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Cui M, Jannig P, Halladjian M, Figueiredo VC, Wen Y, Vechetti IJ, Krogh N, Jude B, Edman S, Lanner J, McCarthy J, Murach KA, Sejersen T, Nielsen H, von Walden F. The rRNA epitranscriptome and myonuclear SNORD landscape in skeletal muscle fibers contributes to ribosome heterogeneity and is altered by a hypertrophic stimulus. Am J Physiol Cell Physiol 2024; 327:C516-C524. [PMID: 38912733 DOI: 10.1152/ajpcell.00301.2024] [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: 05/06/2024] [Revised: 06/03/2024] [Accepted: 06/03/2024] [Indexed: 06/25/2024]
Abstract
In cell biology, ribosomal RNA (rRNA) 2'O-methyl (2'-O-Me) is the most prevalent posttranscriptional chemical modification contributing to ribosome heterogeneity. The modification involves a family of small nucleolar RNAs (snoRNAs) and is specified by box C/D snoRNAs (SNORDs). Given the importance of ribosome biogenesis for skeletal muscle growth, we asked if rRNA 2'-O-Me in nascent ribosomes synthesized in response to a growth stimulus is an unrecognized mode of ribosome heterogeneity in muscle. To determine the pattern and dynamics of 2'-O-Me rRNA, we used a sequencing-based profiling method called RiboMeth-seq (RMS). We applied this method to tissue-derived rRNA of skeletal muscle and rRNA specifically from the muscle fiber using an inducible myofiber-specific RiboTag mouse in sedentary and mechanically overloaded conditions. These analyses were complemented by myonuclear-specific small RNA sequencing to profile SNORDs and link the rRNA epitranscriptome to known regulatory elements generated within the muscle fiber. We demonstrate for the first time that mechanical overload of skeletal muscle 1) induces decreased 2'-O-Me at a subset of skeletal muscle rRNA and 2) alters the SNORD profile in isolated myonuclei. These findings point to a transient diversification of the ribosome pool via 2'-O-Me during growth and adaptation in skeletal muscle. These findings suggest changes in ribosome heterogeneity at the 2'-O-Me level during muscle hypertrophy and lay the foundation for studies investigating the functional implications of these newly identified "growth-induced" ribosomes.NEW & NOTEWORTHY Ribosomal RNAs (rRNAs) are posttranscriptionally modified by 2'O-methyl (2'-O-Me). This study applied RiboMeth-seq (RMS) to detect changes in 2'-O-Me levels during skeletal muscle hypertrophy, uncovering transient diversification of the ribosome pool in skeletal muscle fibers. This work implies a role for ribosome heterogeneity in skeletal muscle growth and adaptation.
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Affiliation(s)
- Minying Cui
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Paulo Jannig
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Maral Halladjian
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Vandré C Figueiredo
- Department of Biological Sciences, Oakland University, Rochester, Michigan, United States
| | - Yuan Wen
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, Kentucky, United States
- Center for Muscle Biology, University of Kentucky, Lexington, Kentucky, United States
- Division of Biomedical Informatics, Department of Internal Medicine, College of Medicine, University of Kentucky, Lexington, Kentucky, United States
| | - Ivan J Vechetti
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Baptiste Jude
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Sebastian Edman
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Johanna Lanner
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - John McCarthy
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, Kentucky, United States
- Center for Muscle Biology, University of Kentucky, Lexington, Kentucky, United States
| | - Kevin A Murach
- Department of Health, Human Performance, and Recreation, Exercise Science Research Center, University of Arkansas, Fayetteville, Arkansas, United States
| | - Thomas Sejersen
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
- Department of Child Neurology, Karolinska University Hospital, Astrid Lindgren Children's Hospital, Stockholm, Sweden
- Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, Hong Kong, People's Republic of China
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ferdinand von Walden
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
- Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, Hong Kong, People's Republic of China
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2
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Chambers TL, Dimet-Wiley A, Keeble AR, Haghani A, Lo WJ, Kang G, Brooke R, Horvath S, Fry CS, Watowich SJ, Wen Y, Murach KA. Methylome-proteome integration after late-life voluntary exercise training reveals regulation and target information for improved skeletal muscle health. J Physiol 2024. [PMID: 39058663 DOI: 10.1113/jp286681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
Exercise is a potent stimulus for combatting skeletal muscle ageing. To study the effects of exercise on muscle in a preclinical setting, we developed a combined endurance-resistance training stimulus for mice called progressive weighted wheel running (PoWeR). PoWeR improves molecular, biochemical, cellular and functional characteristics of skeletal muscle and promotes aspects of partial epigenetic reprogramming when performed late in life (22-24 months of age). In this investigation, we leveraged pan-mammalian DNA methylome arrays and tandem mass-spectrometry proteomics in skeletal muscle to provide detailed information on late-life PoWeR adaptations in female mice relative to age-matched sedentary controls (n = 7-10 per group). Differential CpG methylation at conserved promoter sites was related to transcriptional regulation genes as well as Nr4a3, Hes1 and Hox genes after PoWeR. Using a holistic method of -omics integration called binding and expression target analysis (BETA), methylome changes were associated with upregulated proteins related to global and mitochondrial translation after PoWeR (P = 0.03). Specifically, BETA implicated methylation control of ribosomal, mitoribosomal, and mitochondrial complex I protein abundance after training. DNA methylation may also influence LACTB, MIB1 and UBR4 protein induction with exercise - all are mechanistically linked to muscle health. Computational cistrome analysis predicted several transcription factors including MYC as regulators of the exercise trained methylome-proteome landscape, corroborating prior late-life PoWeR transcriptome data. Correlating the proteome to muscle mass and fatigue resistance revealed positive relationships with VPS13A and NPL levels, respectively. Our findings expose differential epigenetic and proteomic adaptations associated with translational regulation after PoWeR that could influence skeletal muscle mass and function in aged mice. KEY POINTS: Late-life combined endurance-resistance exercise training from 22-24 months of age in mice is shown to improve molecular, biochemical, cellular and in vivo functional characteristics of skeletal muscle and promote aspects of partial epigenetic reprogramming and epigenetic age mitigation. Integration of DNA CpG 36k methylation arrays using conserved sites (which also contain methylation ageing clock sites) with exploratory proteomics in skeletal muscle extends our prior work and reveals coordinated and widespread regulation of ribosomal, translation initiation, mitochondrial ribosomal (mitoribosomal) and complex I proteins after combined voluntary exercise training in a sizeable cohort of female mice (n = 7-10 per group and analysis). Multi-omics integration predicted epigenetic regulation of serine β-lactamase-like protein (LACTB - linked to tumour resistance in muscle), mind bomb 1 (MIB1 - linked to satellite cell and type 2 fibre maintenance) and ubiquitin protein ligase E3 component N-recognin 4 (UBR4 - linked to muscle protein quality control) after training. Computational cistrome analysis identified MYC as a regulator of the late-life training proteome, in agreement with prior transcriptional analyses. Vacuolar protein sorting 13 homolog A (VPS13A) was positively correlated to muscle mass, and the glycoprotein/glycolipid associated sialylation enzyme N-acetylneuraminate pyruvate lyase (NPL) was associated to in vivo muscle fatigue resistance.
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Affiliation(s)
- Toby L Chambers
- Exercise Science Research Center, Molecular Muscle Mass Regulation Laboratory, Department of Health, Human Performance, and Recreation, University of Arkansas, Fayetteville, AR, USA
| | | | - Alexander R Keeble
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- Department of Athletic Training and Clinical Nutrition, University of Kentucky, Lexington, KY, USA
| | - Amin Haghani
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Wen-Juo Lo
- Department of Educational Statistics and Research Methods, University of Arkansas, Fayetteville, AR, USA
| | - Gyumin Kang
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- Department of Physiology, University of Kentucky, Lexington, KY, USA
- Division of Biomedical Informatics, Department of Internal Medicine, University of Kentucky, Lexington, KY, USA
| | - Robert Brooke
- Epigenetic Clock Development Foundation, Los Angeles, CA, USA
| | - Steve Horvath
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
- Epigenetic Clock Development Foundation, Los Angeles, CA, USA
| | - Christopher S Fry
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- Department of Athletic Training and Clinical Nutrition, University of Kentucky, Lexington, KY, USA
| | - Stanley J Watowich
- Ridgeline Therapeutics, Houston, TX, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Yuan Wen
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- Department of Physiology, University of Kentucky, Lexington, KY, USA
- Division of Biomedical Informatics, Department of Internal Medicine, University of Kentucky, Lexington, KY, USA
| | - Kevin A Murach
- Exercise Science Research Center, Molecular Muscle Mass Regulation Laboratory, Department of Health, Human Performance, and Recreation, University of Arkansas, Fayetteville, AR, USA
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Brown A, Parise G, Thomas ACQ, Ng SY, McGlory C, Phillips SM, Kumbhare D, Joanisse S. Low baseline ribosome-related gene expression and resistance training-induced declines in ribosome-related gene expression are associated with skeletal muscle hypertrophy in young men and women. J Cell Physiol 2024; 239:e31182. [PMID: 38214457 DOI: 10.1002/jcp.31182] [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: 07/14/2023] [Revised: 12/04/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024]
Abstract
Ribosomes are essential cellular machinery for protein synthesis. It is hypothesised that ribosome content supports muscle growth and that individuals with more ribosomes have greater increases in muscle size following resistance training (RT). Aerobic conditioning (AC) also elicits distinct physiological adaptations; however, no measures of ribosome content following AC have been conducted. We used ribosome-related gene expression as a proxy measure for ribosome content and hypothesised that AC and RT would increase ribosome-related gene expression. Fourteen young men and women performed 6 weeks of single-legged AC followed by 10 weeks of double-legged RT. Muscle biopsies were taken following AC and following RT in the aerobically conditioned (AC+RT) and unconditioned (RT) legs. No differences in regulatory genes (Ubf, Cyclin D1, Tif-1a and Polr-1b) involved in ribosomal biogenesis or ribosomal RNA (45S, 5.8S, 18S and 28S rRNAs) expression were observed following AC and RT, except for c-Myc (RT > AC+RT) and 5S rRNA (RT < AC+RT at pre-RT) with 18S external transcribed spacer and 5.8S internal transcribed spacer expression decreasing from pre-RT to post-RT in the RT leg only. When divided for change in leg-lean soft tissue mass (ΔLLSTM) following RT, legs with the greatest ΔLLSTM had lower expression in 11/13 measured ribosome-related genes before RT and decreased expression in 9/13 genes following RT. These results indicate that AC and RT did not increase ribosome-related gene expression. Contrary to previous research, the greatest increase in muscle mass was associated with lower changes in ribosome-related gene expression over the course of the 10-week training programme. This may point to the importance of translational efficiency rather than translational capacity (i.e. ribosome content) in mediating long-term exercise-induced adaptations in skeletal muscle.
