97d3e2e9bd63ef99d573cfb5205eb787 300781.pdf 3ea527cbb7b2a38c6af8de86bcd23d657e2be073 300781.pdf fa2d251641380c8195b1c74f9c077b5b1ea15f968a15a1b3af3fb9d3329e28a0 300781.pdf Title: Multi-omics Characterization of Response to PD-1 Inhibitors in Advanced Melanoma Subject: Immunotherapy improves the survival of patients with advanced melanoma, 40% of whom become long-term responders. However, not all patients respond to immunotherapy. Further knowledge of the processes involved in the response and resistance to immunotherapy is still needed. In this study, clinical paraffin samples from fifty-two advanced melanoma patients treated with anti-PD-1 inhibitors were assessed via high-throughput proteomics and RNA-seq. The obtained proteomics and transcriptomics data were analyzed using multi-omics network analyses based on probabilistic graphical models to identify those biological processes involved in the response to immunotherapy. Additionally, proteins related to overall survival were studied. The activity of the node formed by the proteins involved in protein processing in the endoplasmic reticulum and antigen presentation machinery was higher in responders compared to non-responders; the activity of the immune and inflammatory response node was also higher in those with complete or partial responses. A predictor for overall survival based on two proteins (AMBP and PDSM5) was defined. In summary, the response to anti-PD-1 therapy in advanced melanoma is related to protein processing in the endoplasmic reticulum, and also to genes involved in the immune and inflammatory responses. Finally, a two-protein predictor can define survival in advanced disease. The molecular characterization of the mechanisms involved in the response and resistance to immunotherapy in melanoma leads the way to establishing therapeutic alternatives for patients who will not respond to this treatment. Keywords: melanoma; immunotherapy response; multi-omics; inflammatory response; protein processing in the endoplasmic reticulum Author: Lucía Trilla-Fuertes, Angelo Gámez-Pozo, Guillermo Prado-Vázquez, Rocío López-Vacas, Virtudes Soriano, Fernando Garicano, M. José Lecumberri, María Rodríguez de la Borbolla, Margarita Majem, Elisabeth Pérez-Ruiz, María González-Cao, Juana Oramas, Alejandra Magdaleno, Joaquín Fra, Alfonso Martín-Carnicero, Mónica Corral, Teresa Puértolas, Ricardo Ramos-Ruiz, Antje Dittmann, Paolo Nanni, Juan Ángel Fresno Vara and Enrique Espinosa Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Sun Sep 3 11:07:14 2023 CEST ModDate: Sun Sep 3 11:11:54 2023 CEST Custom Metadata: no Metadata Stream: no Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 13 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 1574142 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- EIFDAO+VnURWPalladioL Type 1 Custom yes yes no 10 0 GSECNP+URWPalladioL-Bold Type 1 Custom yes yes no 15 0 OADDOA+URWPalladioL-Roma Type 1 Custom yes yes no 20 0 XBUFXX+URWPalladioL-Ital Type 1 Custom yes yes no 24 0 FFAYKL+VnURWPalladioL-Bold Type 1 Custom yes yes no 28 0 LCJEVJ+TimesNewRomanPS-BoldItalicMT Type 1C WinAnsi yes yes no 47 0 SOSCBV+CMSY10 Type 1 Builtin yes yes no 72 0 VVSYYB+EURM10 Type 1 Builtin yes yes no 76 0 COIBLP+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 94 0 COIBMB+PalatinoLinotype TrueType WinAnsi yes yes no 97 0 COIBMD+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 100 0 COIDBM+PalatinoLinotype TrueType MacRoman yes yes no 103 0 COIBLP+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 114 0 COIBMA+PalatinoLinotype CID TrueType Identity-H yes yes yes 117 0 COIBMB+PalatinoLinotype TrueType WinAnsi yes yes no 123 0 COIBMD+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 126 0 COIDBM+PalatinoLinotype TrueType MacRoman yes yes no 129 0 COIBLP+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 139 0 COIBMB+PalatinoLinotype TrueType WinAnsi yes yes no 142 0 COIBMD+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 145 0 COIDBM+PalatinoLinotype TrueType MacRoman yes yes no 148 0 COIGLH+Arial CID TrueType Identity-H yes yes yes 151 0 COIBLP+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 229 0 COIBMB+PalatinoLinotype TrueType WinAnsi yes yes no 232 0 COIBMD+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 235 0 COIDBM+PalatinoLinotype TrueType MacRoman yes yes no 238 0 COIGLH+Arial CID