Malene Lindholm

All Publications

• Charting the Molecular Terrain of Exercise: The Power of Multi-Omic Mapping. Physiology (Bethesda, Md.) Katz, D. H., Lindholm, M. E., Ashley, E. A. 2024

  Abstract

  Physical activity plays a fundamental role in human health and disease. Exercise has been shown to improve a wide variety of disease states, and the scientific community is committed to understanding the precise molecular mechanisms that underlie the exquisite benefits. This review provides an overview of molecular responses to acute exercise and chronic training, particularly energy mobilization and generation, structural adaptation, inflammation, and immune regulation. Further it offers a detailed discussion on known molecular signals and systemic regulators activated during various forms of exercise and their role in orchestrating health benefits. Critically, the increasing use of multi-omic technologies is explored with an emphasis on how multi-omic and multi-tissue studies contribute to a more profound understanding of exercise biology. These data inform anticipated future advancement in the field and highlight the prospect of integrating exercise with pharmacology for personalized disease prevention and treatment.

  View details for DOI 10.1152/physiol.00024.2024

  View details for PubMedID 39136551

• Physiological Adaptations to Progressive Endurance Exercise Training in Adult and Aged Rats: Insights from the Molecular Transducers of Physical Activity Consortium (MoTrPAC). Function (Oxford, England) Schenk, S., Sagendorf, T. J., Many, G. M., Lira, A. K., de Sousa, L. G., Bae, D., Cicha, M., Kramer, K. S., Muehlbauer, M., Hevener, A. L., Rector, R. S., Thyfault, J. P., Williams, J. P., Goodyear, L. J., Esser, K. A., Newgard, C. B., Bodine, S. C., MoTrPAC Study Group, Adkins, J. N., Albertson, B. G., Amar, D., Amper, M. A., Ashley, E., Bae, D., Bamman, M. M., Barnes, J., Bergman, B. C., Bessesen, D. H., Bodine, S. C., Buford, T. W., Burant, C. F., Cicha, M., Cutter, G. R., De Sousa, L. G., Esser, K. A., Fernandez, F. M., Gaul, D. A., Ge, Y., Goodpaster, B. H., Goodyear, L. J., Guevara, K., Hevener, A. L., Hirshman, M. F., Huffman, K. M., Jackson, B. E., Jankowski, C. M., Jimenez-Morales, D., Kohrt, W. M., Kramer, K. S., Kraus, W. E., Lessard, S. J., Lester, B., Lindholm, M. E., Lira, A. K., Many, G., Marjanovic, N., Marshall, A. G., Melanson, E. L., Miller, M. E., Moreau, K. L., Nair, V. D., Newgard, C. B., Ortlund, E. A., Qian, W., Rasmussen, B. B., Rector, R. S., Richards, C. Z., Rushing, S., Sagendorf, T. J., Sanford, J. A., Schauer, I. E., Schenk, S., Schwartz, R. S., Sealfon, S. C., Seenarine, N., Sparks, L. M., Stowe, C. L., Talton, J. W., Teng, C., Tesfa, N. D., Thalacker-Mercer, A., Thyfault, J. P., Trappe, S., Trappe, T. A., Vasoya, M., Wheeler, M. T., Walkup, M. P., Williams, J. P., Yan, Z., Zhen, J. 2024; 5 (4)

  Abstract

  While regular physical activity is a cornerstone of health, wellness, and vitality, the impact of endurance exercise training on molecular signaling within and across tissues remains to be delineated. The Molecular Transducers of Physical Activity Consortium (MoTrPAC) was established to characterize molecular networks underlying the adaptive response to exercise. Here, we describe the endurance exercise training studies undertaken by the Preclinical Animal Sites Studies component of MoTrPAC, in which we sought to develop and implement a standardized endurance exercise protocol in a large cohort of rats. To this end, Adult (6-mo) and Aged (18-mo) female (n=151) and male (n=143) Fischer 344 rats were subjected to progressive treadmill training (5 d/wk, 70%-75% VO2max) for 1, 2, 4, or 8 wk; sedentary rats were studied as the control group. A total of 18 solid tissues, as well as blood, plasma, and feces, were collected to establish a publicly accessible biorepository and for extensive omics-based analyses by MoTrPAC. Treadmill training was highly effective, with robust improvements in skeletal muscle citrate synthase activity in as little as 1-2 wk and improvements in maximum run speed and maximal oxygen uptake by 4-8 wk. For body mass and composition, notable age- and sex-dependent responses were observed. This work in mature, treadmill-trained rats represents the most comprehensive and publicly accessible tissue biorepository, to date, and provides an unprecedented resource for studying temporal-, sex-, and age-specific responses to endurance exercise training in a preclinical rat model.

  View details for DOI 10.1093/function/zqae014

  View details for PubMedID 38984994

• DNA methylation of exercise-responsive genes differs between trained and untrained men. BMC biology Geiger, C., Needhamsen, M., Emanuelsson, E. B., Norrbom, J., Steindorf, K., Sundberg, C. J., Reitzner, S. M., Lindholm, M. E. 2024; 22 (1): 147

  Abstract

  Physical activity is well known for its multiple health benefits and although the knowledge of the underlying molecular mechanisms is increasing, our understanding of the role of epigenetics in long-term training adaptation remains incomplete. In this intervention study, we included individuals with a history of > 15 years of regular endurance or resistance training compared to age-matched untrained controls performing endurance or resistance exercise. We examined skeletal muscle DNA methylation of genes involved in key adaptation processes, including myogenesis, gene regulation, angiogenesis and metabolism.A greater number of differentially methylated regions and differentially expressed genes were identified when comparing the endurance group with the control group than in the comparison between the strength group and the control group at baseline. Although the cellular composition of skeletal muscle samples was generally consistent across groups, variations were observed in the distribution of muscle fiber types. Slow-twitch fiber type genes MYH7 and MYL3 exhibited lower promoter methylation and elevated expression in endurance-trained athletes, while the same group showed higher methylation in transcription factors such as FOXO3, CREB5, and PGC-1α. The baseline DNA methylation state of those genes was associated with the transcriptional response to an acute bout of exercise. Acute exercise altered very few of the investigated CpG sites.Endurance- compared to resistance-trained athletes and untrained individuals demonstrated a different DNA methylation signature of selected skeletal muscle genes, which may influence transcriptional dynamics following a bout of acute exercise. Skeletal muscle fiber type distribution is associated with methylation of fiber type specific genes. Our results suggest that the baseline DNA methylation landscape in skeletal muscle influences the transcription of regulatory genes in response to an acute exercise bout.

