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Guttery DS, Pandey R, Ferguson DJ, Wall RJ, Brady D, Gupta D, Holder AA, Tewari R. Plasmodium DEH is ER-localized and crucial for oocyst mitotic division during malaria transmission. Life Sci Alliance 2020; 3:e202000879. [PMID: 33106323 PMCID: PMC7652392 DOI: 10.26508/lsa.202000879] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/15/2020] [Accepted: 10/15/2020] [Indexed: 11/24/2022] Open
Abstract
Cells use fatty acids (FAs) for membrane biosynthesis, energy storage, and the generation of signaling molecules. 3-hydroxyacyl-CoA dehydratase-DEH-is a key component of very long chain fatty acid synthesis. Here, we further characterized in-depth the location and function of DEH, applying in silico analysis, live cell imaging, reverse genetics, and ultrastructure analysis using the mouse malaria model Plasmodium berghei DEH is evolutionarily conserved across eukaryotes, with a single DEH in Plasmodium spp. and up to three orthologs in the other eukaryotes studied. DEH-GFP live-cell imaging showed strong GFP fluorescence throughout the life-cycle, with areas of localized expression in the cytoplasm and a circular ring pattern around the nucleus that colocalized with ER markers. Δdeh mutants showed a small but significant reduction in oocyst size compared with WT controls from day 10 postinfection onwards, and endomitotic cell division and sporogony were completely ablated, blocking parasite transmission from mosquito to vertebrate host. Ultrastructure analysis confirmed degeneration of Δdeh oocysts, and a complete lack of sporozoite budding. Overall, DEH is evolutionarily conserved, localizes to the ER, and plays a crucial role in sporogony.
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Affiliation(s)
- David S Guttery
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
- The Leicester Cancer Research Centre, College of Life Sciences, University of Leicester, Leicester, UK
| | - Rajan Pandey
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - David Jp Ferguson
- Department of Biological and Medical Sciences, Faculty of Health and Life Science, Oxford Brookes University, Oxford, UK
- Nuffield Department of Clinical Laboratory Science, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Richard J Wall
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
- Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, UK
| | - Declan Brady
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | | | - Rita Tewari
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
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Regulators of Long-Term Memory Revealed by Mushroom Body-Specific Gene Expression Profiling in Drosophila melanogaster. Genetics 2018; 209:1167-1181. [PMID: 29925565 PMCID: PMC6063240 DOI: 10.1534/genetics.118.301106] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 06/13/2018] [Indexed: 11/20/2022] Open
Abstract
Memory formation is achieved by genetically tightly controlled molecular pathways that result in a change of synaptic strength and synapse organization. While for short-term memory traces, rapidly acting biochemical pathways are in place, the formation of long-lasting memories requires changes in the transcriptional program of a cell. Although many genes involved in learning and memory formation have been identified, little is known about the genetic mechanisms required for changing the transcriptional program during different phases of long-term memory (LTM) formation. With Drosophila melanogaster as a model system, we profiled transcriptomic changes in the mushroom body—a memory center in the fly brain—at distinct time intervals during appetitive olfactory LTM formation using the targeted DamID technique. We describe the gene expression profiles during these phases and tested 33 selected candidate genes for deficits in LTM formation using RNAi knockdown. We identified 10 genes that enhance or decrease memory when knocked-down in the mushroom body. For vajk-1 and hacd1—the two strongest hits—we gained further support for their crucial role in appetitive learning and forgetting. These findings show that profiling gene expression changes in specific cell-types harboring memory traces provides a powerful entry point to identify new genes involved in learning and memory. The presented transcriptomic data may further be used as resource to study genes acting at different memory phases.
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Sawai M, Uchida Y, Ohno Y, Miyamoto M, Nishioka C, Itohara S, Sassa T, Kihara A. The 3-hydroxyacyl-CoA dehydratases HACD1 and HACD2 exhibit functional redundancy and are active in a wide range of fatty acid elongation pathways. J Biol Chem 2017; 292:15538-15551. [PMID: 28784662 DOI: 10.1074/jbc.m117.803171] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 07/19/2017] [Indexed: 12/31/2022] Open
Abstract
Differences among fatty acids (FAs) in chain length and number of double bonds create lipid diversity. FA elongation proceeds via a four-step reaction cycle, in which the 3-hydroxyacyl-CoA dehydratases (HACDs) HACD1-4 catalyze the third step. However, the contribution of each HACD to 3-hydroxyacyl-CoA dehydratase activity in certain tissues or in different FA elongation pathways remains unclear. HACD1 is specifically expressed in muscles and is a myopathy-causative gene. Here, we generated Hacd1 KO mice and observed that these mice had reduced body and skeletal muscle weights. In skeletal muscle, HACD1 mRNA expression was by far the highest among the HACDs However, we observed only an ∼40% reduction in HACD activity and no changes in membrane lipid composition in Hacd1-KO skeletal muscle, suggesting that some HACD activities are redundant. Moreover, when expressed in yeast, both HACD1 and HACD2 participated in saturated and monounsaturated FA elongation pathways. Disruption of HACD2 in the haploid human cell line HAP1 significantly reduced FA elongation activities toward both saturated and unsaturated FAs, and HACD1 HACD2 double disruption resulted in a further reduction. Overexpressed HACD3 exhibited weak activity in saturated and monounsaturated FA elongation pathways, and no activity was detected for HACD4. We therefore conclude that HACD1 and HACD2 exhibit redundant activities in a wide range of FA elongation pathways, including those for saturated to polyunsaturated FAs, with HACD2 being the major 3-hydroxyacyl-CoA dehydratase. Our findings are important for furthering the understanding of the molecular mechanisms in FA elongation and diversity.
