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Mlynska A, Gibavičienė J, Kutanovaitė O, Senkus L, Mažeikaitė J, Kerševičiūtė I, Maskoliūnaitė V, Rupeikaitė N, Sabaliauskaitė R, Gaiževska J, Suveizdė K, Kraśko JA, Dobrovolskienė N, Paberalė E, Žymantaitė E, Pašukonienė V. Defining Melanoma Immune Biomarkers-Desert, Excluded, and Inflamed Subtypes-Using a Gene Expression Classifier Reflecting Intratumoral Immune Response and Stromal Patterns. Biomolecules 2024; 14:171. [PMID: 38397409 PMCID: PMC10886750 DOI: 10.3390/biom14020171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 01/26/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
The spatial distribution of tumor infiltrating lymphocytes (TILs) defines several histologically and clinically distinct immune subtypes-desert (no TILs), excluded (TILs in stroma), and inflamed (TILs in tumor parenchyma). To date, robust classification of immune subtypes still requires deeper experimental evidence across various cancer types. Here, we aimed to investigate, define, and validate the immune subtypes in melanoma by coupling transcriptional and histological assessments of the lymphocyte distribution in tumor parenchyma and stroma. We used the transcriptomic data from The Cancer Genome Atlas melanoma dataset to screen for the desert, excluded, and inflamed immune subtypes. We defined subtype-specific genes and used them to construct a subtype assignment algorithm. We validated the two-step algorithm in the qPCR data of real-world melanoma tumors with histologically defined immune subtypes. The accuracy of a classifier encompassing expression data of seven genes (immune response-related: CD2, CD53, IRF1, and CD8B; and stroma-related: COL5A2, TNFAIP6, and INHBA) in a validation cohort reached 79%. Our findings suggest that melanoma tumors can be classified into transcriptionally and histologically distinct desert, excluded, and inflamed subtypes. Gene expression-based algorithms can assist physicians and pathologists as biomarkers in the rapid assessment of a tumor immune microenvironment while serving as a tool for clinical decision making.
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Affiliation(s)
- Agata Mlynska
- National Cancer Institute, LT-08406 Vilnius, Lithuania; (J.G.); (O.K.); (R.S.); (N.D.); (E.P.); (V.P.)
- Faculty of Fundamental Sciences, Vilnius Gediminas Technical University, LT-10223 Vilnius, Lithuania
| | - Jolita Gibavičienė
- National Cancer Institute, LT-08406 Vilnius, Lithuania; (J.G.); (O.K.); (R.S.); (N.D.); (E.P.); (V.P.)
| | - Otilija Kutanovaitė
- National Cancer Institute, LT-08406 Vilnius, Lithuania; (J.G.); (O.K.); (R.S.); (N.D.); (E.P.); (V.P.)
| | - Linas Senkus
- National Cancer Institute, LT-08406 Vilnius, Lithuania; (J.G.); (O.K.); (R.S.); (N.D.); (E.P.); (V.P.)
| | - Julija Mažeikaitė
- National Cancer Institute, LT-08406 Vilnius, Lithuania; (J.G.); (O.K.); (R.S.); (N.D.); (E.P.); (V.P.)
| | - Ieva Kerševičiūtė
- Life Sciences Center, Vilnius University, LT-01513 Vilnius, Lithuania (N.R.)
| | - Vygantė Maskoliūnaitė
- Life Sciences Center, Vilnius University, LT-01513 Vilnius, Lithuania (N.R.)
- National Center of Pathology, LT-08406 Vilnius, Lithuania
| | - Neda Rupeikaitė
- Life Sciences Center, Vilnius University, LT-01513 Vilnius, Lithuania (N.R.)
| | - Rasa Sabaliauskaitė
- National Cancer Institute, LT-08406 Vilnius, Lithuania; (J.G.); (O.K.); (R.S.); (N.D.); (E.P.); (V.P.)
| | - Justina Gaiževska
- National Cancer Institute, LT-08406 Vilnius, Lithuania; (J.G.); (O.K.); (R.S.); (N.D.); (E.P.); (V.P.)
| | - Karolina Suveizdė
- National Cancer Institute, LT-08406 Vilnius, Lithuania; (J.G.); (O.K.); (R.S.); (N.D.); (E.P.); (V.P.)
| | - Jan Aleksander Kraśko
- National Cancer Institute, LT-08406 Vilnius, Lithuania; (J.G.); (O.K.); (R.S.); (N.D.); (E.P.); (V.P.)
- Faculty of Fundamental Sciences, Vilnius Gediminas Technical University, LT-10223 Vilnius, Lithuania
| | - Neringa Dobrovolskienė
- National Cancer Institute, LT-08406 Vilnius, Lithuania; (J.G.); (O.K.); (R.S.); (N.D.); (E.P.); (V.P.)
| | - Emilija Paberalė
- National Cancer Institute, LT-08406 Vilnius, Lithuania; (J.G.); (O.K.); (R.S.); (N.D.); (E.P.); (V.P.)
- Life Sciences Center, Vilnius University, LT-01513 Vilnius, Lithuania (N.R.)
| | - Eglė Žymantaitė
- National Cancer Institute, LT-08406 Vilnius, Lithuania; (J.G.); (O.K.); (R.S.); (N.D.); (E.P.); (V.P.)
| | - Vita Pašukonienė
- National Cancer Institute, LT-08406 Vilnius, Lithuania; (J.G.); (O.K.); (R.S.); (N.D.); (E.P.); (V.P.)
- Faculty of Fundamental Sciences, Vilnius Gediminas Technical University, LT-10223 Vilnius, Lithuania
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