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"author", "firstName": "Benjamin B.", "lastName": "Currall" }, { "creatorType": "author", "firstName": "Sion", "lastName": "Williams" }, { "creatorType": "author", "firstName": "Daniel", "lastName": "Bilbao Cortes" }, { "creatorType": "author", "firstName": "Melinda", "lastName": "Minucci Boone" }, { "creatorType": "author", "firstName": "Macarena I.", "lastName": "De La Fuente" }, { "creatorType": "author", "firstName": "Sakir H.", "lastName": "Gultekin" }, { "creatorType": "author", "firstName": "Michele", "lastName": "Ceccarelli" }, { "creatorType": "author", "firstName": "Antonio", "lastName": "Iavarone" }, { "creatorType": "author", "firstName": "Anna", "lastName": "Lasorella" } ], "abstractNote": "", "publicationTitle": "Cancer Cell", "publisher": "", "place": "", "date": "9/2025", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "S1535610825003666", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Cancer Cell", "DOI": "10.1016/j.ccell.2025.08.009", "citationKey": "", "url": "https://linkinghub.elsevier.com/retrieve/pii/S1535610825003666", "accessDate": "2025-11-26T22:07:21Z", "PMID": "", "PMCID": "", "ISSN": "15356108", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "DOI.org (Crossref)", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2025-11-26T22:07:21Z", "dateModified": "2025-11-26T22:07:21Z" } }, { "key": "ADLA6HBC", "version": 444, "library": { "type": "group", "id": 265492, "name": "bioinformatics-publications", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/265492/items/ADLA6HBC", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications/items/ADLA6HBC", "type": "text/html" } }, "meta": { 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R.", "lastName": "Noviello" }, { "creatorType": "author", "firstName": "Christopher", "lastName": "Sereduk" }, { "creatorType": "author", "firstName": "Dustin", "lastName": "Grief" }, { "creatorType": "author", "firstName": "Francesca P.", "lastName": "Caruso" }, { "creatorType": "author", "firstName": "Ritin", "lastName": "Sharma" }, { "creatorType": "author", "firstName": "Krystine", "lastName": "Garcia-Mansfield" }, { "creatorType": "author", "firstName": "Patrick", "lastName": "Pirrotte" }, { "creatorType": "author", "firstName": "Jean", "lastName": "Kloss" }, { "creatorType": "author", "firstName": "Fulvio", "lastName": "D’Angelo" }, { "creatorType": "author", "firstName": "Bianca M.", "lastName": "Marin" }, { "creatorType": "author", "firstName": "Kendra", "lastName": "Porath" }, { "creatorType": "author", "firstName": "Sonia", "lastName": "Jain" }, { "creatorType": "author", "firstName": "Benjamin", "lastName": "Rabichow" }, { "creatorType": "author", "firstName": "Shannon P. Fortin", "lastName": "Ensign" }, { "creatorType": "author", "firstName": "Antonio", "lastName": "Iavarone" }, { "creatorType": "author", "firstName": "Antonella", "lastName": "Paladino" }, { "creatorType": "author", "firstName": "Jann N.", "lastName": "Sarkaria" }, { "creatorType": "author", "firstName": "Joseph C.", "lastName": "Loftus" }, { "creatorType": "author", "firstName": "Michele", "lastName": "Ceccarelli" }, { "creatorType": "author", "firstName": "Nhan L.", "lastName": "Tran" } ], "abstractNote": "", "publicationTitle": "Journal of Translational Medicine", "publisher": "", "place": "", "date": "2025-10-21", "volume": "23", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "1153", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J Transl Med", "DOI": "10.1186/s12967-025-07216-5", "citationKey": "", "url": "https://translational-medicine.biomedcentral.com/articles/10.1186/s12967-025-07216-5", "accessDate": "2025-11-26T22:06:41Z", "PMID": "", "PMCID": "", "ISSN": "1479-5876", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "DOI.org (Crossref)", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2025-11-26T22:06:41Z", "dateModified": "2025-11-26T22:06:41Z" } }, { "key": "AZBEWRJC", "version": 443, "library": { "type": "group", "id": 265492, "name": "bioinformatics-publications", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/265492/items/AZBEWRJC", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications/items/AZBEWRJC", "type": "text/html" } }, "meta": { "createdByUser": { "id": 221141, "username": "miccec", "name": "Michele Ceccarelli", "links": { "alternate": { "href": "https://www.zotero.org/miccec", "type": "text/html" } } }, "creatorSummary": "Brandi et al.", "parsedDate": "2025", "numChildren": 0 }, "data": { "key": "AZBEWRJC", "version": 443, "itemType": "journalArticle", "title": "MiDNE a tool for Multi-omics genes and drugs interactions discovery", "creators": [ { "creatorType": "author", "firstName": "Aurora", "lastName": "Brandi" }, { "creatorType": "author", "firstName": "Barbara", "lastName": "Majello" }, { "creatorType": "author", "firstName": "Ines", "lastName": "Simeone" }, { "creatorType": "author", "firstName": "Massimiliano", "lastName": "Romano" }, { "creatorType": "author", "firstName": "Michele", "lastName": "Ceccarelli" }, { "creatorType": "author", "firstName": "Giovanni", "lastName": "Scala" } ], "abstractNote": "", "publicationTitle": "Computational and Structural Biotechnology Journal", "publisher": "", "place": "", "date": "2025", "volume": "27", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "4469-4475", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Computational and Structural Biotechnology Journal", "DOI": "10.1016/j.csbj.2025.10.022", "citationKey": "", "url": "https://linkinghub.elsevier.com/retrieve/pii/S2001037025004258", "accessDate": "2025-11-26T22:06:28Z", "PMID": "", "PMCID": "", "ISSN": "20010370", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "DOI.org (Crossref)", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2025-11-26T22:06:28Z", "dateModified": "2025-11-26T22:06:28Z" } }, { "key": "NAXTMXN9", "version": 442, "library": { "type": "group", "id": 265492, "name": "bioinformatics-publications", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/265492/items/NAXTMXN9", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications/items/NAXTMXN9", "type": "text/html" } }, "meta": { "createdByUser": { "id": 221141, "username": "miccec", "name": "Michele Ceccarelli", "links": { "alternate": { "href": "https://www.zotero.org/miccec", "type": "text/html" } } }, "creatorSummary": "Ciervo et al.", "parsedDate": "2025-10-10", "numChildren": 0 }, "data": { "key": "NAXTMXN9", "version": 442, "itemType": "preprint", "title": "Transposable Elements and Homotypic Niches Drive Immune Dynamics and Resistance in Melanoma Epigenetic-based immunotherapy", "creators": [ { "creatorType": "author", "firstName": "Erika", "lastName": "Ciervo" }, { "creatorType": "author", "firstName": "Francesco", "lastName": "Ceccarelli" }, { "creatorType": "author", "firstName": "Anna Maria", "lastName": "Di Giacomo" }, { "creatorType": "author", "firstName": "Piera", "lastName": "Grisolia" }, { "creatorType": "author", "firstName": "Alessia", "lastName": "Covre" }, { "creatorType": "author", "firstName": "Zein Mersini", "lastName": "Besharat" }, { "creatorType": "author", "firstName": "Antonio", "lastName": "De Falco" }, { "creatorType": "author", "firstName": "Francesca Pia", "lastName": "Caruso" }, { "creatorType": "author", "firstName": "Luigi", "lastName": "Laezza" }, { "creatorType": "author", "firstName": "Luigi", "lastName": "Ferraro" }, { "creatorType": "author", "firstName": "Gloria