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Affiliation(s)
- Megumi Sawai
- From the Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812 and
| | - Yukiko Uchida
- From the Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812 and
| | - Yusuke Ohno
- From the Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812 and
| | - Masatoshi Miyamoto
- From the Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812 and
| | - Chieko Nishioka
- the RIKEN Brain Science Institute, 2-1 Hirosawa, Wako 351-0198, Japan
| | | | - Takayuki Sassa
- From the Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812 and
| | - Akio Kihara
- From the Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812 and
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Kihara A. Synthesis and degradation pathways, functions, and pathology of ceramides and epidermal acylceramides. Prog Lipid Res 2016; 63:50-69. [PMID: 27107674 DOI: 10.1016/j.plipres.2016.04.001] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/08/2016] [Accepted: 04/20/2016] [Indexed: 10/21/2022]
Abstract
Ceramide (Cer) is a structural backbone of sphingolipids and is composed of a long-chain base and a fatty acid. Existence of a variety of Cer species, which differ in chain-length, hydroxylation status, and/or double bond number of either of their hydrophobic chains, has been reported. Ceramide is produced by Cer synthases. Mammals have six Cer synthases (CERS1-6), each of which exhibits characteristic substrate specificity toward acyl-CoAs with different chain-lengths. Knockout mice for each Cer synthase show corresponding, isozyme-specific phenotypes, revealing the functional differences of Cers with different chain-lengths. Cer diversity is especially prominent in epidermis. Changes in Cer levels, composition, and chain-lengths are associated with atopic dermatitis. Acylceramide (acyl-Cer) specifically exists in epidermis and plays an essential role in skin permeability barrier formation. Accordingly, defects in acyl-Cer synthesis cause the cutaneous disorder ichthyosis with accompanying severe skin barrier defects. Although the molecular mechanism by which acyl-Cer is generated was long unclear, most genes involved in its synthesis have been identified recently. In Cer degradation pathways, the long-chain base moiety of Cer is converted to acyl-CoA, which is then incorporated mainly into glycerophospholipids. This pathway generates the lipid mediator sphingosine 1-phosphate. This review will focus on recent advances in our understanding of the synthesis and degradation pathways, physiological functions, and pathology of Cers/acyl-Cers.
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Affiliation(s)
- Akio Kihara
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo, Nishi 6-choume, Kita-ku, Sapporo 060-0812, Japan.
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Pandey R, Mohmmed A, Pierrot C, Khalife J, Malhotra P, Gupta D. Genome wide in silico analysis of Plasmodium falciparum phosphatome. BMC Genomics 2014; 15:1024. [PMID: 25425018 PMCID: PMC4256932 DOI: 10.1186/1471-2164-15-1024] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 11/12/2014] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Eukaryotic cellular machineries are intricately regulated by several molecular mechanisms involving transcriptional control, post-translational control and post-translational modifications of proteins (PTMs). Reversible protein phosphorylation/dephosphorylation process, which involves kinases as well as phosphatases, represents an important regulatory mechanism for diverse pathways and systems in all organisms including human malaria parasite, Plasmodium falciparum. Earlier analysis on P. falciparum protein-phosphatome revealed presence of 34 phosphatases in Plasmodium genome. Recently, we re-analysed P. falciparum phosphatome aimed at identifying parasite specific phosphatases. RESULTS Plasmodium database (PlasmoDB 9.2) search, combined with PFAM and CDD searches, revealed 67 candidate phosphatases in P. falciparum. While this number is far less than the number of phosphatases present in Homo sapiens, it is almost the same as in other Plasmodium species. These Plasmodium phosphatase proteins were classified into 13 super families based on NCBI CDD search. Analysis of proteins expression profiles of the 67 phosphatases revealed that 44 phosphatases are expressed in both schizont as well as gametocytes stages. Fourteen phosphatases are common in schizont, ring and trophozoite stages, four phosphatases are restricted to gametocytes, whereas another three restricted to schizont stage. The phylogenetic trees for each of the known phosphatase super families reveal a considerable phylogenetic closeness amongst apicomplexan organisms and a considerable phylogenetic distance with other eukaryotic model organisms included in the study. The GO assignments and predicted interaction partners of the parasite phosphatases indicate its important role in diverse cellular processes. CONCLUSION In the study presented here, we reviewed the P. falciparum phosphatome to show presence of 67 candidate phosphatases in P. falciparum genomes/proteomes. Intriguingly, amongst these phosphatases, we could identify six Plasmodium specific phosphatases and 33 putative phosphatases that do not have human orthologs, thereby suggesting that these phosphatases have the potential to be explored as novel antimalarial drug targets.