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Affiliation(s)
- Alex Brown
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
| | - Gianni Parise
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
| | - Aaron C Q Thomas
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
| | - Sean Y Ng
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
| | - Chris McGlory
- School of Kinesiology and Health Studies, Queen's University, Kingston, Ontario, Canada
- Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Stuart M Phillips
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
| | - Dinesh Kumbhare
- Toronto Rehabilitation Institute, University of Toronto, Toronto, Ontario, Canada
| | - Sophie Joanisse
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
- Institute of Sport, Manchester Metropolitan University, Manchester, UK
- MRC Versus Arthritis Centre for Musculoskeletal Ageing Research, Nottingha, UK
- School of Life Sciences, University of Nottingham, Nottingham, UK
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Edman S, Jones RG, Jannig PR, Fernandez-Gonzalo R, Norrbom J, Thomas NT, Khadgi S, Koopmans PJ, Morena F, Peterson CS, Scott LN, Greene NP, Figueiredo VC, Fry CS, Zhengye L, Lanner JT, Wen Y, Alkner B, Murach KA, von Walden F. The 24-Hour Time Course of Integrated Molecular Responses to Resistance Exercise in Human Skeletal Muscle Implicates MYC as a Hypertrophic Regulator That is Sufficient for Growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586857. [PMID: 38586026 PMCID: PMC10996609 DOI: 10.1101/2024.03.26.586857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Molecular control of recovery after exercise in muscle is temporally dynamic. A time course of biopsies around resistance exercise (RE) combined with -omics is necessary to better comprehend the molecular contributions of skeletal muscle adaptation in humans. Vastus lateralis biopsies before and 30 minutes, 3-, 8-, and 24-hours after acute RE were collected. A time-point matched biopsy-only group was also included. RNA-sequencing defined the transcriptome while DNA methylomics and computational approaches complemented these data. The post-RE time course revealed: 1) DNA methylome responses at 30 minutes corresponded to upregulated genes at 3 hours, 2) a burst of translation- and transcription-initiation factor-coding transcripts occurred between 3 and 8 hours, 3) global gene expression peaked at 8 hours, 4) ribosome-related genes dominated the mRNA landscape between 8 and 24 hours, 5) methylation-regulated MYC was a highly influential transcription factor throughout the 24-hour recovery and played a primary role in ribosome-related mRNA levels between 8 and 24 hours. The influence of MYC in human muscle adaptation was strengthened by transcriptome information from acute MYC overexpression in mouse muscle. To test whether MYC was sufficient for hypertrophy, we generated a muscle fiber-specific doxycycline inducible model of pulsatile MYC induction. Periodic 48-hour pulses of MYC over 4 weeks resulted in higher muscle mass and fiber size in the soleus of adult female mice. Collectively, we present a temporally resolved resource for understanding molecular adaptations to RE in muscle and reveal MYC as a regulator of RE-induced mRNA levels and hypertrophy.
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Affiliation(s)
- Sebastian Edman
- Karolinska Institute, Division of Pediatric Neurology, Department of Women’s and Children’s Health, Stockholm, Sweden
| | - Ronald G. Jones
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
| | - Paulo R. Jannig
- Karolinska Institute, Division of Pediatric Neurology, Department of Women’s and Children’s Health, Stockholm, Sweden
| | - Rodrigo Fernandez-Gonzalo
- Karolinska Institute, Division of Clinical Physiology, Department of Laboratory Medicine, Stockholm, Sweden
- Unit of Clinical Physiology, Karolinska University Hospital, Huddinge, Sweden
| | - Jessica Norrbom
- Karolinska Institute, Molecular Exercise Physiology Group, Department of Physiology and Pharmacology, Stockholm, Sweden
| | - Nicholas T. Thomas
- University of Kentucky, Center for Muscle Biology, Lexington, KY, USA
- University of Kentucky, Department of Athletic Training and Clinical Nutrition, Lexington, KY, USA
| | - Sabin Khadgi
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
| | - Pieter Jan Koopmans
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
- University of Arkansas, Cell and Molecular Biology Graduate Program, Fayetteville, AR, USA
| | - Francielly Morena
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
| | - Calvin S. Peterson
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
| | - Logan N. Scott
- University of Kentucky, Center for Muscle Biology, Lexington, KY, USA
- University of Kentucky, Department of Physiology, Lexington, KY, USA
- University of Kentucky, Department of Internal Medicine, Division of Biomedical Informatics, Lexington, KY, USA
| | - Nicholas P. Greene
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
| | - Vandre C. Figueiredo
- University of Kentucky, Center for Muscle Biology, Lexington, KY, USA
- Oakland University, Department of Biological Sciences, Rochester Hills, MI, USA
| | - Christopher S. Fry
- University of Kentucky, Center for Muscle Biology, Lexington, KY, USA
- University of Kentucky, Department of Athletic Training and Clinical Nutrition, Lexington, KY, USA
| | - Liu Zhengye
- Karolinska Institute, Molecular Muscle Physiology & Pathophysiology Group, Department of Physiology & Pharmacology, Stockholm, Sweden
| | - Johanna T. Lanner
- Karolinska Institute, Molecular Muscle Physiology & Pathophysiology Group, Department of Physiology & Pharmacology, Stockholm, Sweden
| | - Yuan Wen
- University of Kentucky, Center for Muscle Biology, Lexington, KY, USA
- University of Kentucky, Department of Physiology, Lexington, KY, USA
- University of Kentucky, Department of Internal Medicine, Division of Biomedical Informatics, Lexington, KY, USA
| | - Björn Alkner
- Department of Orthopedics, Eksjö, Region Jönköping County and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Kevin A. Murach
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
- University of Arkansas, Cell and Molecular Biology Graduate Program, Fayetteville, AR, USA
| | - Ferdinand von Walden
- Karolinska Institute, Division of Pediatric Neurology, Department of Women’s and Children’s Health, Stockholm, Sweden
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Guo R, Ma X, Xu H, Ma Y, Zhang R, Liu X, Lu B, Zhang J, Han Y. In silico prediction and a systematic toxicology-based in vivo investigation uncovering the mechanism of aquatic toxicity caused by beta-lactam antibiotics. CHEMOSPHERE 2024; 349:140884. [PMID: 38065262 DOI: 10.1016/j.chemosphere.2023.140884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/18/2023] [Accepted: 12/01/2023] [Indexed: 01/10/2024]
Abstract
Recently, beta-lactam antibiotics have gained attention as significant contributors to public health and environmental issues due to their potential toxicity. Our study employed machine learning to develop a model for assessing the aquatic toxicity of beta-lactam antibiotics on zebrafish. Notably, aztreonam (AZT), a synthetic monobactam and a subclass of beta-lactam antibiotics, demonstrated developmental effects in zebrafish embryos comparable to cephalosporins, indicating a potential for toxicity. Using a systems toxicology-based approach, we identified apoptosis and metabolic disorders as the primary pathways affected by AZT and its impurity F exposure. During the administration of monobactams, we noted that ctsbb, nos2a, and dgat2, genes associated with apoptosis and the metabolic pathway, exhibited significant differential expression. Molecular docking studies were conducted to ascertain the binding affinity between monobactam compounds and their potential targets-Ctsbb, Nos2a, and Dgat2. Furthermore, our research revealed that monobactams influence pre-mRNA alternative splicing, resulting in disruptions in the expression of genes involved in hair cells, brain, spinal cord, and fin regeneration (e.g., krt4, krt5, krt17, cyt1). Notably, we observed a correlation between the levels of rpl3 and rps7 genes, both important ribosomal proteins, and the detected alternative splicing events. Overall, this study enhances our understanding of the toxicity of beta-lactam antibiotics in zebrafish by demonstrating the developmental effects of monobactams and uncovering the underlying mechanisms at the molecular level. It also identifies potential targets for further investigation into the mechanisms of toxicity and provides valuable insights for early assessment of biological toxicity associated with antibiotic pollutants.