Mas", "lastName": "Martin" }, { "creatorType": "author", "firstName": "Maria Fortunata", "lastName": "Lofiego" }, { "creatorType": "author", "firstName": "Tommaso", "lastName": "Sani" }, { "creatorType": "author", "firstName": "Elisabetta", "lastName": "Ferretti" }, { "creatorType": "author", "firstName": "Yan", "lastName": "Guo" }, { "creatorType": "author", "firstName": "Sean Barry", "lastName": "Holden" }, { "creatorType": "author", "firstName": "Roberta", "lastName": "Mortarini" }, { "creatorType": "author", "firstName": "Andrea", "lastName": "Anichini" }, { "creatorType": "author", "firstName": "Michele", "lastName": "Maio" }, { "creatorType": "author", "firstName": "Teresa Maria Rosaria", "lastName": "Noviello" }, { "creatorType": "author", "firstName": "Michele", "lastName": "Ceccarelli" } ], "abstractNote": "Abstract\n \n Melanoma plasticity drives immune evasion and therapy resistance through dynamic cell-state transitions beyond genetic alterations. Epigenetic remodeling critically influences such processes, yet its role in reshaping the tumor ecosystem under therapeutic pressure remains unresolved. Here, we profiled longitudinal biopsies from melanoma patients treated in the phase Ib NIBIT-M4 epi-immunotherapy clinical trial (\n NCT02608437\n ), testing the combination of a DNMT1 inhibitor with anti-CTLA4 using single-cell multiome and high-resolution spatial transcriptomics. Integrated analyses resolved seven malignant meta-programs, including a rare Wnt/β-catenin–driven melanocytic state and a de-differentiated neural crest–like state enriched in non-responders. Spatial modeling revealed that homotypic clustering stabilizes resistant programs, with neural crest–like cells forming compact, centrally localized niches, whereas Wnt/β-catenin subpopulations displayed a bimodal architecture, either cohesive clusters sustained by adhesion or dispersed, transcriptionally plastic cells. Responders exhibited progressive enrichment of an antigen presentation/interferon program and coordinated remodeling of the tumor microenvironment with T and B cell expansion, whereas tumors from non-responder patients maintained stable composition of neural crest–like clusters. Epigenetic therapy reactivated transposable elements, providing both regulatory signals that prime innate immunity within microenvironment and generating antigens that drive immunoediting and immunogenicity of Antigen presentation/interferon cell states in responders. Finally, NFATC2 emerged as a master regulator of neural crests–like transcriptional phenotypes and promoter of resistance to therapeutic interventions in melanoma patients. NFATC2 perturbation was able to shift tumor cells towards more differentiated and immunogenic states. These findings reveal how epigenetic-based immunotherapy reshapes melanoma ecosystems, provide mechanistic insights into how multiple transcriptional programs promote tumor plasticity and resistance to both combinatorial therapies and immune checkpoint blockade, identify spatial clustering as a principle stabilizing resistant niches, and highlight β-catenin and NFATC2 as actionable vulnerabilities to overcome resistance.", "genre": "", "repository": "Genomics", "archiveID": "", "place": "", "date": "2025-10-10", "series": "", "seriesNumber": "", "DOI": "10.1101/2025.10.09.679175", "citationKey": "", "url": "http://biorxiv.org/lookup/doi/10.1101/2025.10.09.679175", "accessDate": "2025-11-26T22:06:09Z", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "DOI.org (Crossref)", "callNumber": "", "rights": "http://creativecommons.org/licenses/by-nc-nd/4.0/", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2025-11-26T22:06:09Z", "dateModified": "2025-11-26T22:06:09Z" } }, { "key": "2LVRLVVI", "version": 441, "library": { "type": "group", "id": 265492, "name": "bioinformatics-publications", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/265492/items/2LVRLVVI", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications/items/2LVRLVVI", "type": "text/html" } }, "meta": { "createdByUser": { "id": 221141, "username": "miccec", "name": "Michele Ceccarelli", "links": { "alternate": { "href": "https://www.zotero.org/miccec", "type": "text/html" } } }, "creatorSummary": "De Falco et al.", "parsedDate": "2025-10-21", "numChildren": 0 }, "data": { "key": "2LVRLVVI", "version": 441, "itemType": "preprint", "title": "Knowledge-informed multimodal cfDNA analysis improves sensitivity and generalization in cancer detection", "creators": [ { "creatorType": "author", "firstName": "Antonio", "lastName": "De Falco" }, { "creatorType": "author", "firstName": "Piera", "lastName": "Grisolia" }, { "creatorType": "author", "firstName": "Raffaella", "lastName": "Giuffrida" }, { "creatorType": "author", "firstName": "Clara", "lastName": "Iannarone" }, { "creatorType": "author", "firstName": "Cinzia", "lastName": "Graziano" }, { "creatorType": "author", "firstName": "Marianna", "lastName": "Scrima" }, { "creatorType": "author", "firstName": "Alessia Maria", "lastName": "Cossu" }, { "creatorType": "author", "firstName": "Rossella", "lastName": "Tufano" }, { "creatorType": "author", "firstName": "Maria Vanessa", "lastName": "Yow" }, { "creatorType": "author", "firstName": "Chloe Marissa", "lastName": "Brown" }, { "creatorType": "author", "firstName": "Palak", "lastName": "Bajaj" }, { "creatorType": "author", "firstName": "Marco", "lastName": "Bocchetti" }, { "creatorType": "author", "firstName": "Pier Vitale", "lastName": "Nuzzo" }, { "creatorType": "author", "firstName": "Floriana", "lastName": "Morgillo" }, { "creatorType": "author", "firstName": "Francesco", "lastName": "Caraglia" }, { "creatorType": "author", "firstName": "Maria Carminia", "lastName": "Delle Corte" }, { "creatorType": "author", "firstName": "Gaetano", "lastName": "Di Guida" }, { "creatorType": "author", "firstName": "Teresa", "lastName": "Troiani" }, { "creatorType": "author", "firstName": "Fortunato", "lastName": "Ciardiello" }, { "creatorType": "author", "firstName": "Maria Rosaria", "lastName": "Rizzo" }, { "creatorType": "author", "firstName": "Alfonso", "lastName": "Fiorelli" }, { "creatorType": "author", "firstName": "Noemi Maria", "lastName": "Giorgiano" }, { "creatorType": "author", "firstName": "Davide", "lastName": "Arcaniolo" }, { "creatorType": "author", "firstName": "Giampiero Della", "lastName": "Rosa" }, { "creatorType": "author", "firstName": "Marco", "lastName": "De Sio" }, { "creatorType": "author", "firstName": "Alessia", "lastName": "Covre" }, { "creatorType": "author", "firstName": "Anna Maria", "lastName": "Di Giacomo" }, { "creatorType": "author", "firstName": "Luana", "lastName": "Calabrò" }, { "creatorType": "author", "firstName": "Paolo", "lastName": "Fontana" }, { "creatorType": "author", "firstName": "Marzia", "lastName": "Mare" }, { "creatorType": "author", "firstName": "Ola", "lastName": "Landgren" }, { "creatorType": "author", "firstName": "Damian J.", "lastName": "Green" }, { "creatorType": "author", "firstName": "Alex", "lastName": "Lesokhin" }, { "creatorType": "author", "firstName": "David G.", "lastName": "Coffey" }, { "creatorType": "author", "firstName": "Nipun", "lastName": "Merchant" }, { "creatorType": "author", "firstName": "Jashodeep", "lastName": "Datta" }, { "creatorType": "author", "firstName": "Stefano", "lastName": "Forte" }, { "creatorType": "author", "firstName": "Michele", "lastName": "Maio" }, { "creatorType": "author", "firstName": "Michele", "lastName": "Caraglia" }, { "creatorType": "author", "firstName": "Michele", "lastName": "Ceccarelli" } ], "abstractNote": "Abstract\n \n Liquid biopsy offers a minimally invasive opportunity to detect and monitor cancers through analysis of cell-free DNA (cfDNA). However, current approaches face challenges of limited sensitivity at low tumor fractions, technical variability, and poor generalization across cohorts. Tumor-informed targeted methods offer high specificity but suffer from low sensitivity due to random sampling, tumor evolution and adaptation (including resistance mechanisms), and other sources of heterogeneity. Conversely, tumor-naive genome-wide methods can increase sensitivity but often sacrifice specificity, particularly at low tumor fractions. We developed Fragmentomics Analysis for Tumor Evaluation with AI (Fate-AI), a multimodal framework that integrates fragmentomic and methylation-derived features from low-pass whole-genome sequencing (LPWGS) and cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq). It employs a knowledge-informed strategy to select recurrently altered genomic regions and tissue-specific methylation loci to combine the advantages of tumor-naive approaches with the specificity of tumor-informed approaches. This approach derives robust per-sample normalized features that mitigate batch effects and enhance cross-cohort reproducibility. We evaluated Fate-AI on a total of 1,219 plasma samples spanning ten cancer types and healthy controls from multiple laboratories and sequencing centers, including 432 newly profiled cases (280 with both cfMeDIP-seq and LPWGS) together with 787 samples from four independent public datasets. Fate-AI achieved superior sensitivity and specificity compared to state-of-the-art methods, detecting tumor-derived signals at fractions as low as 10\n −5\n in experimental dilutions. Fate-AI scores correlated with disease stage and tracked longitudinal progression, anticipating relapse months before clinical progression. Furthermore, Fate-AI enabled tissue-of-origin classification, with AUCs ranging from 0.84 to 0.97 across six cancer types. Collectively, our results demonstrate that Fate-AI provides a sensitive, generalizable, and clinically actionable platform for early detection, minimal residual disease monitoring, and tissue-of-origin classification, supporting its potential as a liquid biopsy framework in precision oncology.", "genre": "", "repository": "Cancer Biology", "archiveID": "", "place": "", "date": "2025-10-21", "series": "", "seriesNumber": "", "DOI": "10.1101/2025.10.20.683167", "citationKey": "", "url": "http://biorxiv.org/lookup/doi/10.1101/2025.10.20.683167", "accessDate": "2025-11-26T22:05:51Z", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "DOI.org (Crossref)", "callNumber": "", "rights": "http://creativecommons.org/licenses/by/4.0/", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2025-11-26T22:05:51Z", "dateModified": "2025-11-26T22:05:51Z" } }, { "key": "F88Z99QK", "version": 461, "library": { "type": "group", "id": 265492, "name": "bioinformatics-publications", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/265492/items/F88Z99QK", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications/items/F88Z99QK", "type": "text/html" } }, "meta": { "createdByUser": { "id": 221141, "username": "miccec", "name": "Michele Ceccarelli", "links": { "alternate": { "href": "https://www.zotero.org/miccec", "type": "text/html" } } }, "creatorSummary": "Anichini et al.", "parsedDate": "2025-07-18", "numChildren": 0 }, "data": { "key": "F88Z99QK", "version": 461, "itemType": "journalArticle", "title": "Integrated multi-omics profiling reveals the role of the DNA methylation landscape in shaping biological heterogeneity and clinical behaviour of metastatic melanoma.", "creators": [ { "creatorType": "author", "firstName": "Andrea", "lastName": "Anichini" }, { "creatorType": "author", "firstName": "Francesca P.", "lastName": "Caruso" }, { "creatorType": "author", "firstName": "Vincenzo", "lastName": "Lagano" }, { "creatorType": "author", "firstName": "Teresa M. R.", "lastName": "Noviello" }, { "creatorType": "author", "firstName": "Rossella", "lastName": "Tufano" }, { "creatorType": "author", "firstName": "Gabriella", "lastName": "Nicolini" }, { "creatorType": "author", "firstName": "Alessandra", "lastName": "Molla" }, { "creatorType": "author", "firstName": "Ilaria", "lastName": "Bersani" }, { "creatorType": "author", "firstName": "Francesco", "lastName": "Sgambelluri" }, { "creatorType": "author", "firstName": "Alessia", "lastName": "Covre" }, { "creatorType": "author", "firstName": "Maria F.", "lastName": "Lofiego" }, { "creatorType": "author", "firstName": "Sandra", "lastName": "Coral" }, { "creatorType": "author", "firstName": "Anna Maria", "lastName": "Di Giacomo" }, { "creatorType": "author", "firstName": "Elena", "lastName": "Simonetti" }, { "creatorType": "author", "firstName": "Barbara", "lastName": "Valeri" }, { "creatorType": "author", "firstName": "Mara", "lastName": "Cossa" }, { "creatorType": "author", "firstName": "Filippo", "lastName": "Ugolini" }, { "creatorType": "author", "firstName": "Sara", "lastName": "Simi" }, { "creatorType": "author", "firstName": "Daniela", "lastName": "Massi" }, { "creatorType": "author", "firstName": "Massimo", "lastName": "Milione" }, { "creatorType": "author", "firstName": "Andrea", "lastName": "Maurichi" }, { "creatorType": "author", "firstName": "Roberto", "lastName": "Patuzzo" }, { "creatorType": "author", "firstName": "Mario", "lastName": "Santinami" }, { "creatorType": "author", "firstName": "Michele", "lastName": "Maio" }, { "creatorType": "author", "firstName": "Michele", "lastName": "Ceccarelli" }, { "creatorType": "author", "firstName": "Roberta", "lastName": "Mortarini" } ], "abstractNote": "BACKGROUND: We developed an integrated multi-omics analysis in metastatic melanoma (MM) cohorts to associate DNA methylation profiles with tumor progression, survival, response to adjuvant immunotherapy, structure of the tumor immune microenvironment and transcriptional programs of immunity and melanoma differentiation. METHODS: Lesions (n = 191) from a fully annotated, retrospective cohort of 165 AJCC 8th Stage III and IV melanoma patients (EPICA cohort) were characterized by reduced representation bisulfite sequencing, RNA sequencing, whole exome sequencing, quantitative immunohistochemistry and multiplex immunofluorescence analysis. The TCGA melanoma datasets were used for validation. Pre-therapy lesions (n = 28) from a cohort of MM patients treated with adjuvant immune checkpoint blockade were characterized for the DNA methylation profile. Impact of a DNMT inhibitor on DNA methylation and transcriptomic profiles of melanoma cell lines was investigated by EPIC arrays and Clariom S arrays. RESULTS: Four tumor subsets (i.e. DEMethylated, LOW, INTermediate and CIMP) with progressively increasing levels of DNA methylation were identified in EPICA, TCGA MM and TCGA primary melanoma cohorts. EPICA patients with LOW methylation tumors exhibited a significantly longer survival and a lower progression rate to more advanced AJCC stages, compared to patients with CIMP tumors. In an adjuvant immune checkpoint blockade cohort, patients with DEM/LOW pre-therapy lesions showed significantly longer relapse-free survival compared to those with INT/CIMP lesions. RNA-seq data analysis revealed that