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Affiliation(s)
| | | | | | - Jamal Khalife
- Structural and Computational Biology group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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Sassa T, Kihara A. Metabolism of very long-chain Fatty acids: genes and pathophysiology. Biomol Ther (Seoul) 2014; 22:83-92. [PMID: 24753812 PMCID: PMC3975470 DOI: 10.4062/biomolther.2014.017] [Citation(s) in RCA: 186] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 03/03/2014] [Indexed: 01/19/2023] Open
Abstract
Fatty acids (FAs) are highly diverse in terms of carbon (C) chain-length and number of double bonds. FAs with C>20 are called very long-chain fatty acids (VLCFAs). VLCFAs are found not only as constituents of cellular lipids such as sphingolipids and glycerophospholipids but also as precursors of lipid mediators. Our understanding on the function of VLCFAs is growing in parallel with the identification of enzymes involved in VLCFA synthesis or degradation. A variety of inherited diseases, such as ichthyosis, macular degeneration, myopathy, mental retardation, and demyelination, are caused by mutations in the genes encoding VLCFA metabolizing enzymes. In this review, we describe mammalian VLCFAs by highlighting their tissue distribution and metabolic pathways, and we discuss responsible genes and enzymes with reference to their roles in pathophysiology.
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Affiliation(s)
- Takayuki Sassa
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-ku, Sapporo 060-0812, Japan
| | - Akio Kihara
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-ku, Sapporo 060-0812, Japan
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Reiterer V, Eyers PA, Farhan H. Day of the dead: pseudokinases and pseudophosphatases in physiology and disease. Trends Cell Biol 2014; 24:489-505. [PMID: 24818526 DOI: 10.1016/j.tcb.2014.03.008] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 03/25/2014] [Accepted: 03/27/2014] [Indexed: 12/19/2022]
Abstract
Pseudophosphatases and pseudokinases are increasingly viewed as integral elements of signaling pathways, and there is mounting evidence that they have frequently retained the ability to interact with cellular 'substrates', and can exert important roles in different diseases. However, these pseudoenzymes have traditionally received scant attention compared to classical kinases and phosphatases. In this review we explore new findings in the emerging pseudokinase and pseudophosphatase fields, and discuss their different modes of action which include exciting new roles as scaffolds, anchors, spatial modulators, traps, and ligand-driven regulators of canonical kinases and phosphatases. Thus, it is now apparent that pseudokinases and pseudophosphatases both support and drive a panoply of signaling networks. Finally, we highlight recent evidence on their involvement in human pathologies, marking them as potential novel drug targets.
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Affiliation(s)
- Veronika Reiterer
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
| | - Hesso Farhan
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland; Department of Biology, University of Konstanz, Konstanz, Germany.
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8
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Muhammad E, Reish O, Ohno Y, Scheetz T, Deluca A, Searby C, Regev M, Benyamini L, Fellig Y, Kihara A, Sheffield VC, Parvari R. Congenital myopathy is caused by mutation of HACD1. Hum Mol Genet 2013; 22:5229-36. [PMID: 23933735 PMCID: PMC3842179 DOI: 10.1093/hmg/ddt380] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Congenital myopathies are heterogeneous inherited diseases of muscle characterized by a range of distinctive histologic abnormalities. We have studied a consanguineous family with congenital myopathy. Genome-wide linkage analysis and whole-exome sequencing identified a homozygous non-sense mutation in 3-hydroxyacyl-CoA dehydratase 1 (HACD1) in affected individuals. The mutation results in non-sense mediated decay of the HACD1 mRNA to 31% of control levels in patient muscle and completely abrogates the enzymatic activity of dehydration of 3-hydroxyacyl-CoA, the third step in the elongation of very long-chain fatty acids (VLCFAs). We describe clinical findings correlated with a deleterious mutation in a gene not previously known to be associated with congenital myopathy in humans. We suggest that the mutation in the HACD1 gene causes a reduction in the synthesis of VLCFAs, which are components of membrane lipids and participants in physiological processes, leading to congenital myopathy. These data indicate that HACD1 is necessary for muscle function.
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Affiliation(s)
- Emad Muhammad
- Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences and
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9
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Cardiomyopathy classification: ongoing debate in the genomics era. Biochem Res Int 2012; 2012:796926. [PMID: 22924131 PMCID: PMC3423823 DOI: 10.1155/2012/796926] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 05/14/2012] [Accepted: 05/31/2012] [Indexed: 01/19/2023] Open
Abstract
Cardiomyopathies represent a group of diseases of the myocardium of the heart and include diseases both primarily of the cardiac muscle and systemic diseases leading to adverse effects on the heart muscle size, shape, and function. Traditionally cardiomyopathies were defined according to phenotypical appearance. Now, as our understanding of the pathophysiology of the different entities classified under each of the different phenotypes improves and our knowledge of the molecular and genetic basis for these entities progresses, the traditional classifications seem oversimplistic and do not reflect current understanding of this myriad of diseases and disease processes. Although our knowledge of the exact basis of many of the disease processes of cardiomyopathies is still in its infancy, it is important to have a classification system that has the ability to incorporate the coming tide of molecular and genetic information. This paper discusses how the traditional classification of cardiomyopathies based on morphology has evolved due to rapid advances in our understanding of the genetic and molecular basis for many of these clinical entities.