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Affiliation(s)
- Ruixian Guo
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China
| | - Xinyan Ma
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; School of Pharmacy, Minzu University of China, Beijing, 100081, China
| | - Huibo Xu
- University of Science and Technology of China, Hefei, 230031, China
| | - Yuanyuan Ma
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Rui Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Xinyan Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Binan Lu
- School of Pharmacy, Minzu University of China, Beijing, 100081, China
| | - Jingpu Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Ying Han
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
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6
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Bajpai AK, Gu Q, Orgil BO, Alberson NR, Towbin JA, Martinez HR, Lu L, Purevjav E. Exploring the Regulation and Function of Rpl3l in the Development of Early-Onset Dilated Cardiomyopathy and Congestive Heart Failure Using Systems Genetics Approach. Genes (Basel) 2023; 15:53. [PMID: 38254943 PMCID: PMC10815855 DOI: 10.3390/genes15010053] [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: 12/05/2023] [Revised: 12/25/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Cardiomyopathies, diseases affecting the myocardium, are common causes of congestive heart failure (CHF) and sudden cardiac death. Recently, biallelic variants in ribosomal protein L3-like (RPL3L) have been reported to be associated with severe neonatal dilated cardiomyopathy (DCM) and CHF. This study employs a systems genetics approach to gain understanding of the regulatory mechanisms underlying the role of RPL3L in DCM. METHODS Genetic correlation, expression quantitative trait loci (eQTL) mapping, differential expression analysis and comparative functional analysis were performed using cardiac gene expression data from the patients and murine genetic reference populations (GRPs) of BXD mice (recombinant inbred strains from a cross of C57BL/6J and DBA/2J mice). Additionally, immune infiltration analysis was performed to understand the relationship between DCM, immune cells and RPL3L expression. RESULTS Systems genetics analysis identified high expression of Rpl3l mRNA, which ranged from 11.31 to 12.16 across murine GRPs of BXD mice, with an ~1.8-fold difference. Pathways such as "diabetic cardiomyopathy", "focal adhesion", "oxidative phosphorylation" and "DCM" were significantly associated with Rpl3l. eQTL mapping suggested Myl4 (Chr 11) and Sdha (Chr 13) as the upstream regulators of Rpl3l. The mRNA expression of Rpl3l, Myl4 and Sdha was significantly correlated with multiple echocardiography traits in BXD mice. Immune infiltration analysis revealed a significant association of RPL3L and SDHA with seven immune cells (CD4, CD8-naive T cell, CD8 T cell, macrophages, cytotoxic T cell, gamma delta T cell and exhausted T cell) that were also differentially infiltrated between heart samples obtained from DCM patients and normal individuals. CONCLUSIONS RPL3L is highly expressed in the heart tissue of humans and mice. Expression of Rpl3l and its upstream regulators, Myl4 and Sdha, correlate with multiple cardiac function traits in murine GRPs of BXD mice, while RPL3L and SDHA correlate with immune cell infiltration in DCM patient hearts, suggesting important roles for RPL3L in DCM and CHF pathogenesis via immune inflammation, necessitating experimental validations of Myl4 and Sdha in Rpl3l regulation.
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Affiliation(s)
- Akhilesh K. Bajpai
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38103, USA; (A.K.B.); (Q.G.)
| | - Qingqing Gu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38103, USA; (A.K.B.); (Q.G.)
| | - Buyan-Ochir Orgil
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
| | - Neely R. Alberson
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
| | - Jeffrey A. Towbin
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
- Cardiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Hugo R. Martinez
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38103, USA; (A.K.B.); (Q.G.)
| | - Enkhsaikhan Purevjav
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
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7
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Reis HBD, Carvalho ME, Espigolan R, Poleti MD, Ambrizi DR, Berton MP, Ferraz JBS, de Mattos Oliveira EC, Eler JP. Genome-Wide Association (GWAS) Applied to Carcass and Meat Traits of Nellore Cattle. Metabolites 2023; 14:6. [PMID: 38276296 PMCID: PMC10818672 DOI: 10.3390/metabo14010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/14/2023] [Accepted: 11/22/2023] [Indexed: 01/27/2024] Open
Abstract
The meat market has enormous importance for the world economy, and the quality of the product offered to the consumer is fundamental for the success of the sector. In this study, we analyzed a database which contained information on 2470 animals from a commercial farm in the state of São Paulo, Brazil. Of this total, 2181 animals were genotyped, using 777,962 single-nucleotide polymorphisms (SNPs). After quality control analysis, 468,321 SNPs provided information on the number of genotyped animals. Genome-wide association analyses (GWAS) were performed for the characteristics of the rib eye area (REA), subcutaneous fat thickness (SFT), shear force at 7 days' ageing (SF7), and intramuscular fat (IMF), with the aid of the single-step genomic best linear unbiased prediction (ssGBLUP) method, with the purpose of identifying possible genomic windows (~1 Mb) responsible for explaining at least 0.5% of the genetic variance of the traits under analysis (≥0.5%). These genomic regions were used in a gene search and enrichment analyses using MeSH terms. The distributed heritability coefficients were 0.14, 0.20, 0.18, and 0.21 for REA, SFT, SF7, and IMF, respectively. The GWAS results indicated significant genomic windows for the traits of interest in a total of 17 chromosomes. Enrichment analyses showed the following significant terms (FDR ≤ 0.05) associated with the characteristics under study: for the REA, heat stress disorders and life cycle stages; for SFT, insulin and nonesterified fatty acids; for SF7, apoptosis and heat shock proteins (HSP27); and for IMF, metalloproteinase 2. In addition, KEGG (Kyoto encyclopedia of genes and genomes) enrichment analysis allowed us to highlight important metabolic pathways related to the studied phenotypes, such as the growth hormone synthesis, insulin-signaling, fatty acid metabolism, and ABC transporter pathways. The results obtained provide a better understanding of the molecular processes involved in the expression of the studied characteristics and may contribute to the design of selection strategies and future studies aimed at improving the productivity of Nellore cattle.
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Affiliation(s)
- Hugo Borges Dos Reis
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| | - Minos Esperândio Carvalho
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| | - Rafael Espigolan
- Department of Animal Science and Biological Sciences, Federal University of Santa Maria (UFSM), Av. Independencia, 3751, Palmeira das Missões 98300-000, RS, Brazil
| | - Mirele Daiana Poleti
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| | - Dewison Ricardo Ambrizi
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| | - Mariana Piatto Berton
- School of Agricultural and Veterinary Studies (FCAV), São Paulo State University, Jaboticabal 14884-900, SP, Brazil;
| | - José Bento Sterman Ferraz
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| | - Elisângela Chicaroni de Mattos Oliveira
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| | - Joanir Pereira Eler
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
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8
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Viggars MR, Sutherland H, Cardozo CP, Jarvis JC. Conserved and species-specific transcriptional responses to daily programmed resistance exercise in rat and mouse. FASEB J 2023; 37:e23299. [PMID: 37994729 DOI: 10.1096/fj.202301611r] [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: 08/23/2023] [Revised: 10/19/2023] [Accepted: 10/26/2023] [Indexed: 11/24/2023]
Abstract
Mice are often used in gain or loss of function studies to understand how genes regulate metabolism and adaptation to exercise in skeletal muscle. Once-daily resistance training with electrical nerve stimulation produces hypertrophy of the dorsiflexors in rat, but not in mouse. Using implantable pulse generators, we assessed the acute transcriptional response (1-h post-exercise) after 2, 10, and 20 days of training in free-living mice and rats using identical nerve stimulation paradigms. RNA sequencing revealed strong concordance in the timecourse of many transcriptional responses in the tibialis anterior muscles of both species including responses related to "stress responses/immediate-early genes, and "collagen homeostasis," "ribosomal subunits," "autophagy," and "focal adhesion." However, pathways associated with energy metabolism including "carbon metabolism," "oxidative phosphorylation," "mitochondrial translation," "propanoate metabolism," and "valine, leucine, and isoleucine degradation" were oppositely regulated between species. These pathways were suppressed in the rat but upregulated in the mouse. Our transcriptional analysis suggests that although many pathways associated with growth show remarkable similarities between species, the absence of an actual growth response in the mouse may be because the mouse prioritizes energy metabolism, specifically the replenishment of fuel stores and intermediate metabolites.
