The resistant and virulence determinants are coded by mobile genetic elements which can easily spread between bacteria populations and co-evolve with its genomic host. In this study, we present the full genomic sequences, insertion sites and phylogenetic analysis of 150 prophages found in 40 K. pneumoniae clinical isolates obtained from an outbreak in a Portuguese hospital. All strains harbored at least one prophage and we identified 104 intact prophages (69.3%). The prophage size ranges from 29.7 to 50.6 kbp, coding between 32 and 78 putative genes. The prophage GC content is 51.2%, lower than the average GC content of 57.1% in K. pneumoniae. Complete prophages were classified into three families in the order Caudolovirales: Myoviridae (59.6%), Siphoviridae (38.5%) and Podoviridae (1.9%). In addition, an alignment and phylogenetic analysis revealed nine distinct clusters. Evidence of recombination was detected within the genome of some prophages but, in most cases, proteins involved in viral structure, transcription, replication and regulation (lysogenic/lysis) were maintained. These results support the knowledge that prophages are diverse and widely disseminated in K. pneumoniae genomes, contributing to the evolution of this species and conferring additional phenotypes. Moreover, we identified K. pneumoniae prophages in a set of endolysin genes, which were found to code for proteins with lysozyme activity, cleaving the β-1,4 linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in the peptidoglycan network and thus representing genes with the potential for lysin phage therapy.
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Affiliation(s)
- Andreia T. Marques
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (L.T.); (J.M.B.V.)
| | - Luís Tanoeiro
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (L.T.); (J.M.B.V.)
| | - Aida Duarte
- Faculty of Pharmacy, Universidade de Lisboa, Av. Gama Pinto, 1649-003 Lisboa, Portugal;
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, 2829-511 Monte da Caparica, Portugal
| | - Luisa Gonçalves
- Clinical Pathology Unit, Hospital SAMS, Cidade de Gabela, 1849-017 Lisboa, Portugal;
| | - Jorge M. B. Vítor
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (L.T.); (J.M.B.V.)
| | - Filipa F. Vale
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (L.T.); (J.M.B.V.)
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161
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Liao Y, Wang Z, Glória LS, Zhang K, Zhang C, Yang R, Luo X, Jia X, Lai SJ, Chen SY. Genome-Wide Association Studies for Growth Curves in Meat Rabbits Through the Single-Step Nonlinear Mixed Model. Front Genet 2021; 12:750939. [PMID: 34691158 PMCID: PMC8531506 DOI: 10.3389/fgene.2021.750939] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/15/2021] [Indexed: 11/13/2022] Open
Abstract
Growth is a complex trait with moderate to high heritability in livestock and must be described by the longitudinal data measured over multiple time points. Therefore, the used phenotype in genome-wide association studies (GWAS) of growth traits could be either the measures at the preselected time point or the fitted parameters of whole growth trajectory. A promising alternative approach was recently proposed that combined the fitting of growth curves and estimation of single-nucleotide polymorphism (SNP) effects into single-step nonlinear mixed model (NMM). In this study, we collected the body weights at 35, 42, 49, 56, 63, 70, and 84 days of age for 401 animals in a crossbred population of meat rabbits and compared five fitting models of growth curves (Logistic, Gompertz, Brody, Von Bertalanffy, and Richards). The logistic model was preferably selected and subjected to GWAS using the approach of single-step NMM, which was based on 87,704 genome-wide SNPs. A total of 45 significant SNPs distributed on five chromosomes were found to simultaneously affect the two growth parameters of mature weight (A) and maturity rate (K). However, no SNP was found to be independently associated with either A or K. Seven positional genes, including KCNIP4, GBA3, PPARGC1A, LDB2, SHISA3, GNA13, and FGF10, were suggested to be candidates affecting growth performances in meat rabbits. To the best of our knowledge, this is the first report of GWAS based on single-step NMM for longitudinal traits in rabbits, which also revealed the genetic architecture of growth traits that are helpful in implementing genome selection.
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Affiliation(s)
- Yonglan Liao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhicheng Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Leonardo S Glória
- Laboratory of Animal Science, State University of Northern of Rio de Janeiro, Campos dos Goytacazes, Brazil
| | - Kai Zhang
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Cuixia Zhang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Rui Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Xinmao Luo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xianbo Jia
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Song-Jia Lai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shi-Yi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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162
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Zakharyuk A, Valyshev A, Plotnikov A, Kopitsyn D, Suzina N, Shcherbakova V. Trichococcus shcherbakoviae subsp. psychrophilus subsp. nov., a psychrotolerant facultative anaerobe isolated from a cold spring. Int J Syst Evol Microbiol 2021; 71. [PMID: 34694985 DOI: 10.1099/ijsem.0.005068] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A psychrotolerant facultative anaerobe, strain SKBGT, was isolated from the bottom sediments of the cold mineral spring Buxichen (Buryatia, Russia). Gram-positive non-motile cocci with a diameter of 1.75-2.5 µm were observed singly or in long chains. Cells grew in the temperature range from ̶ 5-35 °C. Growth was observed within the pH range of 7.0-9.5, with the optimum growth at pH 7.6 and at a NaCl concentration from 0-1.0 % (optimum 0.1 % (w/v)). Strain SKBGT was a chemoorganoheterotroph that used sugars and some organic acids as substrates. The predominant fatty acids in cell walls were С16:1ω9, С18:1ω9, and С16 : 0. The 16S rRNA gene sequence of strain SKBGT shared high similarity (>99 %) with those of the type strains of the genus Trichococcus. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain SKBGT and Trichococcus shcherbakoviae ArtT (=DSM 107162T=VKM B-3260T) were 70.1 and 95.4 %, respectively. The genomic DNA G+C content of strain SKBGT was 47.1 mol%. Compared with the type strain of T. shcherbakoviae, the new strain was characterized by a temperature optimum for growth (10 °C) significantly lower than that of T. shcherbakoviae DSM 107162T (20-30 °C). Based on phenotypic and genomic characteristics, the isolate SKBGT was classified as T. shcherbakoviae subsp. psychrophilus subsp. nov. The type strain is SKBGT (=VKM B-3241Т=JCM 33326T).
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Affiliation(s)
- Anastasiya Zakharyuk
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Prospect Nauki 5, 142290, Pushchino, Moscow Region, Russia
| | - Alexander Valyshev
- Institute of Cellular and Intracellular Symbiosis of the Ural Branch of the Russian Academy of Sciences, Pionerskaya street, 11, 460000, Orenburg, Russia
| | - Andrey Plotnikov
- Institute of Cellular and Intracellular Symbiosis of the Ural Branch of the Russian Academy of Sciences, Pionerskaya street, 11, 460000, Orenburg, Russia
| | - Dmitry Kopitsyn
- Gubkin University, Leninsky Prospect 65-1, 119991, Moscow, Russia
| | - Nataliya Suzina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Prospect Nauki 5, 142290, Pushchino, Moscow Region, Russia
| | - Viktoria Shcherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Prospect Nauki 5, 142290, Pushchino, Moscow Region, Russia
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163
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Maggiori C, Raymond-Bouchard I, Brennan L, Touchette D, Whyte L. MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes. Sci Rep 2021; 11:21041. [PMID: 34702846 PMCID: PMC8548342 DOI: 10.1038/s41598-021-00026-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/30/2021] [Indexed: 01/04/2023] Open
Abstract
Genome reconstruction from metagenomes enables detailed study of individual community members, their metabolisms, and their survival strategies. Obtaining high quality metagenome-assembled genomes (MAGs) is particularly valuable in extreme environments like sea ice cryoconites, where the native consortia are recalcitrant to culture and strong astrobiology analogues. We evaluated three separate approaches for MAG generation from Allen Bay, Nunavut sea ice cryoconites-HiSeq-only, MinION-only, and hybrid (HiSeq + MinION)-where field MinION sequencing yielded a reliable metagenome. The hybrid assembly produced longer contigs, more coding sequences, and more total MAGs, revealing a microbial community dominated by Bacteroidetes. The hybrid MAGs also had the highest completeness, lowest contamination, and highest N50. A putatively novel species of Octadecabacter is among the hybrid MAGs produced, containing the genus's only known instances of genomic potential for nitrate reduction, denitrification, sulfate reduction, and fermentation. This study shows that the inclusion of MinION reads in traditional short read datasets leads to higher quality metagenomes and MAGs for more accurate descriptions of novel microorganisms in this extreme, transient habitat and has produced the first hybrid MAGs from an extreme environment.
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Affiliation(s)
- Catherine Maggiori
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21 111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Ste. Anne-de-Bellevue, Quebec, H9X 3V9, Canada.
| | - Isabelle Raymond-Bouchard
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21 111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Ste. Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Laura Brennan
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21 111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Ste. Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - David Touchette
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21 111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Ste. Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Lyle Whyte
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21 111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Ste. Anne-de-Bellevue, Quebec, H9X 3V9, Canada
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164
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Abstract
The revolution in genome sequencing technologies has enabled the comprehensive detection of genomic variations in human cells, including inherited germline polymorphisms, de novo mutations, and postzygotic mutations. When these technologies are combined with techniques for isolating and expanding single-cell DNA, the landscape of somatic mosaicism in an individual body can be systematically revealed at a single-cell resolution. Here, we summarize three strategies (whole-genome amplification, microdissection of clonal patches in the tissue, and in vitro clonal expansion of single cells) that are currently applied for single-cell mutational analyses. Among these approaches, in vitro clonal expansion, particularly via adult stem cell-derived organoid culture technologies, yields the most sensitive and precise catalog of somatic mutations in single cells. Moreover, because it produces living mutant cells, downstream validation experiments and multiomics profiling are possible. Through the synergistic combination of organoid culture and genome sequencing, researchers can track genome changes at a single-cell resolution, which will lead to new discoveries that were previously impossible.
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Affiliation(s)
- Jeonghwan Youk
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- GENOME INSIGHT Inc, Daejeon, 34051, Republic of Korea
| | - Hyun Woo Kwon
- Department of Nuclear Medicine, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Ryul Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- GENOME INSIGHT Inc, Daejeon, 34051, Republic of Korea.