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10
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Protein tyrosine phosphatase-like A regulates myoblast proliferation and differentiation through MyoG and the cell cycling signaling pathway. Mol Cell Biol 2011; 32:297-308. [PMID: 22106411 DOI: 10.1128/mcb.05484-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Protein tyrosine phosphatase-like A (PTPLa) has been implicated in skeletal myogenesis and cardiogenesis. Mutations in PTPLa correlated with arrhythmogenic right ventricular dysplasia in humans and congenital centronuclear myopathy with severe hypotonia in dogs. The molecular mechanisms of PTPLa in myogenesis are unknown. In this report, we demonstrate that PTPLa is required for myoblast growth and differentiation. The cells lacking PTPLa remained immature and failed to differentiate into mature myotubes. The repressed MyoG expression was responsible for the impaired myoblast differentiation. Meanwhile, impeded cell growth, with an obvious S-phase arrest and compromised G(2)/M transition, was observed in PTPLa-deficient myoblasts. Further study demonstrated that the upregulation of cyclin D1 and cyclin E2 complexes, along with a compromised G(2)/M transition due to the decreased CDK1 (cyclin-dependent kinase 1) activity and upregulated p21, contributed to the mutant cell S-phase arrest and eventually led to the retarded cell growth. Finally, the transcriptional regulation of the PTPLa gene was explored. We identified PTPLa as a new target gene of the serum response factor (SRF). Skeletal- and cardiac-muscle-specific SRF knockouts resulted in significant decreases in PTPLa expression, suggesting a conserved transcriptional regulation of the PTPLa gene in mice.
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Valdés De Hoyos A, Hoz-Rodríguez L, Arzate H, Narayanan AS. Isolation of protein-tyrosine phosphatase-like member-a variant from cementum. J Dent Res 2011; 91:203-9. [PMID: 22067203 DOI: 10.1177/0022034511428155] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Cementum has been shown to contain unique polypeptides that participate in cell recruitment and differentiation during cementum formation. We report the isolation of a cDNA variant for protein-tyrosine phosphatase-like (proline instead of catalytic arginine) member-a (PTPLA) from cementum. A cementifying fibroma-derived λ-ZAP expression library was screened by panning with a monoclonal antibody to cementum attachment protein (CAP), and 1435 bp cDNA (gb AC093525.3) was isolated. This cDNA encodes a 140-amino-acid polypeptide, and its N-terminal 125 amino acids are identical to those of PTPLA. This isoform, designated as PTPLA-CAP, results from a read-through of the PTPLA exon 2 splice donor site, truncating after the second putative transmembrane domain. It contains 15 amino acids encoded within the intron between PTPLA exons 2 and 3, which replace the active site for PTPLA phosphatase activity. The recombinant protein, rhPTPLA-CAP, has Mr 19 kDa and cross-reacts with anti-CAP antibody. Anti-rhPTPLA-CAP antibody immunostained cementum cells, cementum, heart, and liver. Quantitative RT-PCR showed that PTPLA was expressed in all periodontal cells; however, PTPLA-CAP expression was limited to cementum cells. The rhPTPLA-CAP promoted gingival fibroblast attachment. We conclude that PTPLA-CAP is a splice variant of PTPLA, and that, in the periodontium, cementum and cementum cells express this variant.
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Affiliation(s)
- A Valdés De Hoyos
- Laboratorio de Biología Periodontal y Tejidos Mineralizados, Facultad de Odontología, Universidad Nacional Autónoma de México, México
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Tondeur S, Pangault C, Le Carrour T, Lannay Y, Benmahdi R, Cubizolle A, Assou S, Pantesco V, Klein B, Hamamah S, Schved JF, Fest T, De Vos J. Expression map of the human exome in CD34+ cells and blood cells: increased alternative splicing in cell motility and immune response genes. PLoS One 2010; 5:e8990. [PMID: 20126548 PMCID: PMC2813875 DOI: 10.1371/journal.pone.0008990] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Accepted: 01/05/2010] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Hematopoietic cells are endowed with very specific biological functions, including cell motility and immune response. These specific functions are dramatically altered during hematopoietic cell differentiation, whereby undifferentiated hematopoietic stem and progenitor cells (HSPC) residing in bone marrow differentiate into platelets, red blood cells and immune cells that exit into the blood stream and eventually move into lymphoid organs or inflamed tissues. The contribution of alternative splicing (AS) to these functions has long been minimized due to incomplete knowledge on AS events in hematopoietic cells. PRINCIPAL FINDINGS Using Human Exon ST 1.0 microarrays, the entire exome expression profile of immature CD34+ HSPC and mature whole blood cells was mapped, compared to a collection of solid tissues and made freely available as an online exome expression atlas (Amazonia Exon! : http://amazonia.transcriptome.eu/exon.php). At a whole transcript level, HSPC strongly expressed EREG and the pluripotency marker DPPA4. Using a differential splicing index scheme (dsi), a list of 849 transcripts differentially expressed between hematopoietic cells and solid tissues was computed, that included NEDD9 and CD74. Some of these genes also underwent alternative splicing events during hematopoietic differentiation, such as INPP4B, PTPLA or COMMD6, with varied contribution of CD3+ T cells, CD19+ B cells, CD14+ or CD15+ myelomonocytic populations. Strikingly, these genes were significantly enriched for genes involved in cell motility, cell adhesion, response to wounding and immune processes. CONCLUSION The relevance and the precision provided by this exon expression map highlights the contribution of alternative splicing to key feature of blood cells differentiation and function.