  View details for DOI 10.1186/s12915-024-01938-6

  View details for PubMedID 38965555

  View details for PubMedCentralID 4241367

• The impact of exercise on gene regulation in association with complex trait genetics. Nature communications Vetr, N. G., Gay, N. R., MoTrPAC Study Group, Montgomery, S. B., Adkins, J. N., Albertson, B. G., Amar, D., Amper, M. A., Armenteros, J. J., Ashley, E., Avila-Pacheco, J., Bae, D., Balci, A. T., Bamman, M., Bararpour, N., Barton, E. R., Jean Beltran, P. M., Bergman, B. C., Bessesen, D. H., Bodine, S. C., Booth, F. W., Bouverat, B., Buford, T. W., Burant, C. F., Caputo, T., Carr, S., Chambers, T. L., Chavez, C., Chikina, M., Chiu, R., Cicha, M., Clish, C. B., Coen, P. M., Cooper, D., Cornell, E., Cutter, G., Dalton, K. P., Dasari, S., Dennis, C., Esser, K., Evans, C. R., Farrar, R., Fernadez, F. M., Gadde, K., Gagne, N., Gaul, D. A., Ge, Y., Gerszten, R. E., Goodpaster, B. H., Goodyear, L. J., Gritsenko, M. A., Guevara, K., Haddad, F., Hansen, J. R., Harris, M., Hastie, T., Hennig, K. M., Hershman, S. G., Hevener, A., Hirshman, M. F., Hou, Z., Hsu, F., Huffman, K. M., Hung, C., Hutchinson-Bunch, C., Ivanova, A. A., Jackson, B. E., Jankowski, C. M., Jimenez-Morales, D., Jin, C. A., Johannsen, N. M., Newton, R. L., Kachman, M. T., Ke, B. G., Keshishian, H., Kohrt, W. M., Kramer, K. S., Kraus, W. E., Lanza, I., Leeuwenburgh, C., Lessard, S. J., Lester, B., Li, J. Z., Lindholm, M. E., Lira, A. K., Liu, X., Lu, C., Makarewicz, N. S., Maner-Smith, K. M., Mani, D. R., Many, G. M., Marjanovic, N., Marshall, A., Marwaha, S., May, S., Melanson, E. L., Miller, M. E., Monroe, M. E., Moore, S. G., Moore, R. J., Moreau, K. L., Mundorff, C. C., Musi, N., Nachun, D., Nair, V. D., Nair, K. S., Nestor, M. D., Nicklas, B., Nigro, P., Nudelman, G., Ortlund, E. A., Pahor, M., Pearce, C., Petyuk, V. A., Piehowski, P. D., Pincas, H., Powers, S., Presby, D. M., Qian, W., Radom-Aizik, S., Raja, A. N., Ramachandran, K., Ramaker, M. E., Ramos, I., Rankinen, T., Raskind, A. S., Rasmussen, B. B., Ravussin, E., Rector, R. S., Rejeski, W. J., Richards, C. Z., Rirak, S., Robbins, J. M., Rooney, J. L., Rubenstein, A. B., Ruf-Zamojski, F., Rushing, S., Sagendorf, T. J., Samdarshi, M., Sanford, J. A., Savage, E. M., Schauer, I. E., Schenk, S., Schwartz, R. S., Sealfon, S. C., Seenarine, N., Smith, K. S., Smith, G. R., Snyder, M. P., Soni, T., Oliveira De Sousa, L. G., Sparks, L. M., Steep, A., Stowe, C. L., Sun, Y., Teng, C., Thalacker-Mercer, A., Thyfault, J., Tibshirani, R., Tracy, R., Trappe, S., Trappe, T. A., Uppal, K., Vangeti, S., Vasoya, M., Volpi, E., Vornholt, A., Walkup, M. P., Walsh, M. J., Wheeler, M. T., Williams, J. P., Wu, S., Xia, A., Yan, Z., Yu, X., Zang, C., Zaslavsky, E., Zebarjadi, N., Zhang, T., Zhao, B., Zhen, J. 2024; 15 (1): 3346

  Abstract

  Endurance exercise training is known to reduce risk for a range of complex diseases. However, the molecular basis of this effect has been challenging to study and largely restricted to analyses of either few or easily biopsied tissues. Extensive transcriptome data collected across 15 tissues during exercise training in rats as part of the Molecular Transducers of Physical Activity Consortium has provided a unique opportunity to clarify how exercise can affect tissue-specific gene expression and further suggest how exercise adaptation may impact complex disease-associated genes. To build this map, we integrate this multi-tissue atlas of gene expression changes with gene-disease targets, genetic regulation of expression, and trait relationship data in humans. Consensus from multiple approaches prioritizes specific tissues and genes where endurance exercise impacts disease-relevant gene expression. Specifically, we identify a total of 5523 trait-tissue-gene triplets to serve as a valuable starting point for future investigations [Exercise; Transcription; Human Phenotypic Variation].

  View details for DOI 10.1038/s41467-024-45966-w

  View details for PubMedID 38693125

• Temporal dynamics of the multi-omic response to endurance exercise training. Nature 2024; 629 (8010): 174-183

  Abstract

  Regular exercise promotes whole-body health and prevents disease, but the underlying molecular mechanisms are incompletely understood1-3. Here, the Molecular Transducers of Physical Activity Consortium4 profiled the temporal transcriptome, proteome, metabolome, lipidome, phosphoproteome, acetylproteome, ubiquitylproteome, epigenome and immunome in whole blood, plasma and 18 solid tissues in male and female Rattus norvegicus over eight weeks of endurance exercise training. The resulting data compendium encompasses 9,466 assays across 19 tissues, 25 molecular platforms and 4 training time points. Thousands of shared and tissue-specific molecular alterations were identified, with sex differences found in multiple tissues. Temporal multi-omic and multi-tissue analyses revealed expansive biological insights into the adaptive responses to endurance training, including widespread regulation of immune, metabolic, stress response and mitochondrial pathways. Many changes were relevant to human health, including non-alcoholic fatty liver disease, inflammatory bowel disease, cardiovascular health and tissue injury and recovery. The data and analyses presented in this study will serve as valuable resources for understanding and exploring the multi-tissue molecular effects of endurance training and are provided in a public repository ( https://motrpac-data.org/ ).

  View details for DOI 10.1038/s41586-023-06877-w

  View details for PubMedID 38693412

  View details for PubMedCentralID PMC11062907

• Sexual dimorphism and the multi-omic response to exercise training in rat subcutaneous white adipose tissue. Nature metabolism Many, G. M., Sanford, J. A., Sagendorf, T. J., Hou, Z., Nigro, P., Whytock, K. L., Amar, D., Caputo, T., Gay, N. R., Gaul, D. A., Hirshman, M. F., Jimenez-Morales, D., Lindholm, M. E., Muehlbauer, M. J., Vamvini, M., Bergman, B. C., Fernandez, F. M., Goodyear, L. J., Hevener, A. L., Ortlund, E. A., Sparks, L. M., Xia, A., Adkins, J. N., Bodine, S. C., Newgard, C. B., Schenk, S., MoTrPAC Study Group, Armenteros, J. J., Amper, M. A., Ashley, E., Asokan, A. K., Avila-Pacheco, J., Bae, D., Bamman, M. M., Bararpour, N., Barnes, J., Buford, T. W., Burant, C. F., Carbone, N. P., Carr, S. A., Chambers, T. L., Chavez, C., Chiu, R., Clish, C. B., Cutter, G. R., Dasari, S., Dennis, C., Evans, C. R., Fernandez, F. M., Gagne, N., Ge, Y., Goodpaster, B. H., Gritsenko, M. A., Hansen, J. R., Hennig, K. M., Huffman, K. M., Hung, C., Hutchinson-Bunch, C., Ilkayeva, O., Ivanova, A. A., Beltran, P. M., Jin, C. A., Kachman, M. T., Keshishian, H., Kraus, W. E., Lanza, I., Lester, B., Li, J. Z., Lira, A. K., Liu, X., Maner-Smith, K. M., May, S., Monroe, M. R., Montgomery, S., Moore, R. J., Moore, S. G., Nachun, D., Nair, K. S., Nair, V., Raja, A. N., Nestor, M. D., Nudelman, G., Petyuk, V. A., Piehowski, P. D., Pincas, H., Qian, W., Raskind, A., Rasmussen, B. B., Rooney, J. L., Rushing, S., Samdarshi, M., Sealfon, S. C., Smith, K. S., Smith, G. R., Snyder, M., Stowe, C. L., Talton, J. W., Teng, C., Thalacker-Mercer, A., Tracy, R., Trappe, T. A., Vasoya, M., Vetr, N. G., Volpi, E., Walkup, M. P., Walsh, M. J., Wheeler, M. T., Wu, S., Zaslavsky, E., Zebarjadi, N., Zhang, T., Zhao, B., Zhen, J. 2024

  Abstract

  Subcutaneous white adipose tissue (scWAT) is a dynamic storage and secretory organ that regulates systemic homeostasis, yet the impact of endurance exercise training (ExT) and sex on its molecular landscape is not fully established. Utilizing an integrative multi-omics approach, and leveraging data generated by the Molecular Transducers of Physical Activity Consortium (MoTrPAC), we show profound sexual dimorphism in the scWAT of sedentary rats and in the dynamic response of this tissue to ExT. Specifically, the scWAT of sedentary females displays -omic signatures related to insulin signaling and adipogenesis, whereas the scWAT of sedentary males is enriched in terms related to aerobic metabolism. These sex-specific -omic signatures are preserved or amplified with ExT. Integration of multi-omic analyses with phenotypic measures identifies molecular hubs predicted to drive sexually distinct responses to training. Overall, this study underscores the powerful impact of sex on adipose tissue biology and provides a rich resource to investigate the scWAT response to ExT.

