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Kuras M, Betancourt LH, Hong R, Szadai L, Rodriguez J, Horvatovich P, Pla I, Eriksson J, Szeitz B, Deszcz B, Welinder C, Sugihara Y, Ekedahl H, Baldetorp B, Ingvar C, Lundgren L, Lindberg H, Oskolas H, Horvath Z, Rezeli M, Gil J, Appelqvist R, Kemény LV, Malm J, Sanchez A, Szasz AM, Pawłowski K, Wieslander E, Fenyö D, Nemeth IB, Marko-Varga G. Proteogenomic Profiling of Treatment-Naïve Metastatic Malignant Melanoma. Cancers (Basel) 2025; 17:832. [PMID: 40075679 PMCID: PMC11899103 DOI: 10.3390/cancers17050832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2025] [Accepted: 02/12/2025] [Indexed: 03/14/2025] Open
Abstract
BACKGROUND Melanoma is a highly heterogeneous disease, and a deeper molecular classification is essential for improving patient stratification and treatment approaches. Here, we describe the histopathology-driven proteogenomic landscape of 142 treatment-naïve metastatic melanoma samples to uncover molecular subtypes and clinically relevant biomarkers. METHODS We performed an integrative proteogenomic analysis to identify proteomic subtypes, assess the impact of BRAF V600 mutations, and study the molecular profiles and cellular composition of the tumor microenvironment. Clinical and histopathological data were used to support findings related to tissue morphology, disease progression, and patient outcomes. RESULTS Our analysis revealed five distinct proteomic subtypes that integrate immune and stromal microenvironment components and correlate with clinical and histopathological parameters. We demonstrated that BRAF V600-mutated melanomas exhibit biological heterogeneity, where an oncogene-induced senescence-like phenotype is associated with improved survival. This led to a proposed mortality risk-based stratification that may contribute to more personalized treatment strategies. Furthermore, tumor microenvironment composition strongly correlated with disease progression and patient outcomes, highlighting a histopathological connective tissue-to-tumor ratio assessment as a potential decision-making tool. We identified a melanoma-associated SAAV signature linked to extracellular matrix remodeling and SAAV-derived neoantigens as potential targets for anti-tumor immune responses. CONCLUSIONS This study provides a comprehensive stratification of metastatic melanoma, integrating proteogenomic insights with histopathological features. The findings may aid in the development of tailored diagnostic and therapeutic strategies, improving patient management and outcomes.
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Affiliation(s)
- Magdalena Kuras
- Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 214 28 Malmö, Sweden; (M.K.); (J.G.); (J.M.); (A.S.); (K.P.)
- Department of Biomedical Engineering, Lund University, 221 00 Lund, Sweden; (P.H.); (I.P.); (J.E.); (Y.S.); (H.L.); (M.R.); (R.A.); (G.M.-V.)
| | - Lazaro Hiram Betancourt
- Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 214 28 Malmö, Sweden; (M.K.); (J.G.); (J.M.); (A.S.); (K.P.)
- Department of Clinical Sciences Lund, Division of Oncology, Lund University, 221 00 Lund, Sweden; (C.W.); (B.B.); (L.L.); (H.O.)
| | - Runyu Hong
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; (R.H.); (D.F.)
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Leticia Szadai
- Department of Dermatology and Allergology, University of Szeged, 6720 Szeged, Hungary; (L.S.); (I.B.N.)
| | - Jimmy Rodriguez
- Department of Biochemistry and Biophysics, Karolinska Institute, 171 77 Stockholm, Sweden;
| | - Peter Horvatovich
- Department of Biomedical Engineering, Lund University, 221 00 Lund, Sweden; (P.H.); (I.P.); (J.E.); (Y.S.); (H.L.); (M.R.); (R.A.); (G.M.-V.)
- Department of Analytical Biochemistry, Faculty of Science and Engineering, University of Groningen, 9712 CP Groningen, The Netherlands
| | - Indira Pla
- Department of Biomedical Engineering, Lund University, 221 00 Lund, Sweden; (P.H.); (I.P.); (J.E.); (Y.S.); (H.L.); (M.R.); (R.A.); (G.M.-V.)
| | - Jonatan Eriksson
- Department of Biomedical Engineering, Lund University, 221 00 Lund, Sweden; (P.H.); (I.P.); (J.E.); (Y.S.); (H.L.); (M.R.); (R.A.); (G.M.-V.)
| | - Beáta Szeitz
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, 1085 Budapest, Hungary
| | - Bartłomiej Deszcz
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland;
| | - Charlotte Welinder
- Department of Clinical Sciences Lund, Division of Oncology, Lund University, 221 00 Lund, Sweden; (C.W.); (B.B.); (L.L.); (H.O.)
| | - Yutaka Sugihara
- Department of Biomedical Engineering, Lund University, 221 00 Lund, Sweden; (P.H.); (I.P.); (J.E.); (Y.S.); (H.L.); (M.R.); (R.A.); (G.M.-V.)
| | - Henrik Ekedahl
- Department of Clinical Sciences Lund, Division of Oncology, Lund University, 221 00 Lund, Sweden; (C.W.); (B.B.); (L.L.); (H.O.)
