Biology subjects

Murach, K. A.

Publications and source records attributed to Murach, K. A..

9 recordsLinked to original sources

bioRxiv2026

Exercise preconditioning confers skeletal muscle myometaplasticity

Previously exercise trained skeletal muscle is more growth-responsive to retraining. Using a murine training-detraining-retraining approach and multi-omics, we find that Pecam1 gene expression is lower, but capillarization is appreciably higher in previously trained (preconditioned) relative to naive trained control muscle. Greater capillarity could be permissive for accelerated hypertrophic adaptation. Exercise preconditioned myonuclei feature differential promoter CpG regulation in genes related to Wnt signaling. These epigenetic alterations with retraining align with our prior observations of methylation changes within the same pathway after a longer period of chronic training, suggesting a more rapid response due to preconditioning. Methylome-transcriptome integration and single myonucleus RNA-sequencing expose the polyamine metabolism enzyme Smox as a target that relates to heightened hypertrophic adaptability with retraining. Smox induction is sufficient to cause hypertrophy in aligned myotubes cultured on a stiffness-tuned substrate along with a growth-supportive transcriptional program. Integration of our multi-omics data suggests that Smox regulates repression of Ddit4/Redd1 (an inhibitor of mTORC1 signaling) after retraining. Smox may govern a favorable muscle fiber growth environment in previously trained muscle by sensitizing anabolic potential through polyamine metabolism. A lower adaptive threshold mediated by Smox could contribute to myometaplasticity, or a change to how subsequent muscle adaptations are made.

molecular biology↗

bioRxiv2026

Skeletal Muscle Stem Cell-Derived Myonuclei Adopt Divergent Terminal Transcriptional States in Adult and Aged Muscle In Response to a Hypertrophic Stimulus

Skeletal muscle stem cells (MuSCs) give rise to a fusogenic cell population that provide new myonuclei to muscle fibers. Myonuclear functional heterogeneity has recently become appreciated, but the terminal identity of MuSC-Derived myonuclei remains undefined. We performed single-nucleus RNA-sequencing of myonuclei in Adult and Aged muscle to define MuSC-Derived and resident myonuclear responses to mechanical overload (MOV), which induces a hypertrophic stimulus. We found a MuSC-dependent induction of a youthful transcriptional signature in resident myonuclei after MOV in Aged muscle. Age determined terminal transcriptional states of MuSC-Derived myonuclei toward MTJ in Adult, NMJ in Aged, and muscle spindles in both ages. Microtubule-remodeling genes, Macf1, Map1b, and Nav3, along with the transcription factor Runx1, identified this post-fusion specialization with greater expression of these genes in Adult than in Aged MuSC-Derived myonuclei. In-silico transcription factor KO screen identified Runx1 as a regulator of post-fusion specialization and Esrrg as a driver of spindle (intrafusal) MuSC-Derived myonuclear maturation. By defining the age-associated fate of MuSC fusion to muscle fibers, we provide potential targets for modulating muscle plasticity.

molecular biology↗

bioRxiv2026

Myonuclear Dynamics After Skeletal Muscle Surgical Injury

A hallmark of damaged skeletal muscle fibers is displaced myonuclei that are no longer peripherally positioned. Displaced myonuclei are dogmatically thought to be derived exclusively from muscle stem cell (satellite cell) fusion. Using a surgical resection muscle injury model and in vivo recombination-independent resident myonuclear labeling, we detail the prevalence, time course, and origin of displaced myonuclei in response to a non-chemically-mediated muscle trauma. We found that: 1) non-satellite cell-derived (resident) displaced myonuclei emerge seven days after surgical injury in similar proportion to exogenous (satellite cell-derived) displaced myonuclei in intact muscle fibers, with a biased prevalence in myosin heavy chain IIB muscle fibers, 2) muscle fibers with multiple ([≥]2) displaced resident myonuclei was an unexpected but noteworthy feature of muscle fibers 7 days after injury, 3) embryonic myosin-expressing fibers at seven days post-surgery expectedly contain predominantly satellite-cell derived displaced myonuclei, but a subset have displaced resident myonuclei, and 4) satellite cell numbers in intact muscle do not increase until 7 days post-surgery. These data may help inform whether to target satellite cell-initiated processes, myonuclear-initiated processes, or both to facilitate muscle fiber injury repair. This information could lead to more effective therapeutic strategies for treating muscle trauma.

cell biology↗

bioRxiv2026

Myonuclear loss, rather than senescent myonuclei, associates with fiber type-specific atrophy in aging human skeletal muscle