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165
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Zech M, Kumar KR, Reining S, Reunert J, Tchan M, Riley LG, Drew AP, Adam RJ, Berutti R, Biskup S, Derive N, Bakhtiari S, Jin SC, Kruer MC, Bardakjian T, Gonzalez-Alegre P, Keller Sarmiento IJ, Mencacci NE, Lubbe SJ, Kurian MA, Clot F, Méneret A, de Sainte Agathe JM, Fung VSC, Vidailhet M, Baumann M, Marquardt T, Winkelmann J, Boesch S. Biallelic AOPEP Loss-of-Function Variants Cause Progressive Dystonia with Prominent Limb Involvement. Mov Disord 2021; 37:137-147. [PMID: 34596301 DOI: 10.1002/mds.28804] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/01/2021] [Accepted: 09/13/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Monogenic causes of isolated dystonia are heterogeneous. Assembling cohorts of affected individuals sufficiently large to establish new gene-disease relationships can be challenging. OBJECTIVE We sought to expand the catalogue of monogenic etiologies for isolated dystonia. METHODS After the discovery of a candidate variant in a multicenter exome-sequenced cohort of affected individuals with dystonia, we queried online platforms and genomic data repositories worldwide to identify subjects with matching genotypic profiles. RESULTS Seven different biallelic loss-of-function variants in AOPEP were detected in five probands from four unrelated families with strongly overlapping phenotypes. In one proband, we observed a homozygous nonsense variant (c.1477C>T [p.Arg493*]). A second proband harbored compound heterozygous nonsense variants (c.763C>T [p.Arg255*]; c.777G>A [p.Trp259*]), whereas a third proband possessed a frameshift variant (c.696_697delAG [p.Ala234Serfs*5]) in trans with a splice-disrupting alteration (c.2041-1G>A). Two probands (siblings) from a fourth family shared compound heterozygous frameshift alleles (c.1215delT [p.Val406Cysfs*14]; c.1744delA [p.Met582Cysfs*6]). All variants were rare and expected to result in truncated proteins devoid of functionally important amino acid sequence. AOPEP, widely expressed in developing and adult human brain, encodes a zinc-dependent aminopeptidase, a member of a class of proteolytic enzymes implicated in synaptogenesis and neural maintenance. The probands presented with disabling progressive dystonia predominantly affecting upper and lower extremities, with variable involvement of craniocervical muscles. Dystonia was unaccompanied by any additional symptoms in three families, whereas the fourth family presented co-occurring late-onset parkinsonism. CONCLUSIONS Our findings suggest a likely causative role of predicted inactivating biallelic AOPEP variants in cases of autosomal recessive dystonia. Additional studies are warranted to understand the pathophysiology associated with loss-of-function variation in AOPEP. © 2021 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany.,Technical University of Munich, Munich, Germany.,School of Medicine, Technical University of Munich, Institute of Human Genetics, Munich, Germany
| | - Kishore R Kumar
- Molecular Medicine Laboratory and Neurology Department, Concord Clinical School, Concord Repatriation General Hospital, The University of Sydney, Sydney, New South Wales, Australia.,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Sophie Reining
- Department of General Paediatrics, University of Münster, Münster, Germany
| | - Janine Reunert
- Department of General Paediatrics, University of Münster, Münster, Germany
| | - Michel Tchan
- Department of Genetic Medicine, Westmead Hospital, Westmead, New South Wales, Australia.,Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
| | - Lisa G Riley
- Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia.,Rare Diseases Functional Genomics, Kids Research, The Children's Hospital at Westmead and The Children's Medical Research Institute, Sydney, New South Wales, Australia
| | - Alexander P Drew
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Robert J Adam
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia.,Centre for Clinical Research, The University of Queensland, Brisbane, Queensland, Australia
| | - Riccardo Berutti
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany.,Technical University of Munich, Munich, Germany.,School of Medicine, Technical University of Munich, Institute of Human Genetics, Munich, Germany
| | - Saskia Biskup
- CeGaT GmbH und Praxis für Humangenetik Tübingen, Tübingen, Germany
| | - Nicolas Derive
- Laboratoire de Biologie Médicale Multi-Sites SeqOIA, Paris, France
| | - Somayeh Bakhtiari
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, Arizona, USA.,Departments of Child Health, Neurology, and Cellular & Molecular Medicine, and Program in Genetics, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona, USA
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michael C Kruer
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, Arizona, USA.,Departments of Child Health, Neurology, and Cellular & Molecular Medicine, and Program in Genetics, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona, USA
| | - Tanya Bardakjian
- Department of Neurology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Pedro Gonzalez-Alegre
- Department of Neurology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ignacio J Keller Sarmiento
- Ken and Ruth Davee Department of Neurology, and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Niccolo E Mencacci
- Ken and Ruth Davee Department of Neurology, and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Steven J Lubbe
- Ken and Ruth Davee Department of Neurology, and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Manju A Kurian
- Department of Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, United Kingdom.,Department of Neurology, Great Ormond Street Hospital, London, United Kingdom
| | - Fabienne Clot
- Laboratoire de Biologie Médicale Multi-Sites SeqOIA, Paris, France.,AP-HP Sorbonne Université, Département de Génétique, UF de Neurogénétique Moléculaire et Cellulaire, Hôpital Pitié-Salpêtrière, Paris, France
| | - Aurélie Méneret
- Sorbonne Université, Paris Brain Institute-ICM, Inserm, CNRS, Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, DMU Neurosciences, Paris, France
| | - Jean-Madeleine de Sainte Agathe
- Laboratoire de Biologie Médicale Multi-Sites SeqOIA, Paris, France.,AP-HP Sorbonne Université, Laboratoire de Médecine Génomique, Hôpital Pitié-Salpêtrière, Paris, France
| | - Victor S C Fung
- Movement Disorders Unit, Neurology Department, Westmead Hospital, Westmead, New South Wales, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Marie Vidailhet
- Sorbonne Université, Paris Brain Institute-ICM, Inserm, CNRS, Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, DMU Neurosciences, Paris, France
| | - Matthias Baumann
- Department of Pediatrics, Medical University of Innsbruck, Innsbruck, Austria
| | - Thorsten Marquardt
- Department of General Paediatrics, University of Münster, Münster, Germany
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany.,Technical University of Munich, Munich, Germany.,School of Medicine, Technical University of Munich, Institute of Human Genetics, Munich, Germany.,Lehrstuhl für Neurogenetik, Technische Universität München, Munich, Germany.,Munich Cluster for Systems Neurology, SyNergy, Munich, Germany
| | - Sylvia Boesch
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
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166
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Karunarathna NL, Patiranage DSR, Harloff HJ, Sashidhar N, Jung C. Genomic background selection to reduce the mutation load after random mutagenesis. Sci Rep 2021; 11:19404. [PMID: 34593904 PMCID: PMC8484577 DOI: 10.1038/s41598-021-98934-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022] Open
Abstract
Random mutagenesis is a standard procedure to increase allelic variation in a crop species, especially in countries where the use of genetically modified crops is limited due to legal constraints. The chemical mutagen EMS is used in many species to induce random mutations throughout the genome with high mutation density. The major drawback for functional analysis is a high background mutation load in a single plant that must be eliminated by subsequent backcrossing, a time and resource-intensive activity. Here, we demonstrate that genomic background selection combined with marker-assisted selection is an efficient way to select individuals with reduced background mutations within a short period. We identified BC1 plants with a significantly higher share of the recurrent parent genome, thus saving one backcross generation. Furthermore, spring rapeseed as the recurrent parent in a backcrossing program could accelerate breeding by reducing the generation cycle. Our study depicts the potential for reducing the background mutation load while accelerating the generation cycle in EMS-induced winter oilseed rape populations by integrating genomic background selection.
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Affiliation(s)
- Nirosha L Karunarathna
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, 24098, Kiel, Germany
- KWS LOCHOW GMBH, Zuchtstation Wetze, Wetze 3, 37154, Northeim, Germany
| | - Dilan S R Patiranage
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, 24098, Kiel, Germany
| | - Hans-Joachim Harloff
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, 24098, Kiel, Germany
| | - Niharika Sashidhar
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, 24098, Kiel, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Cologne, Germany
| | - Christian Jung
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, 24098, Kiel, Germany.
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstrasse 40, 24118, Kiel, Germany.
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167
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Hescheler DA, Riemann B, Hartmann MJM, Michel M, Faust M, Bruns CJ, Alakus H, Chiapponi C. Targeted Therapy of Papillary Thyroid Cancer: A Comprehensive Genomic Analysis. Front Endocrinol (Lausanne) 2021; 12:748941. [PMID: 34630336 PMCID: PMC8498581 DOI: 10.3389/fendo.2021.748941] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/27/2021] [Indexed: 12/15/2022] Open
Abstract
Background A limited number of targeted therapy options exist for papillary thyroid cancer (PTC) to date. Based on genetic alterations reported by the "The Cancer Genome Atlas (TCGA)", we explored whether PTC shows alterations that may be targetable by drugs approved by the FDA for other solid cancers. Methods Databases of the National Cancer Institute and MyCancerGenome were screened to identify FDA-approved drugs for targeted therapy. Target genes were identified using Drugbank. Genetic alterations were classified into conferring drug sensitivity or resistance using MyCancerGenome, CiViC, TARGET, and OncoKB. Genomic data for PTC were extracted from TCGA and mined for alterations predicting drug response. Results A total of 129 FDA-approved drugs with 128 targetable genes were identified. One hundred ninety-six (70%) of 282 classic, 21 (25%) of 84 follicular, and all 30 tall-cell variant PTCs harbored druggable alterations: 259 occurred in 29, 39 in 19, and 31 in 2 targetable genes, respectively. The BRAF V600 mutation was seen in 68% of classic, 16% of follicular variant, and 93% of tall-cell variant PTCs. The RET gene fusion was seen in 8% of classic PTCs, NTRK1 and 3 gene fusions in 3%, and other alterations in <2% of classic variant PTCs. Ninety-nine of 128 (77%) FDA-approved targetable genes did not show any genetic alteration in PTC. Beside selective and non-selective BRAF-inhibitors, no other FDA-approved drug showed any frequent predicted drug sensitivity (<10%). Conclusion Treatment strategies need to focus on resistance mechanisms to BRAF inhibition and on genetic alteration-independent alternatives rather than on current targeted drugs.
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Affiliation(s)
- Daniel A. Hescheler
- Department of Nuclear Medicine, University Hospital Münster, Münster, Germany
- European Institute for Molecular Imaging (EIMI), University of Münster, Münster, Germany
| | - Burkhard Riemann
- Department of Nuclear Medicine, University Hospital Münster, Münster, Germany
| | - Milan J. M. Hartmann
- Department of General, Visceral, Tumor and Transplant Surgery, University Hospital Cologne, Cologne, Germany
| | - Maximilian Michel
- Institute of Zoology, University of Cologne Germany, Cologne, Germany
| | - Michael Faust
- Policlinic for Prevention, Diabetes and Endocrinology, University of Cologne, Cologne, Germany
| | - Christiane J. Bruns
- Department of General, Visceral, Tumor and Transplant Surgery, University Hospital Cologne, Cologne, Germany
| | - Hakan Alakus
- Department of General, Visceral, Tumor and Transplant Surgery, University Hospital Cologne, Cologne, Germany
| | - Costanza Chiapponi
- Department of General, Visceral, Tumor and Transplant Surgery, University Hospital Cologne, Cologne, Germany
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168
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Pei S, Niu S, Xie F, Wang W, Zhang S, Zhang G. Brevibacterium limosum sp. nov., Brevibacterium pigmenatum sp. nov., and Brevibacterium atlanticum sp. nov., three novel dye decolorizing actinobacteria isolated from ocean sediments. J Microbiol 2021; 59:898-910. [PMID: 34491521 DOI: 10.1007/s12275-021-1235-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/14/2021] [Accepted: 07/21/2021] [Indexed: 10/20/2022]
Abstract
During a study of the marine actinobacterial biodiversity, a large number of Brevibacterium strains were isolated. Of these, five that have relatively low 16S rRNA gene similarity (98.5-99.3%) with validly published Brevibacterium species, were chosen to determine taxonomic positions. On the basis of 16S rRNA gene sequence analysis and BOX-PCR fingerprinting, strains o2T, YB235T, and WO024T were selected as representative strains. Genomic analyses, including average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH), clearly differentiated the three strains from each other and from their closest relatives, with values ranging from 82.8% to 91.5% for ANI and from 26.7% to 46.5% for dDDH that below the threshold for species delineation. Strains YB235T, WO024T, and o2T all exhibited strong and efficient decolorization activity in congo red (CR) dyes, moderate decolorization activity in toluidine blue (TB) dyes and poor decolorization in reactive blue (RB) dyes. Genes coding for peroxidases and laccases were identified and accounted for these strains' ability to effectively oxidize a variety of dyes with different chemical structures. Mining of the whole genome for secondary metabolite biosynthesis gene clusters revealed the presence of gene clusters encoding for bacteriocin, ectoine, NRPS, siderophore, T3PKS, terpene, and thiopeptide. Based on the phylogenetic, genotypic and phenotypic data, strains o2T, YB235T and WO024T clearly represent three novel taxa within the genus Brevibacterium, for which the names Brevibacterium limosum sp. nov. (type strain o2T = JCM 33844T = MCCC 1A09961T), Brevibacterium pigmenatum sp. nov. (type strain YB235T = JCM 33843T = MCCC 1A09842T) and Brevibacterium atlanticum sp. nov. (type strain WO024T = JCM 33846T = MCCC 1A16743T) are proposed.
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169
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Ramírez Toro EJ, Mourão GB, Martínez Sarmiento RA, Cerón-Muñoz MF. Genetic selection indices for growth traits in Blanco-Orejinegro cattle. Transl Anim Sci 2021; 5:txab133. [PMID: 34476348 PMCID: PMC8404612 DOI: 10.1093/tas/txab133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/09/2021] [Indexed: 11/30/2022] Open
Abstract
Selection indices are used in genetic improvement programs, with the purpose of selectins simultaneous for several economically important traits. The objective of this study was to construct equations for selection indices in the Blanco-Orejinegro (BON) breed and to determine the index that would generate the greatest genetic progress. The information used included birth weight (BW), body weights adjusted to 120, 240, 480, and 720 days old (W120, W240, W240, 480 and W720, respectively), age at first calving (AFC) and interval between first and second calving (IBC) estimated breeding values. Two Smith and Hazel indices were calculated using variances (I1) and literature (I2), with a part two indices designed using information from experts and breeders (I3 and I4). All the indices favored the reduction of weight at birth. The I1 focused mainly on W120 and I2, I3 and I4 focused on 720. In general, the estimated indices obtained similar reliability and expected genetic differences I1 generated a decrease in direct BW. I2 generated the largest increases in BW and AFC. I3 and I4 generated positive changes in growth and reproductive traits, with I3 generating the greatest genetic gains in the population, especially for W240.
