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Shi Y, Yuan J, Rraklli V, Maxymovitz E, Cipullo M, Liu M, Li S, Westerlund I, Bedoya-Reina OC, Bullova P, Rorbach J, Juhlin CC, Stenman A, Larsson C, Kogner P, O’Sullivan MJ, Schlisio S, Holmberg J. Aberrant splicing in neuroblastoma generates RNA-fusion transcripts and provides vulnerability to spliceosome inhibitors. Nucleic Acids Res 2021; 49:2509-2521. [PMID: 33555349 PMCID: PMC7969022 DOI: 10.1093/nar/gkab054] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 01/14/2021] [Accepted: 01/21/2021] [Indexed: 11/12/2022] Open
Abstract
The paucity of recurrent mutations has hampered efforts to understand and treat neuroblastoma. Alternative splicing and splicing-dependent RNA-fusions represent mechanisms able to increase the gene product repertoire but their role in neuroblastoma remains largely unexplored. Here we investigate the presence and possible roles of aberrant splicing and splicing-dependent RNA-fusion transcripts in neuroblastoma. In addition, we attend to establish whether the spliceosome can be targeted to treat neuroblastoma. Through analysis of RNA-sequenced neuroblastoma we show that elevated expression of splicing factors is a strong predictor of poor clinical outcome. Furthermore, we identified >900 primarily intrachromosomal fusions containing canonical splicing sites. Fusions included transcripts from well-known oncogenes, were enriched for proximal genes and in chromosomal regions commonly gained or lost in neuroblastoma. As a proof-of-principle that these fusions can generate altered gene products, we characterized a ZNF451-BAG2 fusion, producing a truncated BAG2-protein which inhibited retinoic acid induced differentiation. Spliceosome inhibition impeded neuroblastoma fusion expression, induced apoptosis and inhibited xenograft tumor growth. Our findings elucidate a splicing-dependent mechanism generating altered gene products in neuroblastoma and show that the spliceosome is a potential target for clinical intervention.
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Affiliation(s)
- Yao Shi
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
| | - Juan Yuan
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
| | - Vilma Rraklli
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
| | - Eva Maxymovitz
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
| | - Miriam Cipullo
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, SE-171-65 Solna, Sweden
| | - Mingzhi Liu
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
| | - Shuijie Li
- Department of Microbiology, Tumor- and Cellbiology, Karolinska Institutet, Solnavägen 9, SE-171 65 Solna, Sweden
| | - Isabelle Westerlund
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
| | - Oscar C Bedoya-Reina
- Department of Microbiology, Tumor- and Cellbiology, Karolinska Institutet, Solnavägen 9, SE-171 65 Solna, Sweden
| | - Petra Bullova
- Department of Microbiology, Tumor- and Cellbiology, Karolinska Institutet, Solnavägen 9, SE-171 65 Solna, Sweden
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, SE-171-65 Solna, Sweden
| | - C Christofer Juhlin
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska (CCK), Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Adam Stenman
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska (CCK), Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Catharina Larsson
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska (CCK), Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Per Kogner
- Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Maureen J O’Sullivan
- Department of Histopathology, Our Lady's Children's Hospital, Dublin, Ireland
- Trinity Translational Medicine Institute, Trinity College, Dublin, Ireland
| | - Susanne Schlisio
- Department of Microbiology, Tumor- and Cellbiology, Karolinska Institutet, Solnavägen 9, SE-171 65 Solna, Sweden
| | - Johan Holmberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
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Kawakita T, Mukai T, Yoshida M, Yamada H, Nakayama M, Miyamoto Y, Suzuki M, Nakata N, Takii T, Ryo A, Ohara N, Ato M. Point mutation in the stop codon of MAV_RS14660 increases the growth rate of Mycobacterium avium subspecies hominissuis. Microbiology (Reading) 2021; 167:001007. [PMID: 33357282 PMCID: PMC8131024 DOI: 10.1099/mic.0.001007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/30/2020] [Indexed: 11/18/2022]
Abstract
Mycobacterium avium subspecies hominissuis (MAH) is a pathogen that causes various non-tuberculous mycobacterial diseases in humans and animals worldwide. Among the genus, MAH is characterized by relatively slow growth. Here, we isolated a rapidly growing variant of the MAH 104 strain. The variant strain (named N104) exhibited an enhanced growth rate and higher motility compared to the parent MAH 104 strain (P104). Whole-genome sequencing analysis of N104 revealed the loss of the stop codon of MAV_RS14660 due to a single nucleotide replacement, resulting in the substitution of the codon for tryptophan. Notably, exclusion of the stop codon ligated the open reading frames and caused the fusion of two adjacent proteins. A revertant parent strain, in which a mutation was introduced to restore the stop codon, revealed that elimination of the stop codon in MAV_RS14660 was responsible for the N104 phenotype. Furthermore, we analysed the phenotypes of the parent and mutated strains by determining the functions of the MAV_RS14660 and MAV_RS14655 coding regions flanking the stop codon. The mutant strains, expected to express a fusion protein, exhibited increased resistance to antimicrobial drugs and exogenous copper toxicity compared to that of the parent strains. These findings suggest that the fusion of the MAV_RS14660- and MAV_RS14655-encoding regions in the mutant N104 strain could be related to the modified functions of these intrinsic proteins.
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Affiliation(s)
- Tomomi Kawakita
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Microbiology and Molecular Biodefense Research, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Tetsu Mukai
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mitsunori Yoshida
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroyuki Yamada
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Tokyo, Japan
| | - Masaaki Nakayama
- Department of Oral Microbiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
- Advanced Research Center for Oral and Craniofacial Sciences, Okayama University Dental School, Okayama, Japan
| | - Yuji Miyamoto
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Noboru Nakata
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takemasa Takii
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Tokyo, Japan
| | - Akihide Ryo
- Department of Microbiology and Molecular Biodefense Research, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naoya Ohara
- Department of Oral Microbiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
- Advanced Research Center for Oral and Craniofacial Sciences, Okayama University Dental School, Okayama, Japan
| | - Manabu Ato
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
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3
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Hamnett R, Chesham JE, Maywood ES, Hastings MH. The Cell-Autonomous Clock of VIP Receptor VPAC2 Cells Regulates Period and Coherence of Circadian Behavior. J Neurosci 2021; 41:502-512. [PMID: 33234609 PMCID: PMC7821861 DOI: 10.1523/jneurosci.2015-20.2020] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/28/2020] [Accepted: 10/06/2020] [Indexed: 02/07/2023] Open
Abstract
Circadian (approximately daily) rhythms pervade mammalian behavior. They are generated by cell-autonomous, transcriptional/translational feedback loops (TTFLs), active in all tissues. This distributed clock network is coordinated by the principal circadian pacemaker, the hypothalamic suprachiasmatic nucleus (SCN). Its robust and accurate time-keeping arises from circuit-level interactions that bind its individual cellular clocks into a coherent time-keeper. Cells that express the neuropeptide vasoactive intestinal peptide (VIP) mediate retinal entrainment of the SCN; and in the absence of VIP, or its cognate receptor VPAC2, circadian behavior is compromised because SCN cells cannot synchronize. The contributions to pace-making of other cell types, including VPAC2-expressing target cells of VIP, are, however, not understood. We therefore used intersectional genetics to manipulate the cell-autonomous TTFLs of VPAC2-expressing cells. Measuring circadian behavioral and SCN rhythmicity in these temporally chimeric male mice thus enabled us to determine the contribution of VPAC2-expressing cells (∼35% of SCN cells) to SCN time-keeping. Lengthening of the intrinsic TTFL period of VPAC2 cells by deletion of the CK1εTau allele concomitantly lengthened the period of circadian behavioral rhythms. It also increased the variability of the circadian period of bioluminescent TTFL rhythms in SCN slices recorded ex vivo Abrogation of circadian competence in VPAC2 cells by deletion of Bmal1 severely disrupted circadian behavioral rhythms and compromised TTFL time-keeping in the corresponding SCN slices. Thus, VPAC2-expressing cells are a distinct, functionally powerful subset of the SCN circuit, contributing to computation of ensemble period and maintenance of circadian robustness. These findings extend our understanding of SCN circuit topology.
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Affiliation(s)
- Ryan Hamnett
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge, Cambridgeshire CB2 0QH, United Kingdom
| | - Johanna E Chesham
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge, Cambridgeshire CB2 0QH, United Kingdom
| | - Elizabeth S Maywood
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge, Cambridgeshire CB2 0QH, United Kingdom
| | - Michael H Hastings
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge, Cambridgeshire CB2 0QH, United Kingdom
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Ho JSY, Angel M, Ma Y, Sloan E, Wang G, Martinez-Romero C, Alenquer M, Roudko V, Chung L, Zheng S, Chang M, Fstkchyan Y, Clohisey S, Dinan AM, Gibbs J, Gifford R, Shen R, Gu Q, Irigoyen N, Campisi L, Huang C, Zhao N, Jones JD, van Knippenberg I, Zhu Z, Moshkina N, Meyer L, Noel J, Peralta Z, Rezelj V, Kaake R, Rosenberg B, Wang B, Wei J, Paessler S, Wise HM, Johnson J, Vannini A, Amorim MJ, Baillie JK, Miraldi ER, Benner C, Brierley I, Digard P, Łuksza M, Firth AE, Krogan N, Greenbaum BD, MacLeod MK, van Bakel H, Garcìa-Sastre A, Yewdell JW, Hutchinson E, Marazzi I. Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection. Cell 2020; 181:1502-1517.e23. [PMID: 32559462 PMCID: PMC7323901 DOI: 10.1016/j.cell.2020.05.035] [Citation(s) in RCA: 29] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 02/26/2020] [Accepted: 05/18/2020] [Indexed: 01/12/2023]
Abstract
RNA viruses are a major human health threat. The life cycles of many highly pathogenic RNA viruses like influenza A virus (IAV) and Lassa virus depends on host mRNA, because viral polymerases cleave 5'-m7G-capped host transcripts to prime viral mRNA synthesis ("cap-snatching"). We hypothesized that start codons within cap-snatched host transcripts could generate chimeric human-viral mRNAs with coding potential. We report the existence of this mechanism of gene origination, which we named "start-snatching." Depending on the reading frame, start-snatching allows the translation of host and viral "untranslated regions" (UTRs) to create N-terminally extended viral proteins or entirely novel polypeptides by genetic overprinting. We show that both types of chimeric proteins are made in IAV-infected cells, generate T cell responses, and contribute to virulence. Our results indicate that during infection with IAV, and likely a multitude of other human, animal and plant viruses, a host-dependent mechanism allows the genesis of hybrid genes.
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Affiliation(s)
- Jessica Sook Yuin Ho
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Matthew Angel
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Yixuan Ma
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elizabeth Sloan
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Guojun Wang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carles Martinez-Romero
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marta Alenquer
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Vladimir Roudko
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Liliane Chung
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9PS, UK
| | - Simin Zheng
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Max Chang
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Yesai Fstkchyan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sara Clohisey
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9PS, UK
| | - Adam M Dinan
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 0SP, UK
| | - James Gibbs
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Robert Gifford
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Rong Shen
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Nerea Irigoyen
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 0SP, UK
| | - Laura Campisi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Cheng Huang
- Department of Pathology, the University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Nan Zhao
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joshua D Jones
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 0SP, UK
| | | | - Zeyu Zhu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Natasha Moshkina
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Léa Meyer
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Justine Noel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zuleyma Peralta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Veronica Rezelj
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Robyn Kaake
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Brad Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bo Wang
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9PS, UK
| | - Jiajie Wei
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Slobodan Paessler
- Department of Pathology, the University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Helen M Wise
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9PS, UK
| | - Jeffrey Johnson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alessandro Vannini
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK; Fondazione Human Technopole, Structural Biology Research Centre, 20157 Milan, Italy
| | | | - J Kenneth Baillie
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9PS, UK
| | - Emily R Miraldi
- Divisions of Immunobiology and Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45257, USA
| | - Christopher Benner
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Ian Brierley
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 0SP, UK
| | - Paul Digard
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9PS, UK
| | - Marta Łuksza
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 0SP, UK
| | - Nevan Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Benjamin D Greenbaum
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Megan K MacLeod
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8QQ, UK
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adolfo Garcìa-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jonathan W Yewdell
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Edward Hutchinson
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK.
| | - Ivan Marazzi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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5
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Li H, Jiang S, Li C, Liu L, Lin Z, He H, Deng XW, Zhang Z, Wang X. The hybrid protein interactome contributes to rice heterosis as epistatic effects. Plant J 2020; 102:116-128. [PMID: 31736145 DOI: 10.1111/tpj.14616] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 10/27/2019] [Accepted: 11/01/2019] [Indexed: 05/15/2023]
Abstract
Heterosis is the phenomenon in which hybrid progeny exhibits superior traits in comparison with those of their parents. Genomic variations between the two parental genomes may generate epistasis interactions, which is one of the genetic hypotheses explaining heterosis. We postulate that protein-protein interactions specific to F1 hybrids (F1 -specific PPIs) may occur when two parental genomes combine, as the proteome of each parent may supply novel interacting partners. To test our assumption, an inter-subspecies hybrid interactome was simulated by in silico PPI prediction between rice japonica (cultivar Nipponbare) and indica (cultivar 9311). Four-thousand, six-hundred and twelve F1 -specific PPIs accounting for 20.5% of total PPIs in the hybrid interactome were found. Genes participating in F1 -specific PPIs tend to encode metabolic enzymes and are generally localized in genomic regions harboring metabolic gene clusters. To test the genetic effect of F1 -specific PPIs in heterosis, genomic selection analysis was performed for trait prediction with additive, dominant and epistatic effects separately considered in the model. We found that the removal of single nucleotide polymorphisms associated with F1 -specific PPIs reduced prediction accuracy when epistatic effects were considered in the model, but no significant changes were observed when additive or dominant effects were considered. In summary, genomic divergence widely dispersed between japonica and indica rice may generate F1 -specific PPIs, part of which may accumulatively contribute to heterosis according to our computational analysis. These candidate F1 -specific PPIs, especially for those involved in metabolic biosynthesis pathways, are worthy of experimental validation when large-scale protein interactome datasets are generated in hybrid rice in the future.
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Affiliation(s)
- Hong Li
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Shuqin Jiang
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Lei Liu
- Beijing Key Laboratory of Plant Resources Research and Development, School of Sciences, Beijing Technology and Business University, Beijing, 100048, China
| | - Zechuan Lin
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Xing-Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiangfeng Wang
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
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6
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Oliver GR, Tang X, Schultz-Rogers LE, Vidal-Folch N, Jenkinson WG, Schwab TL, Gaonkar K, Cousin MA, Nair A, Basu S, Chanana P, Oglesbee D, Klee EW. A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease. PLoS One 2019; 14:e0223337. [PMID: 31577830 PMCID: PMC6774566 DOI: 10.1371/journal.pone.0223337] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/18/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND RNA sequencing has been proposed as a means of increasing diagnostic rates in studies of undiagnosed rare inherited disease. Recent studies have reported diagnostic improvements in the range of 7.5-35% by profiling splicing, gene expression quantification and allele specific expression. To-date however, no study has systematically assessed the presence of gene-fusion transcripts in cases of germline disease. Fusion transcripts are routinely identified in cancer studies and are increasingly recognized as having diagnostic, prognostic or therapeutic relevance. Isolated reports exist of fusion transcripts being detected in cases of developmental and neurological phenotypes, and thus, systematic application of fusion detection to germline conditions may further increase diagnostic rates. However, current fusion detection methods are unsuited to the investigation of germline disease due to performance biases arising from their development using tumor, cell-line or in-silico data. METHODS We describe a tailored approach to fusion candidate identification and prioritization in a cohort of 47 undiagnosed, suspected inherited disease patients. We modify an existing fusion transcript detection algorithm by eliminating its cell line-derived filtering steps, and instead, prioritize candidates using a custom workflow that integrates genomic and transcriptomic sequence alignment, biological and technical annotations, customized categorization logic, and phenotypic prioritization. RESULTS We demonstrate that our approach to fusion transcript identification and prioritization detects genuine fusion events excluded by standard analyses and efficiently removes phenotypically unimportant candidates and false positive events, resulting in a reduced candidate list enriched for events with potential phenotypic relevance. We describe the successful genetic resolution of two previously undiagnosed disease cases through the detection of pathogenic fusion transcripts. Furthermore, we report the experimental validation of five additional cases of fusion transcripts with potential phenotypic relevance. CONCLUSIONS The approach we describe can be implemented to enable the detection of phenotypically relevant fusion transcripts in studies of rare inherited disease. Fusion transcript detection has the potential to increase diagnostic rates in rare inherited disease and should be included in RNA-based analytical pipelines aimed at genetic diagnosis.