Age-related reductions in whole-muscle function are attributed, in part, to pronounced atrophy of muscle fibers expressing the fast myosin heavy chain (MyHC) II isoforms. Senescence, a state of irreversible cell cycle arrest that can be characterized by DNA damage ({gamma}H2AX) and chromatin remodeling (loss of nuclear HMGB1), may contribute to skeletal muscle aging. Muscle nuclei (myonuclei) maintain fiber size and function and could exhibit senescence-associated features; however, the prevalence of senescent myonuclei and whether they contribute to fast fiber atrophy in older adults remains unknown. Vastus lateralis biopsies from 20 young (19-34yr; 10 females) and 20 older (65-84yr; 10 females) adults were analyzed via immunohistochemistry for myonuclei positive for {gamma}H2AX ({gamma}H2AX+) and negative for HMGB1 (HMGB1-). MyHC II cross-sectional area (CSA) was [~]70% larger in young compared with old, whereas MyHC I CSA did not differ with age. The relative abundance of {gamma}H2AX+/HMGB1- myonuclei did not differ with age and was not associated with CSA in either fiber type. Single-nucleus RNA-sequencing corroborated no age-related difference in the prevalence of myonuclei with senescence-associated features. Myonuclear content of MyHC II fibers was [~]30% higher in young compared with old and was closely associated with CSA in both fiber types. Size-cluster analysis revealed a pronounced age-related leftward shift in MyHC II CSA that paralleled the reductions in myonuclear number, consistent with myonuclear loss. These data suggest that age-related fast fiber atrophy is not attributed to an increased prevalence of senescent myonuclei but instead occurs concomitantly with fiber type-specific myonuclear loss across the lifespan.

cell biology↗

bioRxiv2025

The Age-Dependent Resident Myonuclear Multi-Omic Response to a Skeletal Muscle Hypertrophic Stimulus

A detailed analysis of how muscle fiber nuclei (myonuclei) respond to a hypertrophic stimulus would provide a critical step toward understanding compromised skeletal muscle plasticity with age. We used recombination-independent doxycycline-inducible myonucleus-specific fluorescent labelling, tissue RNA-sequencing, myonuclear DNA methylation analysis, multi-omic integration, and single myonucleus RNA-sequencing to define the molecular characteristics of adult (6-8 month) and aged (24 month) murine skeletal muscle after acute mechanical overload (MOV). In adult and aged MOV muscles, we found that: 1) similarities in the transcriptional response to loading - specifically in metabolism genes - were partly explained by a post-transcriptional microRNA-mediated mechanism, which we corroborated using an inducible muscle fiber-specific miR-1 knockout model, 2) differences in age-dependent transcriptional responses were linked to the magnitude and location of differential DNA methylation in resident myonuclei, specifically around hypertrophy-associated genes such as Myc, Runx1, Mybph, Ankrd1, collagen genes, and minichromosome maintenance genes, 3) adult and aged resident myonuclear transcriptomes had differing enrichment for innervation-related transcripts as well as unique transcriptional profiles in an Atf3+ "sarcomere assembly" population after MOV, and 4) cellular deconvolution analysis supports a role for neuromuscular junction regulation in age-specific hypertrophic adaptation. These data are a roadmap for uncovering molecular targets to enhance aged muscle adaptability.

cell biology↗

bioRxiv2024

microRNA-1 Regulates Metabolic Flexibility in Skeletal Muscle via Pyruvate Metabolism

MicroRNA-1 (miR-1) is the most abundant miRNA in adult skeletal muscle. To determine the function of miR-1 in adult skeletal muscle, we generated an inducible, skeletal muscle-specific miR-1 knockout (KO) mouse. Integration of RNA-sequencing (RNA-seq) data from miR-1 KO muscle with Argonaute 2 enhanced crosslinking and immunoprecipitation sequencing (AGO2 eCLIP-seq) from human skeletal muscle identified miR-1 target genes involved with glycolysis and pyruvate metabolism. The loss of miR-1 in skeletal muscle induced cancer-like metabolic reprogramming, as shown by higher pyruvate kinase muscle isozyme M2 (PKM2) protein levels, which promoted glycolysis. Comprehensive bioenergetic and metabolic phenotyping combined with skeletal muscle proteomics and metabolomics further demonstrated that miR-1 KO induced metabolic inflexibility as a result of pyruvate oxidation resistance. While the genetic loss of miR-1 reduced endurance exercise performance in mice and in C. elegans, the physiological down-regulation of miR-1 expression in response to a hypertrophic stimulus in both humans and mice causes a similar metabolic reprogramming that supports muscle cell growth. Taken together, these data identify a novel post-translational mechanism of adult skeletal muscle metabolism regulation mediated by miR-1.

physiology↗

bioRxiv2024

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

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.

cell biology↗

bioRxiv2022

The Time-Course of Cancer Cachexia Onset Reveals Biphasic Transcriptional Disruptions in Female Skeletal Muscle Distinct from Males

