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Li J, Lin Y, Li D, He M, Kui H, Bai J, Chen Z, Gou Y, Zhang J, Wang T, Tang Q, Kong F, Jin L, Li M. Building Haplotype-Resolved 3D Genome Maps of Chicken Skeletal Muscle. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2305706. [PMID: 38582509 DOI: 10.1002/advs.202305706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 03/07/2024] [Indexed: 04/08/2024]
Abstract
Haplotype-resolved 3D chromatin architecture related to allelic differences in avian skeletal muscle development has not been addressed so far, although chicken husbandry for meat consumption has been prevalent feature of cultures on every continent for more than thousands of years. Here, high-resolution Hi-C diploid maps (1.2-kb maximum resolution) are generated for skeletal muscle tissues in chicken across three developmental stages (embryonic day 15 to day 30 post-hatching). The sequence features governing spatial arrangement of chromosomes and characterize homolog pairing in the nucleus, are identified. Multi-scale characterization of chromatin reorganization between stages from myogenesis in the fetus to myofiber hypertrophy after hatching show concordant changes in transcriptional regulation by relevant signaling pathways. Further interrogation of parent-of-origin-specific chromatin conformation supported that genomic imprinting is absent in birds. This study also reveals promoter-enhancer interaction (PEI) differences between broiler and layer haplotypes in skeletal muscle development-related genes are related to genetic variation between breeds, however, only a minority of breed-specific variations likely contribute to phenotypic divergence in skeletal muscle potentially via allelic PEI rewiring. Beyond defining the haplotype-specific 3D chromatin architecture in chicken, this study provides a rich resource for investigating allelic regulatory divergence among chicken breeds.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yu Lin
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Diyan Li
- School of Pharmacy, Chengdu University, Chengdu, 610106, China
| | - Mengnan He
- Wildlife Conservation Research Department, Chengdu Research Base of Giant Panda Breeding, Chengdu, 610057, China
| | - Hua Kui
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jingyi Bai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ziyu Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuwei Gou
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiaman Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tao Wang
- School of Pharmacy, Chengdu University, Chengdu, 610106, China
| | - Qianzi Tang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Fanli Kong
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Long Jin
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mingzhou Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
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Stonadge A, Genzor AV, Russell A, Hamed MF, Romero N, Evans G, Pownall ME, Bekker-Jensen S, Blanco G. Myofibrillar myopathy hallmarks associated with ZAK deficiency. Hum Mol Genet 2023; 32:2751-2770. [PMID: 37427997 PMCID: PMC10789240 DOI: 10.1093/hmg/ddad113] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023] Open
Abstract
The ZAK gene encodes two functionally distinct kinases, ZAKα and ZAKβ. Homozygous loss of function mutations affecting both isoforms causes a congenital muscle disease. ZAKβ is the only isoform expressed in skeletal muscle and is activated by muscle contraction and cellular compression. The ZAKβ substrates in skeletal muscle or the mechanism whereby ZAKβ senses mechanical stress remains to be determined. To gain insights into the pathogenic mechanism, we exploited ZAK-deficient cell lines, zebrafish, mice and a human biopsy. ZAK-deficient mice and zebrafish show a mild phenotype. In mice, comparative histopathology data from regeneration, overloading, ageing and sex conditions indicate that while age and activity are drivers of the pathology, ZAKβ appears to have a marginal role in myoblast fusion in vitro or muscle regeneration in vivo. The presence of SYNPO2, BAG3 and Filamin C (FLNC) in a phosphoproteomics assay and extended analyses suggested a role for ZAKβ in the turnover of FLNC. Immunofluorescence analysis of muscle sections from mice and a human biopsy showed evidence of FLNC and BAG3 accumulations as well as other myofibrillar myopathy markers. Moreover, endogenous overloading of skeletal muscle exacerbated the presence of fibres with FLNC accumulations in mice, indicating that ZAKβ signalling is necessary for an adaptive turnover of FLNC that allows for the normal physiological response to sustained mechanical stress. We suggest that accumulation of mislocalized FLNC and BAG3 in highly immunoreactive fibres contributes to the pathogenic mechanism of ZAK deficiency.