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Affiliation(s)
- Gavin R. Oliver
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Xiaojia Tang
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Laura E. Schultz-Rogers
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Noemi Vidal-Folch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - W. Garrett Jenkinson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Tanya L. Schwab
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Krutika Gaonkar
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Margot A. Cousin
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Asha Nair
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Shubham Basu
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Pritha Chanana
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Devin Oglesbee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Medical Genetics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Eric W. Klee
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail:
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7
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Abstract
Gene fusion is one of the hallmarks of cancer genome via chromosomal rearrangement initiated by DNA double-strand breakage. To date, many fusion genes (FGs) have been established as important biomarkers and therapeutic targets in multiple cancer types. To better understand the function of FGs in cancer types and to promote the discovery of clinically relevant FGs, we built FusionGDB (Fusion Gene annotation DataBase) available at https://ccsm.uth.edu/FusionGDB. We collected 48 117 FGs across pan-cancer from three representative fusion gene resources: the improved database of chimeric transcripts and RNA-seq data (ChiTaRS 3.1), an integrative resource for cancer-associated transcript fusions (TumorFusions), and The Cancer Genome Atlas (TCGA) fusions by Gao et al. For these ∼48K FGs, we performed functional annotations including gene assessment across pan-cancer fusion genes, open reading frame (ORF) assignment, and retention search of 39 protein features based on gene structures of multiple isoforms with different breakpoints. We also provided the fusion transcript and amino acid sequences according to multiple breakpoints and transcript isoforms. Our analyses identified 331, 303 and 667 in-frame FGs with retaining kinase, DNA-binding, and epigenetic factor domains, respectively, as well as 976 FGs lost protein-protein interaction. FusionGDB provides six categories of annotations: FusionGeneSummary, FusionProtFeature, FusionGeneSequence, FusionGenePPI, RelatedDrug and RelatedDisease.
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Affiliation(s)
- Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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8
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Duan GF, Ye Y, Xu S, Tao W, Zhao S, Jin T, Nicoll RA, Shi YS, Sheng N. Signal peptide represses GluK1 surface and synaptic trafficking through binding to amino-terminal domain. Nat Commun 2018; 9:4879. [PMID: 30451858 PMCID: PMC6242971 DOI: 10.1038/s41467-018-07403-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 10/17/2018] [Indexed: 01/28/2023] Open
Abstract
Kainate-type glutamate receptors play critical roles in excitatory synaptic transmission and synaptic plasticity in the brain. GluK1 and GluK2 possess fundamentally different capabilities in surface trafficking as well as synaptic targeting in hippocampal CA1 neurons. Here we find that the excitatory postsynaptic currents (EPSCs) are significantly increased by the chimeric GluK1(SPGluK2) receptor, in which the signal peptide of GluK1 is replaced with that of GluK2. Coexpression of GluK1 signal peptide completely suppresses the gain in trafficking ability of GluK1(SPGluK2), indicating that the signal peptide represses receptor trafficking in a trans manner. Furthermore, we demonstrate that the signal peptide directly interacts with the amino-terminal domain (ATD) to inhibit the synaptic and surface expression of GluK1. Thus, we have uncovered a trafficking mechanism for kainate receptors and propose that the cleaved signal peptide behaves as a ligand of GluK1, through binding with the ATD, to repress forward trafficking of the receptor.
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Affiliation(s)
- Gui-Fang Duan
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, The Affliated Hospital of Nanjing University Medical School, and Minister of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, 210032, China
| | - Yaxin Ye
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Sha Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Wucheng Tao
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 94143, CA, USA
| | - Shiping Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Tengchuan Jin
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, 230007, China
| | - Roger A Nicoll
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 94143, CA, USA
- Department of Physiology, University of California, San Francisco, 94143, CA, USA
| | - Yun Stone Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, The Affliated Hospital of Nanjing University Medical School, and Minister of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, 210032, China.
- Institute for Brain Sciences, Nanjing University, Nanjing, 210032, China.
| | - Nengyin Sheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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9
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Wang R, Li J, Yin C, Zhao D, Yin L. Identification of differentially expressed genes and typical fusion genes associated with three subtypes of breast cancer. Breast Cancer 2018; 26:305-316. [PMID: 30446971 DOI: 10.1007/s12282-018-0924-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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] [Received: 06/22/2018] [Accepted: 10/15/2018] [Indexed: 11/25/2022]
Abstract
BACKGROUND This study aimed to identify the differentially expressed genes (DEGs) and the typical fusion genes in different types of breast cancers using RNA-seq. METHODS GSE52643 was downloaded from Gene Expression Omnibus, which included 1 normal sample (MCF10A) and 7 breast cancer samples (BT-474, BT-20, MCF7, MDA-MB-231, MDA-MB-468, T47D, and ZR-75-1). The transcript abundance and the DEGs screening were performed by Cufflinks. The functional and pathway enrichment was analyzed by Gostats. SnowShoes-FTD was applied to identify the fusion genes. RESULTS We screened 430, 445, 397, 417, 369, 557, and 375 DEGs in BT-474, BT-20, MCF7, DA-MB-231, MDA-MB-468, T47D, and ZR-75-1, respectively, compared with MCF10A. DEGs in each comparison group (such as CD40 and CDH1) were significantly enriched in the functions of cell adhesion and extracellular matrix organization and pathways of CAMs and ECM receptor interaction. UCP2 was a common DEG in the 7 comparison groups. SFRP1 and MMP7 were significantly enriched in wnt/-catenin signaling pathway in MDA-MB-231. FAS was significantly enriched in autoimmune thyroid disease pathway in BT-474. Besides, we screened 96 fusion genes, such as ESR1-C6orf97 in ZR-75-1, COBRA1-C9orf167 in BT-20, and VAPB-IKZF3 and ACACA-STAC2 in BT-474. CONCLUSIONS The DEGs such as SFRP1, MMP7, CDH1, FAS, and UCP2 might be the potential biomarkers in breast cancer. Furthermore, some pivotal fusion genes like ESR1-C6orf97 with COBRA1-C9orf167 and VAPB-IKZF3 with ACACA-STAC2 were found in Luminal A and Luminal B breast cancer, respectively.
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Affiliation(s)
- Rong Wang
- National Research Institute for Health and Family Planning, Beijing, 100081, China
| | - Jinbin Li
- Core Laboratory of Translational Medicine, Chinese PLA General Hospital, No. 28, Fuxing Road, Haidian District, Beijing, 100853, China
| | - Chunyu Yin
- Core Laboratory of Translational Medicine, Chinese PLA General Hospital, No. 28, Fuxing Road, Haidian District, Beijing, 100853, China
| | - Di Zhao
- Dermatological of Department, The 309 Hospital of Chinese PLA, Beijing, 100091, China
| | - Ling Yin
- Core Laboratory of Translational Medicine, Chinese PLA General Hospital, No. 28, Fuxing Road, Haidian District, Beijing, 100853, China.
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10
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Wang H, Zhao Q, Fu J, Wang X, Jiang L. Re-assessment of biolistic transient expression: An efficient and robust method for protein localization studies in seedling-lethal mutant and juvenile plants. Plant Sci 2018; 274:2-7. [PMID: 30080604 DOI: 10.1016/j.plantsci.2018.03.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 01/12/2018] [Revised: 03/26/2018] [Accepted: 03/29/2018] [Indexed: 05/09/2023]
Abstract
Knowledge on the subcellular localization of target proteins in a plant mutant background is important for revealing the function of the genes investigated. However, in Arabidopsis and rice, mutant lethality is one major barrier to such studies. Here we describe an optimized bombardment-mediated transient expression approach for studying subcellular protein localization in Arabidopsis seedling of lethal mutants. The whole experiment comprises four stages: cultivation and preparation of plants, coating gold particles with plasmid DNA, delivery of DNA into plants via bombardment, plant incubation and gene expression analysis which include localization and dynamics, co-localization comparison with reporter proteins and functional analysis. The entire process takes about 3-10 days from plant cultivation to protein detection. It has a high efficiency and the results are reproducible. Additionally, this protocol is applicable for the transient expression of chimeric fluorescent fusion proteins in juvenile rice seedlings and leaf sheaths, saving time dramatically in comparison of generating transgenic rice plant.
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Affiliation(s)
- Hao Wang
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Qiong Zhao
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Jiaxin Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-biorecourses, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xiangfeng Wang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China; College of Biological Sciences, China Agricultural University, Beijing 100094, China
| | - Liwen Jiang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China; CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China.
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11
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Hua CK, Gacerez AT, Sentman CL, Ackerman ME. Development of unique cytotoxic chimeric antigen receptors based on human scFv targeting B7H6. Protein Eng Des Sel 2017; 30:713-721. [PMID: 29040754 DOI: 10.1093/protein/gzx051] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 06/20/2017] [Accepted: 08/30/2017] [Indexed: 11/14/2022] Open
Abstract
As a stress-inducible natural killer (NK) cell ligand, B7H6 plays a role in innate tumor immunosurveillance and is a fairly tumor selective marker expressed on a variety of solid and hematologic cancer cells. Here, we describe the isolation and characterization of a new family of single chain fragment variable (scFv) molecules targeting the human B7H6 ligand. Through directed evolution of a yeast surface displayed non-immune human-derived scFv library, eight candidates comprising a single family of clones differing by up to four amino acid mutations and exhibiting nM avidities for soluble B7H6-Ig were isolated. A representative clone re-formatted as an scFv-CH1-Fc molecule demonstrated specific binding to both B7H6-Ig and native membrane-bound B7H6 on tumor cell lines with a binding avidity comparable to the previously characterized B7H6-targeting antibody, TZ47. Furthermore, these clones recognized an epitope distinct from that of TZ47 and the natural NK cell ligand NKp30, and demonstrated specific activity against B7H6-expressing tumor cells when expressed as a chimeric antigen receptor (CAR) in T cells.
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MESH Headings
- Amino Acid Substitution
- Animals
- Antibodies, Neoplasm/biosynthesis
- Antibodies, Neoplasm/chemistry
- Antibodies, Neoplasm/genetics
- B7 Antigens/chemistry
- B7 Antigens/genetics
- B7 Antigens/immunology
- Biomarkers, Tumor/chemistry
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/immunology
- Cell Line, Tumor
- Cell Surface Display Techniques
- Cytotoxicity, Immunologic
- Epitopes/chemistry
- Epitopes/genetics
- Epitopes/immunology
- Gene Expression
- HEK293 Cells
- Humans
- Killer Cells, Natural/cytology
- Killer Cells, Natural/immunology
- Mice
- Models, Molecular
- Mutant Chimeric Proteins/chemistry
- Mutant Chimeric Proteins/genetics
- Mutant Chimeric Proteins/immunology
- Mutation
- Natural Cytotoxicity Triggering Receptor 3/chemistry
- Natural Cytotoxicity Triggering Receptor 3/genetics
- Natural Cytotoxicity Triggering Receptor 3/immunology
- Protein Binding
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Single-Chain Antibodies/biosynthesis
- Single-Chain Antibodies/chemistry
- Single-Chain Antibodies/genetics
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Affiliation(s)
- Casey K Hua
- Thayer School of Engineering, Dartmouth College, 14 Engineering Dr, Hanover, NH 03755, USA
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, 1 Medical Center Dr, Lebanon, NH 03756, USA
| | - Albert T Gacerez
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, 1 Medical Center Dr, Lebanon, NH 03756, USA
- Center for Synthetic Immunity, Geisel School of Medicine, Dartmouth College, 1 Medical Center Dr, Lebanon, NH 03756, USA
| | - Charles L Sentman
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, 1 Medical Center Dr, Lebanon, NH 03756, USA
- Center for Synthetic Immunity, Geisel School of Medicine, Dartmouth College, 1 Medical Center Dr, Lebanon, NH 03756, USA
| | - Margaret E Ackerman
- Thayer School of Engineering, Dartmouth College, 14 Engineering Dr, Hanover, NH 03755, USA
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, 1 Medical Center Dr, Lebanon, NH 03756, USA
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12
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Schaefer B, Moriishi K, Behrends S. Insights into the mechanism of isoenzyme-specific signal peptide peptidase-mediated translocation of heme oxygenase. PLoS One 2017; 12:e0188344. [PMID: 29155886 PMCID: PMC5695791 DOI: 10.1371/journal.pone.0188344] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 11/06/2017] [Indexed: 11/19/2022] Open
Abstract
It has recently been shown that signal peptide peptidase (SPP) can catalyze the intramembrane cleavage of heme oxygenase-1 (HO-1) that leads to translocation of HO-1 into the cytosol and nucleus. While there is consensus that translocated HO-1 promotes tumor progression and drug resistance, the physiological signals leading to SPP-mediated intramembrane cleavage of HO-1 and the specificity of the process remain unclear. In this study, we used co-immunoprecipitation and confocal laser scanning microscopy to investigate the translocation mechanism of HO-1 and its regulation by SPP. We show that HO-1 and the closely related HO-2 isoenzyme bind to SPP under normoxic conditions. Under hypoxic conditions SPP mediates intramembrane cleavage of HO-1, but not HO-2. In experiments with an inactive HO-1 mutant (H25A) we show that translocation is independent of the catalytic activity of HO-1. Studies with HO-1 / HO-2 chimeras indicate that the membrane anchor, the PEST-domain and the nuclear shuttle sequence of HO-1 are necessary for full cleavage and subsequent translocation under hypoxic conditions. In the presence of co-expressed exogenous SPP, the anchor and the PEST-domain are sufficient for translocation. Taken together, we identified the domains involved in HO-1 translocation and showed that SPP-mediated cleavage is isoform-specific and independent of HO-activity. A closer understanding of the translocation mechanism of HO-1 is of particular importance because nuclear HO-1 seems to lead to tumor progression and drug resistance.
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Affiliation(s)
- Bianca Schaefer
- Department of Pharmacology, Toxicology and Clinical Pharmacy, University of Braunschweig—Institute of Technology, Braunschweig, Germany
| | - Kohji Moriishi
- Department of Microbiology, Faculty of Medicine Yamanashi University, Yamanashi, Japan
| | - Soenke Behrends
- Department of Pharmacology, Toxicology and Clinical Pharmacy, University of Braunschweig—Institute of Technology, Braunschweig, Germany
- * E-mail:
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13
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Vdovin AS, Bykova NA, Efimov GA. [T Lymphocytes with Modified Specificity in the Therapy of Malignant Diseases]. Mol Biol (Mosk) 2017; 51:1008-1023. [PMID: 29271964 DOI: 10.7868/s002689841706012x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 05/23/2017] [Indexed: 06/07/2023]
Abstract
Immunotherapy is one of the most rapidly progressing and promising fields in antitumor therapy. It is based on the idea of using immune cells of patient or healthy donors for elimination of malignant cells. T lymphocytes play a key role in cell-mediated immunity including the response to tumors. Recently developed approaches of altering antigen specificity of T cells consist of their genetic modification (introduction of additional T cell receptor or chimeric antigen receptor), as well as the use of bispecific molecules that crosslink target and effector cells. These approaches are used to retarget T lymphocytes with arbitrary specificity against tumor antigens in the context of antitumor immunotherapy. The high potential of T cell immunotherapy was demonstrated in a number of clinical trials. In the future, it is possible to develop approaches to the therapy of a wide spectrum of tumors. The selection of the optimal antigen is the main challenge in successful T cell immunotherapy, as it largely determines the effectiveness of the treatment, as well as the risk of side effects. In this review we discuss potential methods of modification of T cell specificity and targets for immunotherapy.