- SUS University Hospital Lund, 222 42 Lund, Sweden;
| | - Bo Baldetorp
- Department of Clinical Sciences Lund, Division of Oncology, Lund University, 221 00 Lund, Sweden; (C.W.); (B.B.); (L.L.); (H.O.)
| | - Christian Ingvar
- SUS University Hospital Lund, 222 42 Lund, Sweden;
- Department of Surgery, Clinical Sciences, Lund University, SUS, 221 00 Lund, Sweden
| | - Lotta Lundgren
- Department of Clinical Sciences Lund, Division of Oncology, Lund University, 221 00 Lund, Sweden; (C.W.); (B.B.); (L.L.); (H.O.)
- SUS University Hospital Lund, 222 42 Lund, Sweden;
| | - Henrik Lindberg
- Department of Biomedical Engineering, Lund University, 221 00 Lund, Sweden; (P.H.); (I.P.); (J.E.); (Y.S.); (H.L.); (M.R.); (R.A.); (G.M.-V.)
| | - Henriett Oskolas
- Department of Clinical Sciences Lund, Division of Oncology, Lund University, 221 00 Lund, Sweden; (C.W.); (B.B.); (L.L.); (H.O.)
| | - Zsolt Horvath
- Department of Biomedical Engineering, Lund University, 221 00 Lund, Sweden; (P.H.); (I.P.); (J.E.); (Y.S.); (H.L.); (M.R.); (R.A.); (G.M.-V.)
| | - Melinda Rezeli
- Department of Biomedical Engineering, Lund University, 221 00 Lund, Sweden; (P.H.); (I.P.); (J.E.); (Y.S.); (H.L.); (M.R.); (R.A.); (G.M.-V.)
| | - Jeovanis Gil
- Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 214 28 Malmö, Sweden; (M.K.); (J.G.); (J.M.); (A.S.); (K.P.)
| | - Roger Appelqvist
- Department of Biomedical Engineering, Lund University, 221 00 Lund, Sweden; (P.H.); (I.P.); (J.E.); (Y.S.); (H.L.); (M.R.); (R.A.); (G.M.-V.)
| | - Lajos V. Kemény
- HCEMM-SU Translational Dermatology Research Group, Semmelweis University, 1085 Budapest, Hungary;
- Department of Dermatology, Venereology and Dermatooncology, Faculty of Medicine, Semmelweis University, 1085 Budapest, Hungary
- Department of Physiology, Faculty of Medicine, Semmelweis University, 1085 Budapest, Hungary
- MTA-SE Lendület “Momentum” Dermatology Research Group, Hungarian Academy of Sciences and Semmelweis University, 1085 Budapest, Hungary
| | - Johan Malm
- Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 214 28 Malmö, Sweden; (M.K.); (J.G.); (J.M.); (A.S.); (K.P.)
| | - Aniel Sanchez
- Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 214 28 Malmö, Sweden; (M.K.); (J.G.); (J.M.); (A.S.); (K.P.)
| | | | - Krzysztof Pawłowski
- Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 214 28 Malmö, Sweden; (M.K.); (J.G.); (J.M.); (A.S.); (K.P.)
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland;
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Elisabet Wieslander
- Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 214 28 Malmö, Sweden; (M.K.); (J.G.); (J.M.); (A.S.); (K.P.)
| | - David Fenyö
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; (R.H.); (D.F.)
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Istvan Balazs Nemeth
- Department of Dermatology and Allergology, University of Szeged, 6720 Szeged, Hungary; (L.S.); (I.B.N.)
| | - György Marko-Varga
- Department of Biomedical Engineering, Lund University, 221 00 Lund, Sweden; (P.H.); (I.P.); (J.E.); (Y.S.); (H.L.); (M.R.); (R.A.); (G.M.-V.)