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Affiliation(s)
- Amy Stonadge
- York Biomedical Research Institute, Department of Biology, University of York, York, YO10 5DD, UK
| | - Aitana V Genzor
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Alex Russell
- York Biomedical Research Institute, Department of Biology, University of York, York, YO10 5DD, UK
| | - Mohamed F Hamed
- Department of Pathology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Norma Romero
- Unité de Morphologie Neuromusculaire Institut de Myologie - Inserm Sorbonne Université - GHU Pitié-Salpêtrière 47- 83, boulevard de l’Hôpital F-75 651 Paris, Cedex 13, France
| | - Gareth Evans
- York Biomedical Research Institute, Department of Biology, University of York, York, YO10 5DD, UK
| | - Mary Elizabeth Pownall
- York Biomedical Research Institute, Department of Biology, University of York, York, YO10 5DD, UK
| | - Simon Bekker-Jensen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Gonzalo Blanco
- York Biomedical Research Institute, Department of Biology, University of York, York, YO10 5DD, UK
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Sukhareva KS, Smolina NA, Churkina AI, Kalugina KK, Zhuk SV, Khudiakov AA, Khodot AA, Faggian G, Luciani GB, Sejersen T, Kostareva AA. Desmin mutations impact the autophagy flux in C2C12 cell in mutation-specific manner. Cell Tissue Res 2023; 393:357-375. [PMID: 37277577 PMCID: PMC10406715 DOI: 10.1007/s00441-023-03790-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 05/12/2023] [Indexed: 06/07/2023]
Abstract
Desmin is the main intermediate filament of striated and smooth muscle cells and plays a crucial role in maintaining the stability of muscle fiber during contraction and relaxation cycles. Being a component of Z-disk area, desmin integrates autophagic pathways, and the disturbance of Z-disk proteins' structure negatively affects chaperone-assisted selective autophagy (CASA). In the present study, we focused on alteration of autophagy flux in myoblasts expressing various Des mutations. We applied Western blotting, immunocytochemistry, RNA sequencing, and shRNA approach to demonstrate that DesS12F, DesA357P, DesL345P, DesL370P, and DesD399Y mutations. Mutation-specific effect on autophagy flux being most severe in aggregate-prone Des mutations such as DesL345P, DesL370P, and DesD399Y. RNA sequencing data confirmed the most prominent effect of these mutations on expression profile and, in particular, on autophagy-related genes. To verify CASA contribution to desmin aggregate formation, we suppressed CASA by knocking down Bag3 and demonstrated that it promoted aggregate formation and lead to downregulation of Vdac2 and Vps4a and upregulation of Lamp, Pink1, and Prkn. In conclusion, Des mutations showed a mutation-specific effect on autophagy flux in C2C12 cells with either a predominant impact on autophagosome maturation or on degradation and recycling processes. Aggregate-prone desmin mutations lead to the activation of basal autophagy level while suppressing the CASA pathway by knocking down Bag3 can promote desmin aggregate formation.
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Affiliation(s)
- K S Sukhareva
- Institute of Molecular Biology and Genetics, Almazov National Medical Research Centre, Saint-Petersburg, Russia.
- Graduate School of Life and Health Science, University of Verona, Verona, Italy.
| | - N A Smolina
- Institute of Molecular Biology and Genetics, Almazov National Medical Research Centre, Saint-Petersburg, Russia
| | - A I Churkina
- Institute of Molecular Biology and Genetics, Almazov National Medical Research Centre, Saint-Petersburg, Russia
| | - K K Kalugina
- Institute of Molecular Biology and Genetics, Almazov National Medical Research Centre, Saint-Petersburg, Russia
| | - S V Zhuk
- Institute of Molecular Biology and Genetics, Almazov National Medical Research Centre, Saint-Petersburg, Russia
| | - A A Khudiakov
- Institute of Molecular Biology and Genetics, Almazov National Medical Research Centre, Saint-Petersburg, Russia
| | - A A Khodot
- Institute of Molecular Biology and Genetics, Almazov National Medical Research Centre, Saint-Petersburg, Russia
| | - G Faggian
- Graduate School of Life and Health Science, University of Verona, Verona, Italy
| | - G B Luciani
- Graduate School of Life and Health Science, University of Verona, Verona, Italy
| | - T Sejersen
- Department of Women's and Children's Health, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
- Department of Neuropaediatrics, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - A A Kostareva
- Institute of Molecular Biology and Genetics, Almazov National Medical Research Centre, Saint-Petersburg, Russia
- Department of Women's and Children's Health, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
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Casey JG, Kim ES, Joseph R, Li F, Granzier H, Gupta VA. NRAP reduction rescues sarcomere defects in nebulin-related nemaline myopathy. Hum Mol Genet 2023; 32:1711-1721. [PMID: 36661122 PMCID: PMC10162428 DOI: 10.1093/hmg/ddad011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/18/2022] [Accepted: 01/17/2023] [Indexed: 01/21/2023] Open
Abstract
Nemaline myopathy (NM) is a rare neuromuscular disorder associated with congenital or childhood-onset of skeletal muscle weakness and hypotonia, which results in limited motor function. NM is a genetic disorder and mutations in 12 genes are known to contribute to autosomal dominant or recessive forms of the disease. Recessive mutations in nebulin (NEB) are the most common cause of NM affecting about 50% of patients. Because of the large size of the NEB gene and lack of mutational hot spots, developing therapies that can benefit a wide group of patients is challenging. Although there are several promising therapies under investigation, there is no cure for NM. Therefore, targeting disease modifiers that can stabilize or improve skeletal muscle function may represent alternative therapeutic strategies. Our studies have identified Nrap upregulation in nebulin deficiency that contributes to structural and functional deficits in NM. We show that genetic ablation of nrap in nebulin deficiency restored sarcomeric disorganization, reduced protein aggregates and improved skeletal muscle function in zebrafish. Our findings suggest that Nrap is a disease modifier that affects skeletal muscle structure and function in NM; thus, therapeutic targeting of Nrap in nebulin-related NM and related diseases may be beneficial for patients.