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Affiliation(s)
- Mark R Viggars
- Research Institute for Sport & Exercise Science, Liverpool John Moores University, Liverpool, UK
- Department of Physiology and Aging, University of Florida, Gainesville, Florida, USA
- Myology Institute, University of Florida, Gainesville, Florida, USA
| | - Hazel Sutherland
- Research Institute for Sport & Exercise Science, Liverpool John Moores University, Liverpool, UK
| | - Christopher P Cardozo
- Spinal Cord Damage Research Center, James J. Peters VA Medical Center, Bronx, New York, USA
- Icahn School of Medicine, Mount Sinai, New York, New York, USA
| | - Jonathan C Jarvis
- Research Institute for Sport & Exercise Science, Liverpool John Moores University, Liverpool, UK
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9
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Yun Y, Wu R, He X, Qin X, Chen L, Sha L, Yun X, Nishiumi T, Borjigin G. Integrated Transcriptome Analysis of miRNAs and mRNAs in the Skeletal Muscle of Wuranke Sheep. Genes (Basel) 2023; 14:2034. [PMID: 38002977 PMCID: PMC10671749 DOI: 10.3390/genes14112034] [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: 10/08/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
MicroRNAs (miRNAs) are regarded as important regulators in skeletal muscle development. To reveal the regulatory roles of miRNAs and their target mRNAs underlying the skeletal muscle development of Wuranke sheep, we investigated the miRNA and mRNA expression profiles in the biceps femoris of these sheep at the fetal (3 months of gestation) and 3- and 15-month-old postnatal stages. Consequently, a total of 1195 miRNAs and 24,959 genes were identified. Furthermore, 474, 461, and 54 differentially expressed miRNAs (DEMs) and 6783, 7407, and 78 differentially expressed genes (DEGs) were detected among three comparative groups. Functional analysis demonstrated that the target mRNAs of the DEMs were enriched in multiple pathways related to muscle development. Moreover, the interactions among several predicted miRNA-mRNA pairs (oar-miR-133-HDAC1, oar-miR-1185-5p-MYH1/HADHA/OXCT1, and PC-5p-3703_578-INSR/ACTG1) that potentially affect skeletal muscle development were verified using dual-luciferase reporter assays. In this study, we identified the miRNA and mRNA differences in the skeletal muscle of Wuranke sheep at different developmental stages and revealed that a series of candidate miRNA-mRNA pairs may act as modulators of muscle development. These results will contribute to future studies on the function of miRNAs and their target mRNAs during skeletal muscle development in Wuranke sheep.
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Affiliation(s)
- Yueying Yun
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Y.); (X.H.); (X.Q.); (L.C.); (L.S.); (X.Y.)
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China
| | - Rihan Wu
- College of Biochemistry and Engineering, Hohhot Vocational College, Hohhot 010051, China;
| | - Xige He
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Y.); (X.H.); (X.Q.); (L.C.); (L.S.); (X.Y.)
| | - Xia Qin
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Y.); (X.H.); (X.Q.); (L.C.); (L.S.); (X.Y.)
| | - Lu Chen
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Y.); (X.H.); (X.Q.); (L.C.); (L.S.); (X.Y.)
| | - Lina Sha
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Y.); (X.H.); (X.Q.); (L.C.); (L.S.); (X.Y.)
| | - Xueyan Yun
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Y.); (X.H.); (X.Q.); (L.C.); (L.S.); (X.Y.)
| | - Tadayuki Nishiumi
- Division of Life and Food Science, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
| | - Gerelt Borjigin
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Y.); (X.H.); (X.Q.); (L.C.); (L.S.); (X.Y.)
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10
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Roberts MD, McCarthy JJ, Hornberger TA, Phillips SM, Mackey AL, Nader GA, Boppart MD, Kavazis AN, Reidy PT, Ogasawara R, Libardi CA, Ugrinowitsch C, Booth FW, Esser KA. Mechanisms of mechanical overload-induced skeletal muscle hypertrophy: current understanding and future directions. Physiol Rev 2023; 103:2679-2757. [PMID: 37382939 PMCID: PMC10625844 DOI: 10.1152/physrev.00039.2022] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/12/2023] [Accepted: 06/21/2023] [Indexed: 06/30/2023] Open
Abstract
Mechanisms underlying mechanical overload-induced skeletal muscle hypertrophy have been extensively researched since the landmark report by Morpurgo (1897) of "work-induced hypertrophy" in dogs that were treadmill trained. Much of the preclinical rodent and human resistance training research to date supports that involved mechanisms include enhanced mammalian/mechanistic target of rapamycin complex 1 (mTORC1) signaling, an expansion in translational capacity through ribosome biogenesis, increased satellite cell abundance and myonuclear accretion, and postexercise elevations in muscle protein synthesis rates. However, several lines of past and emerging evidence suggest that additional mechanisms that feed into or are independent of these processes are also involved. This review first provides a historical account of how mechanistic research into skeletal muscle hypertrophy has progressed. A comprehensive list of mechanisms associated with skeletal muscle hypertrophy is then outlined, and areas of disagreement involving these mechanisms are presented. Finally, future research directions involving many of the discussed mechanisms are proposed.
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Affiliation(s)
- Michael D Roberts
- School of Kinesiology, Auburn University, Auburn, Alabama, United States
| | - John J McCarthy
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, Kentucky, United States
| | - Troy A Hornberger
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Stuart M Phillips
- Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
| | - Abigail L Mackey
- Institute of Sports Medicine Copenhagen, Department of Orthopedic Surgery, Copenhagen University Hospital-Bispebjerg and Frederiksberg, and Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Gustavo A Nader
- Department of Kinesiology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States
| | - Marni D Boppart
- Department of Kinesiology and Community Health, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States
| | - Andreas N Kavazis
- School of Kinesiology, Auburn University, Auburn, Alabama, United States
| | - Paul T Reidy
- Department of Kinesiology, Nutrition and Health, Miami University, Oxford, Ohio, United States
| | - Riki Ogasawara
- Healthy Food Science Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Cleiton A Libardi
- MUSCULAB-Laboratory of Neuromuscular Adaptations to Resistance Training, Department of Physical Education, Federal University of São Carlos, São Carlos, Brazil
| | - Carlos Ugrinowitsch
- School of Physical Education and Sport, University of São Paulo, São Paulo, Brazil
| | - Frank W Booth
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri, United States
| | - Karyn A Esser
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, Florida, United States
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11
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Ferreira RP, Duarte JA. Protein Turnover in Skeletal Muscle: Looking at Molecular Regulation towards an Active Lifestyle. Int J Sports Med 2023; 44:763-777. [PMID: 36854391 DOI: 10.1055/a-2044-8277] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Skeletal muscle is a highly plastic tissue, able to change its mass and functional properties in response to several stimuli. Skeletal muscle mass is influenced by the balance between protein synthesis and breakdown, which is regulated by several signaling pathways. The relative contribution of Akt/mTOR signaling, ubiquitin-proteasome pathway, autophagy among other signaling pathways to protein turnover and, therefore, to skeletal muscle mass, differs depending on the wasting or loading condition and muscle type. By modulating mitochondria biogenesis, PGC-1α has a major role in the cell's bioenergetic status and, thus, on protein turnover. In fact, rates of protein turnover regulate differently the levels of distinct protein classes in response to atrophic or hypertrophic stimuli. Mitochondrial protein turnover rates may be enhanced in wasting conditions, whereas the increased turnover of myofibrillar proteins triggers muscle mass gain. The present review aims to update the knowledge on the molecular pathways implicated in the regulation of protein turnover in skeletal muscle, focusing on how distinct muscle proteins may be modulated by lifestyle interventions with emphasis on exercise training. The comprehensive analysis of the anabolic effects of exercise programs will pave the way to the tailored management of muscle wasting conditions.
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Affiliation(s)
- Rita Pinho Ferreira
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Jose Alberto Duarte
- TOXRUN - Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal
- CIAFEL, Faculty of Sports, University of Porto and Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal
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12
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Jayaprakash A, Roy A, Thanmalagan RR, Arunachalam A, P T V L. Understanding the mechanism of pathogenicity through interactome studies between Arachis hypogaea L. and Aspergillus flavus. J Proteomics 2023; 287:104975. [PMID: 37482270 DOI: 10.1016/j.jprot.2023.104975] [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: 02/06/2023] [Revised: 06/28/2023] [Accepted: 07/15/2023] [Indexed: 07/25/2023]
Abstract
Aspergillus flavus (A. flavus) infects the peanut seeds during pre-and post-harvest stages, causing seed quality destruction for humans and livestock consumption. Even though many resistant varieties were developed, the molecular mechanism of defense interactions of peanut against A. flavus still needs further investigation. Hence, an interologous host-pathogen protein interaction (HPPI) network was constructed to understand the subcellular level interaction mechanism between peanut and A. flavus. Out of the top 10 hub proteins of both organisms, protein phosphatase 2C and cyclic nucleotide-binding/kinase domain-containing protein and different ribosomal proteins were identified as candidate proteins involved in defense. Functional annotation and subcellular localization based characterization of HPPI identified protein SGT1 homolog, calmodulin and Rac-like GTP-binding proteins to be involved in defense response against fungus. The relevance of HPPI in infectious conditions was assessed using two transcriptome data which identified the interplay of host kinase class R proteins, bHLH TFs and cell wall related proteins to impart resistance against pathogen infection. Further, the pathogenicity analysis identified glycogen phosphorylase and molecular chaperone and allergen Mod-E/Hsp90/Hsp1 as potential pathogen targets to enhance the host defense mechanism. Hence, the computationally predicted host-pathogen PPI network could provide valuable support for molecular biology experiments to understand the host-pathogen interaction. SIGNIFICANCE: Protein-protein interactions execute significant cellular interactions in an organism and are influenced majorly by stress conditions. Here we reported the host-pathogen protein-protein interaction between peanut and A. flavus, and a detailed network analysis based on function, subcellular localization, gene co-expression, and pathogenicity was performed. The network analysis identified key proteins such as host kinase class R proteins, calmodulin, SGT1 homolog, Rac-like GTP-binding proteins bHLH TFs and cell wall related to impart resistance against pathogen infection. We observed the interplay of defense related proteins and cell wall related proteins predominantly, which could be subjected to further studies. The network analysis described in this study could be applied to understand other host-pathogen systems generally.