LOW and CIMP EPICA tumors showed opposite activation of master molecules influencing prognostic target genes, and differential expression of immunotherapy response and melanoma differentiation signatures. Compared to CIMP tumors, LOW lesions showed enrichment for CD8(+) TCF-1(+) PD-1(+) TIM-3(-) pre-exhausted and CD8(+) TCF-1(-) PD-1(+) TIM-3(+) exhausted T cells, more frequent retention of HLA Class I antigens and a de-differentiated melanoma phenotype. The differentiation and immune-related transcriptional features associated with LOW vs CIMP lesions were tumor-intrinsic programs retained in-vitro by melanoma cell lines. Consistently, treatment of differentiated melanoma cell lines with a DNMT inhibitor induced global DNA de-methylation, promoted de-differentiation and upregulated viral mimicry and IFNG predictive signatures of immunotherapy response. CONCLUSIONS: These results reveal the biological, prognostic and therapeutic relevance of DNA methylation classes in MM and support methylome targeting strategies for precision immunotherapy.", "publicationTitle": "Journal of experimental & clinical cancer research : CR", "publisher": "", "place": "", "date": "2025 Jul 18", "volume": "44", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "212", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J Exp Clin Cancer Res", "DOI": "10.1186/s13046-025-03474-9", "citationKey": "", "url": "", "accessDate": "", "PMID": "40682094", "PMCID": "PMC12273276", "ISSN": "1756-9966 0392-9078", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "", "callNumber": "", "rights": "© 2025. The Author(s).", "extra": "Place: England", "tags": [ { "tag": "*DNA Methylation" }, { "tag": "*Melanoma/genetics/pathology" }, { "tag": "Aged" }, { "tag": "DNA methylation" }, { "tag": "DNMT inhibitor" }, { "tag": "Female" }, { "tag": "Gene Expression Regulation, Neoplastic" }, { "tag": "Humans" }, { "tag": "Immune checkpoint blockade" }, { "tag": "Immune contexture" }, { "tag": "Male" }, { "tag": "Melanoma" }, { "tag": "Middle Aged" }, { "tag": "Multiomics" }, { "tag": "Neoplasm Metastasis" }, { "tag": "Prognosis" }, { "tag": "Retrospective Studies" }, { "tag": "Tumor Microenvironment" } ], "collections": [ "3B9BKS6I" ], "relations": {}, "dateAdded": "2025-08-19T18:27:24Z", "dateModified": "2025-08-19T18:27:24Z" } }, { "key": "VPIEBGRP", "version": 435, "library": { "type": "group", "id": 265492, "name": "bioinformatics-publications", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/265492/items/VPIEBGRP", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications/items/VPIEBGRP", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/265492/items/IA678VQA", "type": "application/json" } }, "meta": { "createdByUser": { "id": 221141, "username": "miccec", "name": "Michele Ceccarelli", "links": { "alternate": { "href": "https://www.zotero.org/miccec", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "VPIEBGRP", "version": 435, "parentItem": "IA678VQA", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text", "accessDate": "2025-07-18T13:07:45Z", "url": "https://jeccr.biomedcentral.com/counter/pdf/10.1186/s13046-025-03310-0", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Lofiego et al. - 2025 - DNA methylation status classifies pleural mesothel.pdf", "md5": null, "mtime": null, "tags": [], "relations": {}, "dateAdded": "2025-07-18T13:07:45Z", "dateModified": "2025-07-18T13:07:45Z" } }, { "key": "74VAM6RE", "version": 435, "library": { "type": "group", "id": 265492, "name": "bioinformatics-publications", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/265492/items/74VAM6RE", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications/items/74VAM6RE", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/265492/items/IA678VQA", "type": "application/json" } }, "meta": { "createdByUser": { "id": 221141, "username": "miccec", "name": "Michele Ceccarelli", "links": { "alternate": { "href": "https://www.zotero.org/miccec", "type": "text/html" } } } }, "data": { "key": "74VAM6RE", "version": 435, "parentItem": "IA678VQA", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2025-07-18T13:07:42Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/39966970", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2025-07-18T13:07:42Z", "dateModified": "2025-07-18T13:07:42Z" } }, { "key": "IA678VQA", "version": 460, "library": { "type": "group", "id": 265492, "name": "bioinformatics-publications", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/265492/items/IA678VQA", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications/items/IA678VQA", "type": "text/html" } }, "meta": { "createdByUser": { "id": 221141, "username": "miccec", "name": "Michele Ceccarelli", "links": { "alternate": { "href": "https://www.zotero.org/miccec", "type": "text/html" } } }, "creatorSummary": "Lofiego et al.", "parsedDate": "2025-02-18", "numChildren": 2 }, "data": { "key": "IA678VQA", "version": 460, "itemType": "journalArticle", "title": "DNA methylation status classifies pleural mesothelioma cells according to their immune profile: implication for precision epigenetic therapy", "creators": [ { "creatorType": "author", "firstName": "Maria Fortunata", "lastName": "Lofiego" }, { "creatorType": "author", "firstName": "Rossella", "lastName": "Tufano" }, { "creatorType": "author", "firstName": "Emma", "lastName": "Bello" }, { "creatorType": "author", "firstName": "Laura", "lastName": "Solmonese" }, { "creatorType": "author", "firstName": "Francesco", "lastName": "Marzani" }, { "creatorType": "author", "firstName": "Francesca", "lastName": "Piazzini" }, { "creatorType": "author", "firstName": "Fabrizio", "lastName": "Celesti" }, { "creatorType": "author", "firstName": "Francesca Pia", "lastName": "Caruso" }, { "creatorType": "author", "firstName": "Teresa Maria Rosaria", "lastName": "Noviello" }, { "creatorType": "author", "firstName": "Roberta", "lastName": "Mortarini" }, { "creatorType": "author", "firstName": "Andrea", "lastName": "Anichini" }, { "creatorType": "author", "firstName": "Michele", "lastName": "Ceccarelli" }, { "creatorType": "author", "firstName": "Luana", "lastName": "Calabrò" }, { "creatorType": "author", "firstName": "Michele", "lastName": "Maio" }, { "creatorType": "author", "firstName": "Sandra", "lastName": "Coral" }, { "creatorType": "author", "firstName": "Anna Maria", "lastName": "Di Giacomo" }, { "creatorType": "author", "firstName": "Alessia", "lastName": "Covre" }, { "creatorType": "author", "name": "EPigenetic Immune-oncology Consortium Airc (EPICA) investigators" } ], "abstractNote": "BACKGROUND: Co-targeting of immune checkpoint inhibitors (ICI) CTLA-4 and PD-1 has recently become the new first-line standard of care therapy of pleural mesothelioma (PM) patients, with a significant improvement of overall survival (OS) over conventional chemotherapy. The analysis by tumor histotype demonstrated greater efficacy of ICI therapy compared to standard chemotherapy in non-epithelioid (non-E) vs. epithelioid (E) PM, although some E PM patients also benefit from ICI treatment. This evidence suggests that molecular tumor features, beyond histotype, could be relevant to improve the efficacy of ICI therapy in PM. Among these, tumor DNA methylation emerges as a promising factor to explore, due to its potential role in driving the immune phenotype of cancer cells. Therefore, we utilized a panel of cultured PM cells of different histotype to provide preclinical evidence supporting the role of the tumor methylation landscape, along with its pharmacologic modulation, to prospectively improve the efficacy of ICI therapy of PM patients.