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Affiliation(s)
- Jennifer G Casey
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Euri S Kim
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Remi Joseph
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Frank Li
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Henk Granzier
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Vandana A Gupta
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
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5
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Singh SR, Kadioglu H, Patel K, Carrier L, Agnetti G. Is Desmin Propensity to Aggregate Part of its Protective Function? Cells 2020; 9:cells9020491. [PMID: 32093415 PMCID: PMC7072738 DOI: 10.3390/cells9020491] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 02/17/2020] [Indexed: 12/19/2022] Open
Abstract
Desmin is the major protein component of the intermediate filaments (IFs) cytoskeleton in muscle cells, including cardiac. The accumulation of cleaved and misfolded desmin is a cellular hallmark of heart failure (HF). These desmin alterations are reversed by therapy, suggesting a causal role for the IFs in the development of HF. Though IFs are known to play a role in the protection from stress, a mechanistic model of how that occurs is currently lacking. On the other hand, the heart is uniquely suited to study the function of the IFs, due to its inherent, cyclic contraction. That is, HF can be used as a model to address how IFs afford protection from mechanical, and possibly redox, stress. In this review we provide a brief summary of the current views on the function of the IFs, focusing on desmin. We also propose a new model according to which the propensity of desmin to aggregate may have been selected during evolution as a way to dissipate excessive mechanical and possibly redox stress. According to this model, though desmin misfolding may afford protection from acute injury, the sustained or excessive accumulation of desmin aggregates could impair proteostasis and contribute to disease.
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Affiliation(s)
- Sonia R. Singh
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (S.R.S.); (L.C.)
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Hikmet Kadioglu
- Center for Research on Cardiac Intermediate Filaments, Johns Hopkins University, Baltimore, MD 21205, USA; (H.K.); (K.P.)
| | - Krishna Patel
- Center for Research on Cardiac Intermediate Filaments, Johns Hopkins University, Baltimore, MD 21205, USA; (H.K.); (K.P.)
| | - Lucie Carrier
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (S.R.S.); (L.C.)
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, 20246 Hamburg, Germany
| | - Giulio Agnetti
- Center for Research on Cardiac Intermediate Filaments, Johns Hopkins University, Baltimore, MD 21205, USA; (H.K.); (K.P.)
- DIBINEM, University of Bologna, 40126 Bologna, Italy
- Correspondence:
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6
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Murphy S, Dowling P, Zweyer M, Swandulla D, Ohlendieck K. Proteomic profiling of giant skeletal muscle proteins. Expert Rev Proteomics 2019; 16:241-256. [DOI: 10.1080/14789450.2019.1575205] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland
| | - Margit Zweyer
- Institute of Physiology II, University of Bonn, Bonn, Germany
| | | | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland
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7
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Valberg SJ, Perumbakkam S, McKenzie EC, Finno CJ. Proteome and transcriptome profiling of equine myofibrillar myopathy identifies diminished peroxiredoxin 6 and altered cysteine metabolic pathways. Physiol Genomics 2018; 50:1036-1050. [PMID: 30289745 PMCID: PMC6337024 DOI: 10.1152/physiolgenomics.00044.2018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Equine myofibrillar myopathy (MFM) causes exertional muscle pain and is characterized by myofibrillar disarray and ectopic desmin aggregates of unknown origin. To investigate the pathophysiology of MFM, we compared resting and 3 h postexercise transcriptomes of gluteal muscle and the resting skeletal muscle proteome of MFM and control Arabian horses with RNA sequencing and isobaric tags for relative and absolute quantitation analyses. Three hours after exercise, 191 genes were identified as differentially expressed (DE) in MFM vs. control muscle with >1 log2 fold change (FC) in genes involved in sulfur compound/cysteine metabolism such as cystathionine-beta-synthase ( CBS, ↓4.51), a cysteine and neutral amino acid membrane transporter ( SLC7A10, ↓1.80 MFM), and a cationic transporter (SLC24A1, ↓1.11 MFM). In MFM vs. control at rest, 284 genes were DE with >1 log2 FC in pathways for structure morphogenesis, fiber organization, tissue development, and cell differentiation including > 1 log2 FC in cardiac alpha actin ( ACTC1 ↑2.5 MFM), cytoskeletal desmoplakin ( DSP ↑2.4 MFM), and basement membrane usherin ( USH2A ↓2.9 MFM). Proteome analysis revealed significantly lower antioxidant peroxiredoxin 6 content (PRDX6, ↓4.14 log2 FC MFM), higher fatty acid transport enzyme carnitine palmitoyl transferase (CPT1B, ↑3.49 MFM), and lower sarcomere protein tropomyosin (TPM2, ↓3.24 MFM) in MFM vs. control muscle at rest. We propose that in MFM horses, altered cysteine metabolism and a deficiency of cysteine-containing antioxidants combined with a high capacity to oxidize fatty acids and generate ROS during aerobic exercise causes chronic oxidation and aggregation of key proteins such as desmin.