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MESH Headings
- Antibodies, Bispecific/biosynthesis
- Antibodies, Bispecific/pharmacology
- Antigens, Neoplasm/chemistry
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/immunology
- Cell Engineering
- Cytotoxicity, Immunologic
- Gene Expression
- Humans
- Immunotherapy/methods
- Mutant Chimeric Proteins/chemistry
- Mutant Chimeric Proteins/genetics
- Mutant Chimeric Proteins/immunology
- Neoplasms/genetics
- Neoplasms/immunology
- Neoplasms/pathology
- Neoplasms/therapy
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
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Affiliation(s)
- A S Vdovin
- National Research Center for Hematology, Ministry of Healthcare of the Russian Federation, Moscow, 125167 Russia
| | - N A Bykova
- National Research Center for Hematology, Ministry of Healthcare of the Russian Federation, Moscow, 125167 Russia
| | - G A Efimov
- National Research Center for Hematology, Ministry of Healthcare of the Russian Federation, Moscow, 125167 Russia
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14
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Wang Z, Cheng Y, Abraham JM, Yan R, Liu X, Chen W, Ibrahim S, Schroth GP, Ke X, He Y, Meltzer SJ. RNA sequencing of esophageal adenocarcinomas identifies novel fusion transcripts, including NPC1-MELK, arising from a complex chromosomal rearrangement. Cancer 2017; 123:3916-3924. [PMID: 28640357 PMCID: PMC5626593 DOI: 10.1002/cncr.30837] [Citation(s) in RCA: 9] [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: 04/03/2017] [Revised: 05/14/2017] [Accepted: 05/18/2017] [Indexed: 11/11/2022]
Abstract
BACKGROUND Studies of chromosomal rearrangements and fusion transcripts have elucidated mechanisms of tumorigenesis and led to targeted cancer therapies. This study was aimed at identifying novel fusion transcripts in esophageal adenocarcinoma (EAC). METHODS To identify new fusion transcripts associated with EAC, targeted RNA sequencing and polymerase chain reaction (PCR) verification were performed in 40 EACs and matched nonmalignant specimens from the same patients. Genomic PCR and Sanger sequencing were performed to find the breakpoint of fusion genes. RESULTS Five novel in-frame fusion transcripts were identified and verified in 40 EACs and in a validation cohort of 15 additional EACs (55 patients in all): fibroblast growth factor receptor 2 (FGFR2)-GRB2-associated binding protein 2 (GAB2) in 2 of 55 or 3.6%, Niemann-Pick C1 (NPC1)-maternal embryonic leucine zipper kinase (MELK) in 2 of 55 or 3.6%, ubiquitin-specific peptidase 54 (USP54)-calcium/calmodulin dependent protein kinase II γ (CAMK2G) in 2 of 55 or 3.6%, megakaryoblastic leukemia (translocation) 1 (MKL1)-fibulin 1 (FBLN1) in 1 of 55 or 1.8%, and CCR4-NOT transcription complex subunit 2 (CNOT2)-chromosome 12 open reading frame 49 (C12orf49) in 1 of 55 or 1.8%. A genomic analysis indicated that NPC1-MELK arose from a complex interchromosomal translocation event involving chromosomes 18, 3, and 9 with 3 rearrangement points, and this was consistent with chromoplexy. CONCLUSIONS These data indicate that fusion transcripts occur at a stable frequency in EAC. Furthermore, our results indicate that chromoplexy is an underlying mechanism that generates fusion transcripts in EAC. These and other fusion transcripts merit further study as diagnostic markers and potential therapeutic targets in EAC. Cancer 2017;123:3916-24. © 2017 American Cancer Society.
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Affiliation(s)
- Zhixiong Wang
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Yulan Cheng
- Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, USA
- Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
| | - John M. Abraham
- Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, USA
- Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Rong Yan
- Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Xi Liu
- Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Wei Chen
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Sariat Ibrahim
- Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, USA
- Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
| | | | - Xiquan Ke
- Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Yulong He
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Stephen J. Meltzer
- Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, USA
- Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
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15
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Xavier BM, Hildebrandt E, Jiang F, Ding H, Kappes JC, Urbatsch IL. Substitution of Yor1p NBD1 residues improves the thermal stability of Human Cystic Fibrosis Transmembrane Conductance Regulator. Protein Eng Des Sel 2017; 30:729-741. [PMID: 29053845 PMCID: PMC5914393 DOI: 10.1093/protein/gzx054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 05/26/2017] [Revised: 09/08/2017] [Accepted: 09/15/2017] [Indexed: 01/05/2023] Open
Abstract
The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is a plasma membrane chloride channel protein that regulates vertebrate fluid homeostasis. The inefficiency of wild type human CFTR protein folding/trafficking is exacerbated by genetic mutations that can cause protein misfolding in the endoplasmic reticulum (ER) and subsequent degradation. This project investigates small changes in protein sequence that can alter the thermal stability of the large multi-domain CFTR protein. We target a conserved 70-residue α-subdomain located in the first nucleotide-binding domain that hosts the common misfolding mutation ∆F508. To investigate substitutions that can stabilize this domain, we constructed chimeras between human CFTR and its closest yeast homolog Yor1p. The α-subdomain of Yor1p was replaced with that of CFTR in Saccharomyces cerevisiae. Cellular localization of green fluorescence protein-tagged Yor1p-CFTR chimeras was analyzed by fluorescence microscopy and quantitative multispectral imaging flow cytometry, steady-state protein levels were compared by SDS-PAGE and protein function probed by a phenotypic oligomycin resistance assay. The chimeras exhibited ER retention in yeast characteristic of defective protein folding/processing. Substitution of seven CFTR α-subdomain residues that are highly conserved in Yor1p and other transporters but differ in CFTR (S495P/R516K/F533L/A534P/K536G/I539T/R553K) improved Yor1p-CFTR chimera localization to the yeast plasma membrane. When introduced into human CFTR expressed in mammalian cells, the same substitutions improve the purified protein thermal stability. This stabilized human CFTR protein will be directly useful for structural and biophysical studies that have been limited by the thermal sensitivity of wild type CFTR. The insights into critical structural residues within CFTR could facilitate development of effective therapeutics for CF-causing mutations.
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Affiliation(s)
- B M Xavier
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - E Hildebrandt
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - F Jiang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - H Ding
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - J C Kappes
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Veterans Affairs Medical Center, Research Service, Birmingham, AL 35294, USA
| | - I L Urbatsch
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
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16
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Motl N, Skiba MA, Kabil O, Smith JL, Banerjee R. Structural and biochemical analyses indicate that a bacterial persulfide dioxygenase-rhodanese fusion protein functions in sulfur assimilation. J Biol Chem 2017; 292:14026-14038. [PMID: 28684420 PMCID: PMC5572905 DOI: 10.1074/jbc.m117.790170] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/26/2017] [Indexed: 11/06/2022] Open
Abstract
Hydrogen sulfide (H2S) is a signaling molecule that is toxic at elevated concentrations. In eukaryotes, it is cleared via a mitochondrial sulfide oxidation pathway, which comprises sulfide quinone oxidoreductase, persulfide dioxygenase (PDO), rhodanese, and sulfite oxidase and converts H2S to thiosulfate and sulfate. Natural fusions between the non-heme iron containing PDO and rhodanese, a thiol sulfurtransferase, exist in some bacteria. However, little is known about the role of the PDO-rhodanese fusion (PRF) proteins in sulfur metabolism. Herein, we report the kinetic properties and the crystal structure of a PRF from the Gram-negative endophytic bacterium Burkholderia phytofirmans The crystal structures of wild-type PRF and a sulfurtransferase-inactivated C314S mutant with and without glutathione were determined at 1.8, 2.4, and 2.7 Å resolution, respectively. We found that the two active sites are distant and do not show evidence of direct communication. The B. phytofirmans PRF exhibited robust PDO activity and preferentially catalyzed sulfur transfer in the direction of thiosulfate to sulfite and glutathione persulfide; sulfur transfer in the reverse direction was detectable only under limited turnover conditions. Together with the kinetic data, our bioinformatics analysis reveals that B. phytofirmans PRF is poised to metabolize thiosulfate to sulfite in a sulfur assimilation pathway rather than in sulfide stress response as seen, for example, with the Staphylococcus aureus PRF or sulfide oxidation and disposal as observed with the homologous mammalian proteins.
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Affiliation(s)
- Nicole Motl
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
| | - Meredith A Skiba
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
| | - Omer Kabil
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
| | - Janet L Smith
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
| | - Ruma Banerjee
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600.
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Fisher J, Abramowski P, Wisidagamage Don ND, Flutter B, Capsomidis A, Cheung GWK, Gustafsson K, Anderson J. Avoidance of On-Target Off-Tumor Activation Using a Co-stimulation-Only Chimeric Antigen Receptor. Mol Ther 2017; 25:1234-1247. [PMID: 28341563 PMCID: PMC5417796 DOI: 10.1016/j.ymthe.2017.03.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 03/02/2017] [Accepted: 03/02/2017] [Indexed: 01/13/2023] Open
Abstract
Chimeric antigen receptors (CARs) combine T cell activation with antibody-mediated tumor antigen specificity, bypassing the need for T cell receptor (TCR) ligation. A limitation of CAR technology is on-target off-tumor toxicity caused by target antigen expression on normal cells. Using GD2 as a model cancer antigen, we hypothesized that this could be minimized by using T cells expressing Vγ9Vδ2 TCR, which recognizes transformed cells in a major histocompatibility complex (MHC)-unrestricted manner, in combination with a co-stimulatory CAR that would function independently of the TCR. An anti-GD2 CAR containing a solitary endodomain derived from the NKG2D adaptor DAP10 was expressed in Vγ9Vδ2+ T cells. Differential ligation of the CAR and/or TCR using antibody-coated beads showed that pro-inflammatory cytokine response depended on activation of both receptors. Moreover, in killing assays, GD2-expressing neuroblastoma cells that engaged the Vγ9Vδ2 TCR were efficiently lysed, whereas cells that expressed GD2 equivalently but did not engage the Vγ9Vδ2 TCR were untouched. Differentiation between X-on tumor and X-off tumor offers potential for safer immunotherapy and broader target selection.
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Affiliation(s)
- Jonathan Fisher
- Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Pierre Abramowski
- Institute of Child Health, University College London, London WC1N 1EH, UK
| | | | - Barry Flutter
- Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Anna Capsomidis
- Institute of Child Health, University College London, London WC1N 1EH, UK
| | | | - Kenth Gustafsson
- Institute of Child Health, University College London, London WC1N 1EH, UK
| | - John Anderson
- Institute of Child Health, University College London, London WC1N 1EH, UK.
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18
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Liu X, Wang Y, Yang W, Guan Z, Yu W, Liao DJ. Protein multiplicity can lead to misconduct in western blotting and misinterpretation of immunohistochemical staining results, creating much conflicting data. ACTA ACUST UNITED AC 2016; 51:51-58. [PMID: 27908506 DOI: 10.1016/j.proghi.2016.11.001] [Citation(s) in RCA: 18] [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] [Received: 09/16/2016] [Revised: 11/18/2016] [Accepted: 11/21/2016] [Indexed: 01/18/2023]
Abstract
Western blotting (WB) and immunohistochemical staining (IHC) are common techniques for determining tissue protein expression. Both techniques require a primary antibody specific for the protein in question. WB data is band(s) on a membrane while IHC result is a staining on a tissue section. Most human genes are known to produce multiple protein isoforms; in agreement with that, multiple bands are often found on the WB membrane. However, a common but unspoken practice in WB is to cut away the extra band(s) and present for publication only the band of interest, which implies to the readers that only one form of protein is expressed and thus the data interpretation is straightforward. Similarly, few IHC studies discuss whether the antibody used is isoform-specific and whether the positive staining is derived from only one isoform. Currently, there is no reliable technique to determine the isoform-specificity of an antibody, especially for IHC. Therefore, cutting away extra band(s) on the membrane usually is a form of misconduct in WB, and a positive staining in IHC only indicates the presence of protein product(s) of the to-be-interrogated gene, and not necessarily the presence of the isoform of interest. We suggest that data of WB and IHC involving only one antibody should not be published and that relevant reports should discuss whether there may be protein multiplicity and whether the antibody used is isoform-specific. Hopefully, techniques will soon emerge that allow determination of not only the presence of protein products of genes but also the isoforms expressed.
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Affiliation(s)
- Xingde Liu
- Department of Cardiology Department, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, PR China.
| | - Yiming Wang
- Department of Psychiatry, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, China
| | - Wenxiu Yang
- Department of Pathology, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, PR China.
| | - Zhizhong Guan
- Department of Pathology, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, PR China; Department of Molecular Biology, Guizhou Medical University, Guiyang, Guizhou 550004, PR China.
| | - Wenfeng Yu
- Department of Molecular Biology, Guizhou Medical University, Guiyang, Guizhou 550004, PR China
| | - D Joshua Liao
- Department of Pathology, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, PR China; Department of Molecular Biology, Guizhou Medical University, Guiyang, Guizhou 550004, PR China.
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Yang Y, Tang Z, Fan X, Xu K, Mu Y, Zhou R, Li K. Transcriptome analysis revealed chimeric RNAs, single nucleotide polymorphisms and allele-specific expression in porcine prenatal skeletal muscle. Sci Rep 2016; 6:29039. [PMID: 27352850 PMCID: PMC4926253 DOI: 10.1038/srep29039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 06/14/2016] [Indexed: 01/28/2023] Open
Abstract
Prenatal skeletal muscle development genetically determines postnatal muscle characteristics such as growth and meat quality in pigs. However, the molecular mechanisms underlying prenatal skeletal muscle development remain unclear. Here, we performed the first genome-wide analysis of chimeric RNAs, single nuclear polymorphisms (SNPs) and allele-specific expression (ASE) in prenatal skeletal muscle in pigs. We identified 14,810 protein coding genes and 163 high-confidence chimeric RNAs expressed in prenatal skeletal muscle. More than 94.5% of the chimeric RNAs obeyed the canonical GT/AG splice rule and were trans-splicing events. Ten and two RNAs were aligned to human and mouse chimeric transcripts, respectively. We detected 106,457 high-quality SNPs (6,955 novel), which were mostly (89.09%) located within QTLs for production traits. The high proportion of non-exonic SNPs revealed the incomplete annotation status of the current swine reference genome. ASE analysis revealed that 11,300 heterozygous SNPs showed allelic imbalance, whereas 131 ASE variants were located in the chimeric RNAs. Moreover, 4 ASE variants were associated with various economically relevant traits of pigs. Taken together, our data provide a source for studies of chimeric RNAs and biomarkers for pig breeding, while illuminating the complex transcriptional events underlying prenatal skeletal muscle development in mammals.
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Affiliation(s)
- Yalan Yang
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, P.R.China
| | - Zhonglin Tang
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, P.R.China
| | - Xinhao Fan
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
| | - Kui Xu
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
| | - Yulian Mu
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
| | - Rong Zhou
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
| | - Kui Li
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, P.R.China
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20
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Wang L, Yang SY, Guo MY, Huang YN, Sentenac H, Véry AA, Su YH. The S1-S2 linker determines the distinct pH sensitivity between ZmK2.1 and KAT1. Plant J 2016; 85:675-85. [PMID: 26846460 DOI: 10.1111/tpj.13134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 10/29/2015] [Revised: 01/19/2016] [Accepted: 01/25/2016] [Indexed: 05/12/2023]
Abstract
Efficient stomatal opening requires activation of KAT-type K(+) channels, which mediate K(+) influx into guard cells. Most KAT-type channels are functionally facilitated by extracellular acidification. However, despite sequence and structural homologies, the maize counterpart of Arabidopsis KAT1 (ZmK2.1) is resistant to pH activation. To understand the structural determinant that results in the differential pH activation of these counterparts, we analysed chimeric channels and channels with point mutations for ZmK2.1 and its closest Arabidopsis homologue KAT1. Exchange of the S1-S2 linkers altered the pH sensitivity between the two channels, suggesting that the S1-S2 linker is essentially involved in the pH sensitivity. The effects of D92 mutation within the linker motif together with substitution of the first half of the linker largely resemble the effects of substitution of the complete linker. Topological modelling predicts that one of the two cysteines located on the outer face section of the S5 domain may serve as a potential titratable group that interacts with the S1-S2 linker. The difference between ZmK2.1 and KAT1 is predicted to be the result of the distance of the stabilized linkers from the titratable group. In KAT1, residue K85 within the linker forms a hydrogen bond with C211 that enables the pH activation; conversely, the linker of ZmK2.1 is distantly located and thus does not interact with the equivalent titration group (C208). Thus, in addition to the known structural contributors to the proton activation of KAT channels, we have uncovered a previously unidentified component that is strongly involved in this complex proton activation network.