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Affiliation(s)
- Edison J Ramírez Toro
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Nus Research Center, San Roque, Antioquia, Colombia.,GAMMA Research Group, Faculty of Agrarian Science, Universidad de Antioquia UdeA, Medellín, Colombia
| | | | - Rodrigo A Martínez Sarmiento
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Tibaitata Research Center, Mosquera, Cundinamarca, Colombia
| | - Mario F Cerón-Muñoz
- GAMMA Research Group, Faculty of Agrarian Science, Universidad de Antioquia UdeA, Medellín, Colombia
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170
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Matalonga L, Hernández-Ferrer C, Piscia D, Schüle R, Synofzik M, Töpf A, Vissers LELM, de Voer R, Tonda R, Laurie S, Fernandez-Callejo M, Picó D, Garcia-Linares C, Papakonstantinou A, Corvó A, Joshi R, Diez H, Gut I, Hoischen A, Graessner H, Beltran S. Solving patients with rare diseases through programmatic reanalysis of genome-phenome data. Eur J Hum Genet 2021; 29:1337-1347. [PMID: 34075210 PMCID: PMC8440686 DOI: 10.1038/s41431-021-00852-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/18/2021] [Accepted: 02/26/2021] [Indexed: 11/22/2022] Open
Abstract
Reanalysis of inconclusive exome/genome sequencing data increases the diagnosis yield of patients with rare diseases. However, the cost and efforts required for reanalysis prevent its routine implementation in research and clinical environments. The Solve-RD project aims to reveal the molecular causes underlying undiagnosed rare diseases. One of the goals is to implement innovative approaches to reanalyse the exomes and genomes from thousands of well-studied undiagnosed cases. The raw genomic data is submitted to Solve-RD through the RD-Connect Genome-Phenome Analysis Platform (GPAP) together with standardised phenotypic and pedigree data. We have developed a programmatic workflow to reanalyse genome-phenome data. It uses the RD-Connect GPAP's Application Programming Interface (API) and relies on the big-data technologies upon which the system is built. We have applied the workflow to prioritise rare known pathogenic variants from 4411 undiagnosed cases. The queries returned an average of 1.45 variants per case, which first were evaluated in bulk by a panel of disease experts and afterwards specifically by the submitter of each case. A total of 120 index cases (21.2% of prioritised cases, 2.7% of all exome/genome-negative samples) have already been solved, with others being under investigation. The implementation of solutions as the one described here provide the technical framework to enable periodic case-level data re-evaluation in clinical settings, as recommended by the American College of Medical Genetics.
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Affiliation(s)
- Leslie Matalonga
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Carles Hernández-Ferrer
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Davide Piscia
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Rebecca Schüle
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research (HIH), University of Tübingen, Tübingen, Germany
| | - Matthis Synofzik
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research (HIH), University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Richarda de Voer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Raul Tonda
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Steven Laurie
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Marcos Fernandez-Callejo
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Daniel Picó
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Carles Garcia-Linares
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Anastasios Papakonstantinou
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Alberto Corvó
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Ricky Joshi
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Hector Diez
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Holm Graessner
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- European Reference Network for Rare Neurological Diseases, Tübingen, Germany
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain.
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171
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Novikov RV, Gribkova AK, Kacher JG, Zaytsev PA, Armeev GA, Gluhov GS, Shaytan AK. Design of Nucleic Acid Biosensors Based on CRISPR/Cas Systems and Reporter Split Proteins. Moscow Univ Biol Sci Bull 2021; 76:52-58. [PMID: 34456394 PMCID: PMC8383255 DOI: 10.3103/s0096392521020036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/28/2021] [Accepted: 04/12/2021] [Indexed: 12/13/2022]
Abstract
Highly sensitive, specific, rapid, and easy-to-use diagnostic methods for the detection of nucleic acids of pathogens are required for the diagnosis of many human, animal, and plant diseases and environmental monitoring. The approaches based on the use of the natural ability of bacterial CRISPR/Cas9 systems to recognize DNA sequences with a high specificity under isothermal conditions are an alternative to the polymerase chain reaction method, which requires expensive laboratory equipment. The development of the methods for signal registration with the formation of a DNA/RNA/Cas9 protein complex is a separate bioengineering task. In this work, a design was developed and the applicability of a biosensor system based on the binding of two dCas9 proteins with target DNA sequences (without their cutting) and detection of their colocalization using reporter systems based on split enzymes was studied. Using the methods of molecular modeling, possible mutual positions of two dCas9 proteins at a detectable locus of genomic DNA, allowing the split enzyme domains attached to them to interact in an optimal way, were determined. The optimal distances on DNA between binding sites of dCas9 proteins in different orientations were determined, and the dependence of the complex structure on the distance between the binding sites of dCas9 proteins was modeled. Using the methods of bioinformatics, the genomes of a number of viruses (including SARS-CoV-2) were analyzed, and the presence of genomic loci unique to the species, allowing the possibility of landing pairs of dCas9 proteins in optimal positions, was demonstrated. The possibility of a combined use of dCas9 proteins from different bacteria to expand the spectrum of detected loci was analyzed. The results of the work indicate a fundamental possibility of the creation of highly specific nucleic acid biosensors based on a combination of CRISPR/Cas9 technologies and split enzymes.
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Affiliation(s)
- R V Novikov
- Department of Biology, Moscow State University, 119234 Moscow, Russia.,Sirius University of Science and Technology, 354340 Sochi, Russia
| | - A K Gribkova
- Department of Biology, Moscow State University, 119234 Moscow, Russia.,Sirius University of Science and Technology, 354340 Sochi, Russia
| | - J G Kacher
- Department of Biology, Moscow State University, 119234 Moscow, Russia.,Sirius University of Science and Technology, 354340 Sochi, Russia
| | - P A Zaytsev
- Department of Biology, Moscow State University, 119234 Moscow, Russia.,Sirius University of Science and Technology, 354340 Sochi, Russia
| | - G A Armeev
- Department of Biology, Moscow State University, 119234 Moscow, Russia.,Sirius University of Science and Technology, 354340 Sochi, Russia
| | - G S Gluhov
- Department of Biology, Moscow State University, 119234 Moscow, Russia.,Sirius University of Science and Technology, 354340 Sochi, Russia
| | - A K Shaytan
- Department of Biology, Moscow State University, 119234 Moscow, Russia.,Sirius University of Science and Technology, 354340 Sochi, Russia.,Higher School of Economics University, 109028 Moscow, Russia
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172
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Zhang Y, Han K, Dong X, Hou Q, Li T, Li L, Zhou G, Liu X, Zhao G, Li W. Case Report and Literature Review: Primary Pulmonary NUT-Midline Carcinoma. Front Oncol 2021; 11:700781. [PMID: 34527578 PMCID: PMC8435908 DOI: 10.3389/fonc.2021.700781] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/06/2021] [Indexed: 12/22/2022] Open
Abstract
Nuclear protein of the testis (NUT) carcinoma is a very rare and aggressive carcinoma characterized by chromosomal rearrangement. NUT-midline carcinoma (NMC) can occur anywhere in the body, but most of the tumors are found in the midline anatomic structure or mediastinum. Pulmonary-originated NMC is extremely rare and often difficult to be distinguished from other poorly differentiated tumors, making the diagnosis awfully challenged in clinical practice. There are less than 100 cases of NUT carcinoma reported so far. In this study, the diagnosis and molecular mechanisms of reported NUT carcinoma cases were reviewed. Furthermore, a case of primary pulmonary NUT-midline carcinoma and its pathological features was reported. The process of pathological identification and genomic analysis for establishing the diagnosis was discussed. We found that NUT carcinoma could be identified by combining CT, H&E staining, immunohistochemistry (IHC), and molecular tests. The development of NUT carcinoma might be associated with mutation of MYC, p63, and MED24 genes and the Wnt, MAPK, and PI3K signaling pathways. Our study provided a detailed molecular mechanistic review on NMC and established a procedure to identify pulmonary NMC.
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Affiliation(s)
- Yunxiang Zhang
- Pathology Department, Weifang People’s Hospital, Weifang, China
| | - Kai Han
- Pathology Department, Weifang People’s Hospital, Weifang, China
| | - Xiaotong Dong
- Pathology Department, Weifang People’s Hospital, Weifang, China
| | - Qian Hou
- Pathology Department, Weifang People’s Hospital, Weifang, China
| | - Tianbao Li
- Scientific Research Department, Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Li Li
- Pathology Department, Qilu Hospital of Shandong University, Jinan, China
| | - Gengyin Zhou
- Pathology Department, Qilu Hospital of Shandong University, Jinan, China
| | - Xia Liu
- Ophthalmology Department, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Guifeng Zhao
- Prenatal Diagnosis Department, Weifang People’s Hospital, Weifang, China
| | - Wei Li
- Thoracic Surgery Department, Weifang People’s Hospital, Weifang, China
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173
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UĞUREL OM, ATA O, TURGUT-BALIK D. Genomic chronicle of SARS-CoV-2: a mutational analysis with over 1 million genome sequences. Turk J Biol 2021; 45:425-435. [PMID: 34803444 PMCID: PMC8573839 DOI: 10.3906/biy-2106-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/30/2021] [Indexed: 11/26/2022] Open
Abstract
Use of information technologies to analyse big data on SARS-CoV-2 genome provides an insight for tracking variations and examining the evolution of the virus. Nevertheless, storing, processing, alignment and analyses of these numerous genomes are still a challenge. In this study, over 1 million SARS-CoV-2 genomes have been analysed to show distribution and relationship of variations that could enlighten development and evolution of the virus. In all genomes analysed in this study, a total of over 215M SNVs have been detected and average number of SNV per isolate was found to be 21.83. Single nucleotide variant (SNV) average is observed to reach 31.25 just in March 2021. The average variation number of isolates is increasing and compromising with total case numbers around the world. Remarkably, cytosine deamination, which is one of the most important biochemical processes in the evolutionary development of coronaviruses, accounts for 46% of all SNVs seen in SARS-CoV-2 genomes within 16 months. This study is one of the most comprehensive SARS-CoV-2 genomic analysis study in terms of number of genomes analysed in an academic publication so far, and reported results could be useful in monitoring the development of SARS-CoV-2.
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Affiliation(s)
- Osman Mutluhan UĞUREL
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yıldız Technical University, İstanbulTurkey
- Department of Basic Sciences, School of Engineering and Natural Sciences, Altınbaş University, İstanbulTurkey
| | - Oğuz ATA
- Department of Software Engineering, School of Engineering and Natural Sciences, Altınbaş University, İstanbulTurkey
| | - Dilek TURGUT-BALIK
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yıldız Technical University, İstanbulTurkey
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174
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Morales-Cedeño LR, de Los Santos-Villalobos S, Santoyo G. Functional and Genomic Analysis of Rouxiella badensis SER3 as a Novel Biocontrol Agent of Fungal Pathogens. Front Microbiol 2021; 12:709855. [PMID: 34421868 PMCID: PMC8375033 DOI: 10.3389/fmicb.2021.709855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
In recent decades, various bacterial species have been characterized as biocontrol agents for plant crop diseases; however, only a few genera have been predominantly reported in the literature. Therefore, the identification of new antagonists against phytopathogens is essential for boosting sustainable food production systems. In this study, we evaluated the role of strain SER3 from the recently discovered Rouxiella badensis as a biocontrol agent. SER3 was isolated from the phyllosphere of decaying strawberry fruit (Fragaria × ananassa) and showed different grades of antagonism against 20 fungal pathogens of berries, based on confrontation assays, due to the action of its diffusible and volatile compounds. These fungal pathogens were isolated from decayed strawberry, blackberry, and blueberry fruit and were characterized through internal transcribed spacer (ITS) sequencing and homology searches, exhibiting similarity with well-known postharvest pathogens such as Botrytis, Fusarium, Geotrichum, Mucor, Penicillium, Alternaria, and Botryosphaeria. Koch’s postulates were confirmed for most pathogens by reinfecting berry fruit. SER3 showed good capacity to inhibit the growth of Botrytis cinerea and Fusarium brachygibbosum in strawberry fruit, affecting mycelial development. To gain better understanding of the genetic and metabolic capacities of the SER3 strain, its draft genome was determined and was found to comprise a single chromosome of 5.08 Mb, 52.8% G + C content, and 4,545 protein-coding genes. Phylogenetic analysis indicated that the SER3 strain is affiliated with the R. badensis species, with an average nucleotide identity >96% and a genome-to-genome distance >70%. A comparison of the genomic properties of R. badensis SER3 and other close bacterial relatives showed several genes with potential functions in biocontrol activities, such as those encoding siderophores, non-ribosomal peptide synthetases, and polyketide synthases. This is the first study to demonstrate a novel role of the recently discovered R. badensis species (and any other species of the genus Rouxiella) as a biocontrol agent against postharvest fungal pathogens.