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Affiliation(s)
- Stephanie J Valberg
- McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, Michigan.,Department of Population Sciences, University of Minnesota , St. Paul, Minnesota
| | - Sudeep Perumbakkam
- Department of Large Animal Clinical Sciences, Michigan State University , East Lansing, Michigan
| | - Erica C McKenzie
- Department of Clinical Sciences, Carlson College of Veterinary Medicine, Oregon State University , Corvallis, Oregon
| | - Carrie J Finno
- Department of Population Health and Reproduction, University of California Davis , Davis, California
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Xiong Q, Fischer S, Karow M, Müller R, Meßling S, Eichinger L. ATG16 mediates the autophagic degradation of the 19S proteasomal subunits PSMD1 and PSMD2. Eur J Cell Biol 2018; 97:523-532. [PMID: 30269947 DOI: 10.1016/j.ejcb.2018.09.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 08/06/2018] [Accepted: 09/10/2018] [Indexed: 12/27/2022] Open
Abstract
Autophagy and the ubiquitin proteasome system are the two major cellular processes for protein and organelle recycling and clearance in eukaryotic cells. Evidence is accumulating that these two pathways are interrelated through adaptor proteins. Here, we found that PSMD1 and PSMD2, both components of the 19S regulatory particle of the proteasome, directly interact with Dictyostelium discoideum autophagy 16 (ATG16), a core autophagosomal protein. ATG16 is composed of an N-terminal domain, which is responsible for homo-dimerization and binding to ATG5 and a C-terminal β-propeller structure. Deletion analysis of ATG16 showed that the N-terminal half of ATG16 interacted directly only with PSMD1, while the C-terminal half interacted with both, PSMD1 and PSMD2. RFP-tagged PSMD1 as well as PSMD2 were enriched in large puncta, reminiscent of autophagosomes, in wild-type cells. These puncta were absent in atg16‾ and atg9‾/16‾ cells and weaker and less frequent in atg9‾ cells, showing that ATG16 was crucial and the autophagic process important for their formation. Co-expression of ATG16-GFP or GFP-ATG8a(LC3) with RFP-PSMD1 or RFP-PSMD2, respectively, in atg16‾ or wild-type cells revealed many instances of co-localization, suggesting that RFP-PSMD1 or RFP-PSMD2 positive puncta constitute autophagosomes. LysoTracker® labeling and a proteolytic cleavage assay confirmed that PSMD1 and PSMD2 were present in lysosomes in wild-type cells. In vivo, ATG16 is required for their enrichment in ATG8a positive puncta, which mature into autolysosomes. We propose that ATG16 links autophagy and the ubiquitin proteasome system.
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Affiliation(s)
- Qiuhong Xiong
- Center for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany.; Institute of Biomedical Sciences, Shanxi University, No. 92 Wucheng Road, 030006 Taiyuan, Shanxi, China
| | - Sarah Fischer
- Center for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - Malte Karow
- Center for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - Rolf Müller
- Center for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - Susanne Meßling
- Center for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - Ludwig Eichinger
- Center for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany..
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Lin IH, Chang JL, Hua K, Huang WC, Hsu MT, Chen YF. Skeletal muscle in aged mice reveals extensive transformation of muscle gene expression. BMC Genet 2018; 19:55. [PMID: 30089464 PMCID: PMC6083496 DOI: 10.1186/s12863-018-0660-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 07/26/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Aging leads to decreased skeletal muscle function in mammals and is associated with a progressive loss of muscle mass, quality and strength. Age-related muscle loss (sarcopenia) is an important health problem associated with the aged population. RESULTS We investigated the alteration of genome-wide transcription in mouse skeletal muscle tissue (rectus femoris muscle) during aging using a high-throughput sequencing technique. Analysis revealed significant transcriptional changes between skeletal muscles of mice at 3 (young group) and 24 (old group) months of age. Specifically, genes associated with energy metabolism, cell proliferation, muscle myosin isoforms, as well as immune functions were found to be altered. We observed several interesting gene expression changes in the elderly, many of which have not been reported before. CONCLUSIONS Those data expand our understanding of the various compensatory mechanisms that can occur with age, and further will assist in the development of methods to prevent and attenuate adverse outcomes of aging.
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Affiliation(s)
- I-Hsuan Lin
- VYM Genome Research Center, National Yang-Ming University, Taipei, 112, Taiwan
| | - Junn-Liang Chang
- Department of Pathology & Laboratory Medicine, Taoyuan Armed Forces General Hospital, Taoyuan, 325, Taiwan
| | - Kate Hua
- VYM Genome Research Center, National Yang-Ming University, Taipei, 112, Taiwan
| | - Wan-Chen Huang
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, No.250, Wu-Hsing Street, Taipei, 11031, Taiwan
| | - Ming-Ta Hsu
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, 112, Taiwan
| | - Yi-Fan Chen
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, No.250, Wu-Hsing Street, Taipei, 11031, Taiwan.
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10
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Capitanio D, Moriggi M, Gelfi C. Mapping the human skeletal muscle proteome: progress and potential. Expert Rev Proteomics 2017; 14:825-839. [PMID: 28780899 DOI: 10.1080/14789450.2017.1364996] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
INTRODUCTION Human skeletal muscle represents 40% of our body mass and deciphering its proteome composition to further understand mechanisms regulating muscle function under physiological and pathological conditions has proved a challenge. The inter-individual variability, the presence of structurally and functionally different muscle types and the high protein dynamic range require carefully selected methodologies for the assessment of the muscle proteome. Furthermore, physiological studies are understandingly hampered by ethical issues related to biopsies on healthy subjects, making it difficult to recruit matched controls essential for comparative studies. Areas covered: This review critically analyses studies performed on muscle to date and identifies what still remains unknown or poorly investigated in physiological and pathological states, such as training, aging, metabolic disorders and muscular dystrophies. Expert commentary: Efforts should be made on biological fluid analyses targeting low abundant/low molecular weight fragments generated from muscle cell disruption to improve diagnosis and clinical monitoring. From a methodological point of view, particular attention should be paid to improve the characterization of intact proteins and unknown post translational modifications to better understand the molecular mechanisms of muscle disorders.