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Affiliation(s)
- Li Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shun-Ying Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Man-Yuan Guo
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ya-Nan Huang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hervé Sentenac
- Biochimie & Physiologie Moléculaire des Plantes, UMR 5004, CNRS/386 INRA/SupAgro Montpellier/Université Montpellier, 34060, Montpellier Cedex 2, France
| | - Anne-Aliénor Véry
- Biochimie & Physiologie Moléculaire des Plantes, UMR 5004, CNRS/386 INRA/SupAgro Montpellier/Université Montpellier, 34060, Montpellier Cedex 2, France
| | - Yan-Hua Su
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
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Fouquier J, Rideout JR, Bolyen E, Chase J, Shiffer A, McDonald D, Knight R, Caporaso JG, Kelley ST. Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses. Microbiome 2016; 4:11. [PMID: 26905735 PMCID: PMC4765138 DOI: 10.1186/s40168-016-0153-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 02/05/2016] [Indexed: 05/11/2023]
Abstract
BACKGROUND Fungi play critical roles in many ecosystems, cause serious diseases in plants and animals, and pose significant threats to human health and structural integrity problems in built environments. While most fungal diversity remains unknown, the development of PCR primers for the internal transcribed spacer (ITS) combined with next-generation sequencing has substantially improved our ability to profile fungal microbial diversity. Although the high sequence variability in the ITS region facilitates more accurate species identification, it also makes multiple sequence alignment and phylogenetic analysis unreliable across evolutionarily distant fungi because the sequences are hard to align accurately. To address this issue, we created ghost-tree, a bioinformatics tool that integrates sequence data from two genetic markers into a single phylogenetic tree that can be used for diversity analyses. Our approach starts with a "foundation" phylogeny based on one genetic marker whose sequences can be aligned across organisms spanning divergent taxonomic groups (e.g., fungal families). Then, "extension" phylogenies are built for more closely related organisms (e.g., fungal species or strains) using a second more rapidly evolving genetic marker. These smaller phylogenies are then grafted onto the foundation tree by mapping taxonomic names such that each corresponding foundation-tree tip would branch into its new "extension tree" child. RESULTS We applied ghost-tree to graft fungal extension phylogenies derived from ITS sequences onto a foundation phylogeny derived from fungal 18S sequences. Our analysis of simulated and real fungal ITS data sets found that phylogenetic distances between fungal communities computed using ghost-tree phylogenies explained significantly more variance than non-phylogenetic distances. The phylogenetic metrics also improved our ability to distinguish small differences (effect sizes) between microbial communities, though results were similar to non-phylogenetic methods for larger effect sizes. CONCLUSIONS The Silva/UNITE-based ghost tree presented here can be easily integrated into existing fungal analysis pipelines to enhance the resolution of fungal community differences and improve understanding of these communities in built environments. The ghost-tree software package can also be used to develop phylogenetic trees for other marker gene sets that afford different taxonomic resolution, or for bridging genome trees with amplicon trees. AVAILABILITY ghost-tree is pip-installable. All source code, documentation, and test code are available under the BSD license at https://github.com/JTFouquier/ghost-tree .
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Affiliation(s)
- Jennifer Fouquier
- Graduate Program in Bioinformatics and Medical Informatics, San Diego State University, San Diego, CA, USA.
| | - Jai Ram Rideout
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA.
| | - Evan Bolyen
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA.
| | - John Chase
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA.
| | - Arron Shiffer
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA.
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
| | | | - Rob Knight
- Department of Pediatrics, and Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA.
| | - J Gregory Caporaso
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA.
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
| | - Scott T Kelley
- Graduate Program in Bioinformatics and Medical Informatics, San Diego State University, San Diego, CA, USA.
- Department of Biology, San Diego State University, San Diego, CA, USA.
- San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182-4614, USA.
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Abstract
Using a case study of a 57-year-old man with relapsed/refractory precursor-B (pre-B) acute lymphoblastic leukemia (ALL), this review discusses treatment with immunoconjugates and autologous therapy in acute ALL. Three therapies--blinatumomab, inotuzumab, and CAR T cells--are considered here, each with advantages in specific clinical situations. These therapies represent some of the exciting advances that have been made in the treatment of ALL over the last several years.
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Affiliation(s)
- Anjali Advani
- Inpatient Leukemia Unit, Cleveland Clinic, 9500 Euclid Avenue, R35, Cleveland, OH 44195, USA.
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Wan C, Li C, Ma X, Wang Y, Sun C, Huang R, Zhong P, Gao Z, Chen D, Xu Z, Zhu J, Gao X, Wang P, Deng X. GRY79 encoding a putative metallo-β-lactamase-trihelix chimera is involved in chloroplast development at early seedling stage of rice. Plant Cell Rep 2015; 34:1353-1363. [PMID: 25903544 DOI: 10.1007/s00299-015-1792-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 02/12/2015] [Accepted: 04/11/2015] [Indexed: 06/04/2023]
Abstract
The green - revertible yellow79 mutant resulting from a single-base mutation suggested that the GRY79 gene encoding a putative metallo-β-lactamase-trihelix chimera is involved in chloroplast development at early seedling stage of rice. Functional studies of metallo-β-lactamases and trihelix transcription factors in higher plants remain very sparse. In this study, we isolated the green-revertible yellow79 (gry79) mutant in rice. The mutant developed yellow-green leaves before the three-leaf stage but recovered to normal green at the sixth-leaf stage. Meanwhile, the mutant exhibited reduced level of chlorophylls and arrested development of chloroplasts in the yellow leaves. Genetic analysis suggested that the mutant phenotype was controlled by a single recessive nuclear gene on rice chromosome 2. Map-based cloning revealed that the candidate gene was Os02g33610 encoding a putative metallo-β-lactamase-trihelix chimera. In the gry79 mutant, a single-base mutation occurred in coding region of the gene, resulting in an amino acid change in the encoded protein. Furthermore, the mutant phenotype was rescued by transformation with the wild-type gene. Therefore, we have confirmed that the gry79 mutant phenotype resulted from a single-base mutation in GRY79 (Os02g33610) gene, suggesting that the gene encoding a putative metallo-β-lactamase-trihelix chimera is involved in chloroplast development at early seedling stage of rice. In addition, we considered that the gry79 mutant gene could be applicable as a leaf-color marker gene for efficient identification and elimination of false hybrids in commercial hybrid rice production.
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Affiliation(s)
- Chunmei Wan
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
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Markou A, Sertedaki A, Kaltsas G, Androulakis II, Marakaki C, Pappa T, Gouli A, Papanastasiou L, Fountoulakis S, Zacharoulis A, Karavidas A, Ragkou D, Charmandari E, Chrousos GP, Piaditis GP. Stress-induced Aldosterone Hyper-Secretion in a Substantial Subset of Patients With Essential Hypertension. J Clin Endocrinol Metab 2015; 100:2857-64. [PMID: 25974737 DOI: 10.1210/jc.2015-1268] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
CONTEXT Aldosterone (ALD) secretion is regulated mainly by angiotensin II, K(+), and adrenocorticotropic hormone (ACTH). Mineralocorticoid receptor antagonists (MRAs) have effectively been used for the treatment of patients with hypertension who do not have primary aldosteronism (PA). OBJECTIVE We tested whether chronic stress-related ACTH-mediated ALD hypersecretion and/or zona glomerulosa hypersensitivity could be implicated in the pathogenesis of essential hypertension (ESHT). PATIENTS AND METHODS One hundred thirteen hypertensives without PA and 61 normotensive controls underwent an ultralow-dose (0.03-μg) ACTH stimulation and a treadmill test. Patients with ALD hyper-response according to the cutoffs obtained from controls received treatment with MRAs and underwent genomic DNA testing for the presence of the CYP11B1/CYP11B2 chimeric gene and KCNJ5 gene mutations. A control group of 22 patients with simple ESHT received treatment with MRAs. RESULTS Based on the cutoffs of ALD and aldosterone-to-renin ratio (ARR) post-ACTH stimulation obtained from controls, 30 patients (27%) exhibited an ALD but not cortisol (F) hyper-response (HYPER group). This group had no difference in basal ACTH/renin (REN) concentrations compared with controls and the 83 patients with hypertension (73%) without an ALD hyper-response to ACTH stimulation. Patients in the HYPER group demonstrated significantly higher ALD concentrations, ARR, and ALD/ACTH ratio (AAR) in the treadmill test. Treatment with MRAs alone produced normalization of blood pressure in these patients whereas patients with hypertension with neither PA nor ALD hyper-response to ACTH stimulation who served as a control group failed to lower blood pressure. Also, two novel germline heterozygous KCNJ5 mutations were detected in the HYPER group. CONCLUSIONS A number of patients with hypertension without PA show ACTH-dependent ALD hyper-secretion and benefit from treatment with MRAs. This could be related to chronic stress via ACTH hyper secretion and/or gene-mutations increasing the zona glomerulosa responsiveness to excitatory stimuli.
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Affiliation(s)
- Athina Markou
- Department of Endocrinology and Diabetes Center (A.M., I.I.A., C.M. T.P., A.G., L.P., S.F., D.R., G.P.P.), G. Gennimatas General Hospital, Athens 11527, Greece; Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics (A.S., E.C., G.P.C.), University of Athens Medical School, Aghia Sophia Children's Hospital, Athens 11527, Greece; Department of Pathophysiology (G.K.), University of Athens Medical School, Laikon Hospital, Athens 11527, Greece; and Department of Cardiology (A.Z., A.K.), G. Gennimatas General Hospital, Athens 11527, Greece
| | - Amalia Sertedaki
- Department of Endocrinology and Diabetes Center (A.M., I.I.A., C.M. T.P., A.G., L.P., S.F., D.R., G.P.P.), G. Gennimatas General Hospital, Athens 11527, Greece; Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics (A.S., E.C., G.P.C.), University of Athens Medical School, Aghia Sophia Children's Hospital, Athens 11527, Greece; Department of Pathophysiology (G.K.), University of Athens Medical School, Laikon Hospital, Athens 11527, Greece; and Department of Cardiology (A.Z., A.K.), G. Gennimatas General Hospital, Athens 11527, Greece
| | - Gregory Kaltsas
- Department of Endocrinology and Diabetes Center (A.M., I.I.A., C.M. T.P., A.G., L.P., S.F., D.R., G.P.P.), G. Gennimatas General Hospital, Athens 11527, Greece; Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics (A.S., E.C., G.P.C.), University of Athens Medical School, Aghia Sophia Children's Hospital, Athens 11527, Greece; Department of Pathophysiology (G.K.), University of Athens Medical School, Laikon Hospital, Athens 11527, Greece; and Department of Cardiology (A.Z., A.K.), G. Gennimatas General Hospital, Athens 11527, Greece
| | - Ioannis I Androulakis
- Department of Endocrinology and Diabetes Center (A.M., I.I.A., C.M. T.P., A.G., L.P., S.F., D.R., G.P.P.), G. Gennimatas General Hospital, Athens 11527, Greece; Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics (A.S., E.C., G.P.C.), University of Athens Medical School, Aghia Sophia Children's Hospital, Athens 11527, Greece; Department of Pathophysiology (G.K.), University of Athens Medical School, Laikon Hospital, Athens 11527, Greece; and Department of Cardiology (A.Z., A.K.), G. Gennimatas General Hospital, Athens 11527, Greece
| | - Chrisanthi Marakaki
- Department of Endocrinology and Diabetes Center (A.M., I.I.A., C.M. T.P., A.G., L.P., S.F., D.R., G.P.P.), G. Gennimatas General Hospital, Athens 11527, Greece; Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics (A.S., E.C., G.P.C.), University of Athens Medical School, Aghia Sophia Children's Hospital, Athens 11527, Greece; Department of Pathophysiology (G.K.), University of Athens Medical School, Laikon Hospital, Athens 11527, Greece; and Department of Cardiology (A.Z., A.K.), G. Gennimatas General Hospital, Athens 11527, Greece
| | - Theodora Pappa
- Department of Endocrinology and Diabetes Center (A.M., I.I.A., C.M. T.P., A.G., L.P., S.F., D.R., G.P.P.), G. Gennimatas General Hospital, Athens 11527, Greece; Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics (A.S., E.C., G.P.C.), University of Athens Medical School, Aghia Sophia Children's Hospital, Athens 11527, Greece; Department of Pathophysiology (G.K.), University of Athens Medical School, Laikon Hospital, Athens 11527, Greece; and Department of Cardiology (A.Z., A.K.), G. Gennimatas General Hospital, Athens 11527, Greece
| | - Aggeliki Gouli
- Department of Endocrinology and Diabetes Center (A.M., I.I.A., C.M. T.P., A.G., L.P., S.F., D.R., G.P.P.), G. Gennimatas General Hospital, Athens 11527, Greece; Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics (A.S., E.C., G.P.C.), University of Athens Medical School, Aghia Sophia Children's Hospital, Athens 11527, Greece; Department of Pathophysiology (G.K.), University of Athens Medical School, Laikon Hospital, Athens 11527, Greece; and Department of Cardiology (A.Z., A.K.), G. Gennimatas General Hospital, Athens 11527, Greece
| | - Labrini Papanastasiou
- Department of Endocrinology and Diabetes Center (A.M., I.I.A., C.M. T.P., A.G., L.P., S.F., D.R., G.P.P.), G. Gennimatas General Hospital, Athens 11527, Greece; Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics (A.S., E.C., G.P.C.), University of Athens Medical School, Aghia Sophia Children's Hospital, Athens 11527, Greece; Department of Pathophysiology (G.K.), University of Athens Medical School, Laikon Hospital, Athens 11527, Greece; and Department of Cardiology (A.Z., A.K.), G. Gennimatas General Hospital, Athens 11527, Greece
| | - Stelios Fountoulakis
- Department of Endocrinology and Diabetes Center (A.M., I.I.A., C.M. T.P., A.G., L.P., S.F., D.R., G.P.P.), G. Gennimatas General Hospital, Athens 11527, Greece; Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics (A.S., E.C., G.P.C.), University of Athens Medical School, Aghia Sophia Children's Hospital, Athens 11527, Greece; Department of Pathophysiology (G.K.), University of Athens Medical School, Laikon Hospital, Athens 11527, Greece; and Department of Cardiology (A.Z., A.K.), G. Gennimatas General Hospital, Athens 11527, Greece
| | - Achilles Zacharoulis
- Department of Endocrinology and Diabetes Center (A.M., I.I.A., C.M. T.P., A.G., L.P., S.F., D.R., G.P.P.), G. Gennimatas General Hospital, Athens 11527, Greece; Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics (A.S., E.C., G.P.C.), University of Athens Medical School, Aghia Sophia Children's Hospital, Athens 11527, Greece; Department of Pathophysiology (G.K.), University of Athens Medical School, Laikon Hospital, Athens 11527, Greece; and Department of Cardiology (A.Z., A.K.), G. Gennimatas General Hospital, Athens 11527, Greece
| | - Apostolos Karavidas
- Department of Endocrinology and Diabetes Center (A.M., I.I.A., C.M. T.P., A.G., L.P., S.F., D.R., G.P.P.), G. Gennimatas General Hospital, Athens 11527, Greece; Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics (A.S., E.C., G.P.C.), University of Athens Medical School, Aghia Sophia Children's Hospital, Athens 11527, Greece; Department of Pathophysiology (G.K.), University of Athens Medical School, Laikon Hospital, Athens 11527, Greece; and Department of Cardiology (A.Z., A.K.), G. Gennimatas General Hospital, Athens 11527, Greece
| | - Despoina Ragkou
- Department of Endocrinology and Diabetes Center (A.M., I.I.A., C.M. T.P., A.G., L.P., S.F., D.R., G.P.P.), G. Gennimatas General Hospital, Athens 11527, Greece; Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics (A.S., E.C., G.P.C.), University of Athens Medical School, Aghia Sophia Children's Hospital, Athens 11527, Greece; Department of Pathophysiology (G.K.), University of Athens Medical School, Laikon Hospital, Athens 11527, Greece; and Department of Cardiology (A.Z., A.K.), G. Gennimatas General Hospital, Athens 11527, Greece
| | - Evangelia Charmandari
- Department of Endocrinology and Diabetes Center (A.M., I.I.A., C.M. T.P., A.G., L.P., S.F., D.R., G.P.P.), G. Gennimatas General Hospital, Athens 11527, Greece; Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics (A.S., E.C., G.P.C.), University of Athens Medical School, Aghia Sophia Children's Hospital, Athens 11527, Greece; Department of Pathophysiology (G.K.), University of Athens Medical School, Laikon Hospital, Athens 11527, Greece; and Department of Cardiology (A.Z., A.K.), G. Gennimatas General Hospital, Athens 11527, Greece
| | - George P Chrousos
- Department of Endocrinology and Diabetes Center (A.M., I.I.A., C.M. T.P., A.G., L.P., S.F., D.R., G.P.P.), G. Gennimatas General Hospital, Athens 11527, Greece; Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics (A.S., E.C., G.P.C.), University of Athens Medical School, Aghia Sophia Children's Hospital, Athens 11527, Greece; Department of Pathophysiology (G.K.), University of Athens Medical School, Laikon Hospital, Athens 11527, Greece; and Department of Cardiology (A.Z., A.K.), G. Gennimatas General Hospital, Athens 11527, Greece
| | - George P Piaditis
- Department of Endocrinology and Diabetes Center (A.M., I.I.A., C.M. T.P., A.G., L.P., S.F., D.R., G.P.P.), G. Gennimatas General Hospital, Athens 11527, Greece; Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics (A.S., E.C., G.P.C.), University of Athens Medical School, Aghia Sophia Children's Hospital, Athens 11527, Greece; Department of Pathophysiology (G.K.), University of Athens Medical School, Laikon Hospital, Athens 11527, Greece; and Department of Cardiology (A.Z., A.K.), G. Gennimatas General Hospital, Athens 11527, Greece
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Qin Y, Guo T, Li G, Tang TS, Zhao S, Jiao X, Gong J, Gao F, Guo C, Simpson JL, Chen ZJ. CSB-PGBD3 Mutations Cause Premature Ovarian Failure. PLoS Genet 2015. [PMID: 26218421 PMCID: PMC4517778 DOI: 10.1371/journal.pgen.1005419] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Premature ovarian failure (POF) is a rare, heterogeneous disorder characterized by cessation of menstruation occurring before the age of 40 years. Genetic etiology is responsible for perhaps 25% of cases, but most cases are sporadic and unexplained. In this study, through whole exome sequencing in a non-consanguineous family having four affected members with POF and Sanger sequencing in 432 sporadic cases, we identified three novel mutations in the fusion gene CSB-PGBD3. Subsequently functional studies suggest that mutated CSB-PGBD3 fusion protein was impaired in response to DNA damage, as indicated by delayed or absent recruitment to damaged sites. Our data provide the first evidence that mutations in the CSB-PGBD3 fusion protein can cause human disease, even in the presence of functional CSB, thus potentially explaining conservation of the fusion protein for 43 My since marmoset. The localization of the CSB-PGBD3 fusion protein to UVA-induced nuclear DNA repair foci further suggests that the CSB-PGBD3 fusion protein, like many other proteins that can cause POF, modulates or participates in DNA repair.