  View details for DOI 10.1038/s42255-023-00959-9

  View details for PubMedID 38693320

• Molecular adaptations in response to exercise training are associated with tissue-specific transcriptomic and epigenomic signatures. Cell genomics Nair, V. D., Pincas, H., Smith, G. R., Zaslavsky, E., Ge, Y., Amper, M. A., Vasoya, M., Chikina, M., Sun, Y., Raja, A. N., Mao, W., Gay, N. R., Esser, K. A., Smith, K. S., Zhao, B., Wiel, L., Singh, A., Lindholm, M. E., Amar, D., Montgomery, S., Snyder, M. P., Walsh, M. J., Sealfon, S. C., MoTrPAC Study Group 2024: 100421

  Abstract

  Regular exercise has many physical and brain health benefits, yet the molecular mechanisms mediating exercise effects across tissues remain poorly understood. Here we analyzed 400 high-quality DNA methylation, ATAC-seq, and RNA-seq datasets from eight tissues from control and endurance exercise-trained (EET) rats. Integration of baseline datasets mapped the gene location dependence of epigenetic control features and identified differing regulatory landscapes in each tissue. The transcriptional responses to 8weeks of EET showed little overlap across tissues and predominantly comprised tissue-type enriched genes. We identified sex differences in the transcriptomic and epigenomic changes induced by EET. However, the sex-biased gene responses were linked to shared signaling pathways. We found that many G protein-coupled receptor-encoding genes are regulated by EET, suggesting a role for these receptors in mediating the molecular adaptations to training across tissues. Our findings provide new insights into the mechanisms underlying EET-induced health benefits across organs.

  View details for DOI 10.1016/j.xgen.2023.100421

  View details for PubMedID 38697122

• Molecular Transducers of Physical Activity Consortium (MoTrPAC): Human Studies Design and Protocol. Journal of applied physiology (Bethesda, Md. : 1985) Group, M. R., Jakicic, J. M., Kohrt, W. M., Houmard, J. A., Miller, M. E., Radom-Aizik, S., Rasmussen, B. B., Ravussin, E., Serra, M., Stowe, C. L., Trappe, S., AbouAssi, H., Adkins, J. N., Alekel, D. L., Ashley, E., Bamman, M. M., Bergman, B. C., Bessesen, D. H., Broskey, N. T., Buford, T. W., Burant, C. F., Chen, H., Christle, J. W., Clish, C. B., Coen, P. M., Collier, D., Collins, K. A., Cooper, D. M., Cortes, T., Cutter, G. R., Dubis, G., Fernandez, F. M., Firnhaber, J., Forman, D. E., Gaul, D. A., Gay, N., Gerszten, R. E., Goodpaster, B. H., Gritsenko, M. A., Haddad, F., Huffman, K. M., Ilkayeva, O., Jankowski, C. M., Jin, C., Johannsen, N. M., Johnson, J., Kelly, L., Kershaw, E., Kraus, W. E., Laughlin, M., Lester, B., Lindholm, M. E., Lowe, A., Lu, C. J., McGowan, J., Melanson, E. L., Montgomery, S., Moore, S. G., Moreau, K. L., Muehlbauer, M., Musi, N., Nair, V. D., Newgard, C. B., Newman, A. B., Nicklas, B., Nindle, B. C., Ormond, K., Piehowski, P. D., Qian, W. J., Rankinen, T., Rejeski, W. J., Robbins, J., Rogers, R. J., Rooney, J. L., Rushing, S., Sanford, J. A., Schauer, I. E., Schwartz, R. S., Sealfon, S. C., Slentz, C., Sloan, R., Smith, K. S., Snyder, M., Spahn, J., Sparks, L. M., Stefanovic-Racic, M., Tanner, C. J., Thalacker-Mercer, A., Tracy, R., Trappe, T. A., Volpi, E., Walsh, M. J., Wheeler, M. T., Willis, L. H. 2024

  Abstract

  Physical activity, including structured exercise, is associated with favorable health-related chronic disease outcomes. While there is evidence of various molecular pathways that affect these responses, a comprehensive molecular map of these molecular responses to exercise has not been developed. The Molecular Transducers of Physical Activity Consortium (MoTrPAC) is a multi-center study designed to isolate the effects of structured exercise training on the molecular mechanisms underlying the health benefits of exercise and physical activity. MoTrPAC contains both a pre-clinical and human component. The details of the human studies component of MoTrPAC that include the design and methods are presented here. The human studies contain both an adult and pediatric component. In the adult component, sedentary participants are randomized to 12 weeks of Control, Endurance Exercise Training, or Resistance Exercise Training with outcomes measures completed before and following the 12 weeks. The adult component also includes recruitment of highly active endurance trained or resistance trained participants who only complete measures once. A similar design is used for the pediatric component; however, only endurance exercise is examined. Phenotyping measures include weight, body composition, vital signs, cardiorespiratory fitness, muscular strength, physical activity and diet, and other questionnaires. Participants also complete an acute rest period (adults only) or exercise session (adults, pediatrics) with collection of biospecimens (blood only for pediatrics) to allow for examination of the molecular responses. The design and methods of MoTrPAC may inform other studies. Moreover, MoTrPAC will provide a repository of data that can be used broadly across the scientific community.

  View details for DOI 10.1152/japplphysiol.00102.2024

  View details for PubMedID 38634503

• The mitochondrial multi-omic response to exercise training across rat tissues. Cell metabolism Amar, D., Gay, N. R., Jimenez-Morales, D., Jean Beltran, P. M., Ramaker, M. E., Raja, A. N., Zhao, B., Sun, Y., Marwaha, S., Gaul, D. A., Hershman, S. G., Ferrasse, A., Xia, A., Lanza, I., Fernández, F. M., Montgomery, S. B., Hevener, A. L., Ashley, E. A., Walsh, M. J., Sparks, L. M., Burant, C. F., Rector, R. S., Thyfault, J., Wheeler, M. T., Goodpaster, B. H., Coen, P. M., Schenk, S., Bodine, S. C., Lindholm, M. E. 2024

  Abstract

  Mitochondria have diverse functions critical to whole-body metabolic homeostasis. Endurance training alters mitochondrial activity, but systematic characterization of these adaptations is lacking. Here, the Molecular Transducers of Physical Activity Consortium mapped the temporal, multi-omic changes in mitochondrial analytes across 19 tissues in male and female rats trained for 1, 2, 4, or 8 weeks. Training elicited substantial changes in the adrenal gland, brown adipose, colon, heart, and skeletal muscle. The colon showed non-linear response dynamics, whereas mitochondrial pathways were downregulated in brown adipose and adrenal tissues. Protein acetylation increased in the liver, with a shift in lipid metabolism, whereas oxidative proteins increased in striated muscles. Exercise-upregulated networks were downregulated in human diabetes and cirrhosis. Knockdown of the central network protein 17-beta-hydroxysteroid dehydrogenase 10 (HSD17B10) elevated oxygen consumption, indicative of metabolic stress. We provide a multi-omic, multi-tissue, temporal atlas of the mitochondrial response to exercise training and identify candidates linked to mitochondrial dysfunction.