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Affiliation(s)
- Daniele Capitanio
- a Department of Biomedical Sciences for Health , University of Milan , Segrate , Milan , Italy
| | - Manuela Moriggi
- a Department of Biomedical Sciences for Health , University of Milan , Segrate , Milan , Italy
| | - Cecilia Gelfi
- a Department of Biomedical Sciences for Health , University of Milan , Segrate , Milan , Italy
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11
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Shintani-Domoto Y, Hayasaka T, Maeda D, Masaki N, Ito TK, Sakuma K, Tanaka M, Kabashima K, Takei S, Setou M, Fukayama M. Different desmin peptides are distinctly deposited in cytoplasmic aggregations and cytoplasm of desmin-related cardiomyopathy patients. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:828-836. [PMID: 28341603 DOI: 10.1016/j.bbapap.2017.03.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 11/16/2022]
Abstract
Desmin-related cardiomyopathy is a heterogeneous group of myofibrillar myopathies characterized by aggregates of desmin and related proteins in myocytes. It has been debated how the expression and protein structure are altered in the aggregates and other parts of myocytes in patients. To address this question, we investigated the proteome quantification as well as localization in formalin-fixed and paraffin-embedded specimens of the heart of patients by imaging mass spectrometry and liquid chromatography-mass spectrometry analyses. Fifteen tryptic peptide signals were enriched in the desmin-related cardiomyopathy myocardium, twelve of which were identified as desmin peptides with 14.3- to 27.3-fold increase compared to normal hearts. High-intensity signals at m/z 1032.5 and 1002.5, which were desmin peptides 59-70 at the head portion and 213-222 at the 1B domain, were with infrequent colocalization distributed not only in desmin-positive intracytoplasmic aggregates but also in histologically normal cytoplasm, indicating that desmin protein is fragmented and different types of naturally-occurring truncated proteins ectopically assemble throughout the heart of patients. Thus, in addition to conventional histological identification of protein aggregates, specific desmin peptides show a marked difference in quantity and localization in a tissue section of desmin-related cardiomyopathy and differentiate from other cardiomyopathies. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
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Affiliation(s)
- Yukako Shintani-Domoto
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takahiro Hayasaka
- Laboratory for Advanced Lipid Analysis, Health Innovation & Technology Center, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan; Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Daichi Maeda
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Cellular and Organ Pathology, Akita University, Akita, Japan
| | - Noritaka Masaki
- Department of Medical Spectroscopy, Institute for Medical Photonics Research, Preeminent Medical Photonics Education &Research Center, Hamamatsu University School of Medicine, Hamamatsu, Japan; Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Takashi K Ito
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan; International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kei Sakuma
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Michio Tanaka
- Department of Pathology, Tokyo Metropolitan Hiroo Hospital, Tokyo, Japan
| | - Katsuya Kabashima
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan; International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Shiro Takei
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan; International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Mitsutoshi Setou
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan; International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, Japan; Preeminent Medical Photonics Education & Research Center, Hamamatsu University School of Medicine, Hamamatsu, Japan; Riken Center for Molecular Imaging Science, Kobe, Japan; Department of Anatomy, The University of Hong Kong, Hong Kong, China; Division of Neural Systematics, National Institute for Physiological Sciences, Okazaki, Japan.
| | - Masashi Fukayama
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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12
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Gonzalez-Freire M, Semba RD, Ubaida-Mohien C, Fabbri E, Scalzo P, Højlund K, Dufresne C, Lyashkov A, Ferrucci L. The Human Skeletal Muscle Proteome Project: a reappraisal of the current literature. J Cachexia Sarcopenia Muscle 2017; 8:5-18. [PMID: 27897395 PMCID: PMC5326819 DOI: 10.1002/jcsm.12121] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 03/11/2016] [Accepted: 04/05/2016] [Indexed: 12/14/2022] Open
Abstract
Skeletal muscle is a large organ that accounts for up to half the total mass of the human body. A progressive decline in muscle mass and strength occurs with ageing and in some individuals configures the syndrome of 'sarcopenia', a condition that impairs mobility, challenges autonomy, and is a risk factor for mortality. The mechanisms leading to sarcopenia as well as myopathies are still little understood. The Human Skeletal Muscle Proteome Project was initiated with the aim to characterize muscle proteins and how they change with ageing and disease. We conducted an extensive review of the literature and analysed publically available protein databases. A systematic search of peer-reviewed studies was performed using PubMed. Search terms included 'human', 'skeletal muscle', 'proteome', 'proteomic(s)', and 'mass spectrometry', 'liquid chromatography-mass spectrometry (LC-MS/MS)'. A catalogue of 5431 non-redundant muscle proteins identified by mass spectrometry-based proteomics from 38 peer-reviewed scientific publications from 2002 to November 2015 was created. We also developed a nosology system for the classification of muscle proteins based on localization and function. Such inventory of proteins should serve as a useful background reference for future research on changes in muscle proteome assessed by quantitative mass spectrometry-based proteomic approaches that occur with ageing and diseases. This classification and compilation of the human skeletal muscle proteome can be used for the identification and quantification of proteins in skeletal muscle to discover new mechanisms for sarcopenia and specific muscle diseases that can be targeted for the prevention and treatment.