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Affiliation(s)
- Yingying Qin
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, China
- * E-mail: (YQ); (ZJC)
| | - Ting Guo
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, China
| | - Guangyu Li
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, China
| | - Tie-Shan Tang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shidou Zhao
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, China
| | - Xue Jiao
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, China
| | - Juanjuan Gong
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fei Gao
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Caixia Guo
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Joe Leigh Simpson
- Research and Global Programs March of Dimes Foundation, White Plains, New York, United States of America
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, China
- Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- * E-mail: (YQ); (ZJC)
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26
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Crescenzo R, Abate F, Lasorsa E, Tabbo' F, Gaudiano M, Chiesa N, Di Giacomo F, Spaccarotella E, Barbarossa L, Ercole E, Todaro M, Boi M, Acquaviva A, Ficarra E, Novero D, Rinaldi A, Tousseyn T, Rosenwald A, Kenner L, Cerroni L, Tzankov A, Ponzoni M, Paulli M, Weisenburger D, Chan WC, Iqbal J, Piris MA, Zamo' A, Ciardullo C, Rossi D, Gaidano G, Pileri S, Tiacci E, Falini B, Shultz LD, Mevellec L, Vialard JE, Piva R, Bertoni F, Rabadan R, Inghirami G. Convergent mutations and kinase fusions lead to oncogenic STAT3 activation in anaplastic large cell lymphoma. Cancer Cell 2015; 27:516-32. [PMID: 25873174 PMCID: PMC5898430 DOI: 10.1016/j.ccell.2015.03.006] [Citation(s) in RCA: 326] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 11/14/2014] [Accepted: 03/10/2015] [Indexed: 01/01/2023]
Abstract
A systematic characterization of the genetic alterations driving ALCLs has not been performed. By integrating massive sequencing strategies, we provide a comprehensive characterization of driver genetic alterations (somatic point mutations, copy number alterations, and gene fusions) in ALK(-) ALCLs. We identified activating mutations of JAK1 and/or STAT3 genes in ∼20% of 88 [corrected] ALK(-) ALCLs and demonstrated that 38% of systemic ALK(-) ALCLs displayed double lesions. Recurrent chimeras combining a transcription factor (NFkB2 or NCOR2) with a tyrosine kinase (ROS1 or TYK2) were also discovered in WT JAK1/STAT3 ALK(-) ALCL. All these aberrations lead to the constitutive activation of the JAK/STAT3 pathway, which was proved oncogenic. Consistently, JAK/STAT3 pathway inhibition impaired cell growth in vitro and in vivo.
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Affiliation(s)
- Ramona Crescenzo
- Department of Molecular Biotechnology and Health Science and Center for Experimental Research and Medical Studies, University of Torino, 10126 Torino, Italy; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Francesco Abate
- Department of Molecular Biotechnology and Health Science and Center for Experimental Research and Medical Studies, University of Torino, 10126 Torino, Italy; Department of Control and Computer Engineering, Politecnico di Torino, 10129 Torino, Italy; Department of Biomedical Informatics and Department of Systems Biology, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10027, USA
| | - Elena Lasorsa
- Department of Molecular Biotechnology and Health Science and Center for Experimental Research and Medical Studies, University of Torino, 10126 Torino, Italy
| | - Fabrizio Tabbo'
- Department of Molecular Biotechnology and Health Science and Center for Experimental Research and Medical Studies, University of Torino, 10126 Torino, Italy; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Marcello Gaudiano
- Department of Molecular Biotechnology and Health Science and Center for Experimental Research and Medical Studies, University of Torino, 10126 Torino, Italy; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Nicoletta Chiesa
- Department of Molecular Biotechnology and Health Science and Center for Experimental Research and Medical Studies, University of Torino, 10126 Torino, Italy
| | - Filomena Di Giacomo
- Department of Molecular Biotechnology and Health Science and Center for Experimental Research and Medical Studies, University of Torino, 10126 Torino, Italy
| | - Elisa Spaccarotella
- Department of Molecular Biotechnology and Health Science and Center for Experimental Research and Medical Studies, University of Torino, 10126 Torino, Italy
| | - Luigi Barbarossa
- Department of Molecular Biotechnology and Health Science and Center for Experimental Research and Medical Studies, University of Torino, 10126 Torino, Italy
| | - Elisabetta Ercole
- Department of Molecular Biotechnology and Health Science and Center for Experimental Research and Medical Studies, University of Torino, 10126 Torino, Italy
| | - Maria Todaro
- Department of Molecular Biotechnology and Health Science and Center for Experimental Research and Medical Studies, University of Torino, 10126 Torino, Italy; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Michela Boi
- Department of Molecular Biotechnology and Health Science and Center for Experimental Research and Medical Studies, University of Torino, 10126 Torino, Italy; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Andrea Acquaviva
- Department of Control and Computer Engineering, Politecnico di Torino, 10129 Torino, Italy
| | - Elisa Ficarra
- Department of Control and Computer Engineering, Politecnico di Torino, 10129 Torino, Italy
| | - Domenico Novero
- Department of Pathology, A.O. Città della Salute e della Scienza (Molinette), 10126 Torino, Italy
| | - Andrea Rinaldi
- Lymphoma and Genomics Research Program, Institute of Oncology Research, 6500 Bellinzona, Switzerland
| | - Thomas Tousseyn
- Translational Cell and Tissue Research Lab, KU Leuven, 3000 Leuven, Belgium
| | - Andreas Rosenwald
- Institute of Pathology, University of Würzburg and Comprehensive Cancer Center Mainfranken, 97080 Würzburg, Germany
| | - Lukas Kenner
- Ludwing Boltzmann Institute for Cancer Research, 1090 Vienna, Austria
| | - Lorenzo Cerroni
- Research Unit Dermatopathology of the Medical University of Graz, 8036 Graz, Austria
| | - Alexander Tzankov
- Institute of Pathology, University Hospital Basel, 4031 Basel, Switzerland
| | - Maurilio Ponzoni
- Pathology & Lymphoid Malignancies Units, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Marco Paulli
- Department of Human Pathology, University of Pavia and Scientific Institute Fondazione Policlinico San Matteo, 27100 Pavia, Italy
| | | | - Wing C Chan
- Department of Pathology, City of Hope Medical Center, Duarte, CA 91010, USA
| | - Javeed Iqbal
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Miguel A Piris
- Cancer Genomics, Instituto de Formación e Investigación Marqués de Valdecilla and Department of Pathology, Hospital Universitario Marqués de Valdecilla, 39008 Santander, Spain
| | - Alberto Zamo'
- Department of Pathology and Diagnostics, University of Verona, 37134 Verona, Italy
| | - Carmela Ciardullo
- Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, 28100 Novara, Italy
| | - Davide Rossi
- Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, 28100 Novara, Italy
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, 28100 Novara, Italy
| | - Stefano Pileri
- European Institute of Oncology, 20141 Milano, Italy; Bologna University School of Medicine, 40126 Bologna, Italy
| | - Enrico Tiacci
- Institute of Hematology-Centro di Ricerche Onco-Ematologiche (CREO), Ospedale S. Maria della Misericordia, University of Perugia, 06100 Perugia, Italy
| | - Brunangelo Falini
- Institute of Hematology-Centro di Ricerche Onco-Ematologiche (CREO), Ospedale S. Maria della Misericordia, University of Perugia, 06100 Perugia, Italy
| | | | - Laurence Mevellec
- Janssen Research & Development, a Division of Janssen-Cilag, Campus de Maigremont, CS10615, 27106 Val-de-Reuil Cedex, France
| | - Jorge E Vialard
- Janssen Research & Development, a Division of Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Roberto Piva
- Department of Molecular Biotechnology and Health Science and Center for Experimental Research and Medical Studies, University of Torino, 10126 Torino, Italy; Department of Pathology and NYU Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Francesco Bertoni
- Lymphoma and Genomics Research Program, Institute of Oncology Research, 6500 Bellinzona, Switzerland; Oncology Institute of Southern Switzerland, 6500 Bellinzona, Switzerland
| | - Raul Rabadan
- Department of Biomedical Informatics and Department of Systems Biology, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10027, USA.
| | - Giorgio Inghirami
- Department of Molecular Biotechnology and Health Science and Center for Experimental Research and Medical Studies, University of Torino, 10126 Torino, Italy; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10021, USA; Department of Pathology and NYU Cancer Center, New York University School of Medicine, New York, NY 10016, USA.
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27
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Hwang S, Shin DY, Song MK, Lee EJ. High cut-off value of a chimeric TSH receptor (Mc4)-based bioassay may improve prediction of relapse in Graves' disease for 12 months. Endocrine 2015; 48:89-95. [PMID: 24968734 DOI: 10.1007/s12020-014-0325-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 06/02/2014] [Indexed: 10/25/2022]
Abstract
There are scarce reports regarding a functional prognostic value of thyroid-stimulating autoantibody (TSAb) levels using a thyroid-stimulating hormone receptor chimera (Mc4) in Graves' disease (GD) in iodine sufficient area. The aim of this study was to investigate whether Mc4-TSAb can predict GD remission/relapse after antithyroid drug (ATD) treatment and to compare Mc4-TSAb with a binding assay using M22 monoclonal antibody (M22-TRAb) in GD patients. We retrospectively reviewed the results of M22-TRAb and Mc4-TSAb in GD patients treated with ATD for 12 months. GD patients who underwent ATD treatment for at least 12 months were included. We compared the predictive values of M22-TRAb and Mc4-TSAb for GD remission and relapse. Of the 92 patients, 60 (65.2%) achieved remission and 32 (34.8%) relapsed within 12 months. In receiver operating characteristic analysis, there were no significant differences in the area under the curves (AUCs) between Mc4-TSAb [AUC=0.79 (95% CI 0.69-0.89)] and M22-TRAb [AUC=0.69 (95% CI 0.58-0.81)]. The optimal predictive cut-off values of M22-TRAb and Mc4-TSAb were 2.23 IU/L and 230%, respectively. At a high Mc4-TSAb cut-off, the better specificity of 85.0% and positive predictive value (PPV) of 69.0% were shown compared with those at the best cut-off for M22-TRAb. In conclusion, a high cut-off for an Mc4 assay may improve the predictive value of relapse with superior specificity and PPV compared with M22-TRAb in treated GD.
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Affiliation(s)
- Sena Hwang
- Division of Endocrinology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, 120-752, Republic of Korea
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28
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Lenzini L, Rossi GP. The molecular basis of primary aldosteronism: from chimeric gene to channelopathy. Curr Opin Pharmacol 2014; 21:35-42. [PMID: 25555247 DOI: 10.1016/j.coph.2014.12.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/01/2014] [Accepted: 12/05/2014] [Indexed: 11/19/2022]
Abstract
Primary aldosteronism (PA) is the most common endocrine cause of high blood pressure. Only a minority of the PA cases are familial and due to known (CYP11B2/CYP11B1 chimeric gene or mutations in the KCNJ5 gene) or unknown causes. In the most common sporadic cases the mechanisms by which the excess aldosterone production persists in spite of high blood pressure, sodium retention, suppression of the renin angiotensin system and low potassium levels, all factors that by themselves would be expected to shut off aldosterone production, were a puzzle for decades. Only recently the discovery of functional mutations and down-regulation of potassium channels provided some explanations. We herein reviewed these recent findings and their mechanistic implications. We also propose a clinical molecular classification of familial hyperaldosteronism, which can be important from the practical standpoint as it considers besides the molecular features also the responsiveness to treatment and the imaging features.
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Affiliation(s)
- Livia Lenzini
- Dept. of Medicine-DIMED, Internal Medicine 4, University of Padova, Italy
| | - Gian Paolo Rossi
- Dept. of Medicine-DIMED, Internal Medicine 4, University of Padova, Italy.