  View details for DOI 10.1016/j.cmet.2023.12.021

  View details for PubMedID 38701776

• Remodeling of the human skeletal muscle proteome found after long-term endurance training but not after strength training. iScience Emanuelsson, E. B., Arif, M., Reitzner, S. M., Perez, S., Lindholm, M. E., Mardinoglu, A., Daub, C., Sundberg, C. J., Chapman, M. A. 2024; 27 (1): 108638

  Abstract

  Exercise training has tremendous systemic tissue-specific health benefits, but the molecular adaptations to long-term exercise training are not completely understood. We investigated the skeletal muscle proteome of highly endurance-trained, strength-trained, and untrained individuals and performed exercise- and sex-specific analyses. Of the 6,000+ proteins identified, >650 were differentially expressed in endurance-trained individuals compared with controls. Strikingly, 92% of the shared proteins with higher expression in both the male and female endurance groups were known mitochondrial. In contrast to the findings in endurance-trained individuals, minimal differences were found in strength-trained individuals and between females and males. Lastly, a co-expression network and comparative literature analysis revealed key proteins and pathways related to the health benefits of exercise, which were primarily related to differences in mitochondrial proteins. This network is available as an interactive database resource where investigators can correlate clinical data with global gene and protein expression data for hypothesis generation.

  View details for DOI 10.1016/j.isci.2023.108638

  View details for PubMedID 38213622

  View details for PubMedCentralID PMC10783619

• Comparing the Blood Response to Hyperbaric Oxygen with High-Intensity Interval Training-A Crossover Study in Healthy Volunteers. Antioxidants (Basel, Switzerland) Kjellberg, A., Lindholm, M. E., Zheng, X., Liwenborg, L., Rodriguez-Wallberg, K. A., Catrina, S. B., Lindholm, P. 2023; 12 (12)

  Abstract

  High-intensity interval training (HIIT) and hyperbaric oxygen therapy (HBOT) induce reactive oxygen species (ROS) formation and have immunomodulatory effects. The lack of readily available biomarkers for assessing the dose-response relationship is a challenge in the clinical use of HBOT, motivating this feasibility study to evaluate the methods and variability. The overall hypothesis was that a short session of hyperbaric oxygen (HBO2) would have measurable effects on immune cells in the same physiological range as shown in HIIT; and that the individual response to these interventions can be monitored in venous blood and/or peripheral blood mononuclear cells (PBMCs). Ten healthy volunteers performed two interventions; a 28 min HIIT session and 28 min HBO2 in a crossover design. We evaluated bulk RNA sequencing data from PBMCs, with a separate analysis of mRNA and microRNA. Blood gases, peripheral venous oxygen saturation (SpvO2), and ROS levels were measured in peripheral venous blood. We observed an overlap in the gene expression changes in 166 genes in response to HIIT and HBO2, mostly involved in hypoxic or inflammatory pathways. Both interventions were followed by downregulation of several NF-κB signaling genes in response to both HBO2 and HIIT, while several interferon α/γ signaling genes were upregulated. Only 12 microRNA were significantly changed in HBO2 and 6 in HIIT, without overlap between interventions. ROS levels were elevated in blood at 30 min and 60 min compared to the baseline during HIIT, but not during/after HBO2. In conclusion, HBOT changed the gene expression in a number of pathways measurable in PBMC. The correlation of these changes with the dose and individual response to treatment warrants further investigation.

  View details for DOI 10.3390/antiox12122043

  View details for PubMedID 38136163

  View details for PubMedCentralID PMC10740875

• Exercise is associated with younger methylome and transcriptome profiles in human skeletal muscle. Aging cell Voisin, S., Seale, K., Jacques, M., Landen, S., Harvey, N. R., Haupt, L. M., Griffiths, L. R., Ashton, K. J., Coffey, V. G., Thompson, J. M., Doering, T. M., Lindholm, M. E., Walsh, C., Davison, G., Irwin, R., McBride, C., Hansson, O., Asplund, O., Heikkinen, A. E., Piirila, P., Pietilainen, K. H., Ollikainen, M., Blocquiaux, S., Thomis, M., Dawn, C. K., Sharples, A. P., Eynon, N. 2023: e13859

  Abstract

  Exercise training prevents age-related decline in muscle function. Targeting epigenetic aging is a promising actionable mechanism and late-life exercise mitigates epigenetic aging in rodent muscle. Whether exercise training can decelerate, or reverse epigenetic aging in humans is unknown. Here, we performed a powerful meta-analysis of the methylome and transcriptome of an unprecedented number of human skeletal muscle samples (n=3176). We show that: (1) individuals with higher baseline aerobic fitness have younger epigenetic and transcriptomic profiles, (2) exercise training leads to significant shifts of epigenetic and transcriptomic patterns toward a younger profile, and (3) muscle disuse "ages" the transcriptome. Higher fitness levels were associated with attenuated differential methylation and transcription during aging. Furthermore, both epigenetic and transcriptomic profiles shifted toward a younger state after exercise training interventions, while the transcriptome shifted toward an older state after forced muscle disuse. We demonstrate that exercise training targets many of the age-related transcripts and DNA methylation loci to maintain younger methylome and transcriptome profiles, specifically in genes related to muscle structure, metabolism, and mitochondrial function. Our comprehensive analysis will inform future studies aiming to identify the best combination of therapeutics and exercise regimes to optimize longevity.

  View details for DOI 10.1111/acel.13859

  View details for PubMedID 37128843

• The mitochondrial multi-omic response to exercise training across tissues. bioRxiv : the preprint server for biology Amar, D., Gay, N. R., Jimenez-Morales, D., Beltran, P. M., Ramaker, M. E., Raja, A. N., Zhao, B., Sun, Y., Marwaha, S., Gaul, D., Hershman, S. G., Xia, A., Lanza, I., Fernandez, F. M., Montgomery, S. B., Hevener, A. L., Ashley, E. A., Walsh, M. J., Sparks, L. M., Burant, C. F., Rector, R. S., Thyfault, J., Wheeler, M. T., Goodpaster, B. H., Coen, P. M., Schenk, S., Bodine, S. C., Lindholm, M. E. 2023

  Abstract

  Mitochondria are adaptable organelles with diverse cellular functions critical to whole-body metabolic homeostasis. While chronic endurance exercise training is known to alter mitochondrial activity, these adaptations have not yet been systematically characterized. Here, the Molecular Transducers of Physical Activity Consortium (MoTrPAC) mapped the longitudinal, multi-omic changes in mitochondrial analytes across 19 tissues in male and female rats endurance trained for 1, 2, 4 or 8 weeks. Training elicited substantial changes in the adrenal gland, brown adipose, colon, heart and skeletal muscle, while we detected mild responses in the brain, lung, small intestine and testes. The colon response was characterized by non-linear dynamics that resulted in upregulation of mitochondrial function that was more prominent in females. Brown adipose and adrenal tissues were characterized by substantial downregulation of mitochondrial pathways. Training induced a previously unrecognized robust upregulation of mitochondrial protein abundance and acetylation in the liver, and a concomitant shift in lipid metabolism. The striated muscles demonstrated a highly coordinated response to increase oxidative capacity, with the majority of changes occurring in protein abundance and post-translational modifications. We identified exercise upregulated networks that are downregulated in human type 2 diabetes and liver cirrhosis. In both cases HSD17B10, a central dehydrogenase in multiple metabolic pathways and mitochondrial tRNA maturation, was the main hub. In summary, we provide a multi-omic, cross-tissue atlas of the mitochondrial response to training and identify candidates for prevention of disease-associated mitochondrial dysfunction.

  View details for DOI 10.1101/2023.01.13.523698

  View details for PubMedID 36711881

  View details for PubMedCentralID PMC9882193

• Multiomic identification of key transcriptional regulatory programs during endurance exercise training. bioRxiv : the preprint server for biology Smith, G. R., Zhao, B., Lindholm, M. E., Raja, A., Viggars, M., Pincas, H., Gay, N. R., Sun, Y., Ge, Y., Nair, V. D., Sanford, J. A., S Amper, M. A., Vasoya, M., Smith, K. S., Montgomery, S., Zaslavsky, E., Bodine, S. C., Esser, K. A., Walsh, M. J., Snyder, M. P., Sealfon, S. C., MoTrPAC Study Group 2023

  Abstract

  Transcription factors (TFs) play a key role in regulating gene expression and responses to stimuli. We conducted an integrated analysis of chromatin accessibility and RNA expression across various rat tissues following endurance exercise training (EET) to map epigenomic changes to transcriptional changes and determine key TFs involved. We uncovered tissue-specific changes across both omic layers, including highly correlated differentially accessible regions (DARs) and differentially expressed genes (DEGs). We identified open chromatin regions associated with DEGs (DEGaPs) and found tissue-specific and genomic feature-specific TF motif enrichment patterns among both DARs and DEGaPs. Accessible promoters of up-vs. down-regulated DEGs per tissue showed distinct TF enrichment patterns. Further, some EET-induced TFs in skeletal muscle were either validated at the proteomic level (MEF2C and NUR77) or correlated with exercise-related phenotypic changes. We provide an in-depth analysis of the epigenetic and trans-factor-dependent processes governing gene expression during EET.