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Affiliation(s)
| | - Richard D Semba
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Elisa Fabbri
- National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Paul Scalzo
- National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Kurt Højlund
- Department of Endocrinology, Odense University Hospital, Odense, Denmark.,Institute of Clinical Research and Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | | | - Alexey Lyashkov
- National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Luigi Ferrucci
- National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
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13
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Dowling P, Murphy S, Ohlendieck K. Proteomic profiling of muscle fibre type shifting in neuromuscular diseases. Expert Rev Proteomics 2016; 13:783-99. [DOI: 10.1080/14789450.2016.1209416] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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14
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Exome sequencing identifies variants in two genes encoding the LIM-proteins NRAP and FHL1 in an Italian patient with BAG3 myofibrillar myopathy. J Muscle Res Cell Motil 2016; 37:101-15. [PMID: 27443559 PMCID: PMC5010835 DOI: 10.1007/s10974-016-9451-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/09/2016] [Indexed: 11/06/2022]
Abstract
Myofibrillar myopathies (MFMs) are genetically heterogeneous dystrophies characterized by the disintegration of Z-disks and myofibrils and are associated with mutations in genes encoding Z-disk or Z-disk-related proteins. The c.626 C > T (p.P209L) mutation in the BAG3 gene has been described as causative of a subtype of MFM. We report a sporadic case of a 26-year-old Italian woman, affected by MFM with axonal neuropathy, cardiomyopathy, rigid spine, who carries the c.626 C > T mutation in the BAG3 gene. The patient and her non-consanguineous healthy parents and brother were studied with whole exome sequencing (WES) to further investigate the genetic basis of this complex phenotype. In the patient, we found that the BAG3 mutation is associated with variants in the NRAP and FHL1 genes that encode muscle-specific, LIM domain containing proteins. Quantitative real time PCR, immunohistochemistry and Western blot analysis of the patient’s muscular biopsy showed the absence of NRAP expression and FHL1 accumulation in aggregates in the affected skeletal muscle tissue. Molecular dynamic analysis of the mutated FHL1 domain showed a modification in its surface charge, which could affect its capability to bind its target proteins. To our knowledge this is the first study reporting, in a BAG3 MFM, the simultaneous presence of genetic variants in the BAG3 and FHL1 genes (previously described as independently associated with MFMs) and linking the NRAP gene to MFM for the first time.
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15
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Ruparelia AA, Oorschot V, Ramm G, Bryson-Richardson RJ. FLNC myofibrillar myopathy results from impaired autophagy and protein insufficiency. Hum Mol Genet 2016; 25:2131-2142. [PMID: 26969713 DOI: 10.1093/hmg/ddw080] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 03/07/2016] [Indexed: 01/23/2023] Open
Abstract
Myofibrillar myopathy is a progressive muscle disease characterized by the disintegration of muscle fibers and formation of protein aggregates. Causative mutations have been identified in nine genes encoding Z-disk proteins, including the actin binding protein filamin C (FLNC). To investigate the mechanism of disease in FLNCW2710X myopathy we overexpressed fluorescently tagged FLNC or FLNCW2710X in zebrafish. Expression of FLNCW2710X causes formation of protein aggregates but surprisingly, our studies reveal that the mutant protein localizes correctly to the Z-disk and is capable of rescuing the fiber disintegration phenotype that results from FLNC knockdown. This demonstrates that the functions necessary for muscle integrity are not impaired, and suggests that it is the formation of protein aggregates and subsequent sequestration of FLNC away from the Z-disk that results in myofibrillar disintegration. Similar to those found in patients, the aggregates in FLNCW2710X expressing fish contain the co-chaperone BAG3. FLNC is a target of the BAG3-mediated chaperone assisted selective autophagy (CASA) pathway and therefore we investigated its role, and the role of autophagy in general, in clearing protein aggregates. We reveal that despite BAG3 recruitment to the aggregates they are not degraded via CASA. Additionally, recruitment of BAG3 is sufficient to block alternative autophagy pathways which would otherwise clear the aggregates. This blockage can be relieved by reducing BAG3 levels or by stimulating autophagy. This study therefore identifies both BAG3 reduction and autophagy promotion as potential therapies for FLNCW2710X myofibrillar myopathy, and identifies protein insufficiency due to sequestration, compounded by impaired autophagy, as the cause.
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Affiliation(s)
| | - Viola Oorschot
- The Clive and Vera Ramaciotti Centre for Structural Cryo-Electron Microscopy and and
| | - Georg Ramm
- The Clive and Vera Ramaciotti Centre for Structural Cryo-Electron Microscopy and and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
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16
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Brinkmeier H, Ohlendieck K. Chaperoning heat shock proteins: Proteomic analysis and relevance for normal and dystrophin-deficient muscle. Proteomics Clin Appl 2014; 8:875-95. [DOI: 10.1002/prca.201400015] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 04/24/2014] [Accepted: 05/28/2014] [Indexed: 12/15/2022]
Affiliation(s)
| | - Kay Ohlendieck
- Department of Biology; National University of Ireland; Maynooth Co. Kildare Ireland
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17
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Schessl J, Bach E, Rost S, Feldkirchner S, Kubny C, Müller S, Hanisch FG, Kress W, Schoser B. Novel recessive myotilin mutation causes severe myofibrillar myopathy. Neurogenetics 2014; 15:151-6. [PMID: 24928145 DOI: 10.1007/s10048-014-0410-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 06/02/2014] [Indexed: 01/21/2023]
Abstract
We identified the first homozygous and hence recessive mutation in the myotilin gene (MYOT) in a family affected by a severe myofibrillar myopathy (MFM). MFM is a rare, progressive and devastating disease of human skeletal muscle with distinct histopathological pattern of protein aggregates and myofibrillar degeneration. So far, only heterozygous missense mutations in MYOT have been associated with autosomal dominant myofibrillar myopathy, limb-girdle muscular dystrophy type 1A and distal myopathy. Myotilin itself is highly expressed in skeletal and cardiac muscle and is localized at the Z-disc and therefore interacts in sarcomere assembly. We performed whole-exome sequencing in a German family clinically diagnosed with MFM and identified a homozygous mutation in exon 2, c.16C > G (p.Arg6Gly). Using laser microdissection followed by quantitative mass spectrometry, we identified the myotilin protein as one component showing the highest increased abundance in the aggregates in the index patient. We suggest that the combined approach has a high potential as a new tool for the confirmation of unclassified variants which are found in whole-exome sequencing approaches.
