{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/120366"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/120366","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Comprehensive analysis of cellular contribution to delayed skeletal muscle recovery after disuse","abstract":"Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2025-05-01","abstract_html":"Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2025-05-01","abstract_has_math":false,"creators":["Choi, Sung Jun"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"M.S.","degree_level":"Thesis","degree_discipline":"Kinesiology","degree_department":null,"school":null,"contributors":["Boppart, Marni","Burd, Nicholas"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2023,"date_issued":"2023-05","date_published":"2023-05","updated_at":"2026-07-22T22:24:57Z","subjects":["Pericyte","Skeletal Muscle","Immobilization","Disuse Atrophy","Remobilization","Snrna-seq"],"languages":["en","eng"],"rights":["Copyright 2023 Sung Jun Choi"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/120366","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Boppart, Marni","Burd, Nicholas"]},{"key":"dc:creator","label":"Author","values":["Choi, Sung Jun"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2023-05","2023-04-17"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Kinesiology"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["M.S."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Pericyte","Skeletal Muscle","Immobilization","Disuse Atrophy","Remobilization","Snrna-seq"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en","eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2023 Sung Jun Choi"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/120366"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2025-05-01","The student, Sung Jun Choi, accepted the attached license on 2023-04-13 at 10:24.","The student, Sung Jun Choi, submitted this Thesis for approval on 2023-04-13 at 10:36.","This Thesis was approved for publication on 2023-04-17 at 13:28.","DSpace SAF Submission Ingestion Package generated from Vireo submission #18976 on 2023-09-01 at 17:13:26","Extended periods of inactivity or immobilization often result in significant loss of skeletal muscle mass and function. Physical rehabilitation is the most effective approach to recovery, yet deficits persist during rehabilitation that often become permanent in vulnerable populations. While significant progress has been made in identifying the mechanisms that underlie muscle atrophy during a period of disuse, much less is known about the mechanisms that drive sustained delays in muscle recovery during reload. Our laboratory previously demonstrated that perivascular stem/stromal cells (CD146+ pericytes) are deficient in the capacity to synthesize antioxidants after disuse, and transplantation of healthy pericytes can restore redox imbalance and effectively rebuild muscle structure, suggesting an important role for pericytes in the recovery process. Currently, the precise antioxidants or factors required for recovery remain unknown. PURPOSE: The primary purpose of the study in this thesis was to evaluate single cell transcriptional profiles during recovery after immobilization and identify the cells and precise factors that contribute to prolonged atrophy. METHODS: Young adult wild-type mice underwent 2 weeks of unilateral hindlimb immobilization and 3 days of remobilization before the skeletal muscles (mobile control or remobilized limb; n=15/group) were collected for single nuclei isolation. Single-nuclei RNA sequencing (snRNA-seq) was performed using 10X Genomics Chromium Platform for evaluation of transcriptional differences. RESULTS: A total of 19,059 genes were analyzed by 10X Genomics Cell Ranger software (v7.1.0). Integrated gene expression data were used to identify a total of 14 cell clusters. Gene Ontology (GO) analysis demonstrated similar upregulation of genes associated with skeletal muscle contraction, muscle cell development, cytoskeletal organization, and myofibril assembly across clusters. In contrast, GO terms associated with downregulated genes differed widely among clusters and included acetylation, oxidative phosphorylation, extracellular matrix organization, RNA splicing, angiogenesis. Unexpectedly, the pericyte gene signature suggests that decreased adherence to endothelial cells, rather than antioxidant synthesis, appears to be the primary functional deficit during recovery. CONCLUSION: Overall, this study provides extensive insight on cellular contribution to the lack of recovery at the initial phase of remobilization. Our study suggests that most cells demonstrate an initial attempt to recover cellular structure, yet clear deficits in cellular function remain present in all cells within skeletal muscle. This dataset will provide valuable information to the field and accelerate the design of new cellular and molecular therapeutic targets."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Comprehensive analysis of cellular contribution to delayed skeletal muscle recovery after disuse"]}]}],"canonical_facts":{"dc:contributor":["Boppart, Marni","Burd, Nicholas"],"dc:creator":["Choi, Sung Jun"],"dc:date":["2023-05","2023-04-17"],"dc:description":["Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2025-05-01","The student, Sung Jun Choi, accepted the attached license on 2023-04-13 at 10:24.","The student, Sung Jun Choi, submitted this Thesis for approval on 2023-04-13 at 10:36.","This Thesis was approved for publication on 2023-04-17 at 13:28.","DSpace SAF Submission Ingestion Package generated from Vireo submission #18976 on 2023-09-01 at 17:13:26","Extended periods of inactivity or immobilization often result in significant loss of skeletal muscle mass and function. Physical rehabilitation is the most effective approach to recovery, yet deficits persist during rehabilitation that often become permanent in vulnerable populations. While significant progress has been made in identifying the mechanisms that underlie muscle atrophy during a period of disuse, much less is known about the mechanisms that drive sustained delays in muscle recovery during reload. Our laboratory previously demonstrated that perivascular stem/stromal cells (CD146+ pericytes) are deficient in the capacity to synthesize antioxidants after disuse, and transplantation of healthy pericytes can restore redox imbalance and effectively rebuild muscle structure, suggesting an important role for pericytes in the recovery process. Currently, the precise antioxidants or factors required for recovery remain unknown. PURPOSE: The primary purpose of the study in this thesis was to evaluate single cell transcriptional profiles during recovery after immobilization and identify the cells and precise factors that contribute to prolonged atrophy. METHODS: Young adult wild-type mice underwent 2 weeks of unilateral hindlimb immobilization and 3 days of remobilization before the skeletal muscles (mobile control or remobilized limb; n=15/group) were collected for single nuclei isolation. Single-nuclei RNA sequencing (snRNA-seq) was performed using 10X Genomics Chromium Platform for evaluation of transcriptional differences. RESULTS: A total of 19,059 genes were analyzed by 10X Genomics Cell Ranger software (v7.1.0). Integrated gene expression data were used to identify a total of 14 cell clusters. Gene Ontology (GO) analysis demonstrated similar upregulation of genes associated with skeletal muscle contraction, muscle cell development, cytoskeletal organization, and myofibril assembly across clusters. In contrast, GO terms associated with downregulated genes differed widely among clusters and included acetylation, oxidative phosphorylation, extracellular matrix organization, RNA splicing, angiogenesis. Unexpectedly, the pericyte gene signature suggests that decreased adherence to endothelial cells, rather than antioxidant synthesis, appears to be the primary functional deficit during recovery. CONCLUSION: Overall, this study provides extensive insight on cellular contribution to the lack of recovery at the initial phase of remobilization. Our study suggests that most cells demonstrate an initial attempt to recover cellular structure, yet clear deficits in cellular function remain present in all cells within skeletal muscle. This dataset will provide valuable information to the field and accelerate the design of new cellular and molecular therapeutic targets."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/120366"],"dc:language":["en","eng"],"dc:rights":["Copyright 2023 Sung Jun Choi"],"dc:subject":["Pericyte","Skeletal Muscle","Immobilization","Disuse Atrophy","Remobilization","Snrna-seq"],"dc:title":["Comprehensive analysis of cellular contribution to delayed skeletal muscle recovery after disuse"],"dc:type":["text","Thesis"],"thesis:degree_discipline":["Kinesiology"],"thesis:degree_level":["Thesis"],"thesis:degree_name":["M.S."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:24:57Z"}