  View details for DOI 10.1101/2023.01.10.523450

  View details for PubMedID 36711841

• Mono- and Biallelic Protein-Truncating Variants in Alpha-Actinin 2 Cause Cardiomyopathy Through Distinct Mechanisms. Circulation. Genomic and precision medicine Lindholm, M. E., Jimenez-Morales, D., Zhu, H., Seo, K., Amar, D., Zhao, C., Raja, A., Madhvani, R., Abramowitz, S., Espenel, C., Sutton, S., Caleshu, C., Berry, G. J., Motonaga, K. S., Dunn, K., Platt, J., Ashley, E. A., Wheeler, M. T. 2021: CIRCGEN121003419

  Abstract

  BACKGROUND: ACTN2 (alpha-actinin 2) anchors actin within cardiac sarcomeres. The mechanisms linking ACTN2 mutations to myocardial disease phenotypes are unknown. Here, we characterize patients with novel ACTN2 mutations to reveal insights into the physiological function of ACTN2.METHODS: Patients harboring ACTN2 protein-truncating variants were identified using a custom mutation pipeline. In patient-derived iPSC-cardiomyocytes, we investigated transcriptional profiles using RNA sequencing, contractile properties using video-based edge detection, and cellular hypertrophy using immunohistochemistry. Structural changes were analyzed through electron microscopy. For mechanistic studies, we used coimmunoprecipitation for ACTN2, followed by mass-spectrometry to investigate protein-protein interaction, and protein tagging followed by confocal microscopy to investigate introduction of truncated ACTN2 into the sarcomeres.RESULTS: Patient-derived iPSC-cardiomyocytes were hypertrophic, displayed sarcomeric structural disarray, impaired contractility, and aberrant Ca2+-signaling. In heterozygous indel cells, the truncated protein incorporates into cardiac sarcomeres, leading to aberrant Z-disc ultrastructure. In homozygous stop-gain cells, affinity-purification mass-spectrometry reveals an intricate ACTN2 interactome with sarcomere and sarcolemma-associated proteins. Loss of the C-terminus of ACTN2 disrupts interaction with ACTN1 and GJA1, 2 sarcolemma-associated proteins, which may contribute to the clinical arrhythmic and relaxation defects. The causality of the stop-gain mutation was verified using CRISPR-Cas9 gene editing.CONCLUSIONS: Together, these data advance our understanding of the role of ACTN2 in the human heart and establish recessive inheritance of ACTN2 truncation as causative of disease.

  View details for DOI 10.1161/CIRCGEN.121.003419

  View details for PubMedID 34802252

• Time trajectories in the transcriptomic response to exercise - a meta-analysis. Nature communications Amar, D., Lindholm, M. E., Norrbom, J., Wheeler, M. T., Rivas, M. A., Ashley, E. A. 2021; 12 (1): 3471

  Abstract

  Exercise training prevents multiple diseases, yet the molecular mechanisms that drive exercise adaptation are incompletely understood. To address this, we create a computational framework comprising data from skeletal muscle or blood from 43 studies, including 739 individuals before and after exercise or training. Using linear mixed effects meta-regression, we detect specific time patterns and regulatory modulators of the exercise response. Acute and long-term responses are transcriptionally distinct and we identify SMAD3 as a central regulator of the exercise response. Exercise induces a more pronounced inflammatory response in skeletal muscle of older individuals and our models reveal multiple sex-associated responses. We validate seven of our top genes in a separate human cohort. In this work, we provide a powerful resource ( www.extrameta.org ) that expands the transcriptional landscape of exercise adaptation by extending previously known responses and their regulatory networks, and identifying novel modality-, time-, age-, and sex-associated changes.

  View details for DOI 10.1038/s41467-021-23579-x

  View details for PubMedID 34108459

• Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise. Cell Sanford, J. A., Nogiec, C. D., Lindholm, M. E., Adkins, J. N., Amar, D., Dasari, S., Drugan, J. K., Fernandez, F. M., Radom-Aizik, S., Schenk, S., Snyder, M. P., Tracy, R. P., Vanderboom, P., Trappe, S., Walsh, M. J., Molecular Transducers of Physical Activity Consortium, Adkins, J. N., Amar, D., Dasari, S., Drugan, J. K., Evans, C. R., Fernandez, F. M., Li, Y., Lindholm, M. E., Nogiec, C. D., Radom-Aizik, S., Sanford, J. A., Schenk, S., Snyder, M. P., Tomlinson, L., Tracy, R. P., Trappe, S., Vanderboom, P., Walsh, M. J., Alekel, D. L., Bekirov, I., Boyce, A. T., Boyington, J., Fleg, J. L., Joseph, L. J., Laughlin, M. R., Maruvada, P., Morris, S. A., McGowan, J. A., Nierras, C., Pai, V., Peterson, C., Ramos, E., Roary, M. C., Williams, J. P., Xia, A., Cornell, E., Rooney, J., Miller, M. E., Ambrosius, W. T., Rushing, S., Stowe, C. L., Rejeski, W. J., Nicklas, B. J., Pahor, M., Lu, C., Trappe, T., Chambers, T., Raue, U., Lester, B., Bergman, B. C., Bessesen, D. H., Jankowski, C. M., Kohrt, W. M., Melanson, E. L., Moreau, K. L., Schauer, I. E., Schwartz, R. S., Kraus, W. E., Slentz, C. A., Huffman, K. M., Johnson, J. L., Willis, L. H., Kelly, L., Houmard, J. A., Dubis, G., Broskey, N., Goodpaster, B. H., Sparks, L. M., Coen, P. M., Cooper, D. M., Haddad, F., Rankinen, T., Ravussin, E., Johannsen, N., Harris, M., Jakicic, J. M., Newman, A. B., Forman, D. D., Kershaw, E., Rogers, R. J., Nindl, B. C., Page, L. C., Stefanovic-Racic, M., Barr, S. L., Rasmussen, B. B., Moro, T., Paddon-Jones, D., Volpi, E., Spratt, H., Musi, N., Espinoza, S., Patel, D., Serra, M., Gelfond, J., Burns, A., Bamman, M. M., Buford, T. W., Cutter, G. R., Bodine, S. C., Esser, K., Farrar, R. P., Goodyear, L. J., Hirshman, M. F., Albertson, B. G., Qian, W., Piehowski, P., Gritsenko, M. A., Monore, M. E., Petyuk, V. A., McDermott, J. E., Hansen, J. N., Hutchison, C., Moore, S., Gaul, D. A., Clish, C. B., Avila-Pacheco, J., Dennis, C., Kellis, M., Carr, S., Jean-Beltran, P. M., Keshishian, H., Mani, D. R., Clauser, K., Krug, K., Mundorff, C., Pearce, C., Ivanova, A. A., Ortlund, E. A., Maner-Smith, K., Uppal, K., Zhang, T., Sealfon, S. C., Zavlasky, E., Nair, V., Li, S., Jain, N., Ge, Y., Sun, Y., Nudelman, G., Ruf-Zamojski, F., Smith, G., Pincas, N., Rubenstein, A., Amper, M. A., Seenarine, N., Lappalainen, T., Lanza, I. R., Nair, K. S., Klaus, K., Montgomery, S. B., Smith, K. S., Gay, N. R., Zhao, B., Hung, C. J., Zebarjadi, N., Balliu, B., Fresard, L., Burant, C. F., Li, J. Z., Kachman, M., Soni, T., Raskind, A. B., Gerszten, R., Robbins, J., Ilkayeva, O., Muehlbauer, M. J., Newgard, C. B., Ashley, E. A., Wheeler, M. T., Jimenez-Morales, D., Raja, A., Dalton, K. P., Zhen, J., Kim, Y. S., Christle, J. W., Marwaha, S., Chin, E. T., Hershman, S. G., Hastie, T., Tibshirani, R., Rivas, M. A. 2020; 181 (7): 1464–74