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Affiliation(s)
- Joachim Schessl
- Friedrich-Baur-Institute, Department of Neurology, Ludwig-Maximilians University of Munich, Ziemssenstr. 1 A, 80336, Munich, Germany,
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18
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Abstract
PURPOSE OF REVIEW Myofibrillar myopathies (MFMs) are a heterogeneous group of skeletal and cardiac muscle diseases. In this review, we highlight recent discoveries of new genes and disease mechanisms involved in this group of disorders. RECENT FINDINGS The advent of next-generation sequencing technology, laser microdissection and mass spectrometry-based proteomics has facilitated the discovery of new MFM causative genes and pathomechanisms. New mutations have also been discovered in 'older' genes, helping to find a classification niche for MFM-linked disorders showing variant phenotypes. Cell transfection experiments using primary cultured myoblasts and newer animal models provide insights into the pathogenesis of MFMs. SUMMARY An increasing number of genes are involved in the causation of variant subtypes of MFM. The application of modern technologies in combination with classical histopathological and ultrastructural studies is helping to establish the molecular diagnosis and reach a better understanding of the pathogenic mechanisms of each MFM subtype, thus putting an emphasis on the development of specific means for prevention and therapy of these incapacitating and frequently fatal diseases.
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Ye H, Mandal R, Catherman A, Thomas PM, Kelleher NL, Ikonomidou C, Li L. Top-down proteomics with mass spectrometry imaging: a pilot study towards discovery of biomarkers for neurodevelopmental disorders. PLoS One 2014; 9:e92831. [PMID: 24710523 PMCID: PMC3978070 DOI: 10.1371/journal.pone.0092831] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 02/27/2014] [Indexed: 11/19/2022] Open
Abstract
In the developing mammalian brain, inhibition of NMDA receptor can induce widespread neuroapoptosis, inhibit neurogenesis and cause impairment of learning and memory. Although some mechanistic insights into adverse neurological actions of these NMDA receptor antagonists exist, our understanding of the full spectrum of developmental events affected by early exposure to these chemical agents in the brain is still limited. Here we attempt to gain insights into the impact of pharmacologically induced excitatory/inhibitory imbalance in infancy on the brain proteome using mass spectrometric imaging (MSI). Our goal was to study changes in protein expression in postnatal day 10 (P10) rat brains following neonatal exposure to the NMDA receptor antagonist dizocilpine (MK801). Analysis of rat brains exposed to vehicle or MK801 and comparison of their MALDI MS images revealed differential relative abundances of several proteins. We then identified these markers such as ubiquitin, purkinje cell protein 4 (PEP-19), cytochrome c oxidase subunits and calmodulin, by a combination of reversed-phase (RP) HPLC fractionation and top-down tandem MS platform. More in-depth large scale study along with validation experiments will be carried out in the future. Overall, our findings indicate that a brief neonatal exposure to a compound that alters excitatory/inhibitory balance in the brain has a long term effect on protein expression patterns during subsequent development, highlighting the utility of MALDI-MSI as a discovery tool for potential biomarkers.
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Affiliation(s)
- Hui Ye
- State Key Laboratory of Natural Medicines, Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, PR China
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, PR China
- School of Pharmacy, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Rakesh Mandal
- Department of Neurology, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Adam Catherman
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, United States of America
| | - Paul M. Thomas
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, United States of America
| | - Neil L. Kelleher
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, United States of America
| | - Chrysanthy Ikonomidou
- Department of Neurology, University of Wisconsin Madison, Madison, Wisconsin, United States of America
- * E-mail: (CI); (LL)
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin Madison, Madison, Wisconsin, United States of America
- Department of Chemistry, University of Wisconsin Madison, Madison, Wisconsin, United States of America
- * E-mail: (CI); (LL)
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20
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Bertrand AT, Bönnemann CG, Bonne G. 199th ENMC international workshop: FHL1 related myopathies, June 7-9, 2013, Naarden, The Netherlands. Neuromuscul Disord 2014; 24:453-62. [PMID: 24613424 DOI: 10.1016/j.nmd.2014.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 02/04/2014] [Indexed: 02/04/2023]
Affiliation(s)
- Anne T Bertrand
- Inserm, U974, Paris F-75013, France; Sorbonne Universités, UPMC Univ Paris 06, Myology Center of Research, UM76; CNRS FRE 3617, Institut de Myologie, Paris F-75013, France
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Gisèle Bonne
- Inserm, U974, Paris F-75013, France; Sorbonne Universités, UPMC Univ Paris 06, Myology Center of Research, UM76; CNRS FRE 3617, Institut de Myologie, Paris F-75013, France; AP-HP, Groupe Hospitalier Pitié-Salpêtrière, U.F. Cardiogénétique et Myogénétique Moléculaire, Service de Biochimie Métabolique, Paris F-75013, France.