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Affiliation(s)
- Luzmaria R Morales-Cedeño
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | | | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
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Wang C, Lv H, Ling X, Li H, Diao F, Dai J, Du J, Chen T, Xi Q, Zhao Y, Zhou K, Xu B, Han X, Liu X, Peng M, Chen C, Tao S, Huang L, Liu C, Wen M, Jiang Y, Jiang T, Lu C, Wu W, Wu D, Chen M, Lin Y, Guo X, Huo R, Liu J, Ma H, Jin G, Xia Y, Sha J, Shen H, Hu Z. Association of assisted reproductive technology, germline de novo mutations and congenital heart defects in a prospective birth cohort study. Cell Res 2021; 31:919-928. [PMID: 34108666 PMCID: PMC8324888 DOI: 10.1038/s41422-021-00521-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/17/2021] [Indexed: 01/05/2023] Open
Abstract
Emerging evidence suggests that children conceived through assisted reproductive technology (ART) have a higher risk of congenital heart defects (CHDs) even when there is no family history. De novo mutation (DNM) is a well-known cause of sporadic congenital diseases; however, whether ART procedures increase the number of germline DNM (gDNM) has not yet been well studied. Here, we performed whole-genome sequencing of 1137 individuals from 160 families conceived through ART and 205 families conceived spontaneously. Children conceived via ART carried 4.59 more gDNMs than children conceived spontaneously, including 3.32 paternal and 1.26 maternal DNMs, after correcting for parental age at conception, cigarette smoking, alcohol drinking, and exercise behaviors. Paternal DNMs in offspring conceived via ART are characterized by C>T substitutions at CpG sites, which potentially affect protein-coding genes and are significantly associated with the increased risk of CHD. In addition, the accumulation of non-coding functional mutations was independently associated with CHD and 87.9% of the mutations were originated from the father. Among ART offspring, infertility of the father was associated with elevated paternal DNMs; usage of both recombinant and urinary follicle-stimulating hormone and high-dosage human chorionic gonadotropin trigger was associated with an increase of maternal DNMs. In sum, the increased gDNMs in offspring conceived by ART were primarily originated from fathers, indicating that ART itself may not be a major reason for the accumulation of gDNMs. Our findings emphasize the importance of evaluating the germline status of the fathers in families with the use of ART.
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Affiliation(s)
- Cheng Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hong Lv
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
- State Key Laboratory of Reproductive Medicine (Suzhou Centre), The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China
| | - Xiufeng Ling
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Reproduction, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Hospital, Nanjing, Jiangsu, China
| | - Hong Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Reproductive Genetic Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China
| | - Feiyang Diao
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Clinical Center of Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Juncheng Dai
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jiangbo Du
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Ting Chen
- Scientific Education Section, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Hospital, Nanjing, Jiangsu, China
| | - Qi Xi
- Department of Obstetrics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China
| | - Yang Zhao
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Kun Zhou
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Bo Xu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiumei Han
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiaoyu Liu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Meijuan Peng
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Congcong Chen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shiyao Tao
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lei Huang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Cong Liu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Mingyang Wen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yangqian Jiang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Tao Jiang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Chuncheng Lu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wei Wu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Di Wu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Minjian Chen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yuan Lin
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- State Key Laboratory of Reproductive Medicine (Suzhou Centre), The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China
- Department of Maternal, Child and Adolescent Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Ran Huo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jiayin Liu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- State Key Laboratory of Reproductive Medicine (Suzhou Centre), The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China
- Clinical Center of Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hongxia Ma
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Guangfu Jin
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jiahao Sha
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hongbing Shen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China.
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.
- State Key Laboratory of Reproductive Medicine (Suzhou Centre), The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China.
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China.
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.
- State Key Laboratory of Reproductive Medicine (Suzhou Centre), The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China.
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Abstract
A novel Gram-stain-negative and rod-shaped bacterial strain, designated as 4Y14T, was isolated from aquaculture water and characterized by using a polyphasic taxonomic approach. Strain 4Y14T was found to grow at 10-40 °C (optimum, 28 °C), at pH 7.0-9.0 (optimum, 7.0-8.0) and with 0-2 % NaCl (optimum, 1 %, w/v). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 4Y14T belonged to the genus Chitinilyticum with high levels of similarity to Chitinilyticum litopenaei c1T (97.8 %) and Chitinilyticum aquatile c14T (97.2 %). Phylogenomic analysis indicated that strain 4Y14T formed an independent branch distinct from the two type strains above. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain 4Y14T and the two type strains were, respectively, 25.3 and 25.0 %, and 81.2 and 80.3 %, which were well below the thresholds of 70 % DDH and 95-96 % ANI for species definition, implying that strain 4Y14T should represent a novel genospecies. The predominant cellular fatty acids of strain 4Y14T were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and iso-C16 : 0; the major polar lipids were diphosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine; and the sole respiratory quinone was Q-8. The genomic DNA G+C content was 60.1 mol%. Based on the phenotypic and genotypic analyses, strain 4Y14T is concluded to represent a novel species of the genus Chitinilyticum, for which the name Chitinilyticum piscinae sp. nov. is proposed. The type strain of the species is 4Y14T (=GDMCC 1.1934T=KACC 22080T).
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Affiliation(s)
- Tao Pei
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Juan Du
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Yang Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Ming-Rong Deng
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Honghui Zhu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
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177
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Zhang T, Yin J, Tang S, Li D, Gu X, Zhang S, Suo W, Liu X, Liu Y, Jiang Q, Zhao M, Yin Y, Pan J. Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea). Sci Rep 2021; 11:15021. [PMID: 34294825 PMCID: PMC8298618 DOI: 10.1038/s41598-021-94545-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/13/2021] [Indexed: 11/09/2022] Open
Abstract
The Asian Clam (Corbicula fluminea) is a valuable commercial and medicinal bivalve, which is widely distributed in East and Southeast Asia. As a natural nutrient source, the clam is rich in protein, amino acids, and microelements. The genome of C. fluminea has not yet been characterized; therefore, genome-assisted breeding and improvements cannot yet be implemented. In this work, we present a de novo chromosome-scale genome assembly of C. fluminea using PacBio and Hi-C sequencing technologies. The assembled genome comprised 4728 contigs, with a contig N50 of 521.06 Kb, and 1,215 scaffolds with a scaffold N50 of 70.62 Mb. More than 1.51 Gb (99.17%) of genomic sequences were anchored to 18 chromosomes, of which 1.40 Gb (92.81%) of genomic sequences were ordered and oriented. The genome contains 38,841 coding genes, 32,591 (83.91%) of which were annotated in at least one functional database. Compared with related species, C. fluminea had 851 expanded gene families and 191 contracted gene families. The phylogenetic tree showed that C. fluminea diverged from Ruditapes philippinarum, ~ 228.89 million years ago (Mya), and the genomes of C. fluminea and R. philippinarum shared 244 syntenic blocks. Additionally, we identified 2 MITF members and 99 NLRP members in C. fluminea genome. The high-quality and chromosomal Asian Clam genome will be a valuable resource for a range of development and breeding studies of C. fluminea in future research.
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Affiliation(s)
- Tongqing Zhang
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Jiawen Yin
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.
| | - Shengkai Tang
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Daming Li
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Xiankun Gu
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Shengyu Zhang
- Hongze Lake Fisheries Administration Committee Office of Jiangsu Province, Huai'an, China
| | - Weiguo Suo
- Fisheries Management Commission of Gehu Lake, Changzhou, China
| | - Xiaowei Liu
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Yanshan Liu
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Qicheng Jiang
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Muzi Zhao
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Yue Yin
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Jianlin Pan
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.
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178
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Laruelle A, Manini C, Iñarra E, López JI. Metastasis, an Example of Evolvability. Cancers (Basel) 2021; 13:cancers13153653. [PMID: 34359555 PMCID: PMC8345027 DOI: 10.3390/cancers13153653] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/20/2021] [Accepted: 07/20/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Cancer is a complex disease. Modern molecular technologies are progressively unveiling its genetic and epigenetic complexity, but still many key issues remain unknown. Considering cancer as a social dysfunction in a community of individuals has provided new perspectives of analysis with promising results. This narrative considers both approaches with respect to the metastatic process, the final cause of death in most patients affected by this disease. Abstract This overview focuses on two different perspectives to analyze the metastatic process taking clear cell renal cell carcinoma as a model, molecular and ecological. On the one hand, genomic analyses have demonstrated up to seven different constrained routes of tumor evolution and two different metastatic patterns. On the other hand, game theory applied to cell encounters within a tumor provides a sociological perspective of the possible behaviors of individuals (cells) in a collectivity. This combined approach provides a more comprehensive understanding of the complex rules governing a neoplasm.
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Affiliation(s)
- Annick Laruelle
- Department of Economic Analysis, University of the Basque Country (UPV/EHU), 48015 Bilbao, Spain; (A.L.); (E.I.)
- IKERBASQUE, Basque Foundation of Science, 48011 Bilbao, Spain
| | - Claudia Manini
- Department of Pathology, San Giovanni Bosco Hospital, 10154 Turin, Italy;
| | - Elena Iñarra
- Department of Economic Analysis, University of the Basque Country (UPV/EHU), 48015 Bilbao, Spain; (A.L.); (E.I.)
- Public Economic Institute, University of the Basque Country (UPV/EHU), 48015 Bilbao, Spain
| | - José I. López
- Department of Pathology, Cruces University Hospital, 48903 Barakaldo, Spain
- Biocruces-Bizkaia Health Research Institute, 48903 Barakaldo, Spain
- Correspondence:
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179
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Ceci A, Muñoz-Ballester C, Tegge AN, Brown KL, Umans RA, Michel FM, Patel D, Tewari B, Martin J, Alcoreza O, Maynard T, Martinez-Martinez D, Bordwine P, Bissell N, Friedlander MJ, Sontheimer H, Finkielstein CV. Development and implementation of a scalable and versatile test for COVID-19 diagnostics in rural communities. Nat Commun 2021; 12:4400. [PMID: 34285229 PMCID: PMC8292415 DOI: 10.1038/s41467-021-24552-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/24/2021] [Indexed: 12/23/2022] Open
Abstract
Rapid and widespread testing of severe acute respiratory coronavirus 2 (SARS-CoV-2) is essential for an effective public health response aimed at containing and mitigating the coronavirus disease 2019 (COVID-19) pandemic. Successful health policy implementation relies on early identification of infected individuals and extensive contact tracing. However, rural communities, where resources for testing are sparse or simply absent, face distinctive challenges to achieving this success. Accordingly, we report the development of an academic, public land grant University laboratory-based detection assay for the identification of SARS-CoV-2 in samples from various clinical specimens that can be readily deployed in areas where access to testing is limited. The test, which is a quantitative reverse transcription polymerase chain reaction (RT-qPCR)-based procedure, was validated on samples provided by the state laboratory and submitted for FDA Emergency Use Authorization. Our test exhibits comparable sensitivity and exceeds specificity and inclusivity values compared to other molecular assays. Additionally, this test can be re-configured to meet supply chain shortages, modified for scale up demands, and is amenable to several clinical specimens. Test development also involved 3D engineering critical supplies and formulating a stable collection media that allowed samples to be transported for hours over a dispersed rural region without the need for a cold-chain. These two elements that were critical when shortages impacted testing and when personnel needed to reach areas that were geographically isolated from the testing center. Overall, using a robust, easy-to-adapt methodology, we show that an academic laboratory can supplement COVID-19 testing needs and help local health departments assess and manage outbreaks. This additional testing capacity is particularly germane for smaller cities and rural regions that would otherwise be unable to meet the testing demand.
