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Lin Y, Sun L, Lv Y, Liao R, Zhang K, Zhou J, Zhang S, Xu J, He M, Wu C, Zhang D, Shen X, Dai J, Gao J. Transcriptomic and metabolomic dissection of skeletal muscle of crossbred Chongming white goats with different meat production performance. BMC Genomics 2024; 25:443. [PMID: 38704563 PMCID: PMC11069289 DOI: 10.1186/s12864-024-10304-3] [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: 10/07/2023] [Accepted: 04/12/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND The transcriptome and metabolome dissection of the skeletal muscle of high- and low- growing individuals from a crossbred population of the indigenous Chongming white goat and the Boer goat were performed to discover the potential functional differentially expressed genes (DEGs) and differential expression metabolites (DEMs). RESULTS A total of 2812 DEGs were detected in 6 groups at three time stages (3,6,12 Month) in skeletal muscle using the RNA-seq method. A DEGs set containing seven muscle function related genes (TNNT1, TNNC1, TNNI1, MYBPC2, MYL2, MHY7, and CSRP3) was discovered, and their expression tended to increase as goat muscle development progressed. Seven DEGs (TNNT1, FABP3, TPM3, DES, PPP1R27, RCAN1, LMOD2) in the skeletal muscle of goats in the fast-growing and slow-growing groups was verified their expression difference by reverse transcription-quantitative polymerase chain reaction. Further, through the Liquid chromatography-mass spectrometry (LC-MS) approach, a total of 183 DEMs in various groups of the muscle samples and these DEMs such as Queuine and Keto-PGF1α, which demonstrated different abundance between the goat fast-growing group and slow-growing group. Through weighted correlation network analysis (WGCNA), the study correlated the DEGs with the DEMs and identified 4 DEGs modules associated with 18 metabolites. CONCLUSION This study benefits to dissection candidate genes and regulatory networks related to goat meat production performance, and the joint analysis of transcriptomic and metabolomic data provided insights into the study of goat muscle development.
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Affiliation(s)
- Yuexia Lin
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
| | - Lingwei Sun
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Yuhua Lv
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
| | - Rongrong Liao
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
| | - Keqing Zhang
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
| | - Jinyong Zhou
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
| | - Shushan Zhang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Jiehuan Xu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Mengqian He
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Caifeng Wu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Defu Zhang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Xiaohui Shen
- Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
| | - Jianjun Dai
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China.
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China.
| | - Jun Gao
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China.
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China.
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Yavaş C, Doğan M, Eröz R, Türegün K. A rare TNNT1 gene variant causing creatine kinase elevation in nemaline myopathy: c.271_273del (p.Lys91del). Genes Genomics 2024; 46:613-620. [PMID: 38363456 DOI: 10.1007/s13258-024-01502-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/01/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND Nemaline Myopathy (NM) is a rare genetic disorder that affects muscle function and is characterized by the presence of nemaline rods in muscle fibers. These rods are abnormal structures that interfere with muscle contraction and can cause muscle weakness, respiratory distress, and other complications. NM is caused by variants in several genes, including TNNT1, which encodes the protein troponin T1. NM is inherited in an autosomal recessive pattern. The prevalence of heterozygous TNNT1 variants has been reported to be 1/152,000, indicating that the disease is relatively rare. OBJECTIVE Investigation of TNNT1 gene variants that may cause cretin kinase elevation. METHODS Detailed family histories and clinical data were recorded. Whole exome sequencing was performed and family segregation was done by Sanger sequencing. RESULTS In this study, we report a 5-year-old girl with a novel variant recessive congenital TNNT1 myopathy. The patient had a novel homozygous (c.271_273del) deletion in the TNNT1 gene that is associated with creatine kinase elevation, which is a marker of muscle damage. CONCLUSION This case expands the phenotypic spectrum of TNNT1 myopathy and highlights the importance of genetic testing and counseling for families affected by this rare disorder. In this study provides valuable insights into the genetic basis of NM and highlights the importance of early diagnosis and management for patients with this rare disorder. Further research is needed to better understand the pathophysiology of TNNT1 myopathy and to develop effective treatments for this debilitating condition.
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Affiliation(s)
- Cüneyd Yavaş
- Department of Molecular Biology and Genetics, Biruni University, Karanfil St. No:1H/12, Beylikduzu, Istanbul, 34100, Turkey.
