{"doi":"10.1101/2025.05.16.654579","title":"Deep-learning-enabled multi-omics analyses for prediction of future metastasis in cancer","abstract":"Abstract Metastasis remains the leading cause of cancer-related mortality, yet predicting future metastasis is a major clinical challenge due to the lack of validated biomarkers and effective assessment methods. Here, we present EmitGCL, a deep-learning framework that accurately predicts future metastasis and its corresponding biomarkers. Based on a comprehensive benchmarking comparison, EmitGCL outperformed other computational tools across six cancer types from seven cohorts of patients with superior sensitivity and specificity. It captured occult metastatic cells in a patient with a lymph node-negative breast cancer, who was declared to have no evidence of disease by conventional imaging methods but was later confirmed to have a metastatic disease. Notably, EmitGCL identified HSP90AA1 and HSP90AB1 as predictable biomarkers for future breast cancer metastasis, which was validated across five independent cohorts of patients (n=420). Furthermore, we demonstrated YY1 transcription factor as a key driver of breast cancer metastasis which was validated through in-silico and CRISPR-based migration assays, suggesting that YY1 is a potential therapeutic target for deterring metastasis.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":566517,"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":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9432,"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":1166581,"name":"Maoteng Duan","orcid":null,"position":1,"is_corresponding":false},{"id":1419248,"name":"Po‐Lan Su","orcid":"0000-0002-8470-6590","position":2,"is_corresponding":false},{"id":1470191,"name":"Jianying Li","orcid":"0000-0003-4034-0555","position":3,"is_corresponding":false},{"id":273487,"name":"Jordan E. Krull","orcid":"0000-0001-6507-8085","position":4,"is_corresponding":false},{"id":1470192,"name":"Jiacheng Jin","orcid":"0000-0003-3854-4460","position":5,"is_corresponding":false},{"id":1043210,"name":"Hu Chen","orcid":"0009-0003-5600-5935","position":6,"is_corresponding":false},{"id":1470193,"name":"Yuhan Sun","orcid":"0009-0003-7553-6862","position":7,"is_corresponding":false},{"id":795423,"name":"Weidong Wu","orcid":"0000-0002-7334-8679","position":8,"is_corresponding":false},{"id":889172,"name":"Kai He","orcid":"0000-0002-5805-3354","position":9,"is_corresponding":false},{"id":548400,"name":"Richard L. Carpenter","orcid":"0000-0001-9986-6493","position":10,"is_corresponding":false},{"id":334696,"name":"Chi Zhang","orcid":"0000-0001-9553-0925","position":11,"is_corresponding":false},{"id":455389,"name":"Sha Cao","orcid":"0000-0002-8645-848X","position":12,"is_corresponding":false},{"id":233623,"name":"Dong Xu","orcid":"0000-0002-4809-0514","position":13,"is_corresponding":false},{"id":1214669,"name":"Guangyu Wang","orcid":"0000-0002-5581-6926","position":14,"is_corresponding":false},{"id":1470194,"name":"L. Li","orcid":"0000-0003-2016-0602","position":15,"is_corresponding":false},{"id":642775,"name":"Gang Xin","orcid":"0000-0003-1963-505X","position":16,"is_corresponding":false},{"id":251305,"name":"David P. Carbone","orcid":"0000-0003-3002-1921","position":17,"is_corresponding":false},{"id":270306,"name":"Zihai Li","orcid":"0000-0003-4603-927X","position":18,"is_corresponding":false},{"id":235827,"name":"Qin Ma","orcid":"0000-0002-3264-8392","position":19,"is_corresponding":false},{"id":1166145,"name":"Xiaoying Wang","orcid":"0009-0002-2276-9323","position":0,"is_corresponding":true}],"reference_count":50,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:56:36.440192Z","pmid":"40475399","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}