{"doi":"10.1101/2025.09.17.675534","title":"Cryo-mtscATAC-seq for single-cell mitochondrial DNA genotyping and clonal tracing in archived human tissues","abstract":"High-throughput clonal tracing of primary human samples relies on naturally occurring barcodes, such as somatic mitochondrial DNA (mtDNA) mutations detected via single-cell ATAC-seq (mtscATAC-seq). Fresh-frozen clinical specimens preserve tissue architecture but compromise cell integrity, thereby precluding their use in multiomic approaches such as mitochondrial genotyping at single-cell resolution. Here, we introduce Cryo-mtscATAC-seq, a broadly applicable method for diverse pathophysiological contexts to isolate nuclei with their associated mitochondria (\"CryoCells\") from frozen samples for high-throughput clonal analysis. We applied Cryo-mtscATAC-seq to the neurodegenerated human brain, glioblastoma (GBM), pediatric neuroblastoma, and human aorta, and implemented mitobender, a computational tool to reduce ambient mtDNA in single-cell assays. Our approach revealed regional clonal gliogenesis and microglial expansions in amyotrophic lateral sclerosis (ALS), persistence of oligodendrocyte progenitor cell (OPC)-like clones in GBM recurrence, mtDNA depth heterogeneity after neuroblastoma chemotherapy, and oligoclonal proliferation of smooth muscle cells in human aorta. In conclusion, Cryo-mtscATAC-seq broadly extends mtDNA genotyping to archival frozen specimens across tissue types, opening new avenues for investigation of cell state-informed clonality in human health and disease.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":559157,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9473,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":68826,"name":"Benedikt Obermayer","orcid":"0000-0002-9116-630X","position":1,"is_corresponding":false},{"id":1460386,"name":"Marie Cotta","orcid":"0000-0002-2589-3189","position":2,"is_corresponding":false},{"id":1460387,"name":"Ekaterina Friebel","orcid":"0000-0003-1419-2376","position":3,"is_corresponding":false},{"id":1460945,"name":"Juliana Campo-Garcia","orcid":null,"position":4,"is_corresponding":false},{"id":1460946,"name":"Georgia Charalambous","orcid":null,"position":5,"is_corresponding":false},{"id":1460947,"name":"Roemel Jeusep Bueno","orcid":null,"position":6,"is_corresponding":false},{"id":773117,"name":"Dustin Lieu","orcid":null,"position":7,"is_corresponding":false},{"id":1460948,"name":"Patryk Dabek","orcid":null,"position":8,"is_corresponding":false},{"id":1460949,"name":"Ashley Helmuth","orcid":null,"position":9,"is_corresponding":false},{"id":245131,"name":"George Tellides","orcid":"0000-0001-7042-8190","position":10,"is_corresponding":false},{"id":536474,"name":"Roland Assi","orcid":"0000-0002-0863-9867","position":11,"is_corresponding":false},{"id":689069,"name":"Katrin Bankov","orcid":"0009-0005-4033-4966","position":12,"is_corresponding":false},{"id":1460388,"name":"Marco Lodrini","orcid":"0000-0003-4434-529X","position":13,"is_corresponding":false},{"id":1460389,"name":"Hedwig E. Deubzer","orcid":"0000-0002-6115-4893","position":14,"is_corresponding":false},{"id":636835,"name":"Dieter Beule","orcid":"0000-0002-3284-0632","position":15,"is_corresponding":false},{"id":29707,"name":"Hattie Chung","orcid":"0000-0001-8417-5606","position":16,"is_corresponding":false},{"id":57980,"name":"Helena Radbruch","orcid":"0000-0001-6941-3397","position":17,"is_corresponding":false},{"id":660735,"name":"David Capper","orcid":"0000-0003-1945-497X","position":18,"is_corresponding":false},{"id":57967,"name":"Frank L. Heppner","orcid":"0000-0001-9816-8917","position":19,"is_corresponding":false},{"id":1068950,"name":"Sarah C. Starossom","orcid":"0000-0001-7935-9910","position":20,"is_corresponding":false},{"id":3031,"name":"Caleb A. Lareau","orcid":"0000-0003-4179-4807","position":21,"is_corresponding":false},{"id":25320,"name":"Ilon Liu","orcid":"0000-0002-6186-3630","position":22,"is_corresponding":false},{"id":3035,"name":"Leif S. 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