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Affiliation(s)
- Aiswarya Jayaprakash
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, R. V. Nagar Kalapet, Pondicherry 605014, India
| | - Abhijeet Roy
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, R. V. Nagar Kalapet, Pondicherry 605014, India
| | - Raja Rajeswary Thanmalagan
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, R. V. Nagar Kalapet, Pondicherry 605014, India
| | - Annamalai Arunachalam
- Department of Food Science & Technology, School of Life Sciences, Pondicherry University, R. V. Nagar Kalapet, Pondicherry 605014, India
| | - Lakshmi P T V
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, R. V. Nagar Kalapet, Pondicherry 605014, India.
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13
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Chaillou T, Montiel-Rojas D. Does the blunted stimulation of skeletal muscle protein synthesis by aging in response to mechanical load result from impaired ribosome biogenesis? FRONTIERS IN AGING 2023; 4:1171850. [PMID: 37256189 PMCID: PMC10225510 DOI: 10.3389/fragi.2023.1171850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/04/2023] [Indexed: 06/01/2023]
Abstract
Age-related loss of skeletal muscle mass leads to a reduction of strength. It is likely due to an inadequate stimulation of muscle protein synthesis (MPS) in response to anabolic stimuli, such as mechanical load. Ribosome biogenesis is a major determinant of translational capacity and is essential for the control of muscle mass. This mini-review aims to put forth the hypothesis that ribosome biogenesis is impaired by aging in response to mechanical load, which could contribute to the age-related anabolic resistance and progressive muscle atrophy. Recent animal studies indicate that aging impedes muscle hypertrophic response to mechanical overload. This is associated with an impaired transcription of ribosomal DNA (rDNA) by RNA polymerase I (Pol I), a limited increase in total RNA concentration, a blunted activation of AKT/mTOR pathway, and an increased phosphorylation of AMPK. In contrast, an age-mediated impairment of ribosome biogenesis is unlikely in response to electrical stimulations. In human, the hypertrophic response to resistance exercise training is diminished with age. This is accompanied by a deficit in long-term MPS and an absence of increased total RNA concentration. The results addressing the acute response to resistance exercise suggest an impaired Pol I-mediated rDNA transcription and attenuated activation/expression of several upstream regulators of ribosome biogenesis in muscles from aged individuals. Altogether, emerging evidence indicates that impaired ribosome biogenesis could partly explain age-related anabolic resistance to mechanical load, which may ultimately contribute to progressive muscle atrophy. Future research should develop more advanced molecular tools to provide in-depth analysis of muscle ribosome biogenesis.
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14
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Miyake T, McDermott JC. Re-organization of nucleolar architecture in myogenic differentiation. J Cell Sci 2023; 136:286887. [PMID: 36727534 DOI: 10.1242/jcs.260496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/19/2023] [Indexed: 02/03/2023] Open
Abstract
Myogenesis, the process of muscle differentiation, requires an extensive remodeling of the cellular transcriptome and proteome. Whereas the transcriptional program underpinning myogenesis is well characterized, the required adaptation in protein synthesis is incompletely understood. Enhanced protein synthesis necessitates ribosome biogenesis at the nucleolus. Nucleolar size and activity are inextricably linked with altered gene expression. Here, we report changes in nucleolar morphology and function during myogenic differentiation. Immunofluorescence analysis revealed alterations in nucleolar morphology that were dependent on the cellular state - proliferative or quiescent myogenic progenitors (myoblasts or reserve cells) contained multiple small nucleoli with a characteristic spherical shape, whereas multinucleated myotubes typically contained one large, often irregularly shaped nucleolus. These morphological alterations are consistent with changes to nucleolar phase separation properties. Re-organization of the nucleolar structure was correlated with enhanced rRNA production and protein translation. Inhibition of mTOR signaling with rapamycin perturbed nucleolar re-organization. Conversely, hyperactivated mTOR enhanced alterations in nucleolar morphology. These findings support the idea that there is an mTOR dependent re-organization of nucleolar structure during myogenesis, enhancing our understanding of myogenesis and possibly facilitating new approaches to therapeutic interventions in muscle pathologies.
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Affiliation(s)
- Tetsuaki Miyake
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada.,Muscle Health Research Centre (MHRC), York University, Toronto, ON M3J 1P3, Canada.,Centre for Research in Biomolecular Interactions (CRBI), York University, Toronto, ON M3J 1P3, Canada
| | - John C McDermott
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada.,Muscle Health Research Centre (MHRC), York University, Toronto, ON M3J 1P3, Canada.,Centre for Research in Biomolecular Interactions (CRBI), York University, Toronto, ON M3J 1P3, Canada
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15
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Wang K, Wang S, Zhang Y, Xie L, Song X, Song X. SNORD88C guided 2'-O-methylation of 28S rRNA regulates SCD1 translation to inhibit autophagy and promote growth and metastasis in non-small cell lung cancer. Cell Death Differ 2023; 30:341-355. [PMID: 36376383 PMCID: PMC9950066 DOI: 10.1038/s41418-022-01087-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 11/16/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) have been shown to play critical regulatory roles in cancer development. SNORD88C, which located at the intronic region of C19orf48 in chromosome 19q.33 with a 97-nt length was screened through database and snoRNA-sequencing. We firstly verified this snoRNA was up-regulated in tissue and plasma and served as a non-invasive diagnostic biomarker; then confirmed that SNORD88C promoted proliferation and metastasis of NSCLC in vitro and in vivo. Mechanistically, SNORD88C promoted 2'-O-methylation modification at the C3680 site on 28S rRNA and in turn enhanced downstream SCD1 translation, a central lipogenic enzyme for the synthesis of MUFA that can inhibit autophagy by regulating lipid peroxidation and mTOR, providing the novel insight into the regulation of SNORD88C in NSCLC.
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Affiliation(s)
- Kangyu Wang
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Shiwen Wang
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Yue Zhang
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Li Xie
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Xingguo Song
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China.
| | - Xianrang Song
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China.
- Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China.
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16
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Jones RG, Dimet-Wiley A, Haghani A, da Silva FM, Brightwell CR, Lim S, Khadgi S, Wen Y, Dungan CM, Brooke RT, Greene NP, Peterson CA, McCarthy JJ, Horvath S, Watowich SJ, Fry CS, Murach KA. A molecular signature defining exercise adaptation with ageing and in vivo partial reprogramming in skeletal muscle. J Physiol 2023; 601:763-782. [PMID: 36533424 PMCID: PMC9987218 DOI: 10.1113/jp283836] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Exercise promotes functional improvements in aged tissues, but the extent to which it simulates partial molecular reprogramming is unknown. Using transcriptome profiling from (1) a skeletal muscle-specific in vivo Oct3/4, Klf4, Sox2 and Myc (OKSM) reprogramming-factor expression murine model; (2) an in vivo inducible muscle-specific Myc induction murine model; (3) a translatable high-volume hypertrophic exercise training approach in aged mice; and (4) human exercise muscle biopsies, we collectively defined exercise-induced genes that are common to partial reprogramming. Late-life exercise training lowered murine DNA methylation age according to several contemporary muscle-specific clocks. A comparison of the murine soleus transcriptome after late-life exercise training to the soleus transcriptome after OKSM induction revealed an overlapping signature that included higher JunB and Sun1. Also, within this signature, downregulation of specific mitochondrial and muscle-enriched genes was conserved in skeletal muscle of long-term exercise-trained humans; among these was muscle-specific Abra/Stars. Myc is the OKSM factor most induced by exercise in muscle and was elevated following exercise training in aged mice. A pulse of MYC rewired the global soleus muscle methylome, and the transcriptome after a MYC pulse partially recapitulated OKSM induction. A common signature also emerged in the murine MYC-controlled and exercise adaptation transcriptomes, including lower muscle-specific Melusin and reactive oxygen species-associated Romo1. With Myc, OKSM and exercise training in mice, as well habitual exercise in humans, the complex I accessory subunit Ndufb11 was lower; low Ndufb11 is linked to longevity in rodents. Collectively, exercise shares similarities with genetic in vivo partial reprogramming. KEY POINTS: Advances in the last decade related to cellular epigenetic reprogramming (e.g. DNA methylome remodelling) toward a pluripotent state via the Yamanaka transcription factors Oct3/4, Klf4, Sox2 and Myc (OKSM) provide a window into potential mechanisms for combatting the deleterious effects of cellular ageing. Using global gene expression analysis, we compared the effects of in vivo OKSM-mediated partial reprogramming in skeletal muscle fibres of mice to the effects of late-life murine exercise training in muscle. Myc is the Yamanaka factor most induced by exercise in skeletal muscle, and so we compared the MYC-controlled transcriptome in muscle to Yamanaka factor-mediated and exercise adaptation mRNA landscapes in mice and humans. A single pulse of MYC is sufficient to remodel the muscle methylome. We identify partial reprogramming-associated genes that are innately altered by exercise training and conserved in humans, and propose that MYC contributes to some of these responses.