\nMETHODS: The methylome profile (EPIC array) of distinct E (n = 5) and non-E (n = 9) PM cell lines was analyzed, followed by integrated analysis with their associated transcriptomic profile (Clariom S array), before and after in vitro treatment with the DNA hypomethylating agent (DHA) guadecitabine. The most variable methylated probes were selected to calculate the methylation score (CIMP index) for each cell line at baseline. Genes that were differentially expressed (DE) and differentially methylated (DM) were then selected for gene ontology analysis.\nRESULTS: The CIMP index stratified PM cell lines into two distinct classes, CIMP (hyper-methylated; n = 7) and LOW (hypo-methylated; n = 7), regardless of their E or non-E histotype. Integrated methylome and transcriptome analyses revealed that CIMP PM cells exhibited a substantial number of hyper-methylated, silenced genes, which negatively impacted their immune phenotype compared to LOW PM cells. Treatment with DHA reverted the methylation-driven immune-compromised profile of CIMP PM cells and enhanced the constitutive immune-favorable profile of LOW PM cells.\nCONCLUSION: The study highlighted the relevance of DNA methylation in shaping the constitutive immune classification of PM cells, independent of their histological subtypes. The identified role of DHA in shifting the phenotype of PM cells towards an immune-favorable state highlights its potential for evaluation in phase I/II clinical trials investigating the efficacy of epigenetic-based ICI combinations to reverse cancer immune resistance mechanisms.", "publicationTitle": "Journal of experimental & clinical cancer research: CR", "publisher": "", "place": "", "date": "2025-02-18", "volume": "44", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "58", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J Exp Clin Cancer Res", "DOI": "10.1186/s13046-025-03310-0", "citationKey": "", "url": "", "accessDate": "", "PMID": "39966970", "PMCID": "PMC11834541", "ISSN": "1756-9966", "archive": "", "archiveLocation": "", "shortTitle": "DNA methylation status classifies pleural mesothelioma cells according to their immune profile", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Cell Line, Tumor", "type": 1 }, { "tag": "DNA Methylation", "type": 1 }, { "tag": "DNA methylation", "type": 1 }, { "tag": "Epigenesis, Genetic", "type": 1 }, { "tag": "Epigenetic", "type": 1 }, { "tag": "Gene Expression Regulation, Neoplastic", "type": 1 }, { "tag": "Guadecitabine", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Immunotherapy", "type": 1 }, { "tag": "Mesothelioma", "type": 1 }, { "tag": "Mesothelioma, Malignant", "type": 1 }, { "tag": "Pleural Neoplasms", "type": 1 }, { "tag": "Pleural mesothelioma", "type": 1 }, { "tag": "Precision Medicine", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2025-07-18T13:07:41Z", "dateModified": "2025-07-18T13:07:41Z" } }, { "key": "I4XKCQW7", "version": 460, "library": { "type": "group", "id": 265492, "name": "bioinformatics-publications", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/265492/items/I4XKCQW7", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications/items/I4XKCQW7", "type": "text/html" } }, "meta": { "createdByUser": { "id": 221141, "username": "miccec", "name": "Michele Ceccarelli", "links": { "alternate": { "href": "https://www.zotero.org/miccec", "type": "text/html" } } }, "creatorSummary": "Seetharam et al.", "parsedDate": "2025-03-17", "numChildren": 1 }, "data": { "key": "I4XKCQW7", "version": 460, "itemType": "journalArticle", "title": "Activating antiviral immune responses potentiates immune checkpoint inhibition in glioblastoma models", "creators": [ { "creatorType": "author", "firstName": "Deepa", "lastName": "Seetharam" }, { "creatorType": "author", "firstName": "Jay", "lastName": "Chandar" }, { "creatorType": "author", "firstName": "Christian K.", "lastName": "Ramsoomair" }, { "creatorType": "author", "firstName": "Jelisah F.", "lastName": "Desgraves" }, { "creatorType": "author", "firstName": "Alexandra", "lastName": "Alvarado Medina" }, { "creatorType": "author", "firstName": "Anna Jane", "lastName": "Hudson" }, { "creatorType": "author", "firstName": "Ava", "lastName": "Amidei" }, { "creatorType": "author", "firstName": "Jesus R.", "lastName": "Castro" }, { "creatorType": "author", "firstName": "Vaidya", "lastName": "Govindarajan" }, { "creatorType": "author", "firstName": "Sarah", "lastName": "Wang" }, { "creatorType": "author", "firstName": "Yong", "lastName": "Zhang" }, { "creatorType": "author", "firstName": "Adam M.", "lastName": "Sonabend" }, { "creatorType": "author", "firstName": "Mynor J.", "lastName": "Mendez Valdez" }, { "creatorType": "author", "firstName": "Dragan", "lastName": "Maric" }, { "creatorType": "author", "firstName": "Vasundara", "lastName": "Govindarajan" }, { "creatorType": "author", "firstName": "Sarah R.", "lastName": "Rivas" }, { "creatorType": "author", "firstName": "Victor M.", "lastName": "Lu" }, { "creatorType": "author", "firstName": "Ritika", "lastName": "Tiwari" }, { "creatorType": "author", "firstName": "Nima", "lastName": "Sharifi" }, { "creatorType": "author", "firstName": "Emmanuel", "lastName": "Thomas" }, { "creatorType": "author", "firstName": "Marcus", "lastName": "Alexander" }, { "creatorType": "author", "firstName": "Catherine", "lastName": "DeMarino" }, { "creatorType": "author", "firstName": "Kory", "lastName": "Johnson" }, { "creatorType": "author", "firstName": "Macarena I.", "lastName": "De La Fuente" }, { "creatorType": "author", "firstName": "Ruham", "lastName": "Alshiekh Nasany" }, { "creatorType": "author", "firstName": "Teresa Maria Rosaria", "lastName": "Noviello" }, { "creatorType": "author", "firstName": "Michael E.", "lastName": "Ivan" }, { "creatorType": "author", "firstName": "Ricardo J.", "lastName": "Komotar" }, { "creatorType": "author", "firstName": "Antonio", "lastName": "Iavarone" }, { "creatorType": "author", "firstName": "Avindra", "lastName": "Nath" }, { "creatorType": "author", "firstName": "John", "lastName": "Heiss" }, { "creatorType": "author", "firstName": "Michele", "lastName": "Ceccarelli" }, { "creatorType": "author", "firstName": "Katherine B.", "lastName": "Chiappinelli" }, { "creatorType": "author", "firstName": "Maria E.", "lastName": "Figueroa" }, { "creatorType": "author", "firstName": "Defne", "lastName": "Bayik" }, { "creatorType": "author", "firstName": "Ashish H.", "lastName": "Shah" } ], "abstractNote": "Viral mimicry refers to the activation of innate antiviral immune responses due to the induction of endogenous retroelements (REs). Viral mimicry augments antitumor immune responses and sensitizes solid tumors to immunotherapy. Here, we found that targeting what we believe to be a novel, master epigenetic regulator, Zinc Finger Protein 638 (ZNF638), induces viral mimicry in glioblastoma (GBM) preclinical models and potentiates immune checkpoint inhibition (ICI). ZNF638 recruits the HUSH complex, which precipitates repressive H3K9me3 marks on endogenous REs. In GBM, ZNF638 is associated with marked locoregional immunosuppressive transcriptional signatures, reduced endogenous RE expression, and poor immune cell infiltration. Targeting ZNF638 decreased H3K9 trimethylation, increased REs, and activated