TrueType Identity-H yes yes yes 241 0 WBVKDJ+URWPalladioL-BoldItal Type 1 Custom yes yes no 319 0 COIHPB+PalatinoLinotype,BoldItalic TrueType WinAnsi yes yes no 364 0 COIBLP+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 367 0 COIBMB+PalatinoLinotype TrueType WinAnsi yes yes no 370 0 COIBMD+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 373 0 COIDBM+PalatinoLinotype TrueType MacRoman yes yes no 376 0 Jhove (Rel. 1.28.0, 2023-05-18) Date: 2024-09-18 02:54:29 CEST RepresentationInformation: 300781.pdf ReportingModule: PDF-hul, Rel. 1.12.4 (2023-03-16) LastModified: 2024-09-17 13:59:22 CEST Size: 1574142 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 602 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Destination: section.1 Item: Title: Materials and Methods Destination: section.2 Children: Item: Title: Spanish Melanoma Group Cohort Destination: subsection.2.1 Item: Title: Protein Isolation and Digestion Destination: subsection.2.2 Item: Title: Proteomics Experiments Destination: subsection.2.3 Item: Title: Proteomics Data Preprocessing Destination: subsection.2.4 Item: Title: RNA Isolation Destination: subsection.2.5 Item: Title: RNA Capture and Sequencing Destination: subsection.2.6 Item: Title: Preprocessing of RNA Capture Data Destination: subsection.2.7 Item: Title: Multi-Omics Analysis Using Probabilistic Graphical Models Destination: subsection.2.8 Item: Title: Search of Functional Structure Destination: subsection.2.9 Item: Title: Functional Node Activity Calculation Destination: subsection.2.10 Item: Title: Statistical Analyses Destination: subsection.2.11 Item: Title: Results Destination: section.3 Children: Item: Title: GEM Cohort Destination: subsection.3.1 Item: Title: High-Throughput Proteomics Experiments Destination: subsection.3.2 Item: Title: RNA Capture Experiments Destination: subsection.3.3 Item: Title: Multi-Omics Systems Biology Analyses Destination: subsection.3.4 Item: Title: Proteomics Analyses Destination: subsection.3.5 Item: Title: Discussion Destination: section.4 Item: Title: Conclusions Destination: section.5 Item: Title: References Destination: section.A. Info: Title: Multi-omics Characterization of Response to PD-1 Inhibitors in Advanced Melanoma Author: Lucía Trilla-Fuertes, Angelo Gámez-Pozo, Guillermo Prado-Vázquez, Rocío López-Vacas, Virtudes Soriano, Fernando Garicano, M. José Lecumberri, María Rodríguez de la Borbolla, Margarita Majem, Elisabeth Pérez-Ruiz, María González-Cao, Juana Oramas, Alejandra Magdaleno, Joaquín Fra, Alfonso Martín-Carnicero, Mónica Corral, Teresa Puértolas, Ricardo Ramos-Ruiz, Antje Dittmann, Paolo Nanni, Juan Ángel Fresno Vara and Enrique Espinosa Subject: Immunotherapy improves the survival of patients with advanced melanoma, 40% of whom become long-term responders. However, not all patients respond to immunotherapy. Further knowledge of the processes involved in the response and resistance to immunotherapy is still needed. In this study, clinical paraffin samples from fifty-two advanced melanoma patients treated with anti-PD-1 inhibitors were assessed via high-throughput proteomics and RNA-seq. The obtained proteomics and transcriptomics data were analyzed using multi-omics network analyses based on probabilistic graphical models to identify those biological processes involved in the response to immunotherapy. Additionally, proteins related to overall survival were studied. The activity of the node formed by the proteins involved in protein processing in the endoplasmic reticulum and antigen presentation machinery was higher in responders compared to non-responders; the activity of the immune and inflammatory response node was also higher in those with complete or partial responses. A predictor for overall survival based on two proteins (AMBP and PDSM5) was defined. In summary, the response to anti-PD-1 therapy in advanced melanoma is related to protein processing in the endoplasmic reticulum, and also to genes involved in the immune and inflammatory responses. Finally, a two-protein predictor can define survival in advanced disease. The molecular characterization of the mechanisms involved in the response and resistance to immunotherapy in melanoma leads the way to establishing therapeutic alternatives for patients who will not respond to this treatment. 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