  Abstract

  Exercise provides a robust physiological stimulus that evokes cross-talk among multiple tissues that when repeated regularly (i.e., training) improves physiological capacity, benefits numerous organ systems, and decreases the risk for premature mortality. However, a gap remains in identifying the detailed molecular signals induced by exercise that benefits health and prevents disease. The Molecular Transducers of Physical Activity Consortium (MoTrPAC) was established to address this gap and generate a molecular map of exercise. Preclinical and clinical studies will examine the systemic effects of endurance and resistance exercise across a range of ages and fitness levels by molecular probing of multiple tissues before and after acute and chronic exercise. From this multi-omic and bioinformatic analysis, a molecular map of exercise will be established. Altogether, MoTrPAC will provide a public database that is expected to enhance our understanding of the health benefits of exercise and to provide insight into how physical activity mitigates disease.

  View details for DOI 10.1016/j.cell.2020.06.004

  View details for PubMedID 32589957

• Exercise Induces Different Molecular Responses in Trained and Untrained Human Muscle. Medicine and science in sports and exercise Moberg, M., Lindholm, M. E., Reitzner, S. M., Ekblom, B., Sundberg, C., Psilander, N. 2020

  Abstract

  INTRODUCTION: Human skeletal muscle is thought to have heightened sensitivity to exercise stimulus when it has been previously trained (i.e., it possesses "muscle memory"). We investigated whether basal and acute resistance exercise-induced gene expression and cell signaling events are influenced by previous strength training history.METHODS: Accordingly, 19 training naive women and men completed 10 weeks of unilateral leg strength training, followed by 20 weeks of detraining. Subsequently, an acute resistance exercise session was performed for both legs, with vastus lateralis biopsies taken at rest and 1 h after exercise in both legs (memory and control).RESULTS: The phosphorylation of AMPK and eEF2 was higher in the memory leg than in the control leg at both time points. Post-exercise phosphorylation of 4E-BP1 was higher in the memory leg than in the control leg. The memory leg had lower basal mRNA levels of total PGC1alpha, and, unlike the control leg, exhibited increases in PGC1alpha-ex1a transcripts after exercise. In the genes related to myogenesis (SETD3, MYOD1, and MYOG), mRNA levels differed between the memory and the untrained leg; these effects were evident primarily in the male subjects. Expression of the novel gene SPRYD7 was lower in the memory leg at rest and decreased after exercise only in the control leg, but SPRYD7 protein levels were higher in the memory leg.CONCLUSION: In conclusion, several key regulatory genes and proteins involved in muscular adaptations to resistance exercise are influenced by previous training history. Although the relevance and mechanistic explanation for these findings need further investigation, they support the view of a molecular muscle memory in response to training.

  View details for DOI 10.1249/MSS.0000000000002310

  View details for PubMedID 32079914

• An epigenetic clock for human skeletal muscle. Journal of cachexia, sarcopenia and muscle Voisin, S., Harvey, N. R., Haupt, L. M., Griffiths, L. R., Ashton, K. J., Coffey, V. G., Doering, T. M., Thompson, J. M., Benedict, C., Cedernaes, J., Lindholm, M. E., Craig, J. M., Rowlands, D. S., Sharples, A. P., Horvath, S., Eynon, N. 2020

  Abstract

  BACKGROUND: Ageing is associated with DNA methylation changes in all human tissues, and epigenetic markers can estimate chronological age based on DNA methylation patterns across tissues. However, the construction of the original pan-tissue epigenetic clock did not include skeletal muscle samples and hence exhibited a strong deviation between DNA methylation and chronological age in this tissue.METHODS: To address this, we developed a more accurate, muscle-specific epigenetic clock based on the genome-wide DNA methylation data of 682 skeletal muscle samples from 12 independent datasets (18-89 years old, 22% women, 99% Caucasian), all generated with Illumina HumanMethylation (HM) arrays (HM27, HM450, or HMEPIC). We also took advantage of the large number of samples to conduct an epigenome-wide association study of age-associated DNA methylation patterns in skeletal muscle.RESULTS: The newly developed clock uses 200 cytosine-phosphate-guanine dinucleotides to estimate chronological age in skeletal muscle, 16 of which are in common with the 353 cytosine-phosphate-guanine dinucleotides of the pan-tissue clock. The muscle clock outperformed the pan-tissue clock, with a median error of only 4.6 years across datasets (vs. 13.1 years for the pan-tissue clock, P < 0.0001) and an average correlation of rho = 0.62 between actual and predicted age across datasets (vs. rho = 0.51 for the pan-tissue clock). Lastly, we identified 180 differentially methylated regions with age in skeletal muscle at a false discovery rate < 0.005. However, gene set enrichment analysis did not reveal any enrichment for gene ontologies.CONCLUSIONS: We have developed a muscle-specific epigenetic clock that predicts age with better accuracy than the pan-tissue clock. We implemented the muscle clock in an r package called Muscle Epigenetic Age Test available on Bioconductor to estimate epigenetic age in skeletal muscle samples. This clock may prove valuable in assessing the impact of environmental factors, such as exercise and diet, on muscle-specific biological ageing processes.

  View details for DOI 10.1002/jcsm.12556

  View details for PubMedID 32067420

• Skeletal Muscle Transcriptomic Comparison between Long-Term Trained and Untrained Men and Women. Cell reports Chapman, M. A., Arif, M. n., Emanuelsson, E. B., Reitzner, S. M., Lindholm, M. E., Mardinoglu, A. n., Sundberg, C. J. 2020; 31 (12): 107808

  Abstract

  To better understand the health benefits of lifelong exercise in humans, we conduct global skeletal muscle transcriptomic analyses of long-term endurance- (9 men, 9 women) and strength-trained (7 men) humans compared with age-matched untrained controls (7 men, 8 women). Transcriptomic analysis, Gene Ontology, and genome-scale metabolic modeling demonstrate changes in pathways related to the prevention of metabolic diseases, particularly with endurance training. Our data also show prominent sex differences between controls and that these differences are reduced with endurance training. Additionally, we compare our data with studies examining muscle gene expression before and after a months-long training period in individuals with metabolic diseases. This analysis reveals that training shifts gene expression in individuals with impaired metabolism to become more similar to our endurance-trained group. Overall, our data provide an extensive examination of the accumulated transcriptional changes that occur with decades-long training and identify important "exercise-responsive" genes that could attenuate metabolic disease.