- Chemical Genomics Global Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
- 1st Department of Surgery, Tokyo Medical University, Tokyo 160-8402, Japan
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Ficarro SB, Kothiwal D, Bae HJ, Tavares I, Giordano G, Buratowski S, Marto JA. Leveraging HILIC/ERLIC Separations for Online Nanoscale LC-MS/MS Analysis of Phosphopeptide Isoforms from RNA Polymerase II C-terminal Domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.08.617299. [PMID: 39416017 PMCID: PMC11482835 DOI: 10.1101/2024.10.08.617299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
The eukaryotic RNA polymerase II (Pol II) multi-protein complex transcribes mRNA and coordinates several steps of co-transcriptional mRNA processing and chromatin modification. The largest Pol II subunit, Rpb1, has a C-terminal domain (CTD) comprising dozens of repeated heptad sequences (Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7), each containing five phospho-accepting amino acids. The CTD heptads are dynamically phosphorylated, creating specific patterns correlated with steps of transcription initiation, elongation, and termination. This CTD phosphorylation 'code' choreographs dynamic recruitment of important co-regulatory proteins during gene transcription. Genetic tools were used to engineer protease cleavage sites across the CTD (msCTD), creating tryptic peptides with unique sequences amenable to mass spectrometry analysis. However, phosphorylation isoforms within each msCTD sequence are difficult to resolve by standard reversed phase chromatography typically used for LC-MS/MS applications. Here, we use a panel of synthetic CTD phosphopeptides to explore the potential of hydrophilic interaction and electrostatic repulsion hydrophilic interaction (HILIC and ERLIC) chromatography as alternatives to reversed phase separation for CTD phosphopeptide analysis. Our results demonstrate that ERLIC provides improved performance for separation of singly- and doubly-phosphorylated CTD peptides for sequence analysis by LC-MS/MS. Analysis of native yeast msCTD confirms that phosphorylation on Ser5 and Ser2 represents the major endogenous phosphoisoforms. We expect this methodology will be especially useful in the investigation of pathways where multiple protein phosphorylation events converge in close proximity.
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Sanchez A, Kuras M, Murillo JR, Pla I, Pawlowski K, Szasz AM, Gil J, Nogueira FCS, Perez-Riverol Y, Eriksson J, Appelqvist R, Miliotis T, Kim Y, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Ekedahl H, Horvatovich P, Sugihara Y, Welinder C, Wieslander E, Kwon HJ, Domont GB, Malm J, Rezeli M, Betancourt LH, Marko-Varga G. Novel functional proteins coded by the human genome discovered in metastases of melanoma patients. Cell Biol Toxicol 2020; 36:261-272. [PMID: 31599373 PMCID: PMC7320927 DOI: 10.1007/s10565-019-09494-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/02/2019] [Indexed: 12/18/2022]
Abstract
In the advanced stages, malignant melanoma (MM) has a very poor prognosis. Due to tremendous efforts in cancer research over the last 10 years, and the introduction of novel therapies such as targeted therapies and immunomodulators, the rather dark horizon of the median survival has dramatically changed from under 1 year to several years. With the advent of proteomics, deep-mining studies can reach low-abundant expression levels. The complexity of the proteome, however, still surpasses the dynamic range capabilities of current analytical techniques. Consequently, many predicted protein products with potential biological functions have not yet been verified in experimental proteomic data. This category of 'missing proteins' (MP) is comprised of all proteins that have been predicted but are currently unverified. As part of the initiative launched in 2016 in the USA, the European Cancer Moonshot Center has performed numerous deep proteomics analyses on samples from MM patients. In this study, nine MPs were clearly identified by mass spectrometry in MM metastases. Some MPs significantly correlated with proteins that possess identical PFAM structural domains; and other MPs were significantly associated with cancer-related proteins. This is the first study to our knowledge, where unknown and novel proteins have been annotated in metastatic melanoma tumour tissue.
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Affiliation(s)
- Aniel Sanchez
- Section for Clinical Chemistry, Department of Translational Medicine, Skåne University Hospital Malmö, Lund University, 205 02, Malmö, Sweden.
| | - Magdalena Kuras
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Jimmy Rodriguez Murillo
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Indira Pla
- Section for Clinical Chemistry, Department of Translational Medicine, Skåne University Hospital Malmö, Lund University, 205 02, Malmö, Sweden
| | - Krzysztof Pawlowski
- Section for Clinical Chemistry, Department of Translational Medicine, Skåne University Hospital Malmö, Lund University, 205 02, Malmö, Sweden
- Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - A Marcell Szasz
- Cancer Center, Semmelweis University, Budapest, 1083, Hungary
| | - Jeovanis Gil
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Fábio C S Nogueira
- Proteomics Unit, Department of Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Proteomics, LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD Hinxton, Cambridge, UK
| | - Jonatan Eriksson
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Roger Appelqvist
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | | | - Yonghyo Kim
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Bo Baldetorp
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Christian Ingvar
- Department of Surgery, Clinical Sciences, Skåne University Hospital, Lund University, Lund, Sweden
| | - Håkan Olsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Lotta Lundgren
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Henrik Ekedahl
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Yutaka Sugihara
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Charlotte Welinder
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Elisabet Wieslander
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Ho Jeong Kwon
- Department of Biotechnology, Yonsei University, Seoul, South Korea
| | - Gilberto B Domont
- Proteomics Unit, Department of Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Johan Malm
- Section for Clinical Chemistry, Department of Translational Medicine, Skåne University Hospital Malmö, Lund University, 205 02, Malmö, Sweden
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Lazaro Hiram Betancourt
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden.
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
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