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Affiliation(s)
- A Ceci
- Molecular Diagnostics Laboratory, Fralin Biomedical Research Institute, Virginia Tech, Roanoke, VA, USA
| | - C Muñoz-Ballester
- Center for Glial Biology in Health, Disease, and Cancer, Fralin Biomedical Research Institute at VTC, Roanoke, VA, USA
| | - A N Tegge
- Department of Statistics, Virginia Tech, Blacksburg, VA, USA
| | - K L Brown
- Virginia Tech Carilion School of Medicine, Roanoke, VA, USA
| | - R A Umans
- Center for Glial Biology in Health, Disease, and Cancer, Fralin Biomedical Research Institute at VTC, Roanoke, VA, USA
| | - F M Michel
- Department of Geosciences, Virginia Tech, Blacksburg, VA, USA
| | - D Patel
- Center for Glial Biology in Health, Disease, and Cancer, Fralin Biomedical Research Institute at VTC, Roanoke, VA, USA
| | - B Tewari
- Center for Glial Biology in Health, Disease, and Cancer, Fralin Biomedical Research Institute at VTC, Roanoke, VA, USA
| | - J Martin
- Center for Glial Biology in Health, Disease, and Cancer, Fralin Biomedical Research Institute at VTC, Roanoke, VA, USA
- Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Roanoke, VA, USA
| | - O Alcoreza
- Center for Glial Biology in Health, Disease, and Cancer, Fralin Biomedical Research Institute at VTC, Roanoke, VA, USA
- Virginia Tech Carilion School of Medicine, Roanoke, VA, USA
- Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Roanoke, VA, USA
| | - T Maynard
- Fralin Biomedical Research Institute at VTC, Roanoke, VA, USA
| | - D Martinez-Martinez
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Imperial College London, London, UK
| | - P Bordwine
- Division of Surveillance and Investigation, Office of Epidemiology, Virginia Department of Health, Christiansburg, USA
| | - N Bissell
- New River Valley Health District, Virginia Department of Health, Christiansburg, USA
| | - M J Friedlander
- Fralin Biomedical Research Institute at VTC, Roanoke, VA, USA
| | - H Sontheimer
- Center for Glial Biology in Health, Disease, and Cancer, Fralin Biomedical Research Institute at VTC, Roanoke, VA, USA
| | - C V Finkielstein
- Molecular Diagnostics Laboratory, Fralin Biomedical Research Institute, Virginia Tech, Roanoke, VA, USA.
- Integrated Cellular Responses Laboratory, Fralin Biomedical Research Institute at VTC, Roanoke, VA, USA.
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.
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180
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Sui B, Han L, Ren H, Liu W, Zhang C. A Novel Polyvalent Bacteriophage vB_EcoM_swi3 Infects Pathogenic Escherichia coli and Salmonella enteritidis. Front Microbiol 2021; 12:649673. [PMID: 34335489 PMCID: PMC8317433 DOI: 10.3389/fmicb.2021.649673] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/17/2021] [Indexed: 12/21/2022] Open
Abstract
A novel virulent bacteriophage vB_EcoM_swi3 (swi3), isolated from swine feces, lyzed 9% (6/65) of Escherichia coli and isolates 54% (39/72) of Salmonella enteritidis isolates, which were all clinically pathogenic multidrug-resistant strains. Morphological observation showed that phage swi3 belonged to the Myoviridae family with an icosahedral head (80 nm in diameter) and a contractile sheathed tail (120 nm in length). At the optimal multiplicity of infection of 1, the one-step growth analysis of swi3 showed a 25-min latent period with a burst size of 25-plaque-forming units (PFU)/infected cell. Phage swi3 remained stable both at pH 6.0–8.0 and at less than 50°C for at least 1 h. Genomic sequencing and bioinformatics analysis based on genomic sequences and the terminase large subunit showed that phage swi3 was a novel member that was most closely related to Salmonella phages and belonged to the Rosemountvirus genus. Phage swi3 harbored a 52-kb double-stranded DNA genome with 46.02% GC content. Seventy-two potential open reading frames were identified and annotated, only 15 of which had been assigned to functional genes. No gene associated with pathogenicity and virulence was identified. The effects of phage swi3 in treating pathologic E. coli infections in vivo were evaluated using a mouse model. The administration of a single intraperitoneal injection of swi3 (106 PFU) at 2 h after challenge with the E. coli strain (serotype K88) (108 colony-forming units) sufficiently protected all mice without toxic side effects. This finding highlighted that phage swi3 might be used as an effective antibacterial agent to prevent E. coli and S. enteritidis infection.
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Affiliation(s)
- Bingrui Sui
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Lili Han
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Huiying Ren
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Wenhua Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Can Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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181
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Rampelli S, Turroni S, Debandi F, Alberdi A, Schnorr SL, Hofman CA, Taddia A, Helg R, Biagi E, Brigidi P, D'Amico F, Cattani M, Candela M. The gut microbiome buffers dietary adaptation in Bronze Age domesticated dogs. iScience 2021; 24:102816. [PMID: 34377966 PMCID: PMC8327155 DOI: 10.1016/j.isci.2021.102816] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/14/2021] [Accepted: 07/01/2021] [Indexed: 02/07/2023] Open
Abstract
In an attempt to explore the role of the gut microbiome during recent canine evolutionary history, we sequenced the metagenome of 13 canine coprolites dated ca. 3,600–3,450 years ago from the Bronze Age archaeological site of Solarolo (Italy), which housed a complex farming community. The microbiome structure of Solarolo dogs revealed continuity with that of modern dogs, but it also shared some features with the wild wolf microbiome, as a kind of transitional state between them. The dietary niche, as also inferred from the microbiome composition, was omnivorous, with evidence of consumption of starchy agricultural foods. Of interest, the Solarolo dog microbiome was particularly enriched in sequences encoding alpha-amylases and complemented a low copy number of the host amylase gene. These findings suggest that Neolithic dogs could have responded to the transition to a starch-rich diet by expanding microbial functionalities devoted to starch catabolism, thus compensating for delayed host response. Ancient DNA of Bronze Age canine coprolites from Solarolo was sequenced Solarolo dogs share gut microbiome features with modern wolves and dogs The gut microbiome of Solarolo dogs shows high number of reads for alpha-amylase Neolithic canine gut microbiome complemented delay in host genome adaptation
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Affiliation(s)
- Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Florencia Debandi
- Department of History and Cultures, University of Bologna, Bologna, Italy
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Stephanie L Schnorr
- Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria.,Department of Anthropology, University of Nevada, Las Vegas, NV, USA
| | - Courtney A Hofman
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | - Alberto Taddia
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Riccardo Helg
- Department of History and Cultures, University of Bologna, Bologna, Italy
| | - Elena Biagi
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Patrizia Brigidi
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Federica D'Amico
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.,Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Maurizio Cattani
- Department of History and Cultures, University of Bologna, Bologna, Italy
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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Abstract
Assembly and publication of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome in January 2020 enabled the immediate development of tests to detect the new virus. This began the largest global testing programme in history, in which hundreds of millions of individuals have been tested to date. The unprecedented scale of testing has driven innovation in the strategies, technologies and concepts that govern testing in public health. This Review describes the changing role of testing during the COVID-19 pandemic, including the use of genomic surveillance to track SARS-CoV-2 transmission around the world, the use of contact tracing to contain disease outbreaks and testing for the presence of the virus circulating in the environment. Despite these efforts, widespread community transmission has become entrenched in many countries and has required the testing of populations to identify and isolate infected individuals, many of whom are asymptomatic. The diagnostic and epidemiological principles that underpin such population-scale testing are also considered, as are the high-throughput and point-of-care technologies that make testing feasible on a massive scale.
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Affiliation(s)
- Tim R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia.
- Garvan Institute of Medical Research, Sydney, NSW, Australia.
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia.
| | - Marc Salit
- Departments of Pathology and Bioengineering, Stanford University, Stanford, CA, USA
- Joint Initiative for Metrology in Biology, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
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183
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Yu Z, Song M, Chouchane L, Ma X. Functional Genomic Analysis of Breast Cancer Metastasis: Implications for Diagnosis and Therapy. Cancers (Basel) 2021; 13:cancers13133276. [PMID: 34208889 PMCID: PMC8268362 DOI: 10.3390/cancers13133276] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Metastasis remains the greatest cause of fatalities in breast cancer patients world-wide. The process of metastases is highly complex, and the current research efforts in this area are still rather fragmented. The revolution of genomic profiling methods to analyze samples from human and animal models dramatically improved our understanding of breast cancer metastasis. This article summarizes the recent breakthroughs in genomic analyses of breast cancer metastasis and discusses their implications for prognostic and therapeutic applications. Abstract Breast cancer (BC) is one of the most diagnosed cancers worldwide and is the second cause of cancer related death in women. The most frequent cause of BC-related deaths, like many cancers, is metastasis. However, metastasis is a complicated and poorly understood process for which there is a shortage of accurate prognostic indicators and effective treatments. With the rapid and ever-evolving development and application of genomic sequencing technologies, many novel molecules were identified that play previously unappreciated and important roles in the various stages of metastasis. In this review, we summarize current advancements in the functional genomic analysis of BC metastasis and discuss about the potential prognostic and therapeutic implications from the recent genomic findings.
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Affiliation(s)
- Ziqi Yu
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA;
- Correspondence: (Z.Y.); (X.M.)
| | - Mei Song
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA;
| | - Lotfi Chouchane
- Department of Genetic Medicine, Weill Cornell Medicine-Qatar, Qatar Foundation, Doha P.O. Box 24144, Qatar;
| | - Xiaojing Ma
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA;
- Correspondence: (Z.Y.); (X.M.)
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184
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Abstract
STAT1α is a key transcription factor driving pro-inflammatory responses in macrophages. We found that the interferon gamma (IFNγ)-regulated transcriptional program in macrophages is controlled by ADP-ribosylation (ADPRylation) of STAT1α, a post-translational modification resulting in the site-specific covalent attachment of ADP-ribose moieties. PARP-1, the major nuclear poly(ADP-ribose) polymerase (PARP), supports IFNγ-stimulated enhancer formation by regulating the genome-wide binding and IFNγ-dependent transcriptional activation of STAT1α. It does so by ADPRylating STAT1α on specific residues in its DNA-binding domain (DBD) and transcription activation (TA) domain. ADPRylation of the DBD controls STAT1α binding to its cognate DNA elements, whereas ADPRylation of the TA domain regulates enhancer activation by modulating STAT1α phosphorylation and p300 acetyltransferase activity. Loss of ADPRylation at either site leads to diminished IFNγ-dependent transcription and downstream pro-inflammatory responses. We conclude that PARP-1-mediated ADPRylation of STAT1α drives distinct enhancer activation mechanisms and is a critical regulator of inflammatory responses in macrophages.
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Affiliation(s)
- Rebecca Gupte
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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185
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Simonetti M, Zhang N, Harbers L, Milia MG, Brossa S, Huong Nguyen TT, Cerutti F, Berrino E, Sapino A, Bienko M, Sottile A, Ghisetti V, Crosetto N. COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance. Nat Commun 2021; 12:3903. [PMID: 34162869 PMCID: PMC8222401 DOI: 10.1038/s41467-021-24078-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/01/2021] [Indexed: 11/21/2022] Open
Abstract
While mass-scale vaccination campaigns are ongoing worldwide, genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to monitor the emergence and global spread of viral variants of concern (VOC). Here, we present a streamlined workflow-COVseq-which can be used to generate highly multiplexed sequencing libraries compatible with Illumina platforms from hundreds of SARS-CoV-2 samples in parallel, in a rapid and cost-effective manner. We benchmark COVseq against a standard library preparation method (NEBNext) on 29 SARS-CoV-2 positive samples, reaching 95.4% of concordance between single-nucleotide variants detected by both methods. Application of COVseq to 245 additional SARS-CoV-2 positive samples demonstrates the ability of the method to reliably detect emergent VOC as well as its compatibility with downstream phylogenetic analyses. A cost analysis shows that COVseq could be used to sequence thousands of samples at less than 15 USD per sample, including library preparation and sequencing costs. We conclude that COVseq is a versatile and scalable method that is immediately applicable for SARS-CoV-2 genomic surveillance and easily adaptable to other pathogens such as influenza viruses.