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Affiliation(s)
- Ronald G. Jones
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
| | | | - Amin Haghani
- University of California Los Angeles, Department of Human Genetics, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Francielly Morena da Silva
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
- University of Arkansas, Cachexia Research Laboratory, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
| | - Camille R. Brightwell
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- University of Kentucky, Department of Athletic Training and Clinical Nutrition, Lexington, KY, USA
| | - Seongkyun Lim
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
- University of Arkansas, Cachexia Research Laboratory, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
| | - Sabin Khadgi
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
| | - Yuan Wen
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- University of Kentucky, Department of Physical Therapy, Lexington, KY, USA
| | - Cory M. Dungan
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- University of Kentucky, Department of Physical Therapy, Lexington, KY, USA
| | | | - Nicholas P. Greene
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
- University of Arkansas, Cachexia Research Laboratory, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
- University of Arkansas, Cell and Molecular Biology Graduate Program, Fayetteville, AR, USA
| | - Charlotte A. Peterson
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- University of Kentucky, Department of Physical Therapy, Lexington, KY, USA
- University of Kentucky, Department of Physiology, Lexington, KY, USA
| | - John J. McCarthy
- Altos Labs, San Diego, CA, USA
- University of Kentucky, Department of Physiology, Lexington, KY, USA
| | - Steve Horvath
- University of California Los Angeles, Department of Human Genetics, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Stanley J. Watowich
- Ridgeline Therapeutics, Houston, TX, USA
- University of Texas Medical Branch, Department of Biochemistry and Molecular Biology, Galveston, TX, USA
| | - Christopher S. Fry
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- University of Kentucky, Department of Athletic Training and Clinical Nutrition, Lexington, KY, USA
| | - Kevin A. Murach
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
- University of Arkansas, Cell and Molecular Biology Graduate Program, Fayetteville, AR, USA
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17
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Yang Y, Wang Y, Wang C, Xu X, Liu C, Huang X. Identification of hub genes of Parkinson's disease through bioinformatics analysis. Front Neurosci 2022; 16:974838. [DOI: 10.3389/fnins.2022.974838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/15/2022] [Indexed: 11/11/2022] Open
Abstract
Parkinson's disease (PD) is a common neurodegenerative disease, and there is still a lack of effective diagnostic and treatment methods. This study aimed to search for hub genes that might serve as diagnostic or therapeutic targets for PD. All the analysis was performed in R software. The expression profile data of PD (number: GSE7621) was acquired from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) associated with PD were screened by the “Limma” package of the R software. Key genes associated with PD were screened by the “WGCNA” package of the R software. Target genes were screened by merging the results of “Limma” and “WGCNA.” Enrichment analysis of target genes was performed by Gene Ontology (GO), Disease Ontology (DO), and Kyoto Enrichment of Genes and Genomes (KEGG). Machine learning algorithms were employed to screen for hub genes. Nomogram was constructed using the “rms” package. And the receiver operating characteristic curve (ROC) was plotted to detect and validate our prediction model sensitivity and specificity. Additional expression profile data of PD (number: GSE20141) was acquired from the GEO database to validate the nomogram. GSEA was used to determine the biological functions of the hub genes. Finally, RPL3L, PLEK2, PYCRL, CD99P1, LOC100133130, MELK, LINC01101, and DLG3-AS1 were identified as hub genes of PD. These findings can provide a new direction for the diagnosis and treatment of PD.
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18
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Murach KA, Liu Z, Jude B, Figueiredo VC, Wen Y, Khadgi S, Lim S, Morena da Silva F, Greene NP, Lanner JT, McCarthy JJ, Vechetti IJ, von Walden F. Multi-transcriptome analysis following an acute skeletal muscle growth stimulus yields tools for discerning global and MYC regulatory networks. J Biol Chem 2022; 298:102515. [PMID: 36150502 PMCID: PMC9583450 DOI: 10.1016/j.jbc.2022.102515] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 02/01/2023] Open
Abstract
Myc is a powerful transcription factor implicated in epigenetic reprogramming, cellular plasticity, and rapid growth as well as tumorigenesis. Cancer in skeletal muscle is extremely rare despite marked and sustained Myc induction during loading-induced hypertrophy. Here, we investigated global, actively transcribed, stable, and myonucleus-specific transcriptomes following an acute hypertrophic stimulus in mouse plantaris. With these datasets, we define global and Myc-specific dynamics at the onset of mechanical overload-induced muscle fiber growth. Data collation across analyses reveals an under-appreciated role for the muscle fiber in extracellular matrix remodeling during adaptation, along with the contribution of mRNA stability to epigenetic-related transcript levels in muscle. We also identify Runx1 and Ankrd1 (Marp1) as abundant myonucleus-enriched loading-induced genes. We observed that a strong induction of cell cycle regulators including Myc occurs with mechanical overload in myonuclei. Additionally, in vivo Myc-controlled gene expression in the plantaris was defined using a genetic muscle fiber-specific doxycycline-inducible Myc-overexpression model. We determined Myc is implicated in numerous aspects of gene expression during early-phase muscle fiber growth. Specifically, brief induction of Myc protein in muscle represses Reverbα, Reverbβ, and Myh2 while increasing Rpl3, recapitulating gene expression in myonuclei during acute overload. Experimental, comparative, and in silico analyses place Myc at the center of a stable and actively transcribed, loading-responsive, muscle fiber-localized regulatory hub. Collectively, our experiments are a roadmap for understanding global and Myc-mediated transcriptional networks that regulate rapid remodeling in postmitotic cells. We provide open webtools for exploring the five RNA-seq datasets as a resource to the field.
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Affiliation(s)
- Kevin A. Murach
- Department of Health, Human Performance, and Recreation, Exercise Science Research Center, University of Arkansas, Fayetteville, Arkansas, USA,Cell and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, Arkansas, USA,For correspondence: Kevin A. Murach; Ivan J. Vechetti; Ferdinand von Walden
| | - Zhengye Liu
- Department of Physiology and Pharmacology, Karolinska Institute, Solna, Sweden
| | - Baptiste Jude
- Department of Physiology and Pharmacology, Karolinska Institute, Solna, Sweden,Department of Women’s and Children’s Health, Karolinska Institute, Solna, Sweden
| | - Vandre C. Figueiredo
- Center for Muscle Biology, University of Kentucky, Lexington, Kentucky, USA,Department of Physiology, University of Kentucky, Lexington, Kentucky, USA
| | - Yuan Wen
- Center for Muscle Biology, University of Kentucky, Lexington, Kentucky, USA,Department of Physical Therapy, University of Kentucky, Lexington, Kentucky, USA
| | - Sabin Khadgi
- Department of Health, Human Performance, and Recreation, Exercise Science Research Center, University of Arkansas, Fayetteville, Arkansas, USA
| | - Seongkyun Lim
- Department of Health, Human Performance, and Recreation, Exercise Science Research Center, University of Arkansas, Fayetteville, Arkansas, USA,Cachexia Research Laboratory, University of Arkansas, Fayetteville, Arkansas, USA
| | - Francielly Morena da Silva
- Department of Health, Human Performance, and Recreation, Exercise Science Research Center, University of Arkansas, Fayetteville, Arkansas, USA,Cachexia Research Laboratory, University of Arkansas, Fayetteville, Arkansas, USA
| | - Nicholas P. Greene
- Department of Health, Human Performance, and Recreation, Exercise Science Research Center, University of Arkansas, Fayetteville, Arkansas, USA,Cell and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, Arkansas, USA,Cachexia Research Laboratory, University of Arkansas, Fayetteville, Arkansas, USA
| | - Johanna T. Lanner
- Department of Physiology and Pharmacology, Karolinska Institute, Solna, Sweden
| | - John J. McCarthy
- Center for Muscle Biology, University of Kentucky, Lexington, Kentucky, USA,Department of Physiology, University of Kentucky, Lexington, Kentucky, USA
| | - Ivan J. Vechetti
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Nebraska, USA,For correspondence: Kevin A. Murach; Ivan J. Vechetti; Ferdinand von Walden
| | - Ferdinand von Walden
- Department of Women’s and Children’s Health, Karolinska Institute, Solna, Sweden,For correspondence: Kevin A. Murach; Ivan J. Vechetti; Ferdinand von Walden
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19
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Hammarström D, Øfsteng SJ, Jacobsen NB, Flobergseter KB, Rønnestad BR, Ellefsen S. Ribosome accumulation during early phase resistance training in humans. Acta Physiol (Oxf) 2022; 235:e13806. [PMID: 35213791 PMCID: PMC9540306 DOI: 10.1111/apha.13806] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/04/2022] [Accepted: 02/21/2022] [Indexed: 12/16/2022]
Abstract
Aim To describe ribosome biogenesis during resistance training, its relation to training volume and muscle growth. Methods A training group (n = 11) performed 12 sessions (3‐4 sessions per week) of unilateral knee extension with constant and variable volume (6 and 3‐9 sets per session respectively) allocated to either leg. Ribosome abundance and biogenesis markers were assessed from vastus lateralis biopsies obtained at baseline, 48 hours after sessions 1, 4, 5, 8, 9 and 12, and after eight days of de‐training, and from a control group (n = 8). Muscle thickness was measured before and after the intervention. Results Training led to muscle growth (3.9% over baseline values, 95% CrI: [0.2, 7.5] vs. control) with concomitant increases in total RNA, ribosomal RNA, upstream binding factor (UBF) and ribosomal protein S6 with no differences between volume conditions. Total RNA increased rapidly in response to the first four sessions (8.6% [5.6, 11.7] per session), followed by a plateau and peak values after session 8 (49.5% [34.5, 66.5] above baseline). Total RNA abundance was associated with UBF protein levels (5.0% [0.2, 10.2] per unit UBF), and the rate of increase in total RNA levels predicted hypertrophy (0.3 mm [0.1, 0.4] per %‐point increase in total RNA per session). After de‐training, total RNA decreased (−19.3% [−29.0, −8.1]) without muscle mass changes indicating halted biosynthesis of ribosomes. Conclusion Ribosomes accumulate in the initial phase of resistance training with abundances sensitive to training cessation and associated with UBF protein levels. The average accumulation rate predicts muscle training‐induced hypertrophy.