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Abu-Amero KK, Bosley TM, Kondkar AA, Oystreck DT, Khan AO. CCDD Phenotype Associated with a Small Chromosome 2 Deletion. Semin Ophthalmol 2014; 30:435-42. [PMID: 24475916 DOI: 10.3109/08820538.2013.874474] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE Some individuals are born with congenital limitation of ocular motility, often associated with ptosis and retraction of the globe. Many of these disorders are now known as the congenital cranial dysinnervation disorders (CCDDs). While several genes have been associated with CCDD phenotypes, there are still patients for whom the genetic basis has not been identified. METHODS Clinical evaluation and neuroimaging, sequencing of candidate genes, and array comparative genomic hybridization (array CGH). RESULTS The patient was a four-year-old girl with mild dysmorphism; bilateral mild ptosis; substantial limitation of abduction OS with milder limitations of abduction OD, adduction OS, and vertical gaze OS; and retraction OS > OD on attempted adduction. No mutations were detected in the HOXA1, KIF21A, SALL4, TUBB3, and CHN1 genes. Array CGH revealed a 8 Kb de novo deletion on chromosome 2 (2q24.3) that encompassed a portion of only one gene, the Xin Actin-binding Repeat containing 2 (Gene Symbol XIRP2; NM_001079810). This gene encodes a protein that is involved in muscle development and protecting actin filaments from depolymerization. It interacts functionally with 10 other proteins playing a similar role in muscle development. CONCLUSIONS This patient's chromosomal abnormality affected only one gene that currently seems involved only in muscle development. All other genes currently associated with the CCDDs affect neurologic development. Genetic information from this patient implies that genes involved in development and maintenance of extraocular muscles can cause congenital ocular motility disorders as well.
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Affiliation(s)
- Khaled K Abu-Amero
- a Department of Ophthalmology , College of Medicine, King Saud University , Riyadh , Saudi Arabia .,b Department of Ophthalmology , College of Medicine, University of Florida , Jacksonville , Florida , USA
| | - Thomas M Bosley
- a Department of Ophthalmology , College of Medicine, King Saud University , Riyadh , Saudi Arabia
| | - Altaf A Kondkar
- a Department of Ophthalmology , College of Medicine, King Saud University , Riyadh , Saudi Arabia
| | - Darren T Oystreck
- a Department of Ophthalmology , College of Medicine, King Saud University , Riyadh , Saudi Arabia .,c Division of Ophthalmology, Faculty of Health Sciences , University of Stellenbosch , Tygerberg , South Africa , and
| | - Arif O Khan
- d Division of Pediatric Ophthalmology , King Khaled Eye Specialist Hospital , Riyadh , Saudi Arabia
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Feldkirchner S, Walter MC, Müller S, Kubny C, Krause S, Kress W, Hanisch FG, Schoser B, Schessl J. Proteomic characterization of aggregate components in an intrafamilial variable FHL1-associated myopathy. Neuromuscul Disord 2013; 23:418-26. [DOI: 10.1016/j.nmd.2013.02.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 02/09/2013] [Indexed: 11/28/2022]
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Maerkens A, Kley RA, Olivé M, Theis V, van der Ven PFM, Reimann J, Milting H, Schreiner A, Uszkoreit J, Eisenacher M, Barkovits K, Güttsches AK, Tonillo J, Kuhlmann K, Meyer HE, Schröder R, Tegenthoff M, Fürst DO, Müller T, Goldfarb LG, Vorgerd M, Marcus K. Differential proteomic analysis of abnormal intramyoplasmic aggregates in desminopathy. J Proteomics 2013; 90:14-27. [PMID: 23639843 DOI: 10.1016/j.jprot.2013.04.026] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 04/03/2013] [Accepted: 04/18/2013] [Indexed: 11/27/2022]
Abstract
UNLABELLED Desminopathy is a subtype of myofibrillar myopathy caused by desmin mutations and characterized by protein aggregates accumulating in muscle fibers. The aim of this study was to assess the protein composition of these aggregates. Aggregates and intact myofiber sections were obtained from skeletal muscle biopsies of five desminopathy patients by laser microdissection and analyzed by a label-free spectral count-based proteomic approach. We identified 397 proteins with 22 showing significantly higher spectral indices in aggregates (ratio >1.8, p<0.05). Fifteen of these proteins not previously reported as specific aggregate components provide new insights regarding pathomechanisms of desminopathy. Results of proteomic analysis were supported by immunolocalization studies and parallel reaction monitoring. Three mutant desmin variants were detected directly on the protein level as components of the aggregates, suggesting their direct involvement in aggregate-formation and demonstrating for the first time that proteomic analysis can be used for direct identification of a disease-causing mutation in myofibrillar myopathy. Comparison of the proteomic results in desminopathy with our previous analysis of aggregate composition in filaminopathy, another myofibrillar myopathy subtype, allows to determine subtype-specific proteomic profile that facilitates identification of the specific disorder. BIOLOGICAL SIGNIFICANCE Our proteomic analysis provides essential new insights in the composition of pathological protein aggregates in skeletal muscle fibers of desminopathy patients. The results contribute to a better understanding of pathomechanisms in myofibrillar myopathies and provide the basis for hypothesis-driven studies. The detection of specific proteomic profiles in different myofibrillar myopathy subtypes indicates that proteomic analysis may become a useful tool in differential diagnosis of protein aggregate myopathies.
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Affiliation(s)
- A Maerkens
- Department of Neurology, Neuromuscular Centre Ruhrgebiet, University Hospital Bergmannsheil, Ruhr-University Bochum, Bochum, Germany
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