{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T15:59:25Z","timestamp":1786118365199,"version":"build-2736575974"},"posted":{"date-parts":[[2025,12,5]]},"group-title":"Genetics","reference-count":75,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,12,5]],"date-time":"2025-12-05T00:00:00Z","timestamp":1764892800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"funder":[{"DOI":"10.13039\/100000050","name":"NHLBI","doi-asserted-by":"crossref","award":["R01HL153460"],"award-info":[{"award-number":["R01HL153460"]}],"id":[{"id":"10.13039\/100000050","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,8,4]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>Cachexia is an extrapulmonary manifestation of chronic obstructive pulmonary disease (COPD) characterized by weight loss and muscle wasting. Transcriptomic analysis of skeletal muscle may provide insight to COPD-cachexia-relevant dysregulation, including at the mitochondrial level, where dysfunction is a hallmark of muscle wasting. As muscle biopsies are invasive and yield finite tissue, human muscle derived cultures (HMDCs) can expand limited biopsy material for studying skeletal muscle dysregulation. However, utility of such models depends on their recapitulation of bulk skeletal muscle transcriptomic signatures. To address this, we tested whether COPD and COPD-cachexia dysregulated transcriptional signatures in bulk skeletal muscle are preserved across stages of early differentiation.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>\n                    <jats:italic>Vastus lateralis<\/jats:italic>\n                    biopsies were collected from 15 (7M\/8F, 64\u00b19 years) participants; COPD n=6, COPD cachexia n=4, and n=5 age-matched controls. Cachexia was defined as weight loss coupled with reduced muscle strength, fatigue, anorexia, low muscle mass and\/or systemic inflammation. Satellite cells were isolated and differentiated into HDMCs (myoblasts, myocytes, and myotubes). Transcriptomics data was generated from bulk skeletal muscle and HDMCs. Differential expression analysis identified transcripts significantly dysregulated (p&lt;0.05) in COPD and\/or COPD-cachexia. Weighted gene co-expression network analysis (WGCNA) preformed at the whole transcriptome and mitochondrial transcriptome levels, identified modules of co-expressed genes. Modules were tested for correlation with clinical traits and preservation between bulk tissue and HDMCs (Z-summary &gt;2). Gene set enrichment analysis was performed for all modules.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>\n                    660 genes were significantly differentially expressed between COPD and control bulk skeletal muscle. The top upregulated and downregulated genes were\n                    <jats:italic>IL21R-AS1<\/jats:italic>\n                    (Log2-Fold-Change [L2FC]=5.3, p=4.2\u00d710\n                    <jats:sup>-5<\/jats:sup>\n                    ) and top downregulated\n                    <jats:italic>POU5F1B<\/jats:italic>\n                    (L2FC=-5.8, p=3.1\u00d710\n                    <jats:sup>-2<\/jats:sup>\n                    ), respectively. Among the 492 genes significantly differentially expressed between COPD and COPD-cachexia bulk skeletal muscle. The top upregulated and downregulated genes were\n                    <jats:italic>LINC02274<\/jats:italic>\n                    (L2FC=5.6, p=3.6\u00d710\n                    <jats:sup>-5<\/jats:sup>\n                    ) and\n                    <jats:italic>ZFY<\/jats:italic>\n                    (L2FC=-6.1, p=9.7\u00d710\n                    <jats:sup>-3<\/jats:sup>\n                    ) respectively. Modules 1, 9, A, B, D and H correlated with cachexia-relevant traits, and Modules 3, 7, G, and I correlated most strongly with COPD severity. Most modules (1, 2, 4, 7, 8, 9, A, B, H) were preserved across all states; Modules D and G were preserved in myoblasts only, and Module I in myotubes only. Preserved modules were enriched for contractile, inflammatory, oxidative phosphorylation, and fatty acid metabolism pathways.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>Co-expression modules linked to COPD and COPD-cachexia in bulk skeletal muscle were broadly preserved across all differentiation stages, with myoblast and myotubes most completely recapitulating disease-relevant transcriptional signatures. These findings support HMDCs, as tractable in vitro models preserving contractile, inflammatory, and mitochondrial signatures of COPD-associated muscle dysfunction.<\/jats:p>\n                <\/jats:sec>","DOI":"10.64898\/2025.12.03.692216","type":"posted-content","created":{"date-parts":[[2025,12,8]],"date-time":"2025-12-08T12:43:24Z","timestamp":1765197804000},"source":"Crossref","is-referenced-by-count":0,"title":["Distinct Myogenic Stages Recapitulate Transcriptomic Networks of Skeletal Muscle in COPD Cachexia"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7757-1843","authenticated-orcid":false,"given":"Hanna","family":"Sothers","sequence":"first","affiliation":[{"name":"Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1919-7854","authenticated-orcid":false,"given":"Bitota","family":"Lukusa-Sawalena","sequence":"additional","affiliation":[{"name":"Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1426-8174","authenticated-orcid":false,"given":"Kaleen M","family":"Lavin","sequence":"additional","affiliation":[{"name":"Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenxia","family":"Ma","sequence":"additional","affiliation":[{"name":"Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9935-6319","authenticated-orcid":false,"suffix":"III","given":"Joe W","family":"Chiles","sequence":"additional","affiliation":[{"name":"Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8851-8589","authenticated-orcid":false,"given":"Richard","family":"Casaburi","sequence":"additional","affiliation":[{"name":"Respiratory Research Center, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA; and Division of Respiratory and Critical Care Physiology and Medicine, Harbor-UCLA Medical Center, Torrance, CA, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rakesh","family":"Patel","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA;"},{"name":"Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J Michael","family":"Wells","sequence":"additional","affiliation":[{"name":"Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohamed","family":"Kazamel","sequence":"additional","affiliation":[{"name":"Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7884-0726","authenticated-orcid":false,"given":"Harry B","family":"Rossiter","sequence":"additional","affiliation":[{"name":"Respiratory Research Center, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA; and Division of Respiratory and Critical Care Physiology and Medicine, Harbor-UCLA Medical Center, Torrance, CA, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9124-7927","authenticated-orcid":false,"given":"Anna","family":"Thalacker-Mercer","sequence":"additional","affiliation":[{"name":"Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Merry-Lynn N","family":"McDonald","sequence":"additional","affiliation":[{"name":"Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA;"},{"name":"Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA;"},{"name":"Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026080608350960000_2025.12.03.692216v2.1","unstructured":"Agarwal AK RA , Brown BD. 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