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Affiliation(s)
- Daniel Hammarström
- Section for Health and Exercise Physiology Department of Public Health and Sport Sciences Inland Norway University of Applied Sciences Lillehammer Norway
- Swedish School of Sport and Health Sciences Stockholm Sweden
| | - Sjur J. Øfsteng
- Section for Health and Exercise Physiology Department of Public Health and Sport Sciences Inland Norway University of Applied Sciences Lillehammer Norway
| | - Nicolai B. Jacobsen
- Section for Health and Exercise Physiology Department of Public Health and Sport Sciences Inland Norway University of Applied Sciences Lillehammer Norway
| | - Krister B. Flobergseter
- Section for Health and Exercise Physiology Department of Public Health and Sport Sciences Inland Norway University of Applied Sciences Lillehammer Norway
| | - Bent R. Rønnestad
- Section for Health and Exercise Physiology Department of Public Health and Sport Sciences Inland Norway University of Applied Sciences Lillehammer Norway
| | - Stian Ellefsen
- Section for Health and Exercise Physiology Department of Public Health and Sport Sciences Inland Norway University of Applied Sciences Lillehammer Norway
- Innlandet Hospital Trust Lillehammer Norway
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20
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Henriksson J. The accumulation rate of ribosomes predicts muscle training-induced hypertrophy. Acta Physiol (Oxf) 2022; 235:e13817. [PMID: 35348277 DOI: 10.1111/apha.13817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 12/01/2022]
Affiliation(s)
- Jan Henriksson
- Department of Physiology & Pharmacology Karolinska Institutet Stockholm Sweden
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21
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Mei H, Boom J, El Abdellaoui S, Abdelmohsen K, Munk R, Martindale JL, Kloet S, Kielbasa SM, Sharp TH, Gorospe M, Raz V. Alternative polyadenylation utilization results in ribosome assembly and mRNA translation deficiencies in a model for muscle aging. J Gerontol A Biol Sci Med Sci 2022; 77:1130-1140. [PMID: 35245938 PMCID: PMC9159670 DOI: 10.1093/gerona/glac058] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Indexed: 11/15/2022] Open
Abstract
Aging-associated muscle wasting is regulated by multiple molecular processes, whereby aberrant mRNA processing regulation induces muscle wasting. The poly(A)-binding protein nuclear 1 (PABPN1) regulates polyadenylation site (PAS) utilization, in the absence of PABPN1 the alternative PAS (APA) is utilized. Reduced PABPN1 levels induce muscle wasting where the expression of cellular processes regulating protein homeostasis, the ubiquitin-proteasome system, and translation, are robustly dysregulated. Translation is impacted by mRNA levels, but PABPN1 impact on translation is not fully understood. Here we show that a persistent reduction in PABPN1 levels led to a significant loss of translation efficiency. RNA sequencing of rRNA-depleted libraries from polysome traces revealed reduced mRNA abundance across ribosomal fractions, as well as reduced levels of small RNAs. We show that the abundance of translated mRNAs in the polysomes correlated with PAS switches at the 3'-UTR. Those mRNAs are enriched in cellular processes that are essential for proper muscle function. This study suggests that the effect of PABPN1 on translation efficiency impacts protein homeostasis in aging-associated muscle atrophy.
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Affiliation(s)
- Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Centre, Leiden, The Netherlands
| | - Jasper Boom
- Sequencing Analysis Support Core, Leiden University Medical Centre, Leiden, The Netherlands
| | - Salma El Abdellaoui
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Susan Kloet
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Szymone M Kielbasa
- Sequencing Analysis Support Core, Leiden University Medical Centre, Leiden, The Netherlands
| | - Thomas H Sharp
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden The Netherlands
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Vered Raz
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
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22
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Murach KA, Dungan CM, von Walden F, Wen Y. Epigenetic evidence for distinct contributions of resident and acquired myonuclei during long-term exercise adaptation using timed in vivo myonuclear labeling. Am J Physiol Cell Physiol 2022; 322:C86-C93. [PMID: 34817266 PMCID: PMC8765804 DOI: 10.1152/ajpcell.00358.2021] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Muscle fibers are syncytial postmitotic cells that can acquire exogenous nuclei from resident muscle stem cells, called satellite cells. Myonuclei are added to muscle fibers by satellite cells during conditions such as load-induced hypertrophy. It is difficult to dissect the molecular contributions of resident versus satellite cell-derived myonuclei during adaptation due to the complexity of labeling distinct nuclear populations in multinuclear cells without label transference between nuclei. To sidestep this barrier, we used a genetic mouse model where myonuclear DNA can be specifically and stably labeled via nonconstitutive H2B-GFP at any point in the lifespan. Resident myonuclei (Mn) were GFP-tagged in vivo before 8 wk of progressive weighted wheel running (PoWeR) in adult mice (>4-mo-old). Resident + satellite cell-derived myonuclei (Mn+SC Mn) were labeled at the end of PoWeR in a separate cohort. Following myonuclear isolation, promoter DNA methylation profiles acquired with low-input reduced representation bisulfite sequencing (RRBS) were compared to deduce epigenetic contributions of satellite cell-derived myonuclei during adaptation. Resident myonuclear DNA has hypomethylated promoters in genes related to protein turnover, whereas the addition of satellite cell-derived myonuclei shifts myonuclear methylation profiles to favor transcription factor regulation and cell-cell signaling. By comparing myonucleus-specific methylation profiling to previously published single-nucleus transcriptional analysis in the absence (Mn) versus the presence of satellite cells (Mn+SC Mn) with PoWeR, we provide evidence that satellite cell-derived myonuclei may preferentially supply specific ribosomal proteins to growing myofibers and retain an epigenetic "memory" of prior stem cell identity. These data offer insights on distinct epigenetic myonuclear characteristics and contributions during adult muscle growth.
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Affiliation(s)
- Kevin A. Murach
- 1Molecular Muscle Mass Regulation Laboratory, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, University of Arkansas, Fayetteville, Arkansas,2Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas,3The Center for Muscle Biology, University of Kentucky, Lexington, Kentucky
| | - Cory M. Dungan
- 3The Center for Muscle Biology, University of Kentucky, Lexington, Kentucky,4Department of Physical Therapy, College of Health Sciences, University of Kentucky, Lexington, Kentucky
| | - Ferdinand von Walden
- 5Department of Women’s and Children’s Health, Karolinska Institute, Stockholm, Sweden
| | - Yuan Wen
- 3The Center for Muscle Biology, University of Kentucky, Lexington, Kentucky,6Department of Physiology, College of Medicine, University of Kentucky, Lexington, Kentucky,7Myoanalytics, LLC, Lexington, Kentucky
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23
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Grishin SY, Dzhus UF, Selivanova OM, Balobanov VA, Surin AK, Galzitskaya OV. Comparative Analysis of Aggregation of Thermus thermophilus Ribosomal Protein bS1 and Its Stable Fragment. BIOCHEMISTRY (MOSCOW) 2021; 85:344-354. [PMID: 32564739 DOI: 10.1134/s0006297920030104] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Functionally important multidomain bacterial protein bS1 is the largest ribosomal protein of subunit 30S. It interacts with both mRNA and proteins and is prone to aggregation, although this process has not been studied in detail. Here, we obtained bacterial strains overproducing ribosomal bS1 protein from Thermus thermophilus and its stable fragment bS1(49) and purified these proteins. Using fluorescence spectroscopy, dynamic light scattering, and high-performance liquid chromatography combined with mass spectrometric analysis of products of protein limited proteolysis, we demonstrated that disordered regions at the N- and C-termini of bS1 can play a key role in the aggregation of this protein. The truncated fragment bS1(49) was less prone to aggregation compared to the full-size bS1. The revealed properties of the studied proteins can be used to obtain protein crystals for elucidating the structure of the bS1 stable fragment.