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Affiliation(s)
- Sylvie Tondeur
- CHU Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, Montpellier, France
- INSERM, U847, Montpellier, France
- Université MONTPELLIER1, UFR de médecine, Montpellier, France
| | - Céline Pangault
- CHU Rennes, laboratoire d'Hématologie, Rennes, France
- INSERM U917, Université de Rennes 1, UFR de Médecine, Rennes, France
| | - Tanguy Le Carrour
- CHU Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, Montpellier, France
- INSERM, U847, Montpellier, France
| | - Yoann Lannay
- CHU Montpellier, Unité biologie clinique d'AMP - DPI, Hôpital Arnaud de Villeneuve, Montpellier, France
| | | | | | - Said Assou
- CHU Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, Montpellier, France
- INSERM, U847, Montpellier, France
| | | | - Bernard Klein
- CHU Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, Montpellier, France
- INSERM, U847, Montpellier, France
- Université MONTPELLIER1, UFR de médecine, Montpellier, France
| | - Samir Hamamah
- CHU Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, Montpellier, France
- INSERM, U847, Montpellier, France
- Université MONTPELLIER1, UFR de médecine, Montpellier, France
- CHU Montpellier, Unité biologie clinique d'AMP - DPI, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - Jean-François Schved
- Université MONTPELLIER1, UFR de médecine, Montpellier, France
- CHU Montpellier, Laboratoire d'Hématologie, Hôpital Saint-Eloi, Montpellier, France
| | - Thierry Fest
- CHU Rennes, laboratoire d'Hématologie, Rennes, France
- INSERM U917, Université de Rennes 1, UFR de Médecine, Rennes, France
| | - John De Vos
- CHU Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, Montpellier, France
- INSERM, U847, Montpellier, France
- Université MONTPELLIER1, UFR de médecine, Montpellier, France
- * E-mail:
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Bevilacqua JA, Bitoun M, Biancalana V, Oldfors A, Stoltenburg G, Claeys KG, Lacène E, Brochier G, Manéré L, Laforêt P, Eymard B, Guicheney P, Fardeau M, Romero NB. "Necklace" fibers, a new histological marker of late-onset MTM1-related centronuclear myopathy. Acta Neuropathol 2009; 117:283-91. [PMID: 19084976 DOI: 10.1007/s00401-008-0472-1] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 12/02/2008] [Accepted: 12/03/2008] [Indexed: 12/31/2022]
Abstract
Mutations in the gene encoding the phosphoinositide phosphatase myotubularin 1 protein (MTM1) are usually associated with severe neonatal X-linked myotubular myopathy (XLMTM). However, mutations in MTM1 have also been recognized as the underlying cause of "atypical" forms of XLMTM in newborn boys, female infants, female manifesting carriers and adult men. We reviewed systematically the biopsies of a cohort of patients with an unclassified form of centronuclear myopathy (CNM) and identified four patients presenting a peculiar histological alteration in some muscle fibers that resembled a necklace ("necklace fibers"). We analyzed further the clinical and morphological features and performed a screening of the genes involved in CNM. Muscle biopsies in all four patients demonstrated 4-20% of fibers with internalized nuclei aligned in a basophilic ring (necklace) at 3 microm beneath the sarcolemma. Ultrastructurally, such necklaces consisted of myofibrils of smaller diameter, in oblique orientation, surrounded by mitochondria, sarcoplasmic reticulum and glycogen granules. In the four patients (three women and one man), myopathy developed in early childhood but was slowly progressive. All had mutations in the MTM1 gene. Two mutations have previously been reported (p.E404K and p.R241Q), while two are novel; a c.205_206delinsAACT frameshift change in exon 4 and a c.1234A>G mutation in exon 11 leading to an abnormal splicing and the deletion of nine amino acids in the catalytic domain of MTM1. Necklace fibers were seen neither in DNM2- or BIN1-related CNM nor in males with classical XLMTM. The presence of necklace fibers is useful as a marker to direct genetic analysis to MTM1 in CNM.