  View details for DOI 10.1016/j.celrep.2020.107808

  View details for PubMedID 32579934

• NOVEL ALPHA-ACTININ 2 MUTATIONS ARE ASSOCIATED WITH CARDIOMYOPATHY AND HYPERTROPHY IN HUMAN CARDIAC TISSUE AND IPSC-DERIVED CARDIOMYOCYTES Lindholm, M., Zhu, H., Huang, Y., Ashley, E. A., Wheeler, M. ELSEVIER SCIENCE INC. 2019: 1027

  View details for Web of Science ID 000460565901040

• Metabolic and functional changes in transgender individuals following cross-sex hormone treatment: Design and methods of the GEnder Dysphoria Treatment in Sweden (GETS) study CONTEMPORARY CLINICAL TRIALS COMMUNICATIONS Wiik, A., Andersson, D. P., Brismar, T. B., Chanpen, S., Dhejne, C., Ekstrom, T. J., Flanagan, J. N., Holmberg, M., Kere, J., Lilja, M., Lindholm, M. E., Lundberg, T. R., Maret, E., Melin, M., Olsson, S. M., Rullman, E., Wahlen, K., Arver, S., Gustafsson, T. 2018; 10: 148–53

  Abstract

  Although the divergent male and female differentiation depends on key genes, many biological differences seen in men and women are driven by relative differences in estrogen and testosterone levels. Gender dysphoria denotes the distress that gender incongruence with the assigned sex at birth may cause. Gender-affirming treatment includes medical intervention such as inhibition of endogenous sex hormones and subsequent replacement with cross-sex hormones. The aim of this study is to investigate consequences of an altered sex hormone profile on different tissues and metabolic risk factors. By studying subjects undergoing gender-affirming medical intervention with sex hormones, we have the unique opportunity to distinguish between genetic and hormonal effects.The study is a single center observational cohort study conducted in Stockholm, Sweden. The subjects are examined at four time points; before initiation of treatment, after endogenous sex hormone inhibition, and three and eleven months following sex hormone treatment. Examinations include blood samples, skeletal muscle-, adipose- and skin tissue biopsies, arteriography, echocardiography, carotid Doppler examination, whole body MRI, CT of muscle and measurements of muscle strength.The primary outcome measure is transcriptomic and epigenomic changes in skeletal muscle. Secondary outcome measures include transcriptomic and epigenomic changes associated with metabolism in adipose and skin, muscle strength, fat cell size and ability to release fatty acids from adipose tissue, cardiovascular function, and body composition.This study will provide novel information on the role of sex hormone treatment in skeletal muscle, adipose and skin, and its relation to cardiovascular and metabolic disease.

  View details for DOI 10.1016/j.conctc.2018.04.005

  View details for Web of Science ID 000433315000022

  View details for PubMedID 30023449

  View details for PubMedCentralID PMC6046513

• Medical relevance of protein-truncating variants across 337,205 individuals in the UK Biobank study NATURE COMMUNICATIONS DeBoever, C., Tanigawa, Y., Lindholm, M. E., McInnes, G., Lavertu, A., Ingelsson, E., Chang, C., Ashley, E. A., Bustamante, C. D., Daly, M. J., Rivas, M. A. 2018; 9: 1612

  Abstract

  Protein-truncating variants can have profound effects on gene function and are critical for clinical genome interpretation and generating therapeutic hypotheses, but their relevance to medical phenotypes has not been systematically assessed. Here, we characterize the effect of 18,228 protein-truncating variants across 135 phenotypes from the UK Biobank and find 27 associations between medical phenotypes and protein-truncating variants in genes outside the major histocompatibility complex. We perform phenome-wide analyses and directly measure the effect in homozygous carriers, commonly referred to as "human knockouts," across medical phenotypes for genes implicated as being protective against disease or associated with at least one phenotype in our study. We find several genes with strong pleiotropic or non-additive effects. Our results illustrate the importance of protein-truncating variants in a variety of diseases.

  View details for PubMedID 29691392

• The Impact of Endurance Training on Human Skeletal Muscle Memory, Global Isoform Expression and Novel Transcripts. PLoS genetics Lindholm, M. E., Giacomello, S., Werne Solnestam, B., Fischer, H., Huss, M., Kjellqvist, S., Sundberg, C. J. 2016; 12 (9)

  Abstract

  Regularly performed endurance training has many beneficial effects on health and skeletal muscle function, and can be used to prevent and treat common diseases e.g. cardiovascular disease, type II diabetes and obesity. The molecular adaptation mechanisms regulating these effects are incompletely understood. To date, global transcriptome changes in skeletal muscles have been studied at the gene level only. Therefore, global isoform expression changes following exercise training in humans are unknown. Also, the effects of repeated interventions on transcriptional memory or training response have not been studied before. In this study, 23 individuals trained one leg for three months. Nine months later, 12 of the same subjects trained both legs in a second training period. Skeletal muscle biopsies were obtained from both legs before and after both training periods. RNA sequencing analysis of all 119 skeletal muscle biopsies showed that training altered the expression of 3,404 gene isoforms, mainly associated with oxidative ATP production. Fifty-four genes had isoforms that changed in opposite directions. Training altered expression of 34 novel transcripts, all with protein-coding potential. After nine months of detraining, no training-induced transcriptome differences were detected between the previously trained and untrained legs. Although there were several differences in the physiological and transcriptional responses to repeated training, no coherent evidence of an endurance training induced transcriptional skeletal muscle memory was found. This human lifestyle intervention induced differential expression of thousands of isoforms and several transcripts from unannotated regions of the genome. It is likely that the observed isoform expression changes reflect adaptational mechanisms and processes that provide the functional and health benefits of regular physical activity.

  View details for DOI 10.1371/journal.pgen.1006294

  View details for PubMedID 27657503

  View details for PubMedCentralID PMC5033478

• Skeletal muscle hypoxia-inducible factor-1 and exercise EXPERIMENTAL PHYSIOLOGY Lindholm, M. E., Rundqvist, H. 2016; 101 (1): 28-32

  Abstract

  Reduced oxygen levels in skeletal muscle during exercise are a consequence of increased oxygen consumption. The cellular response to hypoxia is conferred to a large extent by activation of the hypoxia-sensitive transcription factor hypoxia-inducible factor-1 (HIF-1). The target genes of HIF-1 increase oxygen transport through mechanisms such as erythropoietin-mediated erythropoiesis and vascular endothelial growth factor-induced angiogenesis and improve tissue function during low oxygen availability through increased expression of glucose transporters and glycolytic enzymes, which makes HIF-1 an interesting candidate as a mediator of skeletal muscle adaptation to endurance training. However, HIF-1 may also inhibit cellular oxygen consumption and mitochondrial oxidative metabolism, features discordant with the phenotype of a trained muscle. Skeletal muscle readily adjusts to altered functional demands. Adaptation of skeletal muscle to long-term aerobic training enables better aerobic performance at higher intensities through improved metabolic capacity and oxygen supply. The components of acute exercise that act as triggers for adaptation are still largely unknown; however, an early hypothesis was that local hypoxia acts as a possible stimulus for exercise adaptation. The hypoxia-sensitive subunit, HIF-1α, is stabilized in skeletal muscle in response to an acute bout of endurance exercise. However, long-term endurance exercise seems to attenuate the acute HIF-1α response. This attenuation is concurrent with an increase in expression of several negative regulators of the HIF system. We propose that the HIF-1α response is blunted in response to long-term exercise training through induction of its negative regulators and that this inhibition enables the enhanced oxidative metabolism that is part of a local physiological response to exercise.

  View details for DOI 10.1113/EPO85318

  View details for Web of Science ID 000368251900005

  View details for PubMedID 26391197

• The human cardiac and skeletal muscle proteomes defined by transcriptomics and antibody-based profiling BMC GENOMICS Lindskog, C., Linne, J., Fagerberg, L., Hallstrom, B. M., Sundberg, C. J., Lindholm, M., Huss, M., Kampf, C., Choi, H., Liem, D. A., Ping, P., Varemo, L., Mardinoglu, A., Nielsen, J., Larsson, E., Ponten, F., Uhlen, M. 2015; 16

  Abstract

  To understand cardiac and skeletal muscle function, it is important to define and explore their molecular constituents and also to identify similarities and differences in the gene expression in these two different striated muscle tissues. Here, we have investigated the genes and proteins with elevated expression in cardiac and skeletal muscle in relation to all other major human tissues and organs using a global transcriptomics analysis complemented with antibody-based profiling to localize the corresponding proteins on a single cell level.Our study identified a comprehensive list of genes expressed in cardiac and skeletal muscle. The genes with elevated expression were further stratified according to their global expression pattern across the human body as well as their precise localization in the muscle tissues. The functions of the proteins encoded by the elevated genes are well in line with the physiological functions of cardiac and skeletal muscle, such as contraction, ion transport, regulation of membrane potential and actomyosin structure organization. A large fraction of the transcripts in both cardiac and skeletal muscle correspond to mitochondrial proteins involved in energy metabolism, which demonstrates the extreme specialization of these muscle tissues to provide energy for contraction.Our results provide a comprehensive list of genes and proteins elevated in striated muscles. A number of proteins not previously characterized in cardiac and skeletal muscle were identified and localized to specific cellular subcompartments. These proteins represent an interesting starting point for further functional analysis of their role in muscle biology and disease.