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Affiliation(s)
- S Yu Grishin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - U F Dzhus
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - O M Selivanova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - V A Balobanov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - A K Surin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia. .,State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, 142279, Russia.,Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - O V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia. .,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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24
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Sun M, Shen B, Li W, Samir P, Browne CM, Link AJ, Frank J. A Time-Resolved Cryo-EM Study of Saccharomyces cerevisiae 80S Ribosome Protein Composition in Response to a Change in Carbon Source. Proteomics 2020; 21:e2000125. [PMID: 33007145 DOI: 10.1002/pmic.202000125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/31/2020] [Indexed: 12/28/2022]
Abstract
The role of the ribosome in the regulation of gene expression has come into increased focus. It is proposed that ribosomes are catalytic engines capable of changing their protein composition in response to environmental stimuli. Time-resolved cryo-electron microscopy (cryo-EM) techniques are employed to identify quantitative changes in the protein composition and structure of the Saccharomyces cerevisiae 80S ribosomes after shifting the carbon source from glucose to glycerol. Using cryo-EM combined with the computational classification approach, it is found that a fraction of the yeast cells' 80S ribosomes lack ribosomal proteins at the entrance and exit sites for tRNAs, including uL16(RPL10), eS1(RPS1), uS11(RPS14A/B), and eS26(RPS26A/B). This fraction increased after a change from glucose to glycerol medium. The quantitative structural analysis supports the hypothesis that ribosomes are dynamic complexes that alter their composition in response to changes in growth or environmental conditions.
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Affiliation(s)
- Ming Sun
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Bingxin Shen
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Wen Li
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Parimal Samir
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA.,Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA
| | - Christopher M Browne
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA.,Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA
| | - Andrew J Link
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA.,Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA.,Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Joachim Frank
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
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25
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Dupont-Versteegden EE, McCarthy JJ. Translational control of muscle mass. J Appl Physiol (1985) 2020; 127:579-580. [PMID: 31446832 DOI: 10.1152/japplphysiol.00497.2019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
| | - John J McCarthy
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, Kentucky
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26
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Wu F, Sun H, Lu S, Gou X, Yan D, Xu Z, Zhang Z, Qadri QR, Zhang Z, Wang Z, Chen Q, Li M, Wang X, Dong X, Wang Q, Pan Y. Genetic Diversity and Selection Signatures Within Diannan Small-Ear Pigs Revealed by Next-Generation Sequencing. Front Genet 2020; 11:733. [PMID: 32849777 PMCID: PMC7406676 DOI: 10.3389/fgene.2020.00733] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/16/2020] [Indexed: 12/26/2022] Open
Abstract
Genetic characterization of Chinese indigenous pig breeds is essential to promote scientific conservation and sustainable development of pigs. Here, we systematically surveyed the genomes of 75 unrelated Diannan small-ear (DSE) pigs from three diverse regions (Yingjiang County, Jinping County, and Sipsongpanna in Yunnan Province) to describe their population structures, genetic diversity, inbreeding coefficients, and selection signatures. First, these individuals were sequenced and genotyped using the genome reducing and sequencing (GGRS) protocol. A total of 438,038 autosomal single-nucleotide polymorphisms (SNPs) were obtained and used for subsequent statistical analysis. The results showed that these DSE pigs were clearly differentiated into three separate clades revealed by the population structure and principal component analysis, which is consistent with their geographical origins. Diannan small-ear pigs owned lower genetic diversity when compared with some other pig breeds, which demonstrated the need to strengthen the conservation strategies for DSE pigs. In addition, the inbreeding coefficients based on runs of homozygosity (ROH) length (F ROH) were calculated in each ROH length categories, respectively. And the results indicated that the ancient (up to 50 generations ago) inbreeding had greater impacts than recent (within the last five generations) inbreeding within DSE pigs. Some candidate selection signatures within the DSE pig population were detected through the ROH islands and integrated haplotype homozygosity score (iHS) methods. And genes associated with meat quality (COL15A1, RPL3L, and SLC9A3R2), body size (PALM2-AKAP2, NANS, TRAF7, and PACSIN1), adaptability (CLDN9 and E4F1), and appetite (GRM4) were identified. These findings can help to understand the genetic characteristics and provide insights into the molecular background of special phenotypes of DSE pigs to promote conservation and sustainability of the breed.
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Affiliation(s)
- Fen Wu
- Department of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Hao Sun
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Shaoxiong Lu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Xiao Gou
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Dawei Yan
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Zhong Xu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhenyang Zhang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qamar Raza Qadri
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhe Zhang
- Department of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Zhen Wang
- Department of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Qiang Chen
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Mingli Li
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Xiaoyi Wang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Xinxing Dong
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Qishan Wang
- Department of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yuchun Pan
- Department of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China
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Wu H, Qin W, Lu S, Wang X, Zhang J, Sun T, Hu X, Li Y, Chen Q, Wang Y, Zhao H, Piao H, Zhang R, Wei M. Long noncoding RNA ZFAS1 promoting small nucleolar RNA-mediated 2'-O-methylation via NOP58 recruitment in colorectal cancer. Mol Cancer 2020; 19:95. [PMID: 32443980 PMCID: PMC7243338 DOI: 10.1186/s12943-020-01201-w] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 04/15/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Increasing evidence supports the role of small nucleolar RNAs (snoRNAs) and long non-coding RNAs (lncRNAs) as master gene regulators at the epigenetic modification level. However, the underlying mechanism of these functional ncRNAs in colorectal cancer (CRC) has not been well investigated. METHODS The dysregulated expression profiling of lncRNAs-snoRNAs-mRNAs and their correlations and co-expression enrichment were assessed by GeneChip microarray analysis. The candidate lncRNAs, snoRNAs, and target genes were detected by in situ hybridization (ISH), RT-PCR, qPCR and immunofluorescence (IF) assays. The biological functions of these factors were investigated using in vitro and in vivo studies that included CCK8, trans-well, cell apoptosis, IF assay, western blot method, and the xenograft mice models. rRNA 2'-O-methylation (Me) activities were determined by the RTL-P assay and a novel double-stranded primer based on the single-stranded toehold (DPBST) assay. The underlying molecular mechanisms were explored by bioinformatics and RNA stability, RNA fluorescence ISH, RNA pull-down and translation inhibition assays. RESULTS To demonstrate the involvement of lncRNA and snoRNAs in 2'-O-Me modification during tumorigenesis, we uncovered a previously unreported mechanism linking the snoRNPs NOP58 regulated by ZFAS1 in control of SNORD12C, SNORD78 mediated rRNA 2'-O-Me activities in CRC initiation and development. Specifically, ZFAS1 exerts its oncogenic functions and significantly up-regulated accompanied by elevated NOP58, SNORD12C/78 expression in CRC cells and tissues. ZFAS1 knockdown suppressed CRC cell proliferation, migration, and increased cell apoptosis, and this inhibitory effect could be reversed by NOP58 overexpression in vitro and in vivo. Mechanistically, the NOP58 protein could be recognized by the specific motif (AAGA or CAGA) of ZFAS1. This event accelerates the assembly of SNORD12C/78 to allow for further guiding of 2'-O-Me at the corresponding Gm3878 and Gm4593 sites. Importantly, silencing SNORD12C or 78 reduced the rRNAs 2'-O-Me activities, which could be rescued by overexpression ZFAS1, and this subsequently inhibits the RNA stability and translation activity of their downstream targets (e.g., EIF4A3 and LAMC2). CONCLUSION The novel ZFAS1-NOP58-SNORD12C/78-EIF4A3/LAMC2 signaling axis that functions in CRC tumorigenesis provides a better understanding regarding the role of lncRNA-snoRNP-mediated rRNAs 2'-O-Me activities for the prevention and treatment of CRC.
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Affiliation(s)
- Huizhe Wu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, People's Republic of China
| | - Wenyan Qin
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, People's Republic of China
| | - Senxu Lu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, People's Republic of China
| | - Xiufang Wang
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, People's Republic of China
| | - Jing Zhang
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, People's Republic of China
| | - Tong Sun
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, People's Republic of China
| | - Xiaoyun Hu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, People's Republic of China
| | - Yalun Li
- Department of Anorectal Surgery, First Hospital of China Medical University, Shenyang, 110001, People's Republic of China
| | - Qiuchen Chen
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, People's Republic of China
| | - Yuanhe Wang
- Department of Medical Oncology, Cancer Hospital of China Medical University, Shenyang, 110042, People's Republic of China
| | - Haishan Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, People's Republic of China
| | - Haiyan Piao
- Department of Medical Oncology, Cancer Hospital of China Medical University, Shenyang, 110042, People's Republic of China
| | - Rui Zhang
- Department of Medical Oncology, Cancer Hospital of China Medical University, Shenyang, 110042, People's Republic of China.
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China. .,Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, People's Republic of China.
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