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29
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Pyana Pati P, Van Reet N, Mumba Ngoyi D, Ngay Lukusa I, Karhemere Bin Shamamba S, Büscher P. Melarsoprol sensitivity profile of Trypanosoma brucei gambiense isolates from cured and relapsed sleeping sickness patients from the Democratic Republic of the Congo. PLoS Negl Trop Dis 2014; 8:e3212. [PMID: 25275572 PMCID: PMC4183442 DOI: 10.1371/journal.pntd.0003212] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 08/25/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Sleeping sickness caused by Trypanosoma brucei (T.b.) gambiense constitutes a serious health problem in sub-Sahara Africa. In some foci, alarmingly high relapse rates were observed in patients treated with melarsoprol, which used to be the first line treatment for patients in the neurological disease stage. Particularly problematic was the situation in Mbuji-Mayi, East Kasai Province in the Democratic Republic of the Congo with a 57% relapse rate compared to a 5% relapse rate in Masi-Manimba, Bandundu Province. The present study aimed at investigating the mechanisms underlying the high relapse rate in Mbuji-Mayi using an extended collection of recently isolated T.b. gambiense strains from Mbuji-Mayi and from Masi-Manimba. METHODOLOGY/PRINCIPAL FINDINGS Forty five T.b. gambiense strains were used. Forty one were isolated from patients that were cured or relapsed after melarsoprol treatment in Mbuji-Mayi. In vivo drug sensitivity tests provide evidence of reduced melarsoprol sensitivity in these strains. This reduced melarsoprol sensitivity was not attributable to mutations in TbAT1. However, in all these strains, irrespective of the patient treatment outcome, the two aquaglyceroporin (AQP) 2 and 3 genes are replaced by chimeric AQP2/3 genes that may be associated with resistance to pentamidine and melarsoprol. The 4 T.b. gambiense strains isolated in Masi-Manimba contain both wild-type AQP2 and a different chimeric AQP2/3. These findings suggest that the reduced in vivo melarsoprol sensitivity of the Mbuji-Mayi strains and the high relapse rates in that sleeping sickness focus are caused by mutations in the AQP2/AQP3 locus and not by mutations in TbAT1. CONCLUSIONS/SIGNIFICANCE We conclude that mutations in the TbAQP2/3 locus of the local T.b. gambiense strains may explain the high melarsoprol relapse rates in the Mbuji-Mayi focus but other factors must also be involved in the treatment outcome of individual patients.
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Affiliation(s)
- Patient Pyana Pati
- Département de Parasitologie, Institut National de Recherche Biomédicale, Kinshasa Gombe, Democratic Republic of the Congo
- * E-mail:
| | - Nick Van Reet
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Dieudonné Mumba Ngoyi
- Département de Parasitologie, Institut National de Recherche Biomédicale, Kinshasa Gombe, Democratic Republic of the Congo
| | - Ipos Ngay Lukusa
- Département de Parasitologie, Institut National de Recherche Biomédicale, Kinshasa Gombe, Democratic Republic of the Congo
| | - Stomy Karhemere Bin Shamamba
- Département de Parasitologie, Institut National de Recherche Biomédicale, Kinshasa Gombe, Democratic Republic of the Congo
| | - Philippe Büscher
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
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30
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Crescenzo-Chaigne B, Barbezange C, Frigard V, Poulain D, van der Werf S. Chimeric NP non coding regions between type A and C influenza viruses reveal their role in translation regulation. PLoS One 2014; 9:e109046. [PMID: 25268971 PMCID: PMC4182659 DOI: 10.1371/journal.pone.0109046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 09/01/2014] [Indexed: 12/14/2022] Open
Abstract
Exchange of the non coding regions of the NP segment between type A and C influenza viruses was used to demonstrate the importance not only of the proximal panhandle, but also of the initial distal panhandle strength in type specificity. Both elements were found to be compulsory to rescue infectious virus by reverse genetics systems. Interestingly, in type A influenza virus infectious context, the length of the NP segment 5' NC region once transcribed into mRNA was found to impact its translation, and the level of produced NP protein consequently affected the level of viral genome replication.
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Affiliation(s)
- Bernadette Crescenzo-Chaigne
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, Paris, France
- Unité Mixte de Recherche 3569, Centre National de la Recherche Scientifique, Paris, France
| | - Cyril Barbezange
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, Paris, France
- Unité Mixte de Recherche 3569, Centre National de la Recherche Scientifique, Paris, France
| | - Vianney Frigard
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, Paris, France
- Unité Mixte de Recherche 3569, Centre National de la Recherche Scientifique, Paris, France
| | - Damien Poulain
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, Paris, France
- Unité Mixte de Recherche 3569, Centre National de la Recherche Scientifique, Paris, France
| | - Sylvie van der Werf
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, Paris, France
- Unité Mixte de Recherche 3569, Centre National de la Recherche Scientifique, Paris, France
- Université Paris Diderot Sorbonne Paris Cité, Paris, France
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Ng MCY, Shriner D, Chen BH, Li J, Chen WM, Guo X, Liu J, Bielinski SJ, Yanek LR, Nalls MA, Comeau ME, Rasmussen-Torvik LJ, Jensen RA, Evans DS, Sun YV, An P, Patel SR, Lu Y, Long J, Armstrong LL, Wagenknecht L, Yang L, Snively BM, Palmer ND, Mudgal P, Langefeld CD, Keene KL, Freedman BI, Mychaleckyj JC, Nayak U, Raffel LJ, Goodarzi MO, Chen YDI, Taylor HA, Correa A, Sims M, Couper D, Pankow JS, Boerwinkle E, Adeyemo A, Doumatey A, Chen G, Mathias RA, Vaidya D, Singleton AB, Zonderman AB, Igo RP, Sedor JR, Kabagambe EK, Siscovick DS, McKnight B, Rice K, Liu Y, Hsueh WC, Zhao W, Bielak LF, Kraja A, Province MA, Bottinger EP, Gottesman O, Cai Q, Zheng W, Blot WJ, Lowe WL, Pacheco JA, Crawford DC, Grundberg E, Rich SS, Hayes MG, Shu XO, Loos RJF, Borecki IB, Peyser PA, Cummings SR, Psaty BM, Fornage M, Iyengar SK, Evans MK, Becker DM, Kao WHL, Wilson JG, Rotter JI, Sale MM, Liu S, Rotimi CN, Bowden DW. Meta-analysis of genome-wide association studies in African Americans provides insights into the genetic architecture of type 2 diabetes. PLoS Genet 2014; 10:e1004517. [PMID: 25102180 PMCID: PMC4125087 DOI: 10.1371/journal.pgen.1004517] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 06/05/2014] [Indexed: 12/11/2022] Open
Abstract
Type 2 diabetes (T2D) is more prevalent in African Americans than in Europeans. However, little is known about the genetic risk in African Americans despite the recent identification of more than 70 T2D loci primarily by genome-wide association studies (GWAS) in individuals of European ancestry. In order to investigate the genetic architecture of T2D in African Americans, the MEta-analysis of type 2 DIabetes in African Americans (MEDIA) Consortium examined 17 GWAS on T2D comprising 8,284 cases and 15,543 controls in African Americans in stage 1 analysis. Single nucleotide polymorphisms (SNPs) association analysis was conducted in each study under the additive model after adjustment for age, sex, study site, and principal components. Meta-analysis of approximately 2.6 million genotyped and imputed SNPs in all studies was conducted using an inverse variance-weighted fixed effect model. Replications were performed to follow up 21 loci in up to 6,061 cases and 5,483 controls in African Americans, and 8,130 cases and 38,987 controls of European ancestry. We identified three known loci (TCF7L2, HMGA2 and KCNQ1) and two novel loci (HLA-B and INS-IGF2) at genome-wide significance (4.15×10−94<P<5×10−8, odds ratio (OR) = 1.09 to 1.36). Fine-mapping revealed that 88 of 158 previously identified T2D or glucose homeostasis loci demonstrated nominal to highly significant association (2.2×10−23 < locus-wide P<0.05). These novel and previously identified loci yielded a sibling relative risk of 1.19, explaining 17.5% of the phenotypic variance of T2D on the liability scale in African Americans. Overall, this study identified two novel susceptibility loci for T2D in African Americans. A substantial number of previously reported loci are transferable to African Americans after accounting for linkage disequilibrium, enabling fine mapping of causal variants in trans-ethnic meta-analysis studies. Despite the higher prevalence of type 2 diabetes (T2D) in African Americans than in Europeans, recent genome-wide association studies (GWAS) were examined primarily in individuals of European ancestry. In this study, we performed meta-analysis of 17 GWAS in 8,284 cases and 15,543 controls to explore the genetic architecture of T2D in African Americans. Following replication in additional 6,061 cases and 5,483 controls in African Americans, and 8,130 cases and 38,987 controls of European ancestry, we identified two novel and three previous reported T2D loci reaching genome-wide significance. We also examined 158 loci previously reported to be associated with T2D or regulating glucose homeostasis. While 56% of these loci were shared between African Americans and the other populations, the strongest associations in African Americans are often found in nearby single nucleotide polymorphisms (SNPs) instead of the original SNPs reported in other populations due to differential genetic architecture across populations. Our results highlight the importance of performing genetic studies in non-European populations to fine map the causal genetic variants.
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Affiliation(s)
- Maggie C. Y. Ng
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Brian H. Chen
- Program on Genomics and Nutrition, School of Public Health, University of California Los Angeles, Los Angeles, California, United States of America
- Center for Metabolic Disease Prevention, School of Public Health, University of California Los Angeles, Los Angeles, California, United States of America
| | - Jiang Li
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Wei-Min Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Jiankang Liu
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Suzette J. Bielinski
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Lisa R. Yanek
- The GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Michael A. Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mary E. Comeau
- Center for Public Health Genomics, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Laura J. Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Richard A. Jensen
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Daniel S. Evans
- San Francisco Coordinating Center, California Pacific Medical Center Research Institute, San Francisco, California, United States of America
| | - Yan V. Sun
- Department of Epidemiology and Biomedical Informatics, Emory University, Atlanta, Georgia, United States of America
| | - Ping An
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sanjay R. Patel
- Division of Sleep Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Yingchang Lu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Loren L. Armstrong
- Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Lynne Wagenknecht
- Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Lingyao Yang
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Beverly M. Snively
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Nicholette D. Palmer
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Poorva Mudgal
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Carl D. Langefeld
- Center for Public Health Genomics, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Keith L. Keene
- Department of Biology, Center for Health Disparities, East Carolina University, Greenville, North Carolina, United States of America
| | - Barry I. Freedman
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Josyf C. Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Uma Nayak
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Leslie J. Raffel
- Medical Genetics Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Mark O. Goodarzi
- Medical Genetics Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Y-D Ida Chen
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Herman A. Taylor
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
- Jackson State University, Tougaloo College, Jackson, Mississippi, United States of America
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Mario Sims
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - David Couper
- Collaborative Studies Coordinating Center, Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - James S. Pankow
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Ayo Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Rasika A. Mathias
- The GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Division of Allergy and Clinical Immunology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Dhananjay Vaidya
- The GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Andrew B. Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alan B. Zonderman
- Laboratory of Personality and Cognition, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Robert P. Igo
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - John R. Sedor
- Department of Medicine, Case Western Reserve University, MetroHealth System campus, Cleveland, Ohio, United States of America
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | | | - Edmond K. Kabagambe
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - David S. Siscovick
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Barbara McKnight
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Kenneth Rice
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Wen-Chi Hsueh
- Department of Medicine, University of California, San Francisco, California, United States of America
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lawrence F. Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Aldi Kraja
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Michael A. Province
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Erwin P. Bottinger
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Omri Gottesman
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - William J. Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee; International Epidemiology Institute, Rockville, Maryland, United States of America
| | - William L. Lowe
- Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Jennifer A. Pacheco
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Dana C. Crawford
- Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
| | | | | | - Elin Grundberg
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | | | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - M. Geoffrey Hayes
- Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Ingrid B. Borecki
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Patricia A. Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Steven R. Cummings
- San Francisco Coordinating Center, California Pacific Medical Center Research Institute, San Francisco, California, United States of America
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Health Services, University of Washington, Seattle, Washington, United States of America
| | - Myriam Fornage
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Sudha K. Iyengar
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Michele K. Evans
- Health Disparities Unit, National Institute on Aging, National Institutes of Health, Baltimore Maryland, United States of America
| | - Diane M. Becker
- The GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Health Policy and Management, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - W. H. Linda Kao
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Michèle M. Sale
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Simin Liu
- Program on Genomics and Nutrition, School of Public Health, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Epidemiology, University of California Los Angeles, Los Angeles, California, United States of America
- Departments of Epidemiology and Medicine, Brown University, Providence, Rhode Island, United States of America
- * E-mail: (SL); (CNR); (DWB)
| | - Charles N. Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
- * E-mail: (SL); (CNR); (DWB)
| | - Donald W. Bowden
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- * E-mail: (SL); (CNR); (DWB)
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Murashima K, Shimonaka A, Nishimura T, Baba Y, Koga J, Kubota H, Kono T. Exploring Amino Acids Responsible for the Temperature Profile of Glycoside Hydrolase Family 45 Endoglucanase EGL3 fromHumicola grisea. Biosci Biotechnol Biochem 2014; 70:2205-12. [PMID: 16960377 DOI: 10.1271/bbb.60149] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
EGL3 and RCE1 are glycoside hydrolase family 45 endoglucanases isolated from Humicola grisea and Rhizopus oryzae respectively. The amino acid sequences of the two endoglucanases are homologous; on the other hand, the optimum temperature of EGL3 is higher than that of RCE1. In this study, four chimeric endoglucanases, named ER1, ER2, ER3 and ER4, in which one of four sequential amino acid regions of the EGL3 catalytic domain (CAD) was replaced by the corresponding RCE1 amino acids, were constructed to explore the region responsible for the EGL3 temperature profile. Then their temperature profiles were compared with that of the recombinant EGL3. Replacement of the N-terminal region of EGL3 with that of RCE1 caused the EGL3 temperature profile to shift to a lower temperature. These results suggest that the N-terminal amino acids of the EGL3 are responsible for the EGL3 temperature profile.
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Affiliation(s)
- Koichiro Murashima
- Food and Health R & D Laboratories, Meiji Seika Kaisha, Ltd., Sakado-shi, Saitama, Japan.
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Labyntsev AJ, Kolybo DV, Yurchenko ES, Kaberniuk AA, Korotkevych NV, Komisarenko SV. Effect of the T-domain on intracellular transport of diphtheria toxin. Ukr Biochem J 2014; 86:77-87. [PMID: 25033557 DOI: 10.15407/ubj86.03.077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Subunit B of diphtheria toxin (DT), which consists of two domains: R (receptor-binding) and T (transmembrane), plays an important role in toxin-receptor binding on the cell-targets and in transportation of catalytic subunit A to the cell cytosol. Recombinant analogues of the subunit B are promising representatives in the unique class of transporting proteins, able to deliver different types of biologically active molecules to cell cytosol. In the development of these protein constructs understanding of the role of each of the DT fragments in determination of transporting pathways of endocytosed complex toxin-receptor is urgently required. We have studied in this work the T-domain effect on intracellular transport of recombinant fragments of DT. We have compared intracellular transport of the R-domain and the subunit B, the last one consisted of both R-domain and T-domain. Recombinant fragments of DT used in this work were labeled with fluorescent proteins, which allowed applying colocalization technique for our study. Application of confocal microscopy technique revealed differences in transportation of recombinant derivates of DT in Vero cells: R-domain moved faster than subunit B to tubular compartments. Analysis of R-domain and subunit B transportation confirmed almost linear increase of their colocalization with the time regarding to Pearsons correlation coefficient (PCC). However, amount of colocalized with R-domain subunit B were not linearly increased with time according to Manders coefficient (M1), this could indicate the ability of subunit B to transport to such compartments that R-domain do not reach. Possible role of the T-domain in intracellular transportation and compartmentalization of the toxin may be associated with the ability of the T-domain to form a proton channels and its ability to interact with COPI complex.