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MESH Headings
- Adolescent
- Adult
- Age of Onset
- Biopsy
- Female
- Humans
- Immunohistochemistry
- Magnetic Resonance Imaging
- Male
- Microscopy, Electron
- Middle Aged
- Muscle Fibers, Skeletal/metabolism
- Muscle Fibers, Skeletal/pathology
- Muscle Fibers, Skeletal/ultrastructure
- Muscle, Skeletal/pathology
- Muscle, Skeletal/ultrastructure
- Mutation
- Myofibrils/ultrastructure
- Myopathies, Structural, Congenital/genetics
- Myopathies, Structural, Congenital/metabolism
- Myopathies, Structural, Congenital/pathology
- Polymerase Chain Reaction
- Protein Tyrosine Phosphatases, Non-Receptor/genetics
- Protein Tyrosine Phosphatases, Non-Receptor/metabolism
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Affiliation(s)
- Jorge A Bevilacqua
- INSERM, Institut de Myologie, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
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14
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Ikeda M, Kanao Y, Yamanaka M, Sakuraba H, Mizutani Y, Igarashi Y, Kihara A. Characterization of four mammalian 3-hydroxyacyl-CoA dehydratases involved in very long-chain fatty acid synthesis. FEBS Lett 2008; 582:2435-40. [DOI: 10.1016/j.febslet.2008.06.007] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Revised: 05/23/2008] [Accepted: 06/03/2008] [Indexed: 10/22/2022]
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15
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Kihara A, Sakuraba H, Ikeda M, Denpoh A, Igarashi Y. Membrane topology and essential amino acid residues of Phs1, a 3-hydroxyacyl-CoA dehydratase involved in very long-chain fatty acid elongation. J Biol Chem 2008; 283:11199-209. [PMID: 18272525 DOI: 10.1074/jbc.m708993200] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Yeast Phs1 is the 3-hydroxyacyl-CoA dehydratase that catalyzes the third reaction of the four-step cycle in the elongation of very long-chain fatty acids (VLCFAs). In yeast, the hydrophobic backbone of sphingolipids, ceramide, consists of a long-chain base and an amide-linked C26 VLCFA. Therefore, defects in VLCFA synthesis would be expected to greatly affect sphingolipid synthesis. In fact, in this study we found that reduced Phs1 levels result in significant impairment of the conversion of ceramide to inositol phosphorylceramide. Phs1 proteins are conserved among eukaryotes, constituting a novel protein family. Phs1 family members exhibit no sequence similarity to other dehydratase families, so their active site sequence and catalytic mechanism have been completely unknown. Here, by mutating 22 residues conserved among Phs1 family members, we identified six amino acid residues important in Phs1 function, two of which (Tyr-149 and Glu-156) are indispensable. We also examined the membrane topology of Phs1 using an N-glycosylation reporter assay. Our results suggest that Phs1 is a membrane-spanning protein that traverses the membrane six times and has an N terminus and C terminus facing the cytosol. The important amino acids are concentrated in or near two of the six proposed transmembrane regions. Thus, we also propose a catalytic mechanism for Phs1 that is not unlike mechanisms used by other hydratases active in lipid synthesis.
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Affiliation(s)
- Akio Kihara
- Laboratory of Biomembrane and Biofunctional Chemistry, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo, Nishi 6-choume, Kita-ku, Sapporo 060-0812, Japan.
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16
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Moric-Janiszewska E, Markiewicz-Loskot G. Review on the genetics of arrhythmogenic right ventricular dysplasia. Europace 2007; 9:259-66. [PMID: 17363426 DOI: 10.1093/europace/eum034] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Arrhythmogenic right ventricular dysplasia (ARVD) is a clinical and pathologic entity whose diagnosis rests on electrocardiographic and angiographic criteria; pathologic findings, replacement of ventricular myocardium with fatty and fibrous elements, preferentially involve the right ventricular (RV) free wall. There is a familial occurrence in about 50% of cases, with autosomal dominant inheritance with variable penetrance and polymorphic phenotypic expression, and is one of the major genetic causes of juvenile sudden death. When the dysplasia is extensive, it may represent the extensive form of ARVCM (arrhythmogenic right ventricular cardiomyopathy). In this review, we focus on the some candidate genes mutations and information on some genotype-phenotype correlation in the ARVD. Our findings are in agreement with those of European Society of Cardiology who stated that: genetic analysis is usefull in families with RV cardiomyopathy because whenever a pathogenetic mutation is identified, it becomes possible to establish a presymptomatic diagnosis of the disease among family members and to provide them with genetic counseling to monitor the development of the disease and to assess the risk of transmitting the disease offspring. On the basis of current knowledge, genetic analysis does not contribute to risk stratification of arrhythmogenic RV cardiomyopathy.
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Affiliation(s)
- Ewa Moric-Janiszewska
- Department of Biochemistry, Medical University of Silesia, Narcyzów 1, 41-200 Sosnowiec, Poland.
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17
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Schuldiner M, Collins SR, Thompson NJ, Denic V, Bhamidipati A, Punna T, Ihmels J, Andrews B, Boone C, Greenblatt JF, Weissman JS, Krogan NJ. Exploration of the Function and Organization of the Yeast Early Secretory Pathway through an Epistatic Miniarray Profile. Cell 2005; 123:507-19. [PMID: 16269340 DOI: 10.1016/j.cell.2005.08.031] [Citation(s) in RCA: 670] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2005] [Revised: 08/12/2005] [Accepted: 08/22/2005] [Indexed: 10/25/2022]
Abstract
We present a strategy for generating and analyzing comprehensive genetic-interaction maps, termed E-MAPs (epistatic miniarray profiles), comprising quantitative measures of aggravating or alleviating interactions between gene pairs. Crucial to the interpretation of E-MAPs is their high-density nature made possible by focusing on logically connected gene subsets and including essential genes. Described here is the analysis of an E-MAP of genes acting in the yeast early secretory pathway. Hierarchical clustering, together with novel analytical strategies and experimental verification, revealed or clarified the role of many proteins involved in extensively studied processes such as sphingolipid metabolism and retention of HDEL proteins. At a broader level, analysis of the E-MAP delineated pathway organization and components of physical complexes and illustrated the interconnection between the various secretory processes. Extension of this strategy to other logically connected gene subsets in yeast and higher eukaryotes should provide critical insights into the functional/organizational principles of biological systems.