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Affiliation(s)
- Michele Simonetti
- Bienko-Crosetto Lab for Quantitative Genome Biology, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Ning Zhang
- Bienko-Crosetto Lab for Quantitative Genome Biology, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
- Department of Breast Surgery, Qilu hospital of Shandong University, Ji'nan, China
| | - Luuk Harbers
- Bienko-Crosetto Lab for Quantitative Genome Biology, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Maria Grazia Milia
- Laboratory of Microbiology and Virology, Ospedale 'Amedeo di Savoia', Turin, Italy
| | - Silvia Brossa
- Instituto di Candiolo FPO-IRCCS, Candiolo, Turin, Italy
| | - Thi Thu Huong Nguyen
- Bienko-Crosetto Lab for Quantitative Genome Biology, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Francesco Cerutti
- Laboratory of Microbiology and Virology, Ospedale 'Amedeo di Savoia', Turin, Italy
| | - Enrico Berrino
- Instituto di Candiolo FPO-IRCCS, Candiolo, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Anna Sapino
- Instituto di Candiolo FPO-IRCCS, Candiolo, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Magda Bienko
- Bienko-Crosetto Lab for Quantitative Genome Biology, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | | | - Valeria Ghisetti
- Laboratory of Microbiology and Virology, Ospedale 'Amedeo di Savoia', Turin, Italy.
| | - Nicola Crosetto
- Bienko-Crosetto Lab for Quantitative Genome Biology, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Science for Life Laboratory, Solna, Sweden.
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186
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Yu F, Cienfuegos-Gallet AV, Cunningham MH, Jin Y, Wang B, Kreiswirth BN, Chen L. Molecular Evolution and Adaptation of Livestock-Associated Methicillin-Resistant Staphylococcus aureus (LA-MRSA) Sequence Type 9. mSystems 2021; 6:e0049221. [PMID: 34156294 DOI: 10.1128/mSystems.00492-21] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) sequence type 9 (ST9) has emerged and disseminated in Asia. It is associated with colonization or infection in both humans and animal hosts; however, the genetic factors underpinning its adaptation to animal and human population remain to be determined. Here, we conducted a genomic analysis of 191 ST9 S. aureus genomes collected from 12 different countries, including 174 genomes retrieved from public databases and 17 sequenced in this study. In silico spa typing, staphylococcal cassette chromosome mec (SCCmec) typing, and antimicrobial resistance and virulence gene mining were conducted, and the temporal phylogenetic signal was assessed by Bayesian inference. Our results point toward a human methicillin-susceptible S. aureus (MSSA) origin of ST9 that evolved approximately 2 centuries ago. Three major genetic events occurred during ST9 host shift from human to animals: the loss of the immune evasion cluster genes (scn, chp, and sak), which were reported to contribute to virulence in human infections, the acquisition of the SaPIbov4-like element-encoding vwb gene, which is an animal-specific virulence factor responsible for the clotting of animal plasma, and the acquisition of antibiotic resistance genes, including SCCmec, quinolone resistance-determining region (QRDR) mutations, and a multidrug resistance genetic element (MDRST9). Evidence of direct transmission of animal-adapted strains to human hosts also suggest that transmission could potentially reshape the resistance and virulence genetic pool in these isolates. The rapid clonal expansion of MDR ST9 strains in mainland China and Taiwan highlights the increasing need for effective surveillance of antibiotic consumption in animal husbandry to control antimicrobial resistance spread. IMPORTANCEStaphylococcus aureus sequence type 9 (ST9) is the main LA-MRSA clone spreading in the Asian continent. It can colonize and cause mild to severe infections both in animal and humans. Previous work described its genotypic characteristics; however, the molecular history of global spread of ST9 strains remains largely unclear. We conducted a detailed analysis of genomic evolution of global ST9 strains and identified key genetic changes associated with its adaptation to specific hosts. Our results suggest that the ST9 clone originated from human-adapted strains, which lost genes related to the evasion of the immune system. The introduction of ST9 strains in animal populations was aligned with the acquisition of animal-specific virulent factors and mobile elements harboring multiple antimicrobial resistance genes, especially in isolates from mainland China and Taiwan.
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187
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Njau EP, Domelevo Entfellner JB, Machuka EM, Bochere EN, Cleaveland S, Shirima GM, Kusiluka LJ, Upton C, Bishop RP, Pelle R, Okoth EA. The first genotype II African swine fever virus isolated in Africa provides insight into the current Eurasian pandemic. Sci Rep 2021; 11:13081. [PMID: 34158551 PMCID: PMC8219699 DOI: 10.1038/s41598-021-92593-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 05/24/2021] [Indexed: 02/05/2023] Open
Abstract
African swine fever (ASF) caused by the African swine fever virus (ASFV) is ranked by OIE as the most important source of mortality in domestic pigs globally and is indigenous to African wild suids and soft ticks. Despite two ASFV genotypes causing economically devastating epidemics outside the continent since 1961, there have been no genome-level analyses of virus evolution in Africa. The virus was recently transported from south-eastern Africa to Georgia in 2007 and has subsequently spread to Russia, eastern Europe, China, and south-east Asia with devastating socioeconomic consequences. To date, two of the 24 currently described ASFV genotypes defined by sequencing of the p72 gene, namely genotype I and II, have been reported outside Africa, with genotype II being responsible for the ongoing pig pandemic. Multiple complete genotype II genome sequences have been reported from European, Russian and Chinese virus isolates but no complete genome sequences have yet been reported from Africa. We report herein the complete genome of a Tanzanian genotype II isolate, Tanzania/Rukwa/2017/1, collected in 2017 and determined using an Illumina short read strategy. The Tanzania/Rukwa/2017/1 sequence is 183,186 bp in length (in a single contig) and contains 188 open reading frames. Considering only un-gapped sites in the pairwise alignments, the new sequence has 99.961% identity with the updated Georgia 2007/1 reference isolate (FR682468.2), 99.960% identity with Polish isolate Pol16_29413_o23 (MG939586) and 99.957% identity with Chinese isolate ASFV-wbBS01 (MK645909.1). This represents 73 single nucleotide polymorphisms (SNPs) relative to the Polish isolate and 78 SNPs with the Chinese genome. Phylogenetic analysis indicated that Tanzania/Rukwa/2017/1 clusters most closely with Georgia 2007/1. The majority of the differences between Tanzania/Rukwa/2017/1 and Georgia 2007/1 genotype II genomes are insertions/deletions (indels) as is typical for ASFV. The indels included differences in the length and copy number of the terminal multicopy gene families, MGF 360 and 110. The Rukwa2017/1 sequence is the first complete genotype II genome from a precisely mapped locality in Africa, since the exact origin of Georgia2007/1 is unknown. It therefore provides baseline information for future analyses of the diversity and phylogeography of this globally important genetic sub-group of ASF viruses.
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Affiliation(s)
- Emma P Njau
- Biosciences Eastern and Central Africa-International Livestock Research Institute Hub, Nairobi, Kenya.
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania.
- Sokoine University of Agriculture, P. O. Box 3019, Morogoro, Tanzania.
| | | | - Eunice M Machuka
- Biosciences Eastern and Central Africa-International Livestock Research Institute Hub, Nairobi, Kenya
| | - Edwina N Bochere
- Biosciences Eastern and Central Africa-International Livestock Research Institute Hub, Nairobi, Kenya
| | - Sarah Cleaveland
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Gabriel M Shirima
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Lughano J Kusiluka
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
- Mzumbe University, Morogoro, Tanzania
| | - Chris Upton
- Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada
| | - Richard P Bishop
- Biosciences Eastern and Central Africa-International Livestock Research Institute Hub, Nairobi, Kenya
| | - Roger Pelle
- Biosciences Eastern and Central Africa-International Livestock Research Institute Hub, Nairobi, Kenya
| | - Edward A Okoth
- Biosciences Eastern and Central Africa-International Livestock Research Institute Hub, Nairobi, Kenya
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188
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Soukal P, Hrdá Š, Karnkowska A, Milanowski R, Szabová J, Hradilová M, Strnad H, Vlček Č, Čepička I, Hampl V. Heterotrophic euglenid Rhabdomonas costata resembles its phototrophic relatives in many aspects of molecular and cell biology. Sci Rep 2021; 11:13070. [PMID: 34158556 DOI: 10.1038/s41598-021-92174-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 05/28/2021] [Indexed: 02/05/2023] Open
Abstract
Euglenids represent a group of protists with diverse modes of feeding. To date, only a partial genomic sequence of Euglena gracilis and transcriptomes of several phototrophic and secondarily osmotrophic species are available, while primarily heterotrophic euglenids are seriously undersampled. In this work, we begin to fill this gap by presenting genomic and transcriptomic drafts of a primary osmotroph, Rhabdomonas costata. The current genomic assembly length of 100 Mbp is 14× smaller than that of E. gracilis. Despite being too fragmented for comprehensive gene prediction it provided fragments of the mitochondrial genome and comparison of the transcriptomic and genomic data revealed features of its introns, including several candidates for nonconventional types. A set of 39,456 putative R. costata proteins was predicted from the transcriptome. Annotation of the mitochondrial core metabolism provides the first data on the facultatively anaerobic mitochondrion of R. costata, which in most respects resembles the mitochondrion of E. gracilis with a certain level of streamlining. R. costata can synthetise thiamine by enzymes of heterogenous provenances and haem by a mitochondrial-cytoplasmic C4 pathway with enzymes orthologous to those found in E. gracilis. The low percentage of green algae-affiliated genes supports the ancestrally osmotrophic status of this species.
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189
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Shang Y, Sun Q, Chen H, Wu Q, Chen M, Yang S, Du M, Zha F, Ye Q, Zhang J. Isolation and Characterization of a Novel Salmonella Phage vB_SalP_TR2. Front Microbiol 2021; 12:664810. [PMID: 34234757 PMCID: PMC8256156 DOI: 10.3389/fmicb.2021.664810] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 05/12/2021] [Indexed: 11/22/2022] Open
Abstract
Salmonella is a widely distributed foodborne pathogen. The use of Salmonella phages as biocontrol agents has recently gained significant interest. Because the Salmonella genus has high diversity, efforts are necessary to identify lytic Salmonella phages focusing on different serovars. Here, five Salmonella phages were isolated from soil samples, and vB_SalP_TR2 was selected as a novel phage with high lytic potential against the host Salmonella serovar Albany, as well as other tested serovars, including Corvallis, Newport, Kottbus, and Istanbul. Morphological analyses demonstrated that phage vB_SalP_TR2 belongs to the Podoviridae family, with an icosahedral head (62 ± 0.5 nm in diameter and 60 ± 1 nm in length) and a short tail (35 ± 1 nm in length). The latent period and burst size of phage vB_SalP_TR2 was 15 min and 211 PFU/cell, respectively. It contained a linear dsDNA of 71,453 bp, and G + C content was 40.64%. Among 96 putative open reading frames detected, only 35 gene products were found in database searches, with no virulence or antibiotic resistance genes being identified. As a biological control agent, phage vB_SalP_TR2 exhibited a high temperature and pH tolerance. In vitro, it lysed most S. Albany after 24 h at 37°C with multiplicities of infection of 0.0001, 0.001, 0.01, 0.1, 1, 10, and 100. In food matrices (milk and chicken meat), treatment with phage vB_SalP_TR2 also reduced the number of S. Albany compared with that in controls. These findings highlighted phage vB_SalP_TR2 as a potential antibacterial agent for the control of Salmonella in food samples.
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Affiliation(s)
- Yuting Shang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- State Key Laboratory of Food Science and Technology, National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety, Joint International Research Laboratory on Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Qifan Sun
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, China
| | - Hanfang Chen
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Moutong Chen
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Shuanghong Yang
- State Key Laboratory of Food Science and Technology, National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety, Joint International Research Laboratory on Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Mingzhu Du
- State Key Laboratory of Food Science and Technology, National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety, Joint International Research Laboratory on Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Fei Zha
- State Key Laboratory of Food Science and Technology, National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety, Joint International Research Laboratory on Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Qinghua Ye
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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Zhang J, Zhang Y, Kang JY, Chen S, He Y, Han B, Liu MF, Lu L, Li L, Yi Z, Chen L. Potential transmission chains of variant B.1.1.7 and co-mutations of SARS-CoV-2. Cell Discov 2021; 7:44. [PMID: 34127650 PMCID: PMC8203788 DOI: 10.1038/s41421-021-00282-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/15/2021] [Indexed: 02/05/2023] Open
Abstract
The presence of SARS-CoV-2 mutants, including the emerging variant B.1.1.7, has raised great concerns in terms of pathogenesis, transmission, and immune escape. Characterizing SARS-CoV-2 mutations, evolution, and effects on infectivity and pathogenicity is crucial to the design of antibody therapies and surveillance strategies. Here, we analyzed 454,443 SARS-CoV-2 spike genes/proteins and 14,427 whole-genome sequences. We demonstrated that the early variant B.1.1.7 may not have evolved spontaneously in the United Kingdom or within human populations. Our extensive analyses suggested that Canidae, Mustelidae or Felidae, especially the Canidae family (for example, dog) could be a possible host of the direct progenitor of variant B.1.1.7. An alternative hypothesis is that the variant was simply yet to be sampled. Notably, the SARS-CoV-2 whole-genome represents a large number of potential co-mutations. In addition, we used an experimental SARS-CoV-2 reporter replicon system to introduce the dominant co-mutations NSP12_c14408t, 5'UTR_c241t, and NSP3_c3037t into the viral genome, and to monitor the effect of the mutations on viral replication. Our experimental results demonstrated that the co-mutations significantly attenuated the viral replication. The study provides valuable clues for discovering the transmission chains of variant B.1.1.7 and understanding the evolutionary process of SARS-CoV-2.
