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In this study, by deeply integrating single-cell and bulk transcriptome data, we systematically investigated significance of the shared pyroptotic signature at both single-cell and bulk levels in HCC prognosis. Based on the pyroptotic signature, a robust PR risk system was constructed to quantify the prognostic risk of individual patient. To further verify capacity of the pyroptotic signature on predicting patients\u2019 prognosis, an attention mechanism-based deep neural network classification model was constructed. The mechanisms of prognostic difference in the patients with distinct PR risk were dissected on tumor stemness, cancer pathways, transcriptional regulation, immune infiltration and cell communications. A nomogram model combining PR risk with clinicopathologic data was constructed to evaluate the prognosis of individual patients in clinic. The PR risk could also evaluate therapeutic response to neoadjuvant therapies in HCC patients. In conclusion, the constructed PR risk system enables a comprehensive assessment of tumor microenvironment characteristics, accurate prognosis prediction and rational therapeutic options in HCC.<\/jats:p>","DOI":"10.1093\/bib\/bbad487","type":"journal-article","created":{"date-parts":[[2024,1,10]],"date-time":"2024-01-10T09:04:16Z","timestamp":1704877456000},"source":"Crossref","is-referenced-by-count":38,"title":["Integrated bulk and single-cell transcriptomes reveal pyroptotic signature in prognosis and therapeutic options of hepatocellular carcinoma by combining deep learning"],"prefix":"10.1093","volume":"25","author":[{"given":"Yang","family":"Liu","sequence":"first","affiliation":[{"name":"School of Basic Medical Sciences, Southwest Medical University , Luzhou 646000 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hanlin","family":"Li","sequence":"additional","affiliation":[{"name":"School of Basic Medical Sciences, Southwest Medical University , Luzhou 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Southwest Medical University , Luzhou 646000 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1921-1145","authenticated-orcid":false,"given":"Zheng","family":"Shi","sequence":"additional","affiliation":[{"name":"Clinical Genetics Laboratory , Clinical Medical College & Affiliated Hospital, , Chengdu 610106 , China"},{"name":"Chengdu University , Clinical Medical College & Affiliated Hospital, , Chengdu 610106 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8345-343X","authenticated-orcid":false,"given":"Renzhi","family":"Cao","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Pacific Lutheran University , Tacoma, Washington 98447 , 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