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Affiliation(s)
- Maya Schuldiner
- Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California 94143, USA
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18
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Pelé M, Tiret L, Kessler JL, Blot S, Panthier JJ. SINE exonic insertion in the PTPLA gene leads to multiple splicing defects and segregates with the autosomal recessive centronuclear myopathy in dog. Hum Mol Genet 2005. [DOI: 10.1093/hmg/ddi201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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19
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Pelé M, Tiret L, Kessler JL, Blot S, Panthier JJ. SINE exonic insertion in the PTPLA gene leads to multiple splicing defects and segregates with the autosomal recessive centronuclear myopathy in dogs. Hum Mol Genet 2005; 14:1417-27. [PMID: 15829503 DOI: 10.1093/hmg/ddi151] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Human centronuclear and myotubular myopathies belong to a genetically heterogeneous nosological group with clinical variability ranging from fatal disorder to mild weakness. The severe X-linked form is attributed to more than 200 different mutations in the myotubularin encoding gene (MTM1). In contrast, there are no reports regarding the molecular etiology or linkage studies on the autosomal forms of the disease. Labrador retrievers affected by spontaneous centronuclear myopathy (cnm) have clinical and histological features of the human disorder and represent the first model of recessive autosomal centronuclear myopathy. We previously mapped the cnm locus to the centromeric region of canine chromosome 2. No gene of the MTM1 family maps to the human homologous chromosomal region. Described herein is a disease-associated insertion within PTPLA exon 2, found in both alleles of all affected Labradors and in a single allele in obligate carriers. The inserted tRNA-derived short interspersed repeat element (SINE) has a striking effect on the maturation of PTPLA mRNA, whereby it can be spliced out, partially exonized or involved in multiple exon-skipping. As a result, the amount of wild-type transcripts falls to 1% in affected muscles. This example therefore recapitulates cumulative SINE-associated transcriptional defects that have been previously described as exclusive consequences of independent mutations. Although the function of PTPLA in metazoa remains unknown, the characterization of a hypomorphic mutation in Labradors with centronuclear myopathy provides new clues about the molecular complexity of skeletal myofiber homeostasis. These results also suggest that impaired PTPLA signaling might be implicated in human myopathies.
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Affiliation(s)
- Manuel Pelé
- UMR 955 INRA-ENVA de Génétique Moléculaire et Cellulaire, Ecole Nationale Vétérinaire d'Alfort, 7 avenue du Général de Gaulle, 94704 Maisons-Alfort cedex, France
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20
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Bertini E, Biancalana V, Bolino A, Buj Bello A, Clague M, Guicheney P, Jungbluth H, Kress W, Musaro' A, Nandurkar H, Pirola L, Romero N, Senderek J, Suter U, Sewry C, Tronchere H, Wallgren-Pettersson C, Wishart MJ, Laporte J. 118th ENMC International Workshop on Advances in Myotubular Myopathy. 26-28 September 2003, Naarden, The Netherlands. (5th Workshop of the International Consortium on Myotubular Myopathy). Neuromuscul Disord 2004; 14:387-96. [PMID: 15145343 DOI: 10.1016/j.nmd.2004.04.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2004] [Indexed: 11/21/2022]
MESH Headings
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Charcot-Marie-Tooth Disease/genetics
- Charcot-Marie-Tooth Disease/metabolism
- Chromosomes, Human, X
- Humans
- Insulin-Like Growth Factor I/genetics
- Insulin-Like Growth Factor I/metabolism
- Mutation
- Myopathies, Structural, Congenital/congenital
- Myopathies, Structural, Congenital/diagnosis
- Myopathies, Structural, Congenital/genetics
- Myopathies, Structural, Congenital/therapy
- Netherlands
- Protein Tyrosine Phosphatases/genetics
- Protein Tyrosine Phosphatases/physiology
- Protein Tyrosine Phosphatases, Non-Receptor
- Trans-Activators/genetics
- Trans-Activators/metabolism
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Affiliation(s)
- E Bertini
- Department of Laboratories, Unit of Molecular Medicine, Bambino Gesu' Childrens Hospital, P.za S. Onofrio 4, 00165 Rome, Italy.