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Williams RT, Barnhill LM, Kuo HH, Lin WD, Batova A, Yu AL, Diccianni MB. Chimeras of p14ARF and p16: functional hybrids with the ability to arrest growth. PLoS One 2014; 9:e88219. [PMID: 24505435 PMCID: PMC3914946 DOI: 10.1371/journal.pone.0088219] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 01/03/2014] [Indexed: 01/23/2023] Open
Abstract
The INK4A locus codes for two independent tumor suppressors, p14ARF and p16/CDKN2A, and is frequently mutated in many cancers. Here we report a novel deletion/substitution from CC to T in the shared exon 2 of p14ARF/p16 in a melanoma cell line. This mutation aligns the reading frames of p14ARF and p16 mid-transcript, producing one protein which is half p14ARF and half p16, chimera ARF (chARF), and another which is half p16 and half non-p14ARF/non-p16 amino acids, p16-Alternate Carboxyl Terminal (p16-ACT). In an effort to understand the cellular impact of this novel mutation and others like it, we expressed the two protein products in a tumor cell line and analyzed common p14ARF and p16 pathways, including the p53/p21 and CDK4/cyclin D1 pathways, as well as the influence of the two proteins on growth and the cell cycle. We report that chARF mimicked wild-type p14ARF by inducing the p53/p21 pathway, inhibiting cell growth through G2/M arrest and maintaining a certain percentage of cells in G1 during nocodazole-induced G2 arrest. chARF also demonstrated p16 activity by binding CDK4. However, rather than preventing cyclin D1 from binding CDK4, chARF stabilized this interaction through p21 which bound CDK4. p16-ACT had no p16-related function as it was unable to inhibit cyclin D1/CDK4 complex formation and was unable to arrest the cell cycle, though it did inhibit colony formation. We conclude that these novel chimeric proteins, which are very similar to predicted p16/p14ARF chimeric proteins found in other primary cancers, result in maintained p14ARF-p53-p21 signaling while p16-dependent CDK4 inhibition is lost.
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Affiliation(s)
- Richard T. Williams
- Department of Pediatric Hematology/Oncology, University of California San Diego, San Diego, California, United States of America
| | - Lisa M. Barnhill
- Department of Pediatric Hematology/Oncology, University of California San Diego, San Diego, California, United States of America
| | - Huan-Hsien Kuo
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Wen-Der Lin
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Ayse Batova
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Alice L. Yu
- Department of Pediatric Hematology/Oncology, University of California San Diego, San Diego, California, United States of America
| | - Mitchell B. Diccianni
- Department of Pediatric Hematology/Oncology, University of California San Diego, San Diego, California, United States of America
- * E-mail:
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Dumina MV, Zhgun AA, Kerpichnikov IV, Domracheva AG, Novak MI, Valiakhmetov AI, Knorre DA, Severin FF, Él'darov MA, Bartoshevich IÉ. [Functional characteristic of the CefT transporter of the MFS family involved in the transportation of beta-lactam antibiotics in Acremonium chrysogenum and Saccharomyces cerevisiae]. ACTA ACUST UNITED AC 2014; 49:372-81. [PMID: 24455863 DOI: 10.7868/s0555109913040041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Vectors for the expression of the CefT transporter of the MFS family in Acremonium chrysogenum--a producer of beta-lactam antibiotic cephalosporin C--and in Saccharomyces cerevisiae as a fusion with the cyan fluorescent protein (CFP) have been created. The subcellular localization of the CefT-CFP hybrid protein in yeast cells has been investigated. It was shown that the CefT-CFP hybrid protein is capable of complementation of the qdr3, tpo 1, and tpo3 genes encoding for orthologous MFS transporters of Saccharomycetes, making the corresponding strains resistant to spermidine, ethidium bromide, and hygromycin B. High-yield strain VKM F-4081D of A. chrysogenum, expressing the cefT-cfp fusion, was obtained by an agrobacteria conjugated transfer. It was also shown that the constitutive expression of cefT in A. chrysogenum VKM F-4081D led to a change in the biosynthetic profiles of cephalosporin C and its precursors. This resulted in a 25-35% decrease in the finite product accumulated in the cultural liquid with a simultaneous increase in the concentration of its intermediators.
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Román-Ortiz E, Mendizabal Oteiza S, Pinto S, López-Trascasa M, Sánchez-Corral P, Rodríguez de Cordoba S. Eculizumab long-term therapy for pediatric renal transplant in aHUS with CFH/CFHR1 hybrid gene. Pediatr Nephrol 2014; 29:149-53. [PMID: 23982707 DOI: 10.1007/s00467-013-2591-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Revised: 07/17/2013] [Accepted: 07/25/2013] [Indexed: 12/12/2022]
Abstract
BACKGROUND Atypical hemolytic uremic syndrome (aHUS) is a form of thrombotic microangiopathy (TMA) caused by dysregulation of the complement system. Outcomes of kidney transplantation are poor owing to aHUS recurrence and loss of graft. Patients carrying CFH mutations or CFH/CFHR1 hybrid genes present a very high risk of recurrence despite preventive plasmapheresis. Evaluation of recent data suggests that prophylactic eculizumab pretransplant might be the preferred therapy if available. CASE-DIAGNOSIS/TREATMENT We report 3-year follow-up data in a 9-year-old boy with aHUS and successful renal transplant treated with prophylactic eculizumab without recurrence. He presented with aHUS at age 3, irreversible renal failure and uncontrolled severe hypertension with concentric left ventricular hypertrophy, recurrent acute pulmonary edema, and congestive heart failure despite five hypotensive agents and bilateral nephrectomy. Complement analysis demonstrated the presence of a CFH/CFHR1 hybrid gene inherited from his mother and a SNP risk CFH haplotype inherited from his father. Kidney transplant was performed with prophylactic eculizumab and subsequent fortnightly administration. Three years post-transplant, graft function remains stable (serum creatinine 0.9 mg/dl), hypertension is controlled, no left ventricular hypertrophy, no opportunistic infections, and negative clinical chemistry parameters for hemolysis. CONCLUSION Eculizumab is a safe and effective therapy for preventing TMA recurrence and provides long-term graft function in aHUS with the CFH/CFHR1 hybrid gene.
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Affiliation(s)
- Elena Román-Ortiz
- Pediatric Nephrology Unit, Hospital La Fe, Bulevar sur s/n, 46026, Valencia, Spain,
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Chen Q, Wiesener M, Eberhardt HU, Hartmann A, Uzonyi B, Kirschfink M, Amann K, Buettner M, Goodship T, Hugo C, Skerka C, Zipfel PF. Complement factor H-related hybrid protein deregulates complement in dense deposit disease. J Clin Invest 2013; 124:145-55. [PMID: 24334459 DOI: 10.1172/jci71866] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 10/07/2013] [Indexed: 12/16/2022] Open
Abstract
The renal disorder C3 glomerulopathy with dense deposit disease (C3G-DDD) pattern results from complement dysfunction and primarily affects children and young adults. There is no effective treatment, and patients often progress to end-stage renal failure. A small fraction of C3G-DDD cases linked to factor H or C3 gene mutations as well as autoantibodies have been reported. Here, we examined an index family with 2 patients with C3G-DDD and identified a chromosomal deletion in the complement factor H-related (CFHR) gene cluster. This deletion resulted in expression of a hybrid CFHR2-CFHR5 plasma protein. The recombinant hybrid protein stabilized the C3 convertase and reduced factor H-mediated convertase decay. One patient was refractory to plasma replacement and exchange therapy, as evidenced by the hybrid protein quickly returning to pretreatment plasma levels. Subsequently, complement inhibitors were tested on serum from the patient for their ability to block activity of CFHR2-CFHR5. Soluble CR1 restored defective C3 convertase regulation; however, neither eculizumab nor tagged compstatin had any effect. Our findings provide insight into the importance of CFHR proteins for C3 convertase regulation and identify a genetic variation in the CFHR gene cluster that promotes C3G-DDD. Monitoring copy number and sequence variations in the CFHR gene cluster in C3G-DDD and kidney patients with C3G-DDD variations will help guide treatment strategies.
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D'Argenio V, Frisso G, Precone V, Boccia A, Fienga A, Pacileo G, Limongelli G, Paolella G, Calabrò R, Salvatore F. DNA sequence capture and next-generation sequencing for the molecular diagnosis of genetic cardiomyopathies. J Mol Diagn 2013; 16:32-44. [PMID: 24183960 DOI: 10.1016/j.jmoldx.2013.07.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 07/03/2013] [Accepted: 07/30/2013] [Indexed: 12/15/2022] Open
Abstract
Hypertrophic cardiomyopathy is a relatively frequent disease with a prevalence of 0.2% worldwide and a remarkable genetic heterogeneity, with more than 30 causative genes reported to date. Current PCR-based strategies are inadequate for genomic investigations involving many candidate genes. Here, we report a next-generation sequencing procedure associated with DNA sequence capture that is able to sequence 202 cardiomyopathy-related genes simultaneously. We developed a complementary data analysis pipeline to select and prioritize genetic variants. The overall procedure can screen a large number of target genes simultaneously, thereby potentially revealing new disease-causing and modifier genes. By using this procedure, we analyzed hypertrophic cardiomyopathy patients in a shorter time and at a lower cost than with current procedures. The specificity of the next-generation sequencing-based procedure is at least as good as other techniques routinely used for mutation searching, and the sensitivity is much better. Analysis of the results showed some novel variants potentially involved in the pathogenesis of hypertrophic cardiomyopathy: a missense mutation in MYH7 and a nonsense variant in INS-IGF2 (patient 1), a splicing variant in MYBPC3 and an indel/frameshift variant in KCNQ1 (patient 2), and two concomitant variations in CACNA1C (patient 3). Sequencing of DNA from the three patients within a pool allowed detection of most variants identified in each individual patient, indicating that this approach is a feasible and cost-effective procedure.
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Affiliation(s)
- Valeria D'Argenio
- CEINGE-Biotecnologie Avanzate, Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Giulia Frisso
- CEINGE-Biotecnologie Avanzate, Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Vincenza Precone
- CEINGE-Biotecnologie Avanzate, Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | | | - Antonella Fienga
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Giuseppe Pacileo
- Cardiomyopathy and Inherited Heart Disease Clinic, UOC Cardiology, Second University of Naples, Naples, Italy
| | - Giuseppe Limongelli
- Cardiomyopathy and Inherited Heart Disease Clinic, UOC Cardiology, Second University of Naples, Naples, Italy
| | - Giovanni Paolella
- CEINGE-Biotecnologie Avanzate, Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Raffaele Calabrò
- Cardiomyopathy and Inherited Heart Disease Clinic, UOC Cardiology, Second University of Naples, Naples, Italy
| | - Francesco Salvatore
- CEINGE-Biotecnologie Avanzate, Naples, Italy; IRCCS-Fondazione SDN, Naples, Italy.
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Amer AAA, Costa TRD, Farag SI, Avican U, Forsberg Å, Francis MS. Genetically engineered frameshifted YopN-TyeA chimeras influence type III secretion system function in Yersinia pseudotuberculosis. PLoS One 2013; 8:e77767. [PMID: 24098594 PMCID: PMC3789692 DOI: 10.1371/journal.pone.0077767] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 09/05/2013] [Indexed: 12/29/2022] Open
Abstract
Type III secretion is a tightly controlled virulence mechanism utilized by many gram negative bacteria to colonize their eukaryotic hosts. To infect their host, human pathogenic Yersinia spp. translocate protein toxins into the host cell cytosol through a preassembled Ysc-Yop type III secretion device. Several of the Ysc-Yop components are known for their roles in controlling substrate secretion and translocation. Particularly important in this role is the YopN and TyeA heterodimer. In this study, we confirm that Y. pseudotuberculosis naturally produce a 42 kDa YopN-TyeA hybrid protein as a result of a +1 frame shift near the 3 prime of yopN mRNA, as has been previously reported for the closely related Y. pestis. To assess the biological role of this YopN-TyeA hybrid in T3SS by Y. pseudotuberculosis, we used in cis site-directed mutagenesis to engineer bacteria to either produce predominately the YopN-TyeA hybrid by introducing +1 frame shifts to yopN after codon 278 or 287, or to produce only singular YopN and TyeA polypeptides by introducing yopN sequence from Y. enterocolitica, which is known not to produce the hybrid. Significantly, the engineered 42 kDa YopN-TyeA fusions were abundantly produced, stable, and were efficiently secreted by bacteria in vitro. Moreover, these bacteria could all maintain functionally competent needle structures and controlled Yops secretion in vitro. In the presence of host cells however, bacteria producing the most genetically altered hybrids (+1 frameshift after 278 codon) had diminished control of polarized Yop translocation. This corresponded to significant attenuation in competitive survival assays in orally infected mice, although not at all to the same extent as Yersinia lacking both YopN and TyeA proteins. Based on these studies with engineered polypeptides, most likely a naturally occurring YopN-TyeA hybrid protein has the potential to influence T3S control and activity when produced during Yersinia-host cell contact.
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Affiliation(s)
- Ayad A. A. Amer
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Tiago R. D. Costa
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Salah I. Farag
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Ummehan Avican
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Åke Forsberg
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Matthew S. Francis
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
- * E-mail:
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Chang T, Alexopoulos H, Pettingill P, McMenamin M, Deacon R, Erdelyi F, Szabó G, Buckley CJ, Vincent A. Immunization against GAD induces antibody binding to GAD-independent antigens and brainstem GABAergic neuronal loss. PLoS One 2013; 8:e72921. [PMID: 24058450 PMCID: PMC3776810 DOI: 10.1371/journal.pone.0072921] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 07/15/2013] [Indexed: 11/18/2022] Open
Abstract
Stiff person syndrome (SPS) is a highly-disabling neurological disorder of the CNS characterized by progressive muscular rigidity and spasms. In approximately 60–80% of patients there are autoantibodies to glutamic acid decarboxylase (GAD), the enzyme that synthesizes gamma-amino butyric acid (GABA), the predominant inhibitory neurotransmitter of the CNS. Although GAD is intracellular, it is thought that autoimmunity to GAD65 may play a role in the development of SPS. To test this hypothesis, we immunized mice, that expressed enhanced green fluorescent protein (EGFP) under the GAD65 promoter, with either GAD65 (n = 13) or phosphate buffered saline (PBS) (n = 13). Immunization with GAD65 resulted in autoantibodies that immunoprecipitated GAD, bound to CNS tissue in a highly characteristic pattern, and surprisingly bound not only to GAD intracellularly but also to the surface of cerebellar neurons in culture. Moreover, immunization resulted in immunoglobulin diffusion into the brainstem, and a partial loss of GAD-EGFP expressing cells in the brainstem. Although immunization with GAD65 did not produce any behavioral abnormality in the mice, the induction of neuronal-surface antibodies and the trend towards loss of GABAergic neurons in the brainstem, supports a role for humoral autoimmunity in the pathogenesis of SPS and suggests that the mechanisms may involve spread to antigens expressed on the surface of these neurons.
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Affiliation(s)
- Thashi Chang
- Neuroimmunology Group, Weatherall Institute of Molecular Medicine and Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Department of Clinical Medicine, University of Colombo, Colombo, Sri Lanka
| | - Harry Alexopoulos
- Neuroimmunology Group, Weatherall Institute of Molecular Medicine and Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Philippa Pettingill
- Neuroimmunology Group, Weatherall Institute of Molecular Medicine and Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Mary McMenamin
- Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Robert Deacon
- Department of Experimental Psychology, University of Oxford, Oxford, United Kingdom
| | - Ferenc Erdelyi
- Department of Gene Technology and Developmental Neurobiology, Institute of Experimental Medicine, Budapest, Hungary
| | - Gabor Szabó
- Department of Gene Technology and Developmental Neurobiology, Institute of Experimental Medicine, Budapest, Hungary
| | - Camilla J. Buckley
- Neuroimmunology Group, Weatherall Institute of Molecular Medicine and Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Angela Vincent
- Neuroimmunology Group, Weatherall Institute of Molecular Medicine and Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- * E-mail:
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Davila ML, Kloss CC, Gunset G, Sadelain M. CD19 CAR-targeted T cells induce long-term remission and B Cell Aplasia in an immunocompetent mouse model of B cell acute lymphoblastic leukemia. PLoS One 2013; 8:e61338. [PMID: 23585892 PMCID: PMC3621858 DOI: 10.1371/journal.pone.0061338] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Accepted: 03/08/2013] [Indexed: 01/20/2023] Open
Abstract
Although many adults with B cell acute lymphoblastic leukemia (B-ALL) are induced into remission, most will relapse, underscoring the dire need for novel therapies for this disease. We developed murine CD19-specific chimeric antigen receptors (CARs) and an immunocompetent mouse model of B-ALL that recapitulates the disease at genetic, cellular, and pathologic levels. Mouse T cells transduced with an all-murine CD3ζ/CD28-based CAR that is equivalent to the one being used in our clinical trials, eradicate B-ALL in mice and mediate long-term B cell aplasias. In this model, we find that increasing conditioning chemotherapy increases tumor eradication, B cell aplasia, and CAR-modified T cell persistence. Quantification of recipient B lineage cells allowed us to estimate an in vivo effector to endogenous target ratio for B cell aplasia maintenance. In mice exhibiting a dramatic B cell reduction we identified a small population of progenitor B cells in the bone marrow that may serve as a reservoir for long-term CAR-modified T cell stimulation. Lastly, we determine that infusion of CD8+ CAR-modified T cells alone is sufficient to maintain long-term B cell eradication. The mouse model we report here should prove valuable for investigating CAR-based and other therapies for adult B-ALL.