  View details for DOI 10.1186/s12864-015-1686-y

  View details for Web of Science ID 000356761400001

  View details for PubMedID 26109061

• An integrative analysis reveals coordinated reprogramming of the epigenome and the transcriptome in human skeletal muscle after training EPIGENETICS Lindholm, M. E., Marabita, F., Gomez-Cabrero, D., Rundqvist, H., Ekstrom, T. J., Tegner, J., Sundberg, C. J. 2014; 9 (12): 1557-1569

  Abstract

  Regular endurance exercise training induces beneficial functional and health effects in human skeletal muscle. The putative contribution to the training response of the epigenome as a mediator between genes and environment has not been clarified. Here we investigated the contribution of DNA methylation and associated transcriptomic changes in a well-controlled human intervention study. Training effects were mirrored by significant alterations in DNA methylation and gene expression in regions with a homogeneous muscle energetics and remodeling ontology. Moreover, a signature of DNA methylation and gene expression separated the samples based on training and gender. Differential DNA methylation was predominantly observed in enhancers, gene bodies and intergenic regions and less in CpG islands or promoters. We identified transcriptional regulator binding motifs of MRF, MEF2 and ETS proteins in the proximity of the changing sites. A transcriptional network analysis revealed modules harboring distinct ontologies and, interestingly, the overall direction of the changes of methylation within each module was inversely correlated to expression changes. In conclusion, we show that highly consistent and associated modifications in methylation and expression, concordant with observed health-enhancing phenotypic adaptations, are induced by a physiological stimulus.

  View details for DOI 10.4161/15592294.2014.982445

  View details for Web of Science ID 000349364000001

  View details for PubMedID 25484259

  View details for PubMedCentralID PMC4622000

• The human skeletal muscle transcriptome: sex differences, alternative splicing, and tissue homogeneity assessed with RNA sequencing FASEB JOURNAL Lindholm, M. E., Huss, M., Solnestam, B. W., Kjellqvist, S., Lundeberg, J., Sundberg, C. J. 2014; 28 (10): 4571-4581

  Abstract

  Human skeletal muscle health is important for quality of life and several chronic diseases, including type II diabetes, heart disease, and cancer. Skeletal muscle is a tissue widely used to study mechanisms behind different diseases and adaptive effects of controlled interventions. For such mechanistic studies, knowledge about the gene expression profiles in different states is essential. Since the baseline transcriptome has not been analyzed systematically, the purpose of this study was to provide a deep reference profile of female and male skeletal muscle. RNA sequencing data were analyzed from a large set of 45 resting human muscle biopsies. We provide extensive information on the skeletal muscle transcriptome, including 5 previously unannotated protein-coding transcripts. Global transcriptional tissue homogeneity was strikingly high, within both a specific muscle and the contralateral leg. We identified >23,000 known isoforms and found >5000 isoforms that differ between the sexes. The female and male transcriptome was enriched for genes associated with oxidative metabolism and protein catabolic processes, respectively. The data demonstrate remarkably high tissue homogeneity and provide a deep and extensive baseline reference for the human skeletal muscle transcriptome, with regard to alternative splicing, novel transcripts, and sex differences in functional ontology.transcriptome: sex differences, alternative splicing, and tissue homogeneity assessed with RNA sequencing.

  View details for DOI 10.1096/fj.14-255000

  View details for Web of Science ID 000342222700032

  View details for PubMedID 25016029

• Negative regulation of HIF in skeletal muscle of elite endurance athletes: a tentative mechanism promoting oxidative metabolism AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY Lindholm, M. E., Fischer, H., Poellinger, L., Johnson, R. S., Gustafsson, T., Sundberg, C. J., Rundqvist, H. 2014; 307 (3): R248-R255

  Abstract

  The transcription factor hypoxia-inducible factor (HIF) has been suggested as a candidate for mediating training adaptation in skeletal muscle. However, recent evidence rather associates HIF attenuation with a trained phenotype. For example, a muscle-specific HIF deletion increases endurance performance, partly through decreased levels of pyruvate dehydrogenase kinase 1 (PDK-1). HIF activity is regulated on multiple levels: modulation of protein stability, transactivation capacity, and target gene availability. Prolyl hydroxylases (PHD1-3) induces HIF degradation, whereas factor-inhibiting HIF (FIH) and the histone deacetylase sirtuin-6 (SIRT6) repress its transcriptional activity. Together, these negative regulators introduce a mechanism for moderating HIF activity in vivo. We hypothesized that long-term training induces their expression. Negative regulators of HIF were explored by comparing skeletal muscle tissue from moderately active individuals (MA) with elite athletes (EA). In elite athletes, expression of the negative regulators PHD2 (MA 73.54 ± 9.54, EA 98.03 ± 6.58), FIH (MA 4.31 ± 0.25, EA 30.96 ± 7.99) and SIRT6 (MA 0.24 ± 0.07, EA 11.42 ± 2.22) were all significantly higher, whereas the response gene, PDK-1 was lower (MA 0.12 ± 0.03, EA 0.04 ± 0.01). Similar results were observed in a separate 6-wk training study. In vitro, activation of HIF in human primary muscle cell culture by PHD inactivation strongly induced PDK-1 (0.84 ± 0.12 vs 4.70 ± 0.63), providing evidence of a regulatory link between PHD activity and PDK-1 levels in a relevant model system. Citrate synthase activity, closely associated with aerobic exercise adaptation, increased upon PDK-1 silencing. We suggest that training-induced negative regulation of HIF mediates the attenuation of PDK-1 and contributes to skeletal muscle adaptation to exercise.

  View details for DOI 10.1152/ajpregu.00036.2013

  View details for Web of Science ID 000340833300002

  View details for PubMedID 24898836

• An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform EPIGENETICS Marabita, F., Almgren, M., Lindholm, M. E., Ruhrmann, S., Fagerstrom-Billai, F., Jagodic, M., Sundberg, C. J., Ekstrom, T. J., Teschendorff, A. E., Tegner, J., Gomez-Cabrero, D. 2013; 8 (3): 333-346

  Abstract

  The proper identification of differentially methylated CpGs is central in most epigenetic studies. The Illumina HumanMethylation450 BeadChip is widely used to quantify DNA methylation; nevertheless, the design of an appropriate analysis pipeline faces severe challenges due to the convolution of biological and technical variability and the presence of a signal bias between Infinium I and II probe design types. Despite recent attempts to investigate how to analyze DNA methylation data with such an array design, it has not been possible to perform a comprehensive comparison between different bioinformatics pipelines due to the lack of appropriate data sets having both large sample size and sufficient number of technical replicates. Here we perform such a comparative analysis, targeting the problems of reducing the technical variability, eliminating the probe design bias and reducing the batch effect by exploiting two unpublished data sets, which included technical replicates and were profiled for DNA methylation either on peripheral blood, monocytes or muscle biopsies. We evaluated the performance of different analysis pipelines and demonstrated that: (1) it is critical to correct for the probe design type, since the amplitude of the measured methylation change depends on the underlying chemistry; (2) the effect of different normalization schemes is mixed, and the most effective method in our hands were quantile normalization and Beta Mixture Quantile dilation (BMIQ); (3) it is beneficial to correct for batch effects. In conclusion, our comparative analysis using a comprehensive data set suggests an efficient pipeline for proper identification of differentially methylated CpGs using the Illumina 450K arrays.

  View details for DOI 10.4161/epi.24008

  View details for Web of Science ID 000315923300010

  View details for PubMedID 23422812