intracellular dsRNA signaling cascades. Furthermore, ZNF638 knockdown upregulated antiviral immune programs and significantly increased PD-L1 immune checkpoint expression in diverse GBM models. Importantly, targeting ZNF638 sensitized mice to ICI in syngeneic murine orthotopic models through innate IFN signaling. This response was recapitulated in recurrent GBM (rGBM) samples with radiographic responses to checkpoint inhibition with widely increased expression of dsRNA, PD-L1, and perivascular CD8 cell infiltration, suggesting that dsRNA signaling may mediate response to immunotherapy. Finally, low ZNF638 expression was a biomarker of clinical response to ICI and improved survival in patients with rGBM and patients with melanoma. Our findings suggest that ZNF638 could serve as a target to potentiate immunotherapy in gliomas.", "publicationTitle": "The Journal of Clinical Investigation", "publisher": "", "place": "", "date": "2025-03-17", "volume": "135", "issue": "6", "section": "", "partNumber": "", "partTitle": "", "pages": "e183745", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J Clin Invest", "DOI": "10.1172/JCI183745", "citationKey": "", "url": "", "accessDate": "", "PMID": "40091830", "PMCID": "PMC11910234", "ISSN": "1558-8238", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Animals", "type": 1 }, { "tag": "B7-H1 Antigen", "type": 1 }, { "tag": "Brain Neoplasms", "type": 1 }, { "tag": "Brain cancer", "type": 1 }, { "tag": "Cancer immunotherapy", "type": 1 }, { "tag": "Cell Line, Tumor", "type": 1 }, { "tag": "Epigenetics", "type": 1 }, { "tag": "Female", "type": 1 }, { "tag": "Glioblastoma", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Immune Checkpoint Inhibitors", "type": 1 }, { "tag": "Immunity, Innate", "type": 1 }, { "tag": "Mice", "type": 1 }, { "tag": "Oncology", "type": 1 }, { "tag": "Virology", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2025-07-18T13:07:18Z", "dateModified": "2025-07-18T13:07:18Z" } }, { "key": "U7FQHUNK", "version": 434, "library": { "type": "group", "id": 265492, "name": "bioinformatics-publications", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/265492/items/U7FQHUNK", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications/items/U7FQHUNK", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/265492/items/I4XKCQW7", "type": "application/json" } }, "meta": { "createdByUser": { "id": 221141, "username": "miccec", "name": "Michele Ceccarelli", "links": { "alternate": { "href": "https://www.zotero.org/miccec", "type": "text/html" } } } }, "data": { "key": "U7FQHUNK", "version": 434, "parentItem": "I4XKCQW7", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2025-07-18T13:07:18Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/40091830", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2025-07-18T13:07:18Z", "dateModified": "2025-07-18T13:07:18Z" } }, { "key": "SNXSRCII", "version": 460, "library": { "type": "group", "id": 265492, "name": "bioinformatics-publications", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/265492/items/SNXSRCII", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications/items/SNXSRCII", "type": "text/html" } }, "meta": { "createdByUser": { "id": 221141, "username": "miccec", "name": "Michele Ceccarelli", "links": { "alternate": { "href": "https://www.zotero.org/miccec", "type": "text/html" } } }, "creatorSummary": "Guo et al.", "parsedDate": "2025-03-26", "numChildren": 1 }, "data": { "key": "SNXSRCII", "version": 460, "itemType": "journalArticle", "title": "A detailed guide to assessing genome assembly based on long-read sequencing data using Inspector", "creators": [ { "creatorType": "author", "firstName": "Yan", "lastName": "Guo" }, { "creatorType": "author", "firstName": "Yuwei", "lastName": "Song" }, { "creatorType": "author", "firstName": "Limin", "lastName": "Jiang" }, { "creatorType": "author", "firstName": "Yu", "lastName": "Chen" }, { "creatorType": "author", "firstName": "Michele", "lastName": "Ceccarelli" }, { "creatorType": "author", "firstName": "Min", "lastName": "Gao" }, { "creatorType": "author", "firstName": "Zechen", "lastName": "Chong" } ], "abstractNote": "Long-read sequencing technologies yield extended DNA sequences capable of spanning intricate, repetitive genome regions, thereby facilitating the generation of more precise and comprehensive genome assemblies. However, assembly errors are inevitable owing to inherent genomic complexity and limitations of sequencing technology and assembly algorithms, making assembly evaluation crucial. The genome assembly evaluation tool Inspector presents several advantages over existing long-read de novo assembly evaluation tools, including (1) both reference-free and reference-guided assembly evaluation; (2) the ability to detect both small- and large-scale structural errors; (3) the option of assembly error correction, which can improve the quality value of the original assembly; and (4) the ability to perform haplotype-resolved assembly evaluation. Inspector can provide not only basic contig and alignment statistics, but also the precise locations and types of the different structural errors. These advantages provide a robust framework for long-read assembly evaluation. In this Protocol, we showcase four procedures to demonstrate the different applications of Inspector for long-read assembly evaluation. Inspector software and additional guides can be found at https://github.com/ChongLab/Inspector_protocol .", "publicationTitle": "Nature Protocols", "publisher": "", "place": "", "date": "2025-03-26", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat Protoc", "DOI": "10.1038/s41596-025-01149-5", "citationKey": "", "url": "", "accessDate": "", "PMID": "40140633", "PMCID": "", "ISSN": "1750-2799", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2025-07-18T13:07:08Z", "dateModified": "2025-07-18T13:07:08Z" } }, { "key": "IIPLR5KA", "version": 433, "library": { "type": "group", "id": 265492, "name": "bioinformatics-publications", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/265492/items/IIPLR5KA", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications/items/IIPLR5KA", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/265492/items/SNXSRCII", "type": "application/json" } }, "meta": { "createdByUser": { "id": 221141, "username": "miccec", "name": "Michele Ceccarelli", "links": { "alternate": { "href": "https://www.zotero.org/miccec", "type": "text/html" } } } }, "data": { "key": "IIPLR5KA", "version": 433, "parentItem": "SNXSRCII", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2025-07-18T13:07:08Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/40140633", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2025-07-18T13:07:08Z", "dateModified": "2025-07-18T13:07:08Z" } }, { "key": "2CYURE64", "version": 460, "library": { "type": "group", "id": 265492, "name": "bioinformatics-publications", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/265492/items/2CYURE64", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications/items/2CYURE64", "type": "text/html" } }, "meta": { "createdByUser": { "id": 221141, "username": "miccec", "name": "Michele Ceccarelli", "links": { "alternate": { "href": "https://www.zotero.org/miccec", "type": "text/html" } } }, "creatorSummary": "Martins Rodrigues et al.", "parsedDate": "2025-05-01", "numChildren": 1 }, "data": { "key": "2CYURE64", "version": 460, "itemType": "journalArticle", "title": "Precision