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MESH Headings
- Animals
- Antigens, CD19/genetics
- Antigens, CD19/immunology
- Antineoplastic Agents, Alkylating/pharmacology
- B-Lymphocytes/drug effects
- B-Lymphocytes/immunology
- B-Lymphocytes/pathology
- CD28 Antigens/genetics
- CD28 Antigens/immunology
- CD3 Complex/genetics
- CD3 Complex/immunology
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- CD8-Positive T-Lymphocytes/transplantation
- Cell Lineage/immunology
- Cyclophosphamide/pharmacology
- Disease Models, Animal
- Humans
- Immunocompetence
- Immunophenotyping
- Immunotherapy, Adoptive/methods
- Lymphocyte Depletion
- Mice
- Mutant Chimeric Proteins/genetics
- Mutant Chimeric Proteins/immunology
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/immunology
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/pathology
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/therapy
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Remission Induction/methods
- Transduction, Genetic
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Affiliation(s)
- Marco L. Davila
- Leukemia Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- Center for Cell Engineering, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Christopher C. Kloss
- Center for Cell Engineering, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- Biochemistry, Cell, and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York, United States of America
| | - Gertrude Gunset
- Center for Cell Engineering, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Michel Sadelain
- Center for Cell Engineering, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- * E-mail:
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Weiner AM, Gray LT. What role (if any) does the highly conserved CSB-PGBD3 fusion protein play in Cockayne syndrome? Mech Ageing Dev 2013; 134:225-33. [PMID: 23369858 DOI: 10.1016/j.mad.2013.01.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 01/08/2013] [Accepted: 01/15/2013] [Indexed: 11/18/2022]
Abstract
The PGBD3 piggyBac transposon inserted into CSB intron 5 early in the primate lineage. As a result of alternative splicing, the human CSB gene now encodes three proteins: CSB, a CSB-PGBD3 fusion protein that joins the N-terminal CSB domain to the C-terminal PGBD3 transposase domain, and PGBD3 transposase. The fusion protein is as highly conserved as CSB, suggesting that it is advantageous in health; however, expression of the fusion protein in CSB-null cells induces a constitutive interferon (IFN) response. The fusion protein binds in vivo to PGBD3-related MER85 elements, but is also tethered to c-Jun, TEAD1, and CTCF motifs by interactions with the cognate transcription factors. The fusion protein regulates nearby genes from the c-Jun (and to a lesser extent TEAD1 and CTCF) motifs, but not from MER85 elements. We speculate that the fusion protein interferes with CSB-dependent chromatin remodeling, generating double-stranded RNA (dsRNA) that induces an IFN response through endosomal TLR or cytoplasmic RIG-I and/or MDA5 RNA sensors. We suggest that the fusion protein was fixed in primates because an elevated IFN response may help to fight viral infection. We also speculate that an inappropriate IFN response may contribute to the clinical presentation of CS.
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Affiliation(s)
- Alan M Weiner
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA 98195-7350, USA.
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Soejima M, Koda Y. TaqMan real-time polymerase chain reaction for detection of SEC1-FUT2 hybrid alleles: identification of novel hybrid allele. Clin Chim Acta 2013; 415:59-62. [PMID: 22959923 DOI: 10.1016/j.cca.2012.08.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 08/14/2012] [Accepted: 08/22/2012] [Indexed: 12/15/2022]
Abstract
BACKGROUND Two hybrid alleles between the secretor type α(1,2)fucosyltransferase gene (FUT2) and a pseudogene of FUT2 (SEC1) have been reported so far; parts of the SEC1 and FUT2 sequences are suggested to be susceptible to recombination. The se(fus), one of the two hybrid alleles, is found in Japanese populations at relative high frequencies. METHODS A TaqMan assay to distinguish SEC1 and SEC1-FUT2 hybrid alleles was designed for the purpose of dealing with large number of samples. RESULTS The results of the present method were fully consistent with those of the previous method for detection of se(fus) in the Japanese population. In addition, a novel SEC1-FUT2-SEC1 hybrid allele, which contains a 35-bp sequence (between positions 418 and 452) that is identical to the FUT2 sequence including a 13-bp FUT2-specific region (between positions 436 and 448), was encountered in an individual of European descent. CONCLUSIONS The present TaqMan assay is a reliable and powerful method for the large scale association study between disease susceptibility and FUT2 genotypes especially in the Japanese populations because of relative high frequency of se(fus). In addition, this method is a useful tool to find novel SEC1-FUT2 hybrid alleles.
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Affiliation(s)
- Mikiko Soejima
- Department of Forensic Medicine and Human Genetics, Kurume University School of Medicine, Kurume 830-0011, Japan
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Harada Y, Harada H. [Acute promyelocytic leukemia]. Rinsho Ketsueki 2013; 54:49-60. [PMID: 23391647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
MESH Headings
- Age Distribution
- Drug Therapy, Combination/methods
- Humans
- Leukemia, Promyelocytic, Acute/diagnosis
- Leukemia, Promyelocytic, Acute/drug therapy
- Leukemia, Promyelocytic, Acute/genetics
- Leukemia, Promyelocytic, Acute/mortality
- Mutant Chimeric Proteins/genetics
- Mutation/genetics
- Pathology, Molecular/methods
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Tsypik O, Ostash B, Rebets' I, Fedorenko V. [Characterization of Streptomyces globisporus 1912 lnd-cluster region containing lndY, lndYR, lndW2 and lndW genes]. Tsitol Genet 2013; 47:11-16. [PMID: 23427607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Streptomyces globisporus 1912 lnd-cluster region which flanks structural lndZ5-lndZ6 genes contains four open reading frames lndW, lndW2, lndYR and lndY. The latter one encodes putative proteinase which can regulate landomycin production and morphogenesis like LndYR. However, results of lndY overexpression and gene knockout showed that lndY did not participate in regulation of landomycin production and morphogenesis of Streptomyces globisporus 1912. Using transcriptional fusion of promoter lndWp to catechol dioxygenase reporter gene xylE the temporal character of interaction of promoter lndWp and repressor LndYR was studied.
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Guo W, Jiang YX, Li CP. [Prokaryotic expression of chimeric gene derived from the group 1 allergens of dust mites and bioactivity identification]. Zhongguo Ji Sheng Chong Xue Yu Ji Sheng Chong Bing Za Zhi 2012; 30:274-278. [PMID: 23072155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
OBJECTIVE To express a chimeric gene R8 derived from the group 1 allergens of dust mites using prokaryotic expression system and detect their bioactivities. METHODS PCR amplification was performed using specific primers of Derf1 gene and the pUCm-T recombinant plasmid containing the R8 chimeric gene as a template. The PCR products were inserted into the pET28a(+) empty vector after double digestion using restriction endonuclease BamH I and Xho I, respectively. The recombinant plasmid was transferred into E. coli line BL21 and induced by 1 mmol/L isopropyl-beta-D-1-thiogalactopyranoside (IPTG). The expressed product was detected by SDS-PAGE and the target protein was purified. IgE binding assay of the purified protein R8 was detected by ELISA using dust mite allergic patient sera. For determining immunogenicity of R8 protein, 75 BALB/c mice were randomly divided into 5 groups, namely PBS (negative control), rDer f 1 group and rDer p 1 group (positive groups), R8 group and asthma group. The mice were treated with dust mite extract at 0, 7, 14 day by intraperitoneal injection of allergens (100 jl, 0.1 .tg/jl) and inhaled challenge as aerosol (0.5 microg/ml, 30 min/d) on day 21 for 7 days. Before inhalation in immunotherapy groups at 25-27 day, specific allergen immunotherapy was performed using rDerf 1, rDerp 1 and R8 allergens respectively. Mice in negative control group were treated with PBS all the time. Twenty-four hours after the last challenge, mice in every group were sacrificed. The bronchoalveolar lavage fluid (BALF) was collected. ELISA was used to detect the level of interferon-gamma (IFN-gamma) and interleukin 4 (IL-4) in BALF. RESULTS SDS-PAGE analysis revealed that chimeric gene R8 was expressed with a band of approximately M(r) 35 000. Compared with groups of rDerf 1 and rDer p 1 [(80.44 +/- 15.50) and (90.79 +/- 10.38) microg/ml, respectively], IgE binding capacity of the protein R8 (37.03 +/- 12.46) microg/ml was statistically lower (P < 0.001). The level of IFN-gamma in sera of R8 group [(343.43 +/- 38.79) pg/ml] was higher than that of the PBS and asthma groups [(393.93 +/- 50.68) and (208.44 < or = 46.11)pg/ml, respectively] (P < 0.01), but no statistical difference to that of the rDerf 1 and rDer p 1 groups (P > 0.05). IL-4 level in R8 group was lower markedly than the others (P < 0.05 or P < 0.01). CONCLUSION Chimeric protein R8 derived from the group 1 allergens of dust mites has been expressed with low allergenicity and high immunogenicity.
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Affiliation(s)
- Wei Guo
- Department of Medical Parasitology, Wannan Medical College, Wudu 241002, China
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47
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Berry NJ, Marzetta F, Towers GJ, Rose NJ. Diversity of TRIM5α and TRIMCyp sequences in cynomolgus macaques from different geographical origins. Immunogenetics 2012; 64:267-78. [PMID: 22124667 DOI: 10.1007/s00251-011-0585-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 10/17/2011] [Indexed: 12/01/2022]
Abstract
The TRIM5α restriction factor can protect some species of monkeys, but not humans, from HIV infection. It has also emerged that some monkeys have a cyclophilin A domain retrotransposed into the TRIM5 locus resulting in the expression of a TRIMCyp protein with anti-retroviral activity. A high degree of sequence variation in the primate TRIM5 gene has been reported that varies between populations of rhesus macaques, a widely used non-human primate model of HIV/AIDS, and recently shown to correlate with susceptibility to simian immunodeficiency viruses in this species. Cynomolgus macaques are also used widely in HIV research. A non-indigenous population on Mauritius has highly restricted genetic diversity compared with macaques from Indonesia. The relative allelic diversity of TRIM5α and TRIMCyp within these two sub-populations may impact on the susceptibility of the macaques to simian immunodeficiency virus thereby influencing the outcome of studies using these monkeys. We sought to establish the genetic diversity of these alleles in cynomolgus macaques. We identified seven TRIM5α alleles in Indonesian macaques, three of which are novel, but only three in the Mauritian-origin macaques. Strikingly, 87% of Indonesian, but none of the Mauritian macaques, possessed a retrotransposed Cyp domain. A splice acceptor site single-nucleotide polymorphism that allows formation of a TRIMCyp protein was absent for the TRIM5α alleles found in the Mauritian macaques. The level of allelic diversity reported here is greater than previously proposed for cynomolgus macaque species.
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Affiliation(s)
- Neil J Berry
- Division of Retrovirology, National Institute for Biological Standards and Control, A Centre of the Health Protection Agency, Blanche Lane, South Mimms, Potters Bar, Hertfordshire, EN6 3QG, UK
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Song X, Bowen J, Miao W, Liu Y, Gorovsky MA. The nonhistone, N-terminal tail of an essential, chimeric H2A variant regulates mitotic H3-S10 dephosphorylation. Genes Dev 2012; 26:615-29. [PMID: 22426537 PMCID: PMC3315122 DOI: 10.1101/gad.182683.111] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2011] [Accepted: 02/06/2012] [Indexed: 12/21/2022]
Abstract
H2A.Y is an essential, divergent Tetrahymena thermophila histone variant. It has a long nonhistone N terminus that contains leucine-rich repeats (LRR) and an LRR cap domain with similarity to Sds22p, a regulator of yeast protein phosphatase 1 (PP1) activity in the nucleus. In growing cells, H2A.Y is incorporated into micronuclei only during S phase, which occurs immediately after micronuclear mitosis. Depletion of H2A.Y causes prolonged retention of mitosis-associated histone H3-S10 phosphorylation and mitotic abnormalities that mimic S10E mutation. In cells where H2A.Y is depleted, an inducible chimeric gene, in which the H2A.Y N terminus is attached to H2A.X, is shown to regulate micronuclear H3-S10 phosphorylation. H2A.Y can also be specifically coimmunoprecipitated with a Tetrahymena PP1 ortholog (Ppo1p). Taken together, these results argue that the N terminus of H2A.Y functions to regulate H3-S10 dephosphorylation. This striking in vivo case of "cross-talk" between a H2A variant and a specific post-translational modification of another histone demonstrates a novel function for a histone variant.
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Affiliation(s)
- Xiaoyuan Song
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
| | - Josephine Bowen
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
| | - Wei Miao
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
| | - Yifan Liu
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
| | - Martin A. Gorovsky
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
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Wu D, Zhang C, Shen Y, Nephew KP, Wang Q. Androgen receptor-driven chromatin looping in prostate cancer. Trends Endocrinol Metab 2011; 22:474-80. [PMID: 21889355 PMCID: PMC3229688 DOI: 10.1016/j.tem.2011.07.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 07/11/2011] [Accepted: 07/26/2011] [Indexed: 01/22/2023]
Abstract
The androgen receptor (AR) is important for prostate cancer development and progression. Genome-wide mapping of AR binding sites in prostate cancer has found that the majority of AR binding sites are located within non-promoter regions. These distal AR binding regions regulate AR target genes (e.g. UBE2C) involved in prostate cancer growth through chromatin looping. In addition to long-distance gene regulation, looping has been shown to induce spatial proximity of two genes otherwise located far away along the genomic sequence and the formation of double-strand DNA breaks, resulting in aberrant gene fusions (e.g. TMPRSS2-ERG) that also contribute to prostate tumorigenesis. Elucidating the mechanisms of AR-driven chromatin looping will increase our understanding of prostate carcinogenesis and may lead to the identification of new therapeutic targets.
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Affiliation(s)
- Dayong Wu
- Department of Molecular and Cellular Biochemistry and the Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH 43210, USA
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Zhuang Q, Zhang Z, Chen F, Xia G. Comparative and evolutionary analysis of new variants of ω-gliadin genes from three A-genome diploid wheats. J Appl Genet 2011; 53:125-31. [PMID: 22072274 DOI: 10.1007/s13353-011-0075-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2011] [Revised: 10/07/2011] [Accepted: 10/14/2011] [Indexed: 11/25/2022]
Abstract
A genomic polymerase chain reaction (PCR) cloning strategy was applied to isolate ω-gliadin sequences from three A-genome diploid wheats (Triticum monococcum, T. boeoticum and T. urartu). Amplicon lengths varied from 744 and 1,044 bp, and those of the corresponding deduced mature proteins from 248 to 348 residues. The primary structure of the deduced polypeptides comprised a short N- and C-terminal conserved domain, and a long, variable repetitive domain. A phylogenetic analysis recognised several clades: the first consisted of three T. aestivum sequences; the second and the third two T. boeoticum and six T. monococcum sequences; and the rest four T. urartu and three T. aestivum sequences. Among the functional (non-pseudogene) ARQ/E-type ω-gliadin sequences, two were derived from T. boeoticum and three from T. monococcum; one of the latter sequences appeared to be a chimera originating via illegitimate recombination between the other two T. monococcum sequences. None of the 12 intact ω-gliadin sequences contained any cysteine or methionine residues. We discussed the variation and evolution of A-genome ω-gliadin genes.
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Affiliation(s)
- Qianqian Zhuang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100 People's Republic of China
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