Deep proteomic analysis on biobanked paraffine-archived melanoma with prognostic/predictive biomarker read-out
Open accessAbstract
The discovery of novel protein biomarkers in melanoma is crucial. Our introduction of formalin-fixed paraffin-embedded (FFPE) tumor protocol provides new opportunities to understand the progression of melanoma and open the possibility to screen thousands of FFPE samples deposited in tumor biobanks and available at hospital pathology departments. In our retrospective biobank pilot study, 90 FFPE samples from 77 patients were processed. Protein quantitation was performed by high-resolution mass spectrometry and validated by histopathologic analysis. The global protein expression formed six sample clusters. Proteins such as TRAF6 and ARMC10 were upregulated in clusters with enrichment for shorter survival, and proteins such as AIFI1 were upregulated in clusters with enrichment for longer survival. The cohort's heterogeneity was addressed by comparing primary and metastasis samples, as well comparing clinical stages. Within immunotherapy and targeted therapy subgroups, the upregulation of the VEGFA-VEGFR2 pathway, RNA splicing, increased activity of immune cells, extracellular matrix, and metabolic pathways were positively associated with patient outcome. To summarize, we were able to (i) link global protein expression profiles to survival, and they proved to be an independent prognostic indicator, as well as (ii) identify proteins that are potential predictors of a patient's response to immunotherapy and targeted therapy, suggesting new opportunities for precision medicine developments.
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Significance and utility of reference values in occupational medicine
Apostoli, P., Minoia, C., & Hamilton, E. I. (1998) · The Science of The Total Environment · doi:10.1016/s0048-9697(97)00297-0 · Cited by 21 · see citing works
Fejza, A., Polano, M., Camicia, L., Poletto, E., Carobolante, G., Toffoli, G., Mongiat, M., & Andreuzzi, E. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22147511 · Cited by 19 · see citing works
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Regulation of RANKL‐induced osteoclastogenesis by RING finger protein RNF114
Lin, B., Qi, K., Leaman, D. W., Goel, V. K., & Agarwal, A. (2017) · Journal of Orthopaedic Research® · doi:10.1002/jor.23654 · Cited by 15 · see citing works
Patterson, A. R., Bolcas, P. E., Lampe, K., Cantrell, R., Ruff, B. P., Lewkowich, I. P., Hogan, S. P., Janssen, E. M., Bleesing, J., Hershey, G. K. K., et al. (2018) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2018.10.018 · Cited by 14 · see citing works
Velasquez, E., Szadai, L., Zhou, Q., Kim, Y., Pla, I., Sanchez, A., Appelqvist, R., Oskolas, H., Marko‐Varga, M., Lee, B., et al. (2021) · Clinical and Translational Medicine · doi:10.1002/ctm2.466 · Cited by 13 · see citing works
Self-citationHan, W., Wu, Y., Zhao, X., Gong, Z.-H., & Shen, G. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.715173 · Cited by 13 · see citing works
Computational challenges in biomarker discovery from high-throughput proteomic data
Čuklina, J. (2018) · Repository for Publications and Research Data (ETH Zurich) · doi:10.3929/ethz-b-000307772 · Cited by 11 · see citing works
Gimap5 Inhibits Lung Cancer Growth by Interacting With M6PR
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The oncogenic role of NKAP in the growth and invasion of colon cancer cells
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Liu, J., Zhang, M.-Y., Kan, Y., Wang, W., Liu, J., Gong, J.-H., & Yang, J.-G. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.622793 · Cited by 5 · see citing works
de Melo, F. H. M., Gonçalves, D. A., de Sousa, R. X., Icimoto, M. Y., Fernandes, D. C., Laurindo, F. R. M., & Jasiulionis, M. G. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22179556 · Cited by 5 · see citing works
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Flagged first, then by citations
1 of the 105 references couldn’t be matched to a known paper.
Research works printed but not linked: 1
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Predicting immune checkpoint therapy response in three independent metastatic melanoma cohorts
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Li, T., Qin, X., Wang, L., Qin, C., Zhao, B., Cao, H., Yang, X., Wang, Y., Li, Z., Zhou, X., et al. (2023) · Heliyon · doi:10.1016/j.heliyon.2023.e20464 · Cited by 2 · see citing works
Fernández-Coto, D. L., Ayala, M., Alonso-Bastida, R., Palmqvist, A., García, M. F., Balderas-López, S. F., Oskolás, H., Christersson, L., Fülöp, L., Szigeti, B., et al. (2026) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2026.101620 · Cited by 2 · see citing works
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The influence of molecular biology in the dermatopathology
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Fusco, F., Weigel, J., Schliemann, M., Schneider, A., Zhou, Y., Persa, O., Posch, C., Krackhardt, A. M., Förg, S., Schott, C., et al. (2026) · Modern Pathology · doi:10.1016/j.modpat.2026.100995
Guedes, J., Woldmar, N., Baltás, E., Kriston, A., Migh, E., Kovács, F., Oskolás, H., Marko-Varga, M., Appelqvist, R., Wieslander, E., et al. (2026) · npj Precision Oncology · doi:10.1038/s41698-026-01569-w · Cited by 1 · see citing works
Self-citationSpatial Proteomics as a Potential Decision‐Support Layer for Early Melanoma: A Narrative Review
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Self-citation
- Authors
- Szadai, L., Velasquez, E., Szeitz, B., Almeida, N. P. D., Domont, G., Betancourt, L. H., Gil, J., Marko-Varga, M., Oskolas, H., Jánosi, Á. J., Boyano-Adánez, M. D. C., Kemény, L., Baldetorp, B., Malm, J., Horvatovich, P., Szász, A. M., Németh, I. B., & Marko-Varga, G.
- Affiliations
- Department of Dermatology and Allergology, University of Szeged, 6720 Szeged, Hungary
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden
- Semmelweis University (HU)
- Universidade Federal do Rio de Janeiro (BR)
- Lund University (SE)
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden
- University of Szeged (HU)
- Department of Systems Biology, Faculty of Medicine and Health Sciences, University of Alcala de Henares, 28801 Alcalá de Henares, Madrid, Spain
- University of Groningen (NL)
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
- ORCID
- Venue
- Cancers
- Publisher
- MDPI AG
- Published
- 2021-12-03
- Volume
- 13
- Issue
- 23
- Pages
- 6105
- ISSN
- 2072-6694 (ISSN-L)
- PMC
- PMC8657028
- OpenAlex
- W4200329644
- Cited by
- 18
- References
- 105
- Citations by year
- 2026: 5 · 2025: 6 · 2024: 2 · 2023: 4 · 2022: 1
- FWCI
- 0.64
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Cancers (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Lund University Publications (Lund University) (submittedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, cc-by)
- Funders
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
- Lunds Universitet
- Conselho Nacional de Desenvolvimento Científico e Tecnológico
- Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro
- Universidade Federal do Rio de Janeiro
- Innovációs és Technológiai Minisztérium
- Cancer Moonshot
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Health Sciences › Medicine › Oncology › Cutaneous Melanoma Detection and Management
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Melanoma and MAPK Pathways
- Keywords
- melanoma, protein biomarkers, prognostic factors, predictive biomarkers, formalin-fixed paraffin-embedded tissue, survival, TRAF6, RNA splicing, immune cell activity, extracellular matrix, metabolic pathways, immunotherapy response, targeted therapy response, precision medicine, metastasis, clinical stage
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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