| | - Mustafa Doğan
- Genetic Diseases Assessment Center, Basaksehir Cam and Sakura City Hospital, Istanbul, Turkey
| | - Recep Eröz
- Department of Medical Genetics Medical Faculty, Aksaray University, Aksaray, Turkey
| | - Kübra Türegün
- Department of Biotechnology, Institute of Science and Technology, Yıldız Technical University, Istanbul, Turkey
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Strauss KA, Carson VJ, Bolettieri E, Everett M, Bollinger A, Bowser LE, Beiler K, Young M, Edvardson S, Fraenkel N, D'Amico A, Bertini E, Lingappa L, Chowdhury D, Lowes LP, Iammarino M, Alfano LN, Brigatti KW. WiTNNess: An international natural history study of infantile-onset TNNT1 myopathy. Ann Clin Transl Neurol 2023; 10:1972-1984. [PMID: 37632133 PMCID: PMC10647004 DOI: 10.1002/acn3.51884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/10/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
OBJECTIVE We created WiTNNess as a hybrid prospective/cross-sectional observational study to simulate a clinical trial for infantile-onset TNNT1 myopathy. Our aims were to identify populations for future trial enrollment, rehearse outcome assessments, specify endpoints, and refine trial logistics. METHODS Eligible participants had biallelic pathogenic variants of TNNT1 and infantile-onset proximal weakness without confounding conditions. The primary endpoint was ventilator-free survival. "Thriving" was a secondary endpoint defined as the ability to swallow and grow normally without non-oral feeding support. Endpoints of gross motor function included independent sitting and standing as defined by the Word Health Organization, a novel TNNT1 abbreviated motor score, and video mapping of limb movement. We recorded adverse events, concomitant medications, and indices of organ function to serve as comparators of safety in future trials. RESULTS Sixteen children were enrolled in the aggregate cohort (6 prospective, 10 cross-sectional; median census age 2.3 years, range 0.5-13.8). Median ventilator-free survival was 20.2 months and probability of death or permanent mechanical ventilation was 100% by age 60 months. All six children (100%) in the prospective arm failed to thrive by age 12 months. Only 2 of 16 (13%) children in the aggregate cohort sat independently and none stood alone. Novel exploratory motor assessments also proved informative. Laboratory and imaging data suggest that primary manifestations of TNNT1 deficiency are restricted to skeletal muscle. INTERPRETATION WiTNNess allowed us to streamline and economize the collection of historical control data without compromising scientific rigor, and thereby establish a sound operational framework for future clinical trials.
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Affiliation(s)
- Kevin A. Strauss
- Clinic for Special ChildrenStrasburgPennsylvaniaUSA
- Department of PediatricsPenn Medicine‐Lancaster General HospitalPennsylvaniaLancasterUSA
- Department of PediatricsUMass Chan Medical SchoolWorcesterMassachusettsUSA
- Department of Molecular, Cell & Cancer BiologyUMass Chan Medical SchoolWorcesterMassachusettsUSA
| | - Vincent J. Carson
- Clinic for Special ChildrenStrasburgPennsylvaniaUSA
- Department of PediatricsPenn Medicine‐Lancaster General HospitalPennsylvaniaLancasterUSA
| | | | | | | | | | | | - Millie Young
- Clinic for Special ChildrenStrasburgPennsylvaniaUSA
| | - Simon Edvardson
- ALYN Hospital Pediatric and Adolescent Rehabilitation CenterJerusalemIsrael
| | - Nitay Fraenkel
- ALYN Hospital Pediatric and Adolescent Rehabilitation CenterJerusalemIsrael
| | - Adele D'Amico
- Unit of Muscular and Neurodegenerative Disorders, Department of NeurosciencesIRCCS Bambino Gesù Children's HospitalRomeItaly
| | - Enrico Bertini
- Unit of Muscular and Neurodegenerative Disorders, Department of NeurosciencesIRCCS Bambino Gesù Children's HospitalRomeItaly
| | - Lokesh Lingappa
- Department of Pediatric NeurologyRainbow Children's HospitalHyderabadIndia
| | - Devyani Chowdhury
- Cardiology Care for ChildrenLancasterPennsylvaniaUSA
- Department of CardiologyNemours Children's HealthWilmingtonDelawareUSA
| | - Linda P. Lowes
- Center for Gene TherapyNationwide Children's HospitalColumbusOhioUSA
| | - Megan Iammarino
- Center for Gene TherapyNationwide Children's HospitalColumbusOhioUSA
| | - Lindsay N. Alfano
- Center for Gene TherapyNationwide Children's HospitalColumbusOhioUSA
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Laitila J, Wallgren-Pettersson C. Recent advances in nemaline myopathy. Neuromuscul Disord 2021; 31:955-967. [PMID: 34561123 DOI: 10.1016/j.nmd.2021.07.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 11/18/2022]
Abstract
The nemaline myopathies constitute a large proportion of the congenital or structural myopathies. Common to all patients is muscle weakness and the presence in the muscle biopsy of nemaline rods. The causative genes are at least twelve, encoding structural or regulatory proteins of the thin filament, and the clinical picture as well as the histological appearance on muscle biopsy vary widely. Here, we suggest a renewed clinical classification to replace the original one, summarise what is known about the pathogenesis from mutations in each causative gene to the forms of nemaline myopathy described to date, and provide perspectives on pathogenetic mechanisms possibly open to therapeutic modalities.
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Affiliation(s)
- Jenni Laitila
- The Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland; Department of Medical Genetics, Medicum, University of Helsinki, Finland; Department of Biomedical Sciences, University of Copenhagen, Denmark.
| | - Carina Wallgren-Pettersson
- The Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland; Department of Medical Genetics, Medicum, University of Helsinki, Finland
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