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Affiliation(s)
- Jingsong Zhang
- grid.9227.e0000000119573309State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Yang Zhang
- grid.8547.e0000 0001 0125 2443Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jun-Yan Kang
- grid.9227.e0000000119573309State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Shanghai, China
| | - Shuiye Chen
- grid.8547.e0000 0001 0125 2443Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yongqun He
- grid.214458.e0000000086837370Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI USA
| | - Benhao Han
- grid.9227.e0000000119573309State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Mo-Fang Liu
- grid.9227.e0000000119573309State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Shanghai, China
| | - Lina Lu
- grid.9227.e0000000119573309State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Li Li
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA USA
| | - Zhigang Yi
- grid.8547.e0000 0001 0125 2443Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China ,grid.8547.e0000 0001 0125 2443Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Luonan Chen
- grid.9227.e0000000119573309State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China ,grid.440637.20000 0004 4657 8879School of Life Science and Technology, ShanghaiTech University, Shanghai, China ,grid.410726.60000 0004 1797 8419Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China ,Pazhou Lab, Guangzhou, China
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191
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Fan S, Zhan P, Bing J, Jiang N, Huang Y, Chen D, Hu T, Du H, Huang G. A biological and genomic comparison of a drug-resistant and a drug-susceptible strain of Candida auris isolated from Beijing, China. Virulence 2021; 12:1388-1399. [PMID: 34060424 PMCID: PMC8172162 DOI: 10.1080/21505594.2021.1928410] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The fungal pathogen Candida auris has emerged as a new threat to human health. We previously reported the first isolate of C. auris (BJCA001) in China, which belongs to the South Asian clade (I) and was susceptible to all antifungals tested. In this study, we report the isolation of a drug-resistant C. auris strain (BJCA002) from the same city (Beijing). Strain BJCA002 belongs to the South African clade (III) and is resistant to fluconazole and amphotericin B based on the tentative MIC breakpoints. Taking advantage of the two isolates with distinct antifungal susceptibility and genetic origins, we performed a biological and genomic comparative study. Besides antifungal susceptibility, strains BJCA001 and BJCA002 showed differences in multiple aspects including morphologies, expression of virulence factors, virulence, mating type, and genomic sequence and organization. Notably, strain BJCA002 was less virulent than BJCA001 in both the Galleria mellonella and mouse systemic infection models. Genomic analysis demonstrated that strain BJCA002 but not BJCA001 had multiple mutations in drug resistance-associated genes, including a hot-spot mutation of ERG11 (VF125AL, namely V125A and F126L) and some missense mutations in CDR1, MDR1, and TAC1. Notably, strain BJCA001 carried 64 copies of the Zorro3 retrotransposon, whereas BJCA002 had only 3 copies in the genome. Taken together, our findings not only reveal the genetic and phenotypic diversities of the two isolates from Beijing, China, but also shed new light on the genetic basis of the antifungal resistance and virulence of C. auris.
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Affiliation(s)
- Shuru Fan
- Department of Infectious Diseases, Huashan Hospital and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Ping Zhan
- Institute of Clinical Medicine and Dermatology Department, Jiangxi Provincial People's Hospital Affiliated to Nanchang Univercity, Nanchang, China
| | - Jian Bing
- Department of Infectious Diseases, Huashan Hospital and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Ning Jiang
- Department of Infectious Diseases, Huashan Hospital and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yingnan Huang
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Dongke Chen
- Department of Laboratory Medicine, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Tianren Hu
- Department of Infectious Diseases, Huashan Hospital and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Han Du
- Department of Infectious Diseases, Huashan Hospital and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Guanghua Huang
- Department of Infectious Diseases, Huashan Hospital and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University
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192
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Toro Ospina AM, Aguilar I, Vargas de Oliveira MH, Cruz Dos Santos Correia LE, Vercesi Filho AE, Albuquerque LG, de Vasconcelos Silva JAI. Assessing the accuracy of imputation in the Gyr breed using different SNP panels. Genome 2021; 64:893-899. [PMID: 34057850 DOI: 10.1139/gen-2020-0081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The aim of this study was to evaluate the accuracy of imputation in a Gyr population using two medium-density panels (Bos taurus - Bos indicus) and to test whether the inclusion of the Nellore breed increases the imputation accuracy in the Gyr population. The database consisted of 289 Gyr females from Brazil genotyped with the GGP Bovine LDv4 chip containing 30 000 SNPs and 158 Gyr females from Colombia genotyped with the GGP indicus chip containing 35 000 SNPs. A customized chip was created that contained the information of 9109 SNPs (9K) to test the imputation accuracy in Gyr populations; 604 Nellore animals with information of LD SNPs tested in the scenarios were included in the reference population. Four scenarios were tested: LD9K_30KGIR, LD9K_35INDGIR, LD9K_30KGIR_NEL, and LD9K_35INDGIR_NEL. Principal component analysis (PCA) was computed for the genomic matrix and sample-specific imputation accuracies were calculated using Pearson's correlation (CS) and the concordance rate (CR) for imputed genotypes. The results of PCA of the Colombian and Brazilian Gyr populations demonstrated the genomic relationship between the two populations. The CS and CR ranged from 0.88 to 0.94 and from 0.93 to 0.96, respectively. Among the scenarios tested, the highest CS (0.94) was observed for the LD9K_30KGIR scenario. The present results highlight the importance of the choice of chip for imputation in the Gyr breed. However, the variation in SNPs may reduce the imputation accuracy even when the chip of the Bos indicus subspecies is used.
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Affiliation(s)
| | - Ignacio Aguilar
- Instituto Nacional de Investigación Agropecuaria, INIA, Montevideo, Uruguay
| | | | | | | | - Lucia Galvão Albuquerque
- Faculdade de Ciências Agrárias e Veterinárias - Unesp, CEP 14.884-900, Jaboticabal, São Paulo, Brasil
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193
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Gershoni M, Weller JI, Ezra E. Genetic and Genome-Wide Association Analysis of Yearling Weight Gain in Israel Holstein Dairy Calves. Genes (Basel) 2021; 12:708. [PMID: 34068476 DOI: 10.3390/genes12050708] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 01/19/2023] Open
Abstract
Yearling weight gain in male and female Israeli Holstein calves, defined as 365 × ((weight - 35)/age at weight) + 35, was analyzed from 814,729 records on 368,255 animals from 740 herds recorded between 1994 and 2021. The variance components were calculated based on valid records from 2008 through 2017 for each sex separately and both sexes jointly by a single-trait individual animal model analysis, which accounted for repeat records on animals. The analysis model also included the square root, linear, and quadratic effects of age at weight. Heritability and repeatability were 0.35 and 0.71 in the analysis of both sexes and similar in the single sex analyses. The regression of yearling weight gain on birth date in the complete data set was -0.96 kg/year. The complete data set was also analyzed by the same model as the variance component analysis, including both sexes and accounting for differing variance components for each sex. The genetic trend for yearling weight gain, including both sexes, was 1.02 kg/year. Genetic evaluations for yearling weight gain was positively correlated with genetic evaluations for milk, fat, protein production, and cow survival but negatively correlated with female fertility. Yearling weight gain was also correlated with the direct effect on dystocia, and increased yearling weight gain resulted in greater frequency of dystocia. Of the 1749 Israeli Holstein bulls genotyped with reliabilities >50%, 1445 had genetic evaluations. As genotyping of these bulls was performed using several single nucleotide polymorhphism (SNP) chip platforms, we included only those markers that were genotyped in >90% of the tested cohort. A total of 40,498 SNPs were retained. More than 400 markers had significant effects after permutation and correction for multiple testing (pnominal < 1 × 10-8). Considering all SNPs simultaneously, 0.69 of variance among the sires' transmitting ability was explained. There were 24 markers with coefficients of determination for yearling weight gain >0.04. One marker, BTA-75458-no-rs on chromosome 5, explained ≈6% of the variance among the estimated breeding values for yearling weight gain. ARS-BFGL-NGS-39379 had the fifth largest coefficient of determination in the current study and was also found to have a significant effect on weight at an age of 13-14 months in a previous study on Holsteins. Significant genomic effects on yearling weight gain were mainly associated with milk production quantitative trait loci, specifically with kappa casein metabolism.
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194
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Ono R, Ueno H, Yoshida K, Takahashi S, Yoshihara H, Nozaki T, Suzuki K, Nakazawa A, Saiki R, Seki M, Takita J, Ogawa S, Manabe A, Hasegawa D. Clonal evidence for the development of neuroblastoma with extensive copy-neutral loss of heterozygosity arising in a mature teratoma. Cancer Sci 2021; 112:2921-2927. [PMID: 33934450 PMCID: PMC8253283 DOI: 10.1111/cas.14931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 11/27/2022] Open
Abstract
Mature teratomas are usually benign tumors that rarely undergo malignant transformation. We report an advanced neuroblastoma arising in a mature teratoma of the ovary. Whole-exome sequencing identified extensive copy-neutral loss of heterozygosity (LOH) in both neuroblastoma and teratoma elements, suggesting that the neuroblastoma evolved from the teratoma. In addition, several truncating germline heterozygous variants in tumor suppressor genes, including RBL2 and FBXW12, became homozygous as a result of LOH. Collectively, we speculate that extensive LOH in teratoma cells may force heterozygous germline variants to become homozygous, which, in turn, may contribute to the development of neuroblastoma with the acquisition of additional chromosomal changes.
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Affiliation(s)
- Rintaro Ono
- Department of Pediatrics, St. Luke's International Hospital, Tokyo, Japan
| | - Hiroo Ueno
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Satoko Takahashi
- Department of Pediatrics, St. Luke's International Hospital, Tokyo, Japan.,Department of Pediatrics, Japanese Red Cross Narita Hospital, Chiba, Japan
| | - Hiroki Yoshihara
- Department of Pediatrics, St. Luke's International Hospital, Tokyo, Japan
| | - Taiki Nozaki
- Department of Diagnostic Radiology, St. Luke's International Hospital, Tokyo, Japan
| | - Koyu Suzuki
- Department of Pathology, St. Luke's International Hospital, Tokyo, Japan
| | - Atsuko Nakazawa
- Department of Clinical Research, Saitama Children's Medical Center, Saitama, Japan
| | - Ryunosuke Saiki
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masafumi Seki
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Atsushi Manabe
- Department of Pediatrics, St. Luke's International Hospital, Tokyo, Japan.,Department of Pediatrics, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Daisuke Hasegawa
- Department of Pediatrics, St. Luke's International Hospital, Tokyo, Japan
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195
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Yang H, Gu W, Li Z, Zhang L, Liao D, Song J, Shi B, Hasimu J, Li Z, Yang Z, Zhong Q, Li H. Novel putative bluetongue virus serotype 29 isolated from inapparently infected goat in Xinjiang of China. Transbound Emerg Dis 2021; 68:2543-2555. [PMID: 33190404 DOI: 10.1111/tbed.13927] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/29/2020] [Accepted: 11/10/2020] [Indexed: 02/04/2023]
Abstract
Bluetongue virus (BTV) is the 'type' species of the genus Orbivirus causing bluetongue (BT) in sheep, bovine and other ruminants. Twenty-four serotypes and several atypical serotypes of BTV were identified worldwide. In present study, a novel strain of BTV (V196/XJ/2014) was isolated from an asymptomatic sentinel goat in Yuli County, Xinjiang of China. Serotype identification of this isolate exhibited uniform negative results by serotype-specific conventional RT-PCR and real-time RT-PCR for BTV-1 to BTV-27, and virus neutralization tests using reference sera of BTV-1 to BTV-24. Genomic analysis showed V196/XJ/2014 grouped with atypical serotypes of BTV-25 to BTV-28, BTV-X/XJ1407, BTV-X/ITL2015 and BTV-Y/TUN2017, while segment 2 and VP2 protein of V196/XJ/2014 shared <63.4%/61.4% nucleic acids and amino acids sequence identities with other recognized BTV serotypes and its segment 2 formed a separate 'nucleotype' in phylogenetic tree. These results indicated V196/XJ/2014 does not belong to any reported serotypes of BTV. Further studies of infectivity and pathogenicity showed that goats infected with V196/XJ/2014 did not exhibit observed clinical symptoms, but high level of virus amplification and homologous neutralization antibodies were detected post-infection. Our studies suggested a novel putative serotype of BTV-29 was isolated in Xinjiang of China, which expands our knowledge about the diversity of BTV.