BackgroundCancer-cachexia (CC) is experienced by 80% of cancer patients, representing 40% of cancer-related deaths. Evidence suggests biological sex dimorphism is associated with CC. Assessments of the female transcriptome in CC are lacking and direct comparisons between biological sex are scarce. The purpose of this study was to define the time course of LLC-induced CC in females using transcriptomics, while directly comparing the effects of biological sex. MethodsEight-week-old female mice were injected with LLC cells (1x106) or sterile PBS to the hind flank. Tumors developed for 1, 2, 3 or 4-weeks. Due to dimorphism between tumor weight in 3- and 4-weeks of development, these were reorganized as low-tumor weight (LT, tumor-weight [≤]1.2g), or high-tumor weight (HT, tumor-weight [≥]2g). Gastrocnemius muscle was collected for RNA-sequencing (RNA-seq). Differentially expressed genes (DEGs) were defined as FDR<0.05. Data were further compared to RNA-seq of male mice from a previous study. ResultsGlobal gene expression of female gastrocnemius muscle reveals consistent DEGs at all timepoints, all associated with type-II interferon signaling (FDR<0.05). Early transcriptomic upregulation of extracellular-matrix pathways was noted at 1wk (p<0.05), JAK-STAT pathway was upregulated in 2wk, LT, and HT. Type II interferon signaling was downregulated in 1wk, LT, and HT (p<0.05). A second major transcriptomic downregulation in oxidative phosphorylation, electron transport chain and TCA cycle were noted in cachectic (HT) muscle only (p<0.05). Male-female comparison of cachectic groups revealed 69% of DEGs were distinct between sex (FDR<0.05). Comparison of the top 10-up and down DEGs revealed downregulation of type-II Interferon genes was unique to female, while males show upregulation of interferon-signaling pathways. ConclusionWe demonstrate biphasic disruptions in transcriptome of female LLC tumor-bearing mice: an early phase associated with ECM remodeling and a late phase, accompanied by onset of systemic cachexia, affecting overall skeletal muscle energy metabolism. Comparison of cachectic female-male mice reveals ~2/3 of DEGs are biological sex specific, providing evidence of dimorphic mechanisms of cachexia between sexes. Alterations to Type-II Interferon signaling appears specific to CC development in females, suggesting a new biological sex-specific marker of CC. Our data support biological sex dimorphisms in development of CC. HighlightsO_LIWhile males show impairments in skeletal muscle energy metabolism in early stages of CC, early transcriptomic alterations impact ECM remodeling that precedes impairments in skeletal muscle energy metabolism in female tumor-bearing mice. C_LIO_LI2/3 of differently expressed genes in skeletal muscle undergoing cachexia are biological sex specific. C_LIO_LIDownregulation of Type-II Interferon genes is unique to female mice, which displayed preserved gastrocnemius mass despite systemic cachexia, representing a potential therapeutic target for muscle mass maintenance in cancer-induced atrophy. C_LIO_LIMechanisms of LLC-induced cachexia appear to be biological sex specific which needs to be considered in further study of mechanisms and therapeutic modalities. C_LI

bioinformatics↗

bioRxiv2020

Genetic and Epigenetic Regulation of Skeletal Muscle Ribosome Biogenesis with Exercise

Ribosomes are the macromolecular engines of protein synthesis. Skeletal muscle ribosome biogenesis is stimulated by exercise, but the contribution of ribosomal DNA (rDNA) copy number and methylation to exercise-induced rDNA transcription is unclear. To investigate the genetic and epigenetic regulation of ribosome biogenesis with exercise, a time course of skeletal muscle biopsies was obtained from 30 participants (18 men and 12 women; 31 {+/-}8 yrs, 25 {+/-}4 kg/m2) at rest and 30 min, 3h, 8h, and 24h after acute endurance (n=10, 45 min cycling, 70% VO2max) or resistance exercise (n=10, 4 x 7 x 2 exercises); 10 control participants underwent biopsies without exercise. rDNA transcription and dosage were assessed using qPCR and whole genome sequencing. rDNA promoter methylation was investigated using massARRAY EpiTYPER, and global rDNA CpG methylation was assessed using reduced-representation bisulfite sequencing. Ribosome biogenesis and MYC transcription were associated with resistance but not endurance exercise, indicating preferential up-regulation during hypertrophic processes. With resistance exercise, ribosome biogenesis was associated with rDNA gene dosage as well as epigenetic changes in enhancer and non-canonical MYC-associated areas in rDNA, but not the promoter. A mouse model of in vivo metabolic RNA labeling and genetic myonuclear fluorescent labeling validated the effects of an acute hypertrophic stimulus on ribosome biogenesis and Myc transcription, and corroborated rDNA enhancer and Myc-associated methylation alterations specifically in myonuclei. This study provides the first information on skeletal muscle genetic and rDNA gene-wide epigenetic regulation of ribosome biogenesis in response to exercise, revealing novel roles for rDNA dosage and CpG methylation. GRAPHICAL ABSTRACT O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

cell biology↗