Molecular profiling of driver events in metastatic uveal melanoma

Joakim Karlsson; Lisa M. Nilsson; Suman Mitra; Samuel Alsén; Ganesh Vilas Shelke; Vasu R. Sah; Elin M.V. Forsberg; Ulrika Stierner; Charlotta All-Eriksson; Berglind Einarsdottir; Henrik Jespersen; Lars Ny; Per Lindnér; Erik Larsson; Roger Olofsson Bagge; Jonas A. Nilsson

doi:10.1038/s41467-020-15606-0

Molecular profiling of driver events in metastatic uveal melanoma

Joakim Karlsson, Lisa M. Nilsson, Suman Mitra, Samuel Alsén, Ganesh Vilas Shelke, Vasu R. Sah, Elin M.V. Forsberg, Ulrika Stierner, Charlotta All-Eriksson, Berglind Einarsdottir, Henrik Jespersen, Lars Ny, Per Lindnér, Erik Larsson, Roger Olofsson Bagge, Jonas A. Nilsson^*

^*Corresponding author for this work

University of Iceland

Research output: Contribution to journal › Article › peer-review

21 Citations (Scopus)

Abstract

Metastatic uveal melanoma is less well understood than its primary counterpart, has a distinct biology compared to skin melanoma, and lacks effective treatments. Here we genomically profile metastatic tumors and infiltrating lymphocytes. BAP1 alterations are overrepresented and found in 29/32 of cases. Reintroducing a functional BAP1 allele into a deficient patient-derived cell line, reveals a broad shift towards a transcriptomic subtype previously associated with better prognosis of the primary disease. One outlier tumor has a high mutational burden associated with UV-damage. CDKN2A deletions also occur, which are rarely present in primaries. A focused knockdown screen is used to investigate overexpressed genes associated withcopy number gains. Tumor-infiltrating lymphocytes are in several cases found tumor-reactive, but expression of the immune checkpoint receptors TIM-3, TIGIT and LAG3 is also abundant. This study represents the largest whole-genome analysis of uveal melanoma to date, and presents an updated view of the metastatic disease.

Original language	English
Article number	1894
Journal	Nature Communications
Volume	11
Issue number	1
DOIs	https://doi.org/10.1038/s41467-020-15606-0
Publication status	Published - 1 Dec 2020

Bibliographical note

Funding Information:
The results published here are in part based upon data generated by the TCGA Research Network (cancergenome.nih.gov/). We thank Sofia Stenqvist for animal care, Ola Nilsson and Gülay Altiparmak for histology, Carina Karlsson for technical assistance and Therese Bengtsson, Valerio Belgrano and surgeons in the SCANDIUM trial for patient sampling and registrations. Quantitative proteomic analysis was performed by Britt-Marie Olssen and Evelin Berger at the Proteomics Core Facility of Sahlgrenska Academy, University of Gothenburg. The GeneCoreSU and SciLifeLab facilities are acknowledged for sequencing services, partly financed by a National Genomics Initiative grant to J.A.N. Other funding sources included Knut and Alice Wallenberg Foundation, Cancerfonden, Vetenskaps-rådet, Sjöbergstiftelsen, Familjen Erling Perssons stiftelse, Wilhelm & Martina Lundgrens Vetenskapsfond, the Assar Gabrielsson foundation and Västra Götalandsregionen.

Publisher Copyright:
© 2020, The Author(s).

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Karlsson, J., Nilsson, L. M., Mitra, S., Alsén, S., Shelke, G. V., Sah, V. R., Forsberg, E. M. V., Stierner, U., All-Eriksson, C., Einarsdottir, B., Jespersen, H., Ny, L., Lindnér, P., Larsson, E., Olofsson Bagge, R., & Nilsson, J. A. (2020). Molecular profiling of driver events in metastatic uveal melanoma. Nature Communications, 11(1), [1894]. https://doi.org/10.1038/s41467-020-15606-0

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title = "Molecular profiling of driver events in metastatic uveal melanoma",

abstract = "Metastatic uveal melanoma is less well understood than its primary counterpart, has a distinct biology compared to skin melanoma, and lacks effective treatments. Here we genomically profile metastatic tumors and infiltrating lymphocytes. BAP1 alterations are overrepresented and found in 29/32 of cases. Reintroducing a functional BAP1 allele into a deficient patient-derived cell line, reveals a broad shift towards a transcriptomic subtype previously associated with better prognosis of the primary disease. One outlier tumor has a high mutational burden associated with UV-damage. CDKN2A deletions also occur, which are rarely present in primaries. A focused knockdown screen is used to investigate overexpressed genes associated withcopy number gains. Tumor-infiltrating lymphocytes are in several cases found tumor-reactive, but expression of the immune checkpoint receptors TIM-3, TIGIT and LAG3 is also abundant. This study represents the largest whole-genome analysis of uveal melanoma to date, and presents an updated view of the metastatic disease.",

author = "Joakim Karlsson and Nilsson, {Lisa M.} and Suman Mitra and Samuel Als{\'e}n and Shelke, {Ganesh Vilas} and Sah, {Vasu R.} and Forsberg, {Elin M.V.} and Ulrika Stierner and Charlotta All-Eriksson and Berglind Einarsdottir and Henrik Jespersen and Lars Ny and Per Lindn{\'e}r and Erik Larsson and {Olofsson Bagge}, Roger and Nilsson, {Jonas A.}",

note = "Funding Information: The results published here are in part based upon data generated by the TCGA Research Network (cancergenome.nih.gov/). We thank Sofia Stenqvist for animal care, Ola Nilsson and G{\"u}lay Altiparmak for histology, Carina Karlsson for technical assistance and Therese Bengtsson, Valerio Belgrano and surgeons in the SCANDIUM trial for patient sampling and registrations. Quantitative proteomic analysis was performed by Britt-Marie Olssen and Evelin Berger at the Proteomics Core Facility of Sahlgrenska Academy, University of Gothenburg. The GeneCoreSU and SciLifeLab facilities are acknowledged for sequencing services, partly financed by a National Genomics Initiative grant to J.A.N. Other funding sources included Knut and Alice Wallenberg Foundation, Cancerfonden, Vetenskaps-r{\aa}det, Sj{\"o}bergstiftelsen, Familjen Erling Perssons stiftelse, Wilhelm & Martina Lundgrens Vetenskapsfond, the Assar Gabrielsson foundation and V{\"a}stra G{\"o}talandsregionen. Publisher Copyright: {\textcopyright} 2020, The Author(s).",

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Karlsson, J, Nilsson, LM, Mitra, S, Alsén, S, Shelke, GV, Sah, VR, Forsberg, EMV, Stierner, U, All-Eriksson, C, Einarsdottir, B, Jespersen, H, Ny, L, Lindnér, P, Larsson, E, Olofsson Bagge, R & Nilsson, JA 2020, 'Molecular profiling of driver events in metastatic uveal melanoma', Nature Communications, vol. 11, no. 1, 1894. https://doi.org/10.1038/s41467-020-15606-0

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AU - Karlsson, Joakim

AU - Nilsson, Lisa M.

AU - Mitra, Suman

AU - Alsén, Samuel

AU - Shelke, Ganesh Vilas

AU - Sah, Vasu R.

AU - Forsberg, Elin M.V.

AU - Stierner, Ulrika

AU - All-Eriksson, Charlotta

AU - Einarsdottir, Berglind

AