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Alkailani MI, Gibbings D. The Regulation and Immune Signature of Retrotransposons in Cancer. Cancers (Basel) 2023; 15:4340. [PMID: 37686616 PMCID: PMC10486412 DOI: 10.3390/cancers15174340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023] Open
Abstract
Advances in sequencing technologies and the bioinformatic analysis of big data facilitate the study of jumping genes' activity in the human genome in cancer from a broad perspective. Retrotransposons, which move from one genomic site to another by a copy-and-paste mechanism, are regulated by various molecular pathways that may be disrupted during tumorigenesis. Active retrotransposons can stimulate type I IFN responses. Although accumulated evidence suggests that retrotransposons can induce inflammation, the research investigating the exact mechanism of triggering these responses is ongoing. Understanding these mechanisms could improve the therapeutic management of cancer through the use of retrotransposon-induced inflammation as a tool to instigate immune responses to tumors.
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Affiliation(s)
- Maisa I. Alkailani
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha P.O. Box 34110, Qatar
| | - Derrick Gibbings
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada;
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2
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Min J, Zhao J, Zagelbaum J, Lee J, Takahashi S, Cummings P, Schooley A, Dekker J, Gottesman ME, Rabadan R, Gautier J. Mechanisms of insertions at a DNA double-strand break. Mol Cell 2023; 83:2434-2448.e7. [PMID: 37402370 PMCID: PMC10527084 DOI: 10.1016/j.molcel.2023.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 04/06/2023] [Accepted: 06/08/2023] [Indexed: 07/06/2023]
Abstract
Insertions and deletions (indels) are common sources of structural variation, and insertions originating from spontaneous DNA lesions are frequent in cancer. We developed a highly sensitive assay called insertion and deletion sequencing (Indel-seq) to monitor rearrangements in human cells at the TRIM37 acceptor locus that reports indels stemming from experimentally induced and spontaneous genome instability. Templated insertions, which derive from sequences genome wide, require contact between donor and acceptor loci, require homologous recombination, and are stimulated by DNA end-processing. Insertions are facilitated by transcription and involve a DNA/RNA hybrid intermediate. Indel-seq reveals that insertions are generated via multiple pathways. The broken acceptor site anneals with a resected DNA break or invades the displaced strand of a transcription bubble or R-loop, followed by DNA synthesis, displacement, and then ligation by non-homologous end joining. Our studies identify transcription-coupled insertions as a critical source of spontaneous genome instability that is distinct from cut-and-paste events.
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Affiliation(s)
- Jaewon Min
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
| | - Junfei Zhao
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jennifer Zagelbaum
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jina Lee
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Sho Takahashi
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Portia Cummings
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Allana Schooley
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Max E Gottesman
- Department of Biochemistry and Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Raul Rabadan
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jean Gautier
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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3
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Caniels TG, Medina-Ramírez M, Zhang J, Sarkar A, Kumar S, LaBranche A, Derking R, Allen JD, Snitselaar JL, Capella-Pujol J, Sánchez IDM, Yasmeen A, Diaz M, Aldon Y, Bijl TPL, Venkatayogi S, Martin Beem JS, Newman A, Jiang C, Lee WH, Pater M, Burger JA, van Breemen MJ, de Taeye SW, Rantalainen K, LaBranche C, Saunders KO, Montefiori D, Ozorowski G, Ward AB, Crispin M, Moore JP, Klasse PJ, Haynes BF, Wilson IA, Wiehe K, Verkoczy L, Sanders RW. Germline-targeting HIV-1 Env vaccination induces VRC01-class antibodies with rare insertions. Cell Rep Med 2023; 4:101003. [PMID: 37044090 PMCID: PMC10140475 DOI: 10.1016/j.xcrm.2023.101003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/23/2023] [Accepted: 03/17/2023] [Indexed: 04/14/2023]
Abstract
Targeting germline (gl-) precursors of broadly neutralizing antibodies (bNAbs) is acknowledged as an important strategy for HIV-1 vaccines. The VRC01-class of bNAbs is attractive because of its distinct genetic signature. However, VRC01-class bNAbs often require extensive somatic hypermutation, including rare insertions and deletions. We describe a BG505 SOSIP trimer, termed GT1.2, to optimize binding to gl-CH31, the unmutated common precursor of the CH30-34 bNAb lineage that acquired a large CDRH1 insertion. The GT1.2 trimer activates gl-CH31 naive B cells in knock-in mice, and B cell responses could be matured by selected boosting immunogens to generate cross-reactive Ab responses. Next-generation B cell sequencing reveals selection for VRC01-class mutations, including insertions in CDRH1 and FWR3 at positions identical to VRC01-class bNAbs, as well as CDRL1 deletions and/or glycine substitutions to accommodate the N276 glycan. These results provide proof of concept for vaccine-induced affinity maturation of B cell lineages that require rare insertions and deletions.
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Affiliation(s)
- Tom G Caniels
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Max Medina-Ramírez
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Jinsong Zhang
- Applied Biomedical Science Institute, San Diego, CA, USA
| | - Anita Sarkar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sonu Kumar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Alex LaBranche
- Applied Biomedical Science Institute, San Diego, CA, USA
| | - Ronald Derking
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Jonne L Snitselaar
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Joan Capella-Pujol
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Iván Del Moral Sánchez
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Anila Yasmeen
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Marilyn Diaz
- Applied Biomedical Science Institute, San Diego, CA, USA
| | - Yoann Aldon
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Tom P L Bijl
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | | | | | - Amanda Newman
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Chuancang Jiang
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Maarten Pater
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Judith A Burger
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Mariëlle J van Breemen
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Steven W de Taeye
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Kimmo Rantalainen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Celia LaBranche
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Kevin O Saunders
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - David Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Per Johan Klasse
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA.
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4
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Kostyusheva AP, Brezgin SA, Ponomareva NI, Goptar IA, Nikiforova AV, Gegechkori VI, Poluektova VB, Turkadze KA, Sudina AE, Chulanov VP, Kostyushev DS. [Antiviral Activity of CRISPR/Cas9 Ribonucleoprotein Complexes on a Hepatitis B Virus Model In Vivo]. Mol Biol (Mosk) 2022; 56:884-891. [PMID: 36475475 DOI: 10.31857/s002689842206012x] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/23/2022] [Indexed: 12/13/2022]
Abstract
Chronic hepatitis B (CHB) is caused by hepatitis B virus (HBV) infection. This disease is a key issue for global health. Modern methods of therapy do not completely eliminate HBV from infected cells and do not cure chronic infection. The CRISPR/Cas9 systems of site-specific nucleases can effectively cleave do not target DNA including viral genomes. The cleavage of the major form of the HBV genome, i.e., covalently closed circular DNA (cccDNA), leads to a robust reduction in viral replication and degradation or mutational inactivation of cccDNA. CRISPR/Cas9-based approaches are one of the most promising ways to achieve a 'sterilizing' cure of CHB, i.e., complete elimination of the virus from the body. Here, the HBV mouse model in vivo has been used to analyze the antiviral activity of the high-specific Cas9 protein and sgRNA targeting HBV genome. We have found that a single injection of short-lived ribonucleoprotein complexes of CRISPR/Cas9 results in a ~10-fold reduction in HBV DNA levels in the serum and liver of mice as early as 48 h after the start of the experiment. The remaining HBV DNAs have been found to harbor rare indel mutations. Developing new antivirals for treating CHB based on CRISPR/Cas9 ribonucleoprotein complexes could substantially reduce the duration of CHB therapy and, potentially, achieve complete elimination of viral infection.
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Affiliation(s)
- A P Kostyusheva
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases (Sechenov University), Moscow, 119048 Russia
| | - S A Brezgin
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases (Sechenov University), Moscow, 119048 Russia.,Sirius University of Science and Technology, Sochi, 354340 Russia
| | - N I Ponomareva
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases (Sechenov University), Moscow, 119048 Russia.,Sirius University of Science and Technology, Sochi, 354340 Russia
| | - I A Goptar
- Izmerov Research Institute of Occupational Health, Moscow, 105275 Russia
| | - A V Nikiforova
- Izmerov Research Institute of Occupational Health, Moscow, 105275 Russia
| | - V I Gegechkori
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases (Sechenov University), Moscow, 119048 Russia
| | - V B Poluektova
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases (Sechenov University), Moscow, 119048 Russia
| | - K A Turkadze
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases (Sechenov University), Moscow, 119048 Russia
| | - A E Sudina
- Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Moscow, 119121 Russia
| | - V P Chulanov
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases (Sechenov University), Moscow, 119048 Russia.,Sirius University of Science and Technology, Sochi, 354340 Russia.,Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency, Moscow, 119121 Russia
| | - D S Kostyushev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases (Sechenov University), Moscow, 119048 Russia.,Sirius University of Science and Technology, Sochi, 354340 Russia.,
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5
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Hobson CA, Pierrat G, Tenaillon O, Bonacorsi S, Bercot B, Jaouen E, Jacquier H, Birgy A. Klebsiella pneumoniae Carbapenemase Variants Resistant to Ceftazidime-Avibactam: an Evolutionary Overview. Antimicrob Agents Chemother 2022; 66:e0044722. [PMID: 35980232 DOI: 10.1128/aac.00447-22] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
First variants of the Klebsiella pneumoniae carbapenemase (KPC), KPC-2 and KPC-3, have encountered a worldwide success, particularly in K. pneumoniae isolates. These beta-lactamases conferred resistance to most beta-lactams including carbapenems but remained susceptible to new beta-lactam/beta-lactamase inhibitors, such as ceftazidime-avibactam. After the marketing of ceftazidime-avibactam, numerous variants of KPC resistant to this association have been described among isolates recovered from clinical samples or derived from experimental studies. In KPC variants resistant to ceftazidime-avibactam, point mutations, insertions and/or deletions have been described in various hot spots. Deciphering the impact of these mutations is crucial, not only from a therapeutic point of view, but also to follow the evolution in time and space of KPC variants resistant to ceftazidime-avibactam. In this review, we describe the mutational landscape of the KPC beta-lactamase toward ceftazidime-avibactam resistance based on a multidisciplinary approach including epidemiology, microbiology, enzymology, and thermodynamics. We show that resistance is associated with three hot spots, with a high representation of insertions and deletions compared with other class A beta-lactamases. Moreover, extension of resistance to ceftazidime-avibactam is associated with a trade-off in the resistance to other beta-lactams and a decrease in enzyme stability. Nevertheless, the high natural stability of KPC could underlay the propensity of this enzyme to acquire in vivo mutations conferring resistance to ceftazidime-avibactam (CAZavi), particularly via insertions and deletions.
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6
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Liu X, Guo L, Xu T, Lu X, Ma M, Sheng W, Wu Y, Peng H, Cao L, Zheng F, Huang S, Yang Z, Du J, Shi M, Guo D. A comprehensive evolutionary and epidemiological characterization of insertion and deletion mutations in SARS-CoV-2 genomes. Virus Evol 2022; 7:veab104. [PMID: 35039785 PMCID: PMC8754802 DOI: 10.1093/ve/veab104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 11/07/2021] [Revised: 11/29/2021] [Accepted: 12/11/2021] [Indexed: 12/19/2022] Open
Abstract
SARS-CoV-2, which causes the current pandemic of respiratory illness, is evolving continuously and generating new variants. Nevertheless, most of the sequence analyses thus far focused on nucleotide substitutions despite the fact that insertions and deletions (indels) are equally important in the evolution of SARS-CoV-2. In this study, we analyzed 1,099,664 high-quality sequences of SARS-CoV-2 genomes to re-construct the evolutionary and epidemiological histories of indels. Our analysis revealed 289 circulating indel types (237 deletion and 52 insertion types, each represented by more than ten genomic sequences), among which eighteen were recurrent indel types, each represented by more than 500 genome sequences. Although indels were identified across the entire genome, most of them were identified in nsp6, S, ORF8, and N genes, among which ORF8 indel types had the highest frequencies of frameshift. Geographical and temporal analyses of these variants revealed a few alterations of dominant indel types, each accompanied by geographic expansion to different countries and continents, which resulted in the fixation of several types of indels in the field, including the current variants of concern. Evolutionary and structural analyses revealed that indels involving S N-terminal domain regions were linked to the 3/4 variants of concern, resulting in significantly altered S protein that might contribute to the selective advantage of the corresponding variant. In sum, our study highlights the important role of insertions and deletions in the evolution and spread of SARS-CoV-2.
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Affiliation(s)
- Xue Liu
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Liping Guo
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Tiefeng Xu
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xiaoyu Lu
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Mingpeng Ma
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Wenyu Sheng
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yinxia Wu
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Hong Peng
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Liu Cao
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Fuxiang Zheng
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Siyao Huang
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Zixiao Yang
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jie Du
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Mang Shi
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Deyin Guo
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
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7
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Ahmed SF, Quadeer AA, McKay MR. SARS-CoV-2 T Cell Responses Elicited by COVID-19 Vaccines or Infection Are Expected to Remain Robust against Omicron. Viruses 2022; 14:79. [PMID: 35062283 PMCID: PMC8781795 DOI: 10.3390/v14010079] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [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: 12/13/2021] [Revised: 12/26/2021] [Accepted: 12/31/2021] [Indexed: 02/06/2023] Open
Abstract
Omicron, the most recent SARS-CoV-2 variant of concern (VOC), harbours multiple mutations in the spike protein that were not observed in previous VOCs. Initial studies suggest Omicron to substantially reduce the neutralizing capability of antibodies induced from vaccines and previous infection. However, its effect on T cell responses remains to be determined. Here, we assess the effect of Omicron mutations on known T cell epitopes and report data suggesting T cell responses to remain broadly robust against this new variant.
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Affiliation(s)
- Syed Faraz Ahmed
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China;
| | - Ahmed Abdul Quadeer
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China;
| | - Matthew R. McKay
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China;
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Department of Electrical and Electronic Engineering, University of Melbourne, Parkville, VIC 3010, Australia
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
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8
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Korotkov EV, Yakovleva IV, Kamionskaya AM. Use of Mathematical Methods for the Biosafety Assessment of Agricultural Crops. APPL BIOCHEM MICRO+ 2021; 57:271-279. [PMID: 33727728 PMCID: PMC7952145 DOI: 10.1134/s000368382102006x] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 12/01/2022]
Abstract
In Russia and around the world, there are important questions regarding the potential threats to national and biological safety created by genetic technologies and the need to improve or introduce new, justified, and adequate measures for their control, regulation, and prevention. The article shows that a significant volume of the global market is occupied by five major transgenic crops, and producers are ready to switch to crops with an edited genome that has been approved in the United States, Argentina, and other countries. We propose a qualitatively new approach to the risk assessment of edited plants, "Safe Design," and we have also developed an extremely important, fundamentally new approach to the development of methods that combine next-generation sequencing (NGS) and Bioinformatics for the assessment of the crop import biosafety. The proposed mathematical approach provides a detailed analysis of the possible insertions of DNA fragments into the genome of edited crops and a clarification of their biological significance. The developed method can be used in the rapid screening of plants for the presence of potentially dangerous genes, viral sequences, and nonspecific promoter sequences.
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Affiliation(s)
- E. V. Korotkov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - I. V. Yakovleva
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - A. M. Kamionskaya
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
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9
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Chowdhury R, Grisewood MJ, Boorla VS, Yan Q, Pfleger BF, Maranas CD. IPRO+/-: Computational Protein Design Tool Allowing for Insertions and Deletions. Structure 2020; 28:1344-1357.e4. [PMID: 32857964 DOI: 10.1016/j.str.2020.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 07/01/2020] [Accepted: 08/07/2020] [Indexed: 12/30/2022]
Abstract
Insertions and deletions (indels) in protein sequences alter the residue spacing along the polypeptide backbone and consequently open up possibilities for tuning protein function in a way that is inaccessible by amino acid substitution alone. We describe an optimization-based computational protein redesign approach centered around predicting beneficial combinations of indels along with substitutions and also obtain putative substrate-docked structures for these protein variants. This modified algorithmic capability would be of interest for enzyme engineering and broadly inform other protein design tasks. We highlight this capability by (1) identifying active variants of a bacterial thioesterase enzyme ('TesA) with experimental corroboration, (2) recapitulating existing active TEM-1 β-Lactamase sequences of different sizes, and (3) identifying shorter 4-Coumarate:CoA ligases with enhanced in vitro activities toward non-native substrates. A separate PyRosetta-based open-source tool, Indel-Maker (http://www.maranasgroup.com/software.htm), has also been created to construct computational models of user-defined protein variants with specific indels and substitutions.
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Affiliation(s)
- Ratul Chowdhury
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Matthew J Grisewood
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Veda Sheersh Boorla
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Qiang Yan
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA.
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10
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Abstract
Arynes and donor-acceptor (D-A) cyclopropanes are two classes of strained systems having the potential for numerous applications in organic synthesis. The last two decades have witnessed a renaissance of interest in the chemistry of these species primarily because of the mild and robust methods for their generation or activation. Commonly, arynes as easily polarizable systems result in 1,2-disubstitution, whereas D-A cyclopropanes as polarized systems lead to 1,3-bisfunctionalization thereby showing striking similarities. Transformations with 1,2- and 1,3-dipoles afford cyclic structures. With arynes, emerging four-membered rings as intermediates might react further, whereas the analogous five-membered rings obtained from D-A cyclopropanes are most often the final products. However, there are a few cases where these intermediates behave surprisingly differently. This Minireview highlights the parallels in reactivity between arynes and D-A cyclopropanes thereby shedding light on the neglected similarities of these two reactive species.
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Affiliation(s)
- Daniel B. Werz
- Technische Universität BraunschweigInstitut für Organische ChemieHagenring 3038106BraunschweigGermany
| | - Akkattu T. Biju
- Department of Organic ChemistryIndian Institute of ScienceBangalore560012India
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11
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Wellenreuther M, Mérot C, Berdan E, Bernatchez L. Going beyond SNPs: The role of structural genomic variants in adaptive evolution and species diversification. Mol Ecol 2019; 28:1203-1209. [PMID: 30834648 DOI: 10.1111/mec.15066] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 02/28/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Maren Wellenreuther
- The New Zealand Institute for Plant & Food Research Ltd, Nelson, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Emma Berdan
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
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12
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Barton HJ, Zeng K. The Impact of Natural Selection on Short Insertion and Deletion Variation in the Great Tit Genome. Genome Biol Evol 2019; 11:1514-1524. [PMID: 30924871 PMCID: PMC6543879 DOI: 10.1093/gbe/evz068] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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] [Accepted: 03/27/2019] [Indexed: 12/11/2022] Open
Abstract
Insertions and deletions (INDELs) remain understudied, despite being the most common form of genetic variation after single nucleotide polymorphisms. This stems partly from the challenge of correctly identifying the ancestral state of an INDEL and thus identifying it as an insertion or a deletion. Erroneously assigned ancestral states can skew the site frequency spectrum, leading to artificial signals of selection. Consequently, the selective pressures acting on INDELs are, at present, poorly resolved. To tackle this issue, we have recently published a maximum likelihood approach to estimate the mutation rate and the distribution of fitness effects for INDELs. Our approach estimates and controls for the rate of ancestral state misidentification, overcoming issues plaguing previous INDEL studies. Here, we apply the method to INDEL polymorphism data from ten high coverage (∼44×) European great tit (Parus major) genomes. We demonstrate that coding INDELs are under strong purifying selection with a small proportion making it into the population (∼4%). However, among fixed coding INDELs, 71% of insertions and 86% of deletions are fixed by positive selection. In noncoding regions, we estimate ∼80% of insertions and ∼52% of deletions are effectively neutral, the remainder show signatures of purifying selection. Additionally, we see evidence of linked selection reducing INDEL diversity below background levels, both in proximity to exons and in areas of low recombination.
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Affiliation(s)
- Henry J Barton
- Department of Animal and Plant Sciences, University of Sheffield, United Kingdom
| | - Kai Zeng
- Department of Animal and Plant Sciences, University of Sheffield, United Kingdom
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13
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Ledwaba J, Sayed Y, Pillay V, Morris L, Hunt G. Low Frequency of Protease Inhibitor Resistance Mutations and Insertions in HIV-1 Subtype C Protease Inhibitor-Naïve Sequences. AIDS Res Hum Retroviruses 2019; 35:673-678. [PMID: 30793914 DOI: 10.1089/aid.2019.0012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 11/13/2022] Open
Abstract
Human immunodeficiency virus-1 (HIV-1) protease sequences from 2,225 protease inhibitor (PI)-naïve HIV-1 subtype C-infected individuals collected over a 14-year period were analyzed for polymorphisms. Over 50% of sequences differed from an HIV-1 subtype B consensus sequence at 8 of the 99 amino acids at residues 12, 15, 19, 36, 41, 69, 89, and 93, but not in the functionally important regions. The frequency of primary resistance and accessory mutations occurred in <1% of the sequences. Of note, 11 sequences (0.5%) harbored amino acid insertions between residues 36 and 39, located in the elbow of the flap region. The insertions were found throughout the 13-year period. Occurrence of insertions in subtype C viruses is rare and viruses remain sensitive to currently used PIs (lopinavir/r, atazanavir/r, and darunavir/r). However, ongoing characterization of isolates is required to identify changes that may impact PI treatment since PIs are part of standard SA regimens.
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Affiliation(s)
- Johanna Ledwaba
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Yasien Sayed
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Visva Pillay
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
- Department of Virology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gillian Hunt
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa
- Department of Virology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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14
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Okoroh EM, Kane DJ, Gee RE, Kieltyka L, Frederiksen BN, Baca KM, Rankin KM, Goodman DA, Kroelinger CD, Barfield WD. Policy change is not enough: engaging provider champions on immediate postpartum contraception. Am J Obstet Gynecol 2018. [PMID: 29530670 DOI: 10.1016/j.ajog.2018.03.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Rates of short-interval pregnancies that result in unintended pregnancies remain high in the United States and contribute to adverse reproductive health outcomes. Long-acting reversible contraception methods have annual failure rates of <1%, compared with 9% for oral contraceptive pills, and are an effective strategy to reduce unintended pregnancies. To increase access to long-acting reversible contraception in the immediate postpartum period, several State Medicaid programs, which include those in Iowa and Louisiana, recently established reimbursement policies to remove the barriers to reimbursement of immediate postpartum long-acting reversible contraception insertion. We used a mixed-methods approach to analyze 2013-2015 linked Medicaid and vital records data from both Iowa and Louisiana and to describe trends in immediate postpartum long-acting reversible contraception provision 1 year before and after the Medicaid reimbursement policy change. We also used data from key informant interviews with state program staff to understand how provider champions affected policy uptake. We found that the monthly average for the number of insertions in Iowa increased from 4.6 per month before the policy to 6.6 per month after the policy; in Louisiana, the average number of insertions increased from 2.6 per month before the policy to 45.2 per month. In both states, the majority of insertions occurred at 1 academic/teaching hospital. In Louisiana, the additional increase may be due to the engagement of a provider champion who worked at both the state and facility level. Recruiting, training, engaging, and supporting provider champions, as facilitators, with influence at state and facility levels, is an important component of a multipart strategy for increasing successful implementation of state-level Medicaid payment reform policies that allow reimbursement for immediate postpartum long-acting reversible contraception insertions.
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Affiliation(s)
- Ekwutosi M Okoroh
- Division of Reproductive Health, National Center for Chronic Disease Prevention and Health Promotion, Centers for Disease Control and Prevention, Atlanta, GA; Louisiana Department of Health, Medicaid Quality Management, Statistics and Reporting, Baton Rouge, LA
| | - Debra J Kane
- Division of Reproductive Health, National Center for Chronic Disease Prevention and Health Promotion, Centers for Disease Control and Prevention, Atlanta, GA; Iowa Department of Public Health, Bureau of Family Health, Des Moines, IA
| | - Rebekah E Gee
- Louisiana Department of Health, Medicaid Quality Management, Statistics and Reporting, Baton Rouge, LA; Louisiana State University Department of Obstetrics and Gynecology and School of Public Health, New Orleans, LA
| | - Lyn Kieltyka
- Division of Reproductive Health, National Center for Chronic Disease Prevention and Health Promotion, Centers for Disease Control and Prevention, Atlanta, GA; Louisiana Department of Health, Bureau of Family Health, New Orleans, LA
| | - Brittni N Frederiksen
- Division of Reproductive Health, National Center for Chronic Disease Prevention and Health Promotion, Centers for Disease Control and Prevention, Atlanta, GA; Iowa Department of Public Health, Bureau of Family Health, Des Moines, IA
| | - Katharyn M Baca
- Louisiana Department of Health, Bureau of Family Health, New Orleans, LA
| | - Kristin M Rankin
- Division of Epidemiology and Biostatistics, School of Public Health, University of Illinois at Chicago, Chicago, IL
| | - David A Goodman
- Division of Reproductive Health, National Center for Chronic Disease Prevention and Health Promotion, Centers for Disease Control and Prevention, Atlanta, GA
| | - Charlan D Kroelinger
- Division of Reproductive Health, National Center for Chronic Disease Prevention and Health Promotion, Centers for Disease Control and Prevention, Atlanta, GA
| | - Wanda D Barfield
- Division of Reproductive Health, National Center for Chronic Disease Prevention and Health Promotion, Centers for Disease Control and Prevention, Atlanta, GA
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15
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Andreatta M, Jurtz VI, Kaever T, Sette A, Peters B, Nielsen M. Machine learning reveals a non-canonical mode of peptide binding to MHC class II molecules. Immunology 2017; 152:255-264. [PMID: 28542831 DOI: 10.1111/imm.12763] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 03/07/2017] [Revised: 04/21/2017] [Accepted: 05/15/2017] [Indexed: 02/01/2023] Open
Abstract
MHC class II molecules play a fundamental role in the cellular immune system: they load short peptide fragments derived from extracellular proteins and present them on the cell surface. It is currently thought that the peptide binds lying more or less flat in the MHC groove, with a fixed distance of nine amino acids between the first and last residue in contact with the MHCII. While confirming that the great majority of peptides bind to the MHC using this canonical mode, we report evidence for an alternative, less common mode of interaction. A fraction of observed ligands were shown to have an unconventional spacing of the anchor residues that directly interact with the MHC, which could only be accommodated to the canonical MHC motif either by imposing a more stretched out peptide backbone (an 8mer core) or by the peptide bulging out of the MHC groove (a 10mer core). We estimated that on average 2% of peptides bind with a core deletion, and 0·45% with a core insertion, but the frequency of such non-canonical cores was as high as 10% for certain MHCII molecules. A mutational analysis and experimental validation of a number of these anomalous ligands demonstrated that they could only fit to their MHC binding motif with a non-canonical binding core of length different from nine. This previously undescribed mode of peptide binding to MHCII molecules gives a more complete picture of peptide presentation by MHCII and allows us to model more accurately this event.
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Affiliation(s)
- Massimo Andreatta
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Vanessa I Jurtz
- Centre for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Thomas Kaever
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Morten Nielsen
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina.,Centre for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
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16
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Abstract
The processes of yeast selection for using as wine fermentation starters have revealed a great phenotypic diversity both at interspecific and intraspecific level, which is explained by a corresponding genetic variation among different yeast isolates. Thus, the mechanisms involved in promoting these genetic changes are the main engine generating yeast biodiversity. Currently, an important task to understand biodiversity, population structure and evolutionary history of wine yeasts is the study of the molecular mechanisms involved in yeast adaptation to wine fermentation, and on remodeling the genomic features of wine yeast, unconsciously selected since the advent of winemaking. Moreover, the availability of rapid and simple molecular techniques that show genetic polymorphisms at species and strain levels have enabled the study of yeast diversity during wine fermentation. This review will summarize the mechanisms involved in generating genetic polymorphisms in yeasts, the molecular methods used to unveil genetic variation, and the utility of these polymorphisms to differentiate strains, populations, and species in order to infer the evolutionary history and the adaptive evolution of wine yeasts, and to identify their influence on their biotechnological and sensorial properties.
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Affiliation(s)
- José M Guillamón
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos - Consejo Superior de Investigaciones Científicas (CSIC)Valencia, Spain
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos - Consejo Superior de Investigaciones Científicas (CSIC)Valencia, Spain.,Departamento de Genética, Universidad de ValenciaValencia, Spain
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17
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Vatte C, Al Amri AM, Cyrus C, Chathoth S, Acharya S, Hashim TM, Al Ali Z, Alshreadah ST, Alsayyah A, Al-Ali AK. Tyrosine kinase domain mutations of EGFR gene in head and neck squamous cell carcinoma. Onco Targets Ther 2017; 10:1527-1533. [PMID: 28352186 PMCID: PMC5359136 DOI: 10.2147/ott.s132187] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 12/27/2022] Open
Abstract
Background Epidermal growth factor receptor (EGFR) is a commonly altered gene that is identified in various cancers, including head and neck squamous cell carcinoma (HNSCC). Therefore, EGFR is a promising molecular marker targeted by monoclonal antibodies and small molecule inhibitors targeting the tyrosine kinase (TK) domain. Objective The objective of this study was to investigate the spectrum of mutations in exons 18, 19, 20, and 21 of the EGFR gene in HNSCC patients. Materials and methods This retrospective study included 47 confirmed HNSCC cases. Mutations in the TK domain, exons 18, 19, 20, and 21 of the EGFR gene, were detected by Scorpion® chemistry and ARMS® technologies on Rotor-Gene Q real-time polymerase chain reaction. Results The tumors exhibited EGFR-TK domain mutations in 57% of cases. Four cases of T790M mutations were reported for the first time among HNSCC patients. Out of the total mutations, L861Q (exon 21), exon 20 insertions and deletions of exon 19 accounted for the majority of mutations (21%, 19%, and 17%, respectively). EGFR mutation status was correlated with the higher grade (P=0.026) and advanced stage (P=0.034) of HNSCC tumors. Conclusion Higher frequency of EGFR-TK domain mutations together with the presence of the T790M mutation suggests that identification of these mutations might streamline the therapy and provide a better prognosis in HNSCC cases.
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Affiliation(s)
- Chittibabu Vatte
- Department of Genetic Research, Institute for Research and Medical Consultation, University of Dammam, Dammam
| | - Ali M Al Amri
- Department of Internal Medicine, King Fahd Hospital of the University, University of Dammam, Al-Khobar
| | - Cyril Cyrus
- Department of Genetic Research, Institute for Research and Medical Consultation, University of Dammam, Dammam
| | - Shahanas Chathoth
- Department of Genetic Research, Institute for Research and Medical Consultation, University of Dammam, Dammam
| | - Sadananda Acharya
- Department of Stemcell Research, Institute for Research and Medical Consultation
| | - Tariq Mohammad Hashim
- Department of Pathology, King Fahd Hospital of the University, University of Dammam, Al-Khobar
| | - Zhara Al Ali
- Department of Internal Medicine, King Fahd Hospital of the University, University of Dammam, Al-Khobar
| | - Saleh Tawfeeq Alshreadah
- Department of Internal Medicine, King Fahd Hospital of the University, University of Dammam, Al-Khobar
| | - Ahmed Alsayyah
- Department of Pathology, King Fahd Hospital of the University, University of Dammam, Al-Khobar
| | - Amein K Al-Ali
- Department of Biochemistry, College of Medicine, University of Dammam, Dammam, Kingdom of Saudi Arabia
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18
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Noronha V, Choughule A, Patil VM, Joshi A, Kumar R, Susan Joy Philip D, Banavali S, Dutt A, Prabhash K. Epidermal growth factor receptor exon 20 mutation in lung cancer: types, incidence, clinical features and impact on treatment. Onco Targets Ther 2017; 10:2903-2908. [PMID: 28652772 PMCID: PMC5476719 DOI: 10.2147/ott.s133245] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND There are limited data available on the treatment and outcome of epidermal growth factor receptor (EGFR) exon 20-mutated lung cancer patients. Hence, we planned an analysis of the demographic details, clinical profile and survival of lung cancer patients with exon 20 mutations. We compared our results to patients with EGFR tyrosine kinase inhibitor (TKI)-sensitizing activating and EGFR/anaplastic lymphoma kinase (ALK)-negative mutations. METHODS This was a retrospective analysis of lung cancer patients who were treated at our center between January 2010 and August 2014. We reviewed the results of EGFR mutation testing by real-time polymerase chain reaction and Sanger sequencing. We also reviewed the data relating to baseline demographics, clinical profile, patient treatment and outcome measures in terms of response and overall survival (OS). RESULTS A total of 580 patients fulfilled the selection criteria. In all, 227 (39.1%) patients had EGFR TKI-sensitizing activating mutations, 20 (3.4%) patients had exon 20 insertion mutations and 333 patients were EGFR/ALK mutation negative (57.5%). The median OS was 5 months (95% confidence interval [CI] 0.17-9.8 months) in exon 20 insertion mutations, 16.1 months (95% CI 12.8-19.5 months) in EGFR TKI-sensitizing activating mutations and 10 months (95% CI 7.9-12.1 months) in EGFR/ALK mutation-negative patients. The median OS was significantly better for the EGFR TKI-sensitizing activating mutation group (P=0.000, log-rank test) and for the EGFR/ALK-negative group (P=0.037, log-rank test) compared to the exon 20-mutated group. CONCLUSION Exon 20 mutation results in a poorer OS prognosis compared to EGFR- and ALK-negative patients and patients harboring EGFR TKI-sensitizing activating mutations. The incidence of de novo exon 20 insertions was 3.4%. Different types of exon mutations seem to have different outcomes.
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Affiliation(s)
| | | | | | | | - Rajiv Kumar
- Department of Pathology, Tata Memorial Hospital
| | | | | | - Amit Dutt
- Dutt Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai, India
| | - Kumar Prabhash
- Department of Medical Oncology-Molecular Laboratory
- Correspondence: Kumar Prabhash, Department of Medical Oncology, Medical Oncology Molecular Laboratory, Tata Memorial Hospital, 1108, HBB, Parel, Mumbai 400012, India Tel +91 92 2418 2898, Email
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19
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Kumar V, Khan AW, Saxena RK, Garg V, Varshney RK. First-generation HapMap in Cajanus spp. reveals untapped variations in parental lines of mapping populations. Plant Biotechnol J 2016; 14:1673-81. [PMID: 26821983 PMCID: PMC5066660 DOI: 10.1111/pbi.12528] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 12/06/2015] [Accepted: 12/10/2015] [Indexed: 05/02/2023]
Abstract
Whole genome re-sequencing (WGRS) was conducted on a panel of 20 Cajanus spp. accessions (crossing parentals of recombinant inbred lines, introgression lines, multiparent advanced generation intercross and nested association mapping population) comprising of two wild species and 18 cultivated species accessions. A total of 791.77 million paired-end reads were generated with an effective mapping depth of ~12X per accession. Analysis of WGRS data provided 5 465 676 genome-wide variations including 4 686 422 SNPs and 779 254 InDels across the accessions. Large structural variations in the form of copy number variations (2598) and presence and absence variations (970) were also identified. Additionally, 2 630 904 accession-specific variations comprising of 2 278 571 SNPs (86.6%), 166 243 deletions (6.3%) and 186 090 insertions (7.1%) were also reported. Identified polymorphic sites in this study provide the first-generation HapMap in Cajanus spp. which will be useful in mapping the genomic regions responsible for important traits.
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Affiliation(s)
- Vinay Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Aamir W Khan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- School of Plant Biology and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
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20
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Fan S, Meyer A. Evolution of genomic structural variation and genomic architecture in the adaptive radiations of African cichlid fishes. Front Genet 2014; 5:163. [PMID: 24917883 PMCID: PMC4042683 DOI: 10.3389/fgene.2014.00163] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [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: 02/07/2014] [Accepted: 05/15/2014] [Indexed: 12/30/2022] Open
Abstract
African cichlid fishes are an ideal system for studying explosive rates of speciation and the origin of diversity in adaptive radiation. Within the last few million years, more than 2000 species have evolved in the Great Lakes of East Africa, the largest adaptive radiation in vertebrates. These young species show spectacular diversity in their coloration, morphology and behavior. However, little is known about the genomic basis of this astonishing diversity. Recently, five African cichlid genomes were sequenced, including that of the Nile Tilapia (Oreochromis niloticus), a basal and only relatively moderately diversified lineage, and the genomes of four representative endemic species of the adaptive radiations, Neolamprologus brichardi, Astatotilapia burtoni, Metriaclima zebra, and Pundamila nyererei. Using the Tilapia genome as a reference genome, we generated a high-resolution genomic variation map, consisting of single nucleotide polymorphisms (SNPs), short insertions and deletions (indels), inversions and deletions. In total, around 18.8, 17.7, 17.0, and 17.0 million SNPs, 2.3, 2.2, 1.4, and 1.9 million indels, 262, 306, 162, and 154 inversions, and 3509, 2705, 2710, and 2634 deletions were inferred to have evolved in N. brichardi, A. burtoni, P. nyererei, and M. zebra, respectively. Many of these variations affected the annotated gene regions in the genome. Different patterns of genetic variation were detected during the adaptive radiation of African cichlid fishes. For SNPs, the highest rate of evolution was detected in the common ancestor of N. brichardi, A. burtoni, P. nyererei, and M. zebra. However, for the evolution of inversions and deletions, we found that the rates at the terminal taxa are substantially higher than the rates at the ancestral lineages. The high-resolution map provides an ideal opportunity to understand the genomic bases of the adaptive radiation of African cichlid fishes.
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Affiliation(s)
- Shaohua Fan
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz Konstanz, Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz Konstanz, Germany
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21
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Adhikari AN, Peng J, Wilde M, Xu J, Freed KF, Sosnick TR. Modeling large regions in proteins: applications to loops, termini, and folding. Protein Sci 2012; 21:107-21. [PMID: 22095743 PMCID: PMC3323786 DOI: 10.1002/pro.767] [Citation(s) in RCA: 16] [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] [Subscribe] [Scholar Register] [Received: 08/20/2011] [Revised: 11/02/2011] [Accepted: 11/06/2011] [Indexed: 11/10/2022]
Abstract
Template-based methods for predicting protein structure provide models for a significant portion of the protein but often contain insertions or chain ends (InsEnds) of indeterminate conformation. The local structure prediction "problem" entails modeling the InsEnds onto the rest of the protein. A well-known limit involves predicting loops of ≤12 residues in crystal structures. However, InsEnds may contain as many as ~50 amino acids, and the template-based model of the protein itself may be imperfect. To address these challenges, we present a free modeling method for predicting the local structure of loops and large InsEnds in both crystal structures and template-based models. The approach uses single amino acid torsional angle "pivot" moves of the protein backbone with a C(β) level representation. Nevertheless, our accuracy for loops is comparable to existing methods. We also apply a more stringent test, the blind structure prediction and refinement categories of the CASP9 tournament, where we improve the quality of several homology based models by modeling InsEnds as long as 45 amino acids, sizes generally inaccessible to existing loop prediction methods. Our approach ranks as one of the best in the CASP9 refinement category that involves improving template-based models so that they can function as molecular replacement models to solve the phase problem for crystallographic structure determination.
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Affiliation(s)
- Aashish N Adhikari
- Department of Chemistry, The University of ChicagoChicago, Illinois 60637
- The James Franck Institute, The University of ChicagoChicago, Illinois 60637
| | - Jian Peng
- Toyota Technological Institute at ChicagoChicago, Illinois 60637
| | - Michael Wilde
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicago, Illinois 60637
| | - Jinbo Xu
- Toyota Technological Institute at ChicagoChicago, Illinois 60637
| | - Karl F Freed
- Department of Chemistry, The University of ChicagoChicago, Illinois 60637
- The James Franck Institute, The University of ChicagoChicago, Illinois 60637
- Computation Institute, The University of Chicago and Argonne National LaboratoryChicago, Illinois 60637
| | - Tobin R Sosnick
- Computation Institute, The University of Chicago and Argonne National LaboratoryChicago, Illinois 60637
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicago, Illinois 60637
- Institute for Biophysical Dynamics, The University of ChicagoChicago, Illinois 60637
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22
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Rogozin IB, Basu MK, Csürös M, Koonin EV. Analysis of rare genomic changes does not support the unikont-bikont phylogeny and suggests cyanobacterial symbiosis as the point of primary radiation of eukaryotes. Genome Biol Evol 2009; 1:99-113. [PMID: 20333181 PMCID: PMC2817406 DOI: 10.1093/gbe/evp011] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [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] [Accepted: 05/21/2009] [Indexed: 11/29/2022] Open
Abstract
The deep phylogeny of eukaryotes is an important but extremely difficult problem of evolutionary biology. Five eukaryotic supergroups are relatively well established but the relationship between these supergroups remains elusive, and their divergence seems to best fit a “Big Bang” model. Attempts were made to root the tree of eukaryotes by using potential derived shared characters such as unique fusions of conserved genes. One popular model of eukaryotic evolution that emerged from this type of analysis is the unikont–bikont phylogeny: The unikont branch consists of Metazoa, Choanozoa, Fungi, and Amoebozoa, whereas bikonts include the rest of eukaryotes, namely, Plantae (green plants, Chlorophyta, and Rhodophyta), Chromalveolata, excavates, and Rhizaria. We reexamine the relationships between the eukaryotic supergroups using a genome-wide analysis of rare genomic changes (RGCs) associated with multiple, conserved amino acids (RGC_CAMs and RGC_CAs), to resolve trifurcations of major eukaryotic lineages. The results do not support the basal position of Chromalveolata with respect to Plantae and unikonts or the monophyly of the bikont group and appear to be best compatible with the monophyly of unikonts and Chromalveolata. Chromalveolata show a distinct, additional signal of affinity with Plantae, conceivably, owing to genes transferred from the secondary, red algal symbiont. Excavates are derived forms, with extremely long branches that complicate phylogenetic inference; nevertheless, the RGC analysis suggests that they are significantly more likely to cluster with the unikont–Chromalveolata assemblage than with the Plantae. Thus, the first split in eukaryotic evolution might lie between photosynthetic and nonphotosynthetic forms and so could have been triggered by the endosymbiosis between an ancestral unicellular eukaryote and a cyanobacterium that gave rise to the chloroplast.
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Affiliation(s)
- Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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23
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Berg PE, Gayda R, Avni H, Zehnbauer B, Markovitz A. Cloning of Escherichia coli DNA that controls cell division and capsular polysaccharide synthesis. Proc Natl Acad Sci U S A 1976; 73:697-701. [PMID: 768981 PMCID: PMC335985 DOI: 10.1073/pnas.73.3.697] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A 2 x 10(6) dalton DNA fragment that controls cell division, capsular polysaccharide synthesis, and enzymes of capsular polysaccharide synthesis has been cloned.
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