proteogenomics reveals pan-cancer impact of germline variants", "creators": [ { "creatorType": "author", "firstName": "Fernanda", "lastName": "Martins Rodrigues" }, { "creatorType": "author", "firstName": "Nadezhda V.", "lastName": "Terekhanova" }, { "creatorType": "author", "firstName": "Kathleen J.", "lastName": "Imbach" }, { "creatorType": "author", "firstName": "Karl R.", "lastName": "Clauser" }, { "creatorType": "author", "firstName": "Myvizhi", "lastName": "Esai Selvan" }, { "creatorType": "author", "firstName": "Isabel", "lastName": "Mendizabal" }, { "creatorType": "author", "firstName": "Yifat", "lastName": "Geffen" }, { "creatorType": "author", "firstName": "Yo", "lastName": "Akiyama" }, { "creatorType": "author", "firstName": "Myranda", "lastName": "Maynard" }, { "creatorType": "author", "firstName": "Tomer M.", "lastName": "Yaron" }, { "creatorType": "author", "firstName": "Yize", "lastName": "Li" }, { "creatorType": "author", "firstName": "Song", "lastName": "Cao" }, { "creatorType": "author", "firstName": "Erik P.", "lastName": "Storrs" }, { "creatorType": "author", "firstName": "Olivia S.", "lastName": "Gonda" }, { "creatorType": "author", "firstName": "Adrian", "lastName": "Gaite-Reguero" }, { "creatorType": "author", "firstName": "Akshay", "lastName": "Govindan" }, { "creatorType": "author", "firstName": "Emily A.", "lastName": "Kawaler" }, { "creatorType": "author", "firstName": "Matthew A.", "lastName": "Wyczalkowski" }, { "creatorType": "author", "firstName": "Robert J.", "lastName": "Klein" }, { "creatorType": "author", "firstName": "Berk", "lastName": "Turhan" }, { "creatorType": "author", "firstName": "Karsten", "lastName": "Krug" }, { "creatorType": "author", "firstName": "D. R.", "lastName": "Mani" }, { "creatorType": "author", "firstName": "Felipe da Veiga", "lastName": "Leprevost" }, { "creatorType": "author", "firstName": "Alexey I.", "lastName": "Nesvizhskii" }, { "creatorType": "author", "firstName": "Steven A.", "lastName": "Carr" }, { "creatorType": "author", "firstName": "David", "lastName": "Fenyö" }, { "creatorType": "author", "firstName": "Michael A.", "lastName": "Gillette" }, { "creatorType": "author", "firstName": "Antonio", "lastName": "Colaprico" }, { "creatorType": "author", "firstName": "Antonio", "lastName": "Iavarone" }, { "creatorType": "author", "firstName": "Ana I.", "lastName": "Robles" }, { "creatorType": "author", "firstName": "Kuan-Lin", "lastName": "Huang" }, { "creatorType": "author", "firstName": "Chandan", "lastName": "Kumar-Sinha" }, { "creatorType": "author", "firstName": "François", "lastName": "Aguet" }, { "creatorType": "author", "firstName": "Alexander J.", "lastName": "Lazar" }, { "creatorType": "author", "firstName": "Lewis C.", "lastName": "Cantley" }, { "creatorType": "author", "firstName": "Urko M.", "lastName": "Marigorta" }, { "creatorType": "author", "firstName": "Zeynep H.", "lastName": "Gümüş" }, { "creatorType": "author", "firstName": "Matthew H.", "lastName": "Bailey" }, { "creatorType": "author", "firstName": "Gad", "lastName": "Getz" }, { "creatorType": "author", "firstName": "Eduard", "lastName": "Porta-Pardo" }, { "creatorType": "author", "firstName": "Li", "lastName": "Ding" }, { "creatorType": "author", "name": "Clinical Proteomic Tumor Analysis Consortium" } ], "abstractNote": "We investigate the impact of germline variants on cancer patients' proteomes, encompassing 1,064 individuals across 10 cancer types. We introduced an approach, \"precision peptidomics,\" mapping 337,469 coding germline variants onto peptides from patients' mass spectrometry data, revealing their potential impact on post-translational modifications, protein stability, allele-specific expression, and protein structure by leveraging the relevant protein databases. We identified rare pathogenic and common germline variants in cancer genes potentially affecting proteomic features, including variants altering protein abundance and structure and variants in kinases (ERBB2 and MAP2K2) impacting phosphorylation. Precision peptidome analysis predicted destabilizing events in signal-regulatory protein alpha (SIRPA) and glial fibrillary acid protein (GFAP), relevant to immunomodulation and glioblastoma diagnostics, respectively. Genome-wide association studies identified quantitative trait loci for gene expression and protein levels, spanning millions of SNPs and thousands of proteins. Polygenic risk scores correlated with distal effects from risk variants. Our findings emphasize the contribution of germline genetics to cancer heterogeneity and high-throughput precision peptidomics.", "publicationTitle": "Cell", "publisher": "", "place": "", "date": "2025-05-01", "volume": "188", "issue": "9", "section": "", "partNumber": "", "partTitle": "", "pages": "2312-2335.e26", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Cell", "DOI": "10.1016/j.cell.2025.03.026", "citationKey": "", "url": "", "accessDate": "", "PMID": "40233739", "PMCID": "", "ISSN": "1097-4172", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "CPTAC", "type": 1 }, { "tag": "Genome-Wide Association Study", "type": 1 }, { "tag": "Germ-Line Mutation", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Neoplasms", "type": 1 }, { "tag": "Polymorphism, Single Nucleotide", "type": 1 }, { "tag": "Protein Processing, Post-Translational", "type": 1 }, { "tag": "Proteogenomics", "type": 1 }, { "tag": "Proteome", "type": 1 }, { "tag": "Quantitative Trait Loci", "type": 1 }, { "tag": "Receptor, ErbB-2", "type": 1 }, { "tag": "germline", "type": 1 }, { "tag": "pan-cancer", "type": 1 }, { "tag": "precision peptidomics", "type": 1 }, { "tag": "proteogenomics", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2025-07-18T13:06:57Z", "dateModified": "2025-07-18T13:06:57Z" } }, { "key": "9PSUQXMS", "version": 432, "library": { "type": "group", "id": 265492, "name": "bioinformatics-publications", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/265492/items/9PSUQXMS", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications/items/9PSUQXMS", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/265492/items/2CYURE64", "type": "application/json" } }, "meta": { "createdByUser": { "id": 221141, "username": "miccec", "name": "Michele Ceccarelli", "links": { "alternate": { "href": "https://www.zotero.org/miccec", "type": "text/html" } } } }, "data": { "key": "9PSUQXMS", "version": 432, "parentItem": "2CYURE64", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2025-07-18T13:06:57Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/40233739", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2025-07-18T13:06:57Z", "dateModified": "2025-07-18T13:06:57Z" } }, { "key": "KIKR9HPP", "version": 460, "library": { "type": "group", "id": 265492, "name": "bioinformatics-publications", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/265492/items/KIKR9HPP", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications/items/KIKR9HPP", "type": "text/html" } }, "meta": { "createdByUser": { "id": 221141, "username": "miccec", "name": "Michele Ceccarelli", "links": { "alternate": { "href": "https://www.zotero.org/miccec", "type": "text/html" } } }, "creatorSummary": "Kołodziejczak-Guglas et al.", "parsedDate": "2025-06-11", "numChildren": 1 }, "data": { "key": "KIKR9HPP", "version": 460, "itemType": "journalArticle", "title": "Proteomic-based stemness score measures oncogenic dedifferentiation and enables the identification of druggable