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21
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Wang B, Pelletier J, Massaad MJ, Herscovics A, Shore GC. The yeast split-ubiquitin membrane protein two-hybrid screen identifies BAP31 as a regulator of the turnover of endoplasmic reticulum-associated protein tyrosine phosphatase-like B. Mol Cell Biol 2004; 24:2767-78. [PMID: 15024066 PMCID: PMC371098 DOI: 10.1128/mcb.24.7.2767-2778.2004] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
In the past decade, traditional yeast two-hybrid techniques have identified a plethora of interactions among soluble proteins operating within diverse cellular pathways. The discovery of associations between membrane proteins by genetic approaches, on the other hand, is less well established due to technical limitations. Recently, a split-ubiquitin system was developed to overcome this barrier, but so far, this system has been limited to the analysis of known membrane protein interactions. Here, we constructed unique split-ubiquitin-linked cDNA libraries and provide details for implementing this system to screen for binding partners of a bait protein, in this case BAP31. BAP31 is a resident integral protein of the endoplasmic reticulum, where it operates as a chaperone or cargo receptor and regulator of apoptosis. Here we describe a novel human member of the protein tyrosine phosphatase-like B (PTPLB) family, an integral protein of the endoplasmic reticulum membrane with four membrane-spanning alpha helices, as a BAP31-interacting protein. PTPLB turns over rapidly through degradation by the proteasome system. Comparisons of mouse cells with a deletion of Bap31 or reconstituted with human BAP31 indicate that BAP31 is required to maintain PTPLB, consistent with a chaperone or quality control function for BAP31 in the endoplasmic reticulum membrane.
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Affiliation(s)
- Bing Wang
- Department of Biochemistry. McGill Cancer Center, McGill University, Montreal, Quebec, Canada H3G 1Y6
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22
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Lorvidhaya P, Stephen Huang SK. Sudden Cardiac Death in Athletes. Cardiology 2004; 100:186-95. [PMID: 14713730 DOI: 10.1159/000074812] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2003] [Accepted: 09/26/2003] [Indexed: 11/19/2022]
Abstract
Sudden cardiac death in athletes, although relatively uncommon, is a well-recognized condition generally associated with some congenital abnormalities. It, however, continues to be of vast interest to the public as athletes are seen as a distinct group of individuals who are especially able to tolerate more intense physical activities than the general population. Obviously, intense activities predispose susceptible athletes to sudden cardiac death, hence the importance of pre-participation screening tests. As the cost of healthcare continues to be on the rise, there will be increasing difficulty justifying a nation-wide method of screening cost-effectively. This article is intended to describe the possible underlying causes of sudden cardiac death discovered thus far, as well as methods for detection, pre-participation guidelines, and emerging therapy.
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MESH Headings
- Cause of Death
- Cost-Benefit Analysis
- Death, Sudden, Cardiac/etiology
- Death, Sudden, Cardiac/pathology
- Death, Sudden, Cardiac/prevention & control
- Heart Defects, Congenital/mortality
- Heart Defects, Congenital/pathology
- Heart Diseases/mortality
- Heart Diseases/pathology
- Humans
- Mass Screening/economics
- Practice Guidelines as Topic
- Risk
- Sports
- Tachycardia, Ventricular/complications
- Tachycardia, Ventricular/mortality
- United States
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Affiliation(s)
- Peem Lorvidhaya
- Division of Cardiology, Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, Tex. 79430-9410, USA
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23
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Rampazzo A, Beffagna G, Nava A, Occhi G, Bauce B, Noiato M, Basso C, Frigo G, Thiene G, Towbin J, Danieli GA. Arrhythmogenic right ventricular cardiomyopathy type 1 (ARVD1): confirmation of locus assignment and mutation screening of four candidate genes. Eur J Hum Genet 2003; 11:69-76. [PMID: 12529708 DOI: 10.1038/sj.ejhg.5200914] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2002] [Revised: 07/10/2002] [Accepted: 10/10/2002] [Indexed: 11/09/2022] Open
Abstract
Arrhythmogenic right ventricular cardiomyopathy type 1 (ARVD1) is an autosomal dominant disorder characterised by progressive degeneration of right ventricular myocardium, arrhythmias and risk of sudden death. By linkage analysis, we previously mapped the involved gene to chromosome 14q24.3. In the present study we report on linkage analysis of one additional and unrelated family, which enabled to confirm previous locus assignment. Another family is reported, in which genetic and clinical data suggest linkage to the same locus. Direct sequencing of DNA from individuals belonging to established ARVD1 families failed to detect causative mutations in exonic sequences of four genes (POMT2, TGFbeta3, KIAAA1036 and KIAA0759) expressed in the heart and which defects could possibly induce plasma membrane instability or apoptosis, key features of ARVD pathogenesis.
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24
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Abstract
Recent advances in molecular genetics of arrhythmogenic right ventricular cardiomyopathy (ARVD) are reviewed. In particular, the finding of mutations in the gene coding for cardiac ryanodine receptor (hRYR2), both in patients affected with ARVD2 and in patients affected with catecholaminergic ventricular arrhythmias or with familial ventricular tachyarrhythmia, is discussed. Novel data support the hypothesis that apoptosis may be a key step in molecular pathogenesis of ARVDs. A series of studies on drugs with apparent protective effect against apoptosis in myocardial cells might open new perspectives in the therapeutic approach.
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Affiliation(s)
- Gian Antonio Danieli
- Human Molecular Genetics Unit, Department of Biology, University of Padua, Italy.
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25
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