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Affiliation(s)
- Heng Yang
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan Province, China
| | - Wenxi Gu
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Autonomous Region, China
| | - Zhanhong Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan Province, China
| | - Ling Zhang
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Autonomous Region, China
| | - Defang Liao
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan Province, China
| | - Jianling Song
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan Province, China
| | - Baoxin Shi
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Autonomous Region, China
| | - Jiapaer Hasimu
- Yuli Animal Husbandry and Veterinary Station, Yuli, Xinjiang Autonomous Region, China
| | - Zhuoran Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan Province, China
| | - Zhenxing Yang
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan Province, China
| | - Qi Zhong
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Autonomous Region, China
| | - Huachun Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan Province, China
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196
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Yang SK, Tan NP, Chong CW, Abushelaibi A, Lim SHE, Lai KS. The Missing Piece: Recent Approaches Investigating the Antimicrobial Mode of Action of Essential Oils. Evol Bioinform Online 2021; 17:1176934320938391. [PMID: 34017165 PMCID: PMC8114247 DOI: 10.1177/1176934320938391] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/03/2020] [Indexed: 01/03/2023] Open
Abstract
Antibiotic resistance is a major global health issue that has seen alarming rates of increase in all parts of the world over the past two decades. The surge in antibiotic resistance has resulted in longer hospital stays, higher medical costs, and elevated mortality rates. Constant attempts have been made to discover newer and more effective antimicrobials to reduce the severity of antibiotic resistance. Plant secondary metabolites, such as essential oils, have been the major focus due to their complexity and bioactive nature. However, the underlying mechanism of their antimicrobial effect remains largely unknown. Understanding the antimicrobial mode of action of essential oils is crucial in developing potential strategies for the use of essential oils in a clinical setting. Recent advances in genomics and proteomics have enhanced our understanding of the antimicrobial mode of action of essential oils. We might well be at the dawn of completing a mystery on how essential oils carry out their antimicrobial activities. Therefore, an overview of essential oils with regard to their antimicrobial activities and mode of action is discussed in this review. Recent approaches used in identifying the antimicrobial mode of action of essential oils, specifically from the perspective of genomics and proteomics, are also synthesized. Based on the information gathered from this review, we offer recommendations for future strategies and prospects for the study of essential oils and their function as antimicrobials.
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Affiliation(s)
- Shun-Kai Yang
- Health Sciences Division, Abu Dhabi Women's College, Higher Colleges of Technology, Abu Dhabi, United Arab Emirates
| | - Ngai-Paing Tan
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, Selangor, Malaysia
| | - Chun-Wie Chong
- School of Pharmacy, Monash University Malaysia, Subang Jaya, Malaysia
| | - Aisha Abushelaibi
- Health Sciences Division, Abu Dhabi Women's College, Higher Colleges of Technology, Abu Dhabi, United Arab Emirates
| | - Swee-Hua-Erin Lim
- Health Sciences Division, Abu Dhabi Women's College, Higher Colleges of Technology, Abu Dhabi, United Arab Emirates
| | - Kok-Song Lai
- Health Sciences Division, Abu Dhabi Women's College, Higher Colleges of Technology, Abu Dhabi, United Arab Emirates
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197
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Li K, Wang H, Zhang HF, Zhao XX, Lai YJ, Liu FF. Genomic analysis of host gene responses to cerebral Plasmodium falciparum malaria. Immun Inflamm Dis 2021; 9:819-826. [PMID: 33942992 PMCID: PMC8342194 DOI: 10.1002/iid3.436] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/16/2021] [Accepted: 03/31/2021] [Indexed: 11/09/2022]
Abstract
Introduction A vaccine for malaria is urgently required but no vaccine has yet shown satisfactory protective efficacy especially for Plasmodium falciparum. P. falciparum infection can progress to cerebral malaria (CM), a neurological syndrome with exceedingly high mortality. Designing effective P. falciparum vaccines require more understanding of the protective immune response while the host immune response to CM and the mechanisms are still elusive. Here, we aim to identify host gene responses to CM and host gene networks associated with CM pathogenesis. Methods An innovative genomic analysis strategy, the weighted gene coexpression network analysis (WGCNA) combined with differential gene expression analysis, was used in this study. Data for analysis contain 93 whole blood samples, derived from two previous public transcriptome datasets. Results This approach led to the identification of numerous differentially expressed human transcripts and dozens of coexpression gene modules. We further identified nine key genes, including MBP, SAMSN1, PSMF1, SLC39A8, EIF3B, SMPDL3A, FABP5, SPSB3, and SHARPIN, of which the last four genes were first identified to be related to CM in the present study. Conclusion The results provided a comprehensive characterization of host gene expression profiles in CM and offered some new insight into malaria vaccine design. These identified key genes could be potential targets or immune modulators for novel therapeutic interventions of CM.
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Affiliation(s)
- Ke Li
- Department of Blood Transfusion, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Han Wang
- Department of Pharmacy, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Hong-Feng Zhang
- Department of Pathology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao-Xiao Zhao
- Department of Pathology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yong-Ji Lai
- Department of Pharmacy, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fang-Fang Liu
- Department of Pathology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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198
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Ocejo M, Oporto B, Lavín JL, Hurtado A. Whole genome-based characterisation of antimicrobial resistance and genetic diversity in Campylobacter jejuni and Campylobacter coli from ruminants. Sci Rep 2021; 11:8998. [PMID: 33903652 PMCID: PMC8076188 DOI: 10.1038/s41598-021-88318-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/06/2021] [Indexed: 11/09/2022] Open
Abstract
Campylobacter, a leading cause of gastroenteritis in humans, asymptomatically colonises the intestinal tract of a wide range of animals.Although antimicrobial treatment is restricted to severe cases, the increase of antimicrobial resistance (AMR) is a concern. Considering the significant contribution of ruminants as reservoirs of resistant Campylobacter, Illumina whole-genome sequencing was used to characterise the mechanisms of AMR in Campylobacter jejuni and Campylobacter coli recovered from beef cattle, dairy cattle, and sheep in northern Spain. Genome analysis showed extensive genetic diversity that clearly separated both species. Resistance genotypes were identified by screening assembled sequences with BLASTn and ABRicate, and additional sequence alignments were performed to search for frameshift mutations and gene modifications. A high correlation was observed between phenotypic resistance to a given antimicrobial and the presence of the corresponding known resistance genes. Detailed sequence analysis allowed us to detect the recently described mosaic tet(O/M/O) gene in one C. coli, describe possible new alleles of blaOXA-61-like genes, and decipher the genetic context of aminoglycoside resistance genes, as well as the plasmid/chromosomal location of the different AMR genes and their implication for resistance spread. Updated resistance gene databases and detailed analysis of the matched open reading frames are needed to avoid errors when using WGS-based analysis pipelines for AMR detection in the absence of phenotypic data.
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Affiliation(s)
- Medelin Ocejo
- Animal Health Department, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Bizkaia, Spain
| | - Beatriz Oporto
- Animal Health Department, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Bizkaia, Spain
| | - José Luis Lavín
- Applied Mathematics Department, Bioinformatics Unit, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Bizkaia, Spain
| | - Ana Hurtado
- Animal Health Department, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Bizkaia, Spain.
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199
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Ferreira R, Amado R, Padrão J, Ferreira V, Dias NM, Melo LDR, Santos SB, Nicolau A. The first sequenced Sphaerotilus natans bacteriophage- characterization and potential to control its filamentous bacterium host. FEMS Microbiol Ecol 2021; 97:6136272. [PMID: 33587121 DOI: 10.1093/femsec/fiab029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 02/12/2021] [Indexed: 01/01/2023] Open
Abstract
Bacteriophages (phages) are ubiquitous entities present in every conceivable habitat as a result of their bacterial parasitism. Their prevalence and impact in the ecology of bacterial communities and their ability to control pathogens make their characterization essential, particularly of new phages, improving knowledge and potential application. The isolation and characterization of a new lytic phage against Sphaerotilus natans strain DSM 6575, named vB_SnaP-R1 (SnaR1), is here described. Besides being the first sequenced genome of a Sphaerotilus natans infecting phage, 99% of its 41507 bp genome lacks homology with any other sequenced phage, revealing its uniqueness and previous lack of knowledge. Moreover, SnaR1 is the first Podoviridae phage described infecting this bacterium. Sphaerotilus natans is an important filamentous bacterium due to its deleterious effect on wastewater treatment plants (WWTP) and thus, phages may play a role as novel biotechnological tools against filamentous overgrowth in WWTP. The lytic spectrum of SnaR1 was restricted to its host strain, infecting only one out of three S. natans strains and infection assays revealed its ability to reduce bacterial loads. Results suggest SnaR1 as the prototype of a new phage genus and demonstrates its potential as a non-chemical alternative to reduce S. natans DSM 6575 cells.
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Affiliation(s)
- Rute Ferreira
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Rui Amado
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Jorge Padrão
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Vânia Ferreira
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Nicolina M Dias
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Luís D R Melo
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Sílvio B Santos
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Ana Nicolau
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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Yao J, Tang YC, Yi B, Yang J, Chai Y, Yin N, Zhang ZX, Wei YJ, Li DC, Zhou J. Signature of gene aberrant alternative splicing events in pancreatic adenocarcinoma prognosis. J Cancer 2021; 12:3164-3179. [PMID: 33976726 PMCID: PMC8100795 DOI: 10.7150/jca.48661] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 03/15/2021] [Indexed: 12/17/2022] Open
Abstract
Alternative splicing (AS), as an effective and universal mechanism of transcriptional regulation, is involved in the development and progression of cancer. Therefore, systematic analysis of alternative splicing in pancreatic adenocarcinoma (PAAD) is warranted. The corresponding clinical information of the RNA-Seq data and PAAD cohort was downloaded from the TCGA data portal. Then, a java application, SpliceSeq, was used to evaluate the RNA splicing pattern and calculate the splicing percentage index (PSI). Differentially expressed AS events (DEAS) were identified based on PSI values between PAAD cancer samples and normal samples of adjacent tissues. Kaplan-Meier and Cox regression analyses were used to assess the association between DEAS and patient clinical characteristics. Unsupervised cluster analysis used to reveal four clusters with different survival patterns. At the same time, GEO and TCGA combined with GTEx to verify the differential expression of AS gene and splicing factor. After rigorous filtering, a total of 45,313 AS events were identified, 1,546 of which were differentially expressed AS events. Nineteen DEAS were found to be associated with OS with a five-year overall survival rate of 0.946. And the subtype clusters results indicate that there are differences in the nature of individual AS that affect clinical outcomes. Results also identified 15 splicing factors associated with the prognosis of PAAD. And the splicing factors ESRP1 and RBM5 played an important role in the PAAD-associated AS events. The PAAD-associated AS events, splicing networks, and clusters identified in this study are valuable for deciphering the underlying mechanisms of AS in PAAD and may facilitate the establishment of therapeutic goals for further validation.
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Affiliation(s)
- Jun Yao
- Department of General Surgery, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
- Pancreatic Disease Research Centre, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Yu-Chen Tang
- Department of General Surgery, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
- Pancreatic Disease Research Centre, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Bin Yi
- Department of General Surgery, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
- Pancreatic Disease Research Centre, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Jian Yang
- Department of General Surgery, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
- Pancreatic Disease Research Centre, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Yun Chai
- Department of Plastic Surgery, Suzhou Municipal Hospital, Suzhou, Jiangsu, 215006, China
| | - Ni Yin
- Department of Oncology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Zi-Xiang Zhang
- Department of General Surgery, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
- Pancreatic Disease Research Centre, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Yi-Jun Wei
- Department of General Surgery, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
- Pancreatic Disease Research Centre, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - De-Chun Li
- Department of General Surgery, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
- Pancreatic Disease Research Centre, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Jian Zhou
- Department of General Surgery, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
- Pancreatic Disease Research Centre, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
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