targets", "creators": [ { "creatorType": "author", "firstName": "Iga", "lastName": "Kołodziejczak-Guglas" }, { "creatorType": "author", "firstName": "Renan L. S.", "lastName": "Simões" }, { "creatorType": "author", "firstName": "Emerson", "lastName": "de Souza Santos" }, { "creatorType": "author", "firstName": "Elizabeth G.", "lastName": "Demicco" }, { "creatorType": "author", "firstName": "Rossana N.", "lastName": "Lazcano Segura" }, { "creatorType": "author", "firstName": "Weiping", "lastName": "Ma" }, { "creatorType": "author", "firstName": "Pei", "lastName": "Wang" }, { "creatorType": "author", "firstName": "Yifat", "lastName": "Geffen" }, { "creatorType": "author", "firstName": "Erik", "lastName": "Storrs" }, { "creatorType": "author", "firstName": "Francesca", "lastName": "Petralia" }, { "creatorType": "author", "firstName": "Antonio", "lastName": "Colaprico" }, { "creatorType": "author", "firstName": "Felipe", "lastName": "da Veiga Leprevost" }, { "creatorType": "author", "firstName": "Pietro", "lastName": "Pugliese" }, { "creatorType": "author", "firstName": "Michele", "lastName": "Ceccarelli" }, { "creatorType": "author", "firstName": "Houtan", "lastName": "Noushmehr" }, { "creatorType": "author", "firstName": "Alexey I.", "lastName": "Nesvizhskii" }, { "creatorType": "author", "firstName": "Bożena", "lastName": "Kamińska" }, { "creatorType": "author", "firstName": "Waldemar", "lastName": "Priebe" }, { "creatorType": "author", "firstName": "Jan", "lastName": "Lubiński" }, { "creatorType": "author", "firstName": "Bing", "lastName": "Zhang" }, { "creatorType": "author", "firstName": "Alexander J.", "lastName": "Lazar" }, { "creatorType": "author", "firstName": "Paweł", "lastName": "Kurzawa" }, { "creatorType": "author", "firstName": "Mehdi", "lastName": "Mesri" }, { "creatorType": "author", "firstName": "Ana I.", "lastName": "Robles" }, { "creatorType": "author", "name": "Clinical Proteomic Tumor Analysis Consortium" }, { "creatorType": "author", "firstName": "Li", "lastName": "Ding" }, { "creatorType": "author", "firstName": "Tathiane M.", "lastName": "Malta" }, { "creatorType": "author", "firstName": "Maciej", "lastName": "Wiznerowicz" } ], "abstractNote": "Cancer progression and therapeutic resistance are closely linked to a stemness phenotype. Here, we introduce a protein-expression-based stemness index (PROTsi) to evaluate oncogenic dedifferentiation in relation to histopathology, molecular features, and clinical outcomes. Utilizing datasets from the Clinical Proteomic Tumor Analysis Consortium across 11 tumor types, we validate PROTsi's effectiveness in accurately quantifying stem-like features. Through integration of PROTsi with multi-omics, including protein post-translational modifications, we identify molecular features associated with stemness and proteins that act as active nodes within transcriptional networks, driving tumor aggressiveness. Proteins highly correlated with stemness were identified as potential drug targets, both shared and tumor specific. These stemness-associated proteins demonstrate predictive value for clinical outcomes, as confirmed by immunohistochemistry in multiple samples. The findings emphasize PROTsi's efficacy as a valuable tool for selecting predictive protein targets, a crucial step in customizing anti-cancer therapy and advancing the clinical development of cures for cancer patients.", "publicationTitle": "Cell Genomics", "publisher": "", "place": "", "date": "2025-06-11", "volume": "5", "issue": "6", "section": "", "partNumber": "", "partTitle": "", "pages": "100851", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Cell Genom", "DOI": "10.1016/j.xgen.2025.100851", "citationKey": "", "url": "", "accessDate": "", "PMID": "40250426", "PMCID": "PMC12230239", "ISSN": "2666-979X", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Biomarkers, Tumor", "type": 1 }, { "tag": "Cell Dedifferentiation", "type": 1 }, { "tag": "Gene Expression Regulation, Neoplastic", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Neoplasms", "type": 1 }, { "tag": "Neoplastic Stem Cells", "type": 1 }, { "tag": "Protein Processing, Post-Translational", "type": 1 }, { "tag": "Proteomics", "type": 1 }, { "tag": "biomarkers", "type": 1 }, { "tag": "cancer", "type": 1 }, { "tag": "drug targets", "type": 1 }, { "tag": "kinase activity", "type": 1 }, { "tag": "machine learning", "type": 1 }, { "tag": "mass spectrometry", "type": 1 }, { "tag": "multiomics", "type": 1 }, { "tag": "proteomics", "type": 1 }, { "tag": "stemness", "type": 1 }, { "tag": "tumor plasticity", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2025-07-18T13:06:47Z", "dateModified": "2025-07-18T13:06:47Z" } }, { "key": "CPS9P5RZ", "version": 431, "library": { "type": "group", "id": 265492, "name": "bioinformatics-publications", "links": { "alternate": { "href": "https://www.zotero.org/groups/bioinformatics-publications", "type": "text/html" } } }, "links": { "self": { "href": 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"creatorType": "author", "firstName": "Charalampos S.", "lastName": "Floudas" }, { "creatorType": "author", "firstName": "Siranush", "lastName": "Sarkizova" }, { "creatorType": "author", "firstName": "Michele", "lastName": "Ceccarelli" }, { "creatorType": "author", "firstName": "Wei", "lastName": "Zheng" } ], "abstractNote": "The application of messenger RNA (mRNA) technology in antigen-based immuno-oncology therapies represents a significant advancement in cancer treatment. Cancer vaccines are an effective combinatorial partner to sensitize the host immune system to the tumor and boost the efficacy of immune therapies. Selecting suitable tumor antigens is the key step to devising effective vaccinations and amplifying the immune response. Tumor neoantigens are de novo epitopes derived from somatic mutations, avoiding T-cell central tolerance of self-epitopes and inducing immune responses to tumors. The identification and prioritization of patient-specific tumor neoantigens are based on advanced computational algorithms taking advantage of the profiling with next-generation sequencing considering factors involved in human leukocyte antigen (HLA)-peptide-T-cell receptor (TCR) complex formation, including peptide presentation, HLA-peptide affinity, and TCR recognition. This review discusses the development and clinical application of mRNA vaccines in oncology, with a particular focus on recent clinical trials and the computational workflows and methodologies for identifying both shared and individual antigens. While this review centers on therapeutic mRNA vaccines targeting existing tumors, it does not cover preventative vaccines. Preclinical experimental validations are crucial in cancer vaccine development, but we emphasize the computational approaches that facilitate neoantigen selection and design, highlighting their role in advancing mRNA vaccine development. The versatility and rapid development potential of mRNA make it an ideal platform for personalized neoantigen immunotherapy. We explore various strategies for antigen target identification, including tumor-associated and tumor-specific antigens and the computational tools used to predict epitopes capable of eliciting strong immune responses. We address key design considerations for enhancing the immunogenicity and stability of mRNA vaccines, as well as emerging trends and challenges in the field. 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