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Myopathies occur in many different diseases, but the mechanisms that drive these muscle pathologies are still largely unknown, partly because conventional approaches cannot link histopathological features to molecular states at single-fiber resolution. To address this challenge, we brought histopathology and spatial transcriptomics together by applying high-resolution Seq-Scope technology to a rodent model of mTORC1 hyperactivation, which produces diverse pathological alterations within individual myofibers. Cross-sections from extensor digitorum longus (EDL) and soleus (SOL), two muscles with distinct fiber-type compositions, were profiled to determine how transcriptome changes are linked to histopathological outcomes. Our analyses reveal that mTORC1 hyperactivation elicits distinct, fiber-type\u2013dependent pathological programs. Type I and IIa fibers, abundant in SOL but scarce in EDL, were largely resistant to mTORC1-induced pathology, exhibiting only minimal morphological alterations and no fiber type-specific responses beyond those commonly observed throughout the tissue. In contrast, type IIx fibers, shared between both muscles, diverged into opposing fates: in SOL, they underwent abnormal enlargement driven by sustained growth signaling, cytoskeletal remodeling, and impaired proteostasis with defective autophagy; whereas in EDL, they developed basophilia characterized by lipid-supported respiration fueling excessive ribonucleotide synthesis and RNA accumulation. Within the same muscle, type IIb fibers displayed striking heterogeneity with discrete transcriptional states encompassing canonical stress responses, oxidative metabolic activation, and developmental reprogramming. In parallel, non-myocytic populations, including activated macrophages and fibroblasts, accumulated preferentially in SOL, forming a fibrotic microenvironment supporting inflammation, tissue remodeling and hypertrophy. Taken together, these findings reveal that sustained mTORC1 signaling disrupts muscle homeostasis through distinct metabolic and structural routes, directly linking histopathological phenotypes to their molecular states at single-fiber resolution.<\/jats:p>","DOI":"10.64898\/2025.12.03.692123","type":"posted-content","created":{"date-parts":[[2025,12,8]],"date-time":"2025-12-08T12:42:42Z","timestamp":1765197762000},"source":"Crossref","is-referenced-by-count":0,"title":["Histopathology and spatial transcriptomics jointly map myofiber-specific pathological programs in mTORC1-driven myopathy"],"prefix":"10.64898","author":[{"given":"Jer-En","family":"Hsu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingyang","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiqiu","family":"Cheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3631-3979","authenticated-orcid":false,"given":"Hyun-Min","family":"Kang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susan V.","family":"Brooks","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Myungjin","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun Hee","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2025120913150788000_2025.12.03.692123v1.1","doi-asserted-by":"publisher","DOI":"10.1152\/physrev.00031.2010"},{"key":"2025120913150788000_2025.12.03.692123v1.2","doi-asserted-by":"publisher","DOI":"10.1002\/1097-0029(20000915)50:6<500::AID-JEMT7>3.0.CO;2-7"},{"key":"2025120913150788000_2025.12.03.692123v1.3","doi-asserted-by":"publisher","DOI":"10.1038\/nrm3025"},{"key":"2025120913150788000_2025.12.03.692123v1.4","doi-asserted-by":"publisher","DOI":"10.1038\/ncb2763"},{"key":"2025120913150788000_2025.12.03.692123v1.5","doi-asserted-by":"publisher","DOI":"10.1126\/science.1232044"},{"issue":"10","key":"2025120913150788000_2025.12.03.692123v1.6","doi-asserted-by":"crossref","first-page":"2303","DOI":"10.1080\/15548627.2021.2016255","article-title":"Simultaneous loss of TSC1 and DEPDC5 in skeletal and cardiac muscles produces early-onset myopathy and cardiac dysfunction associated with oxidative damage and SQSTM1\/p62 accumulation","volume":"18","year":"2022","journal-title":"Autophagy"},{"key":"2025120913150788000_2025.12.03.692123v1.7","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.RA118.005970"},{"key":"2025120913150788000_2025.12.03.692123v1.8","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmet.2013.03.015"},{"key":"2025120913150788000_2025.12.03.692123v1.9","doi-asserted-by":"publisher","DOI":"10.1038\/ncb2152"},{"key":"2025120913150788000_2025.12.03.692123v1.10","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.exphem.2017.02.004","article-title":"Role of mTORC1-S6K1 signaling pathway in regulation of hematopoietic stem cell and acute myeloid leukemia","volume":"50","year":"2017","journal-title":"Exp Hematol"},{"key":"2025120913150788000_2025.12.03.692123v1.11","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2005.10.024"},{"key":"2025120913150788000_2025.12.03.692123v1.12","doi-asserted-by":"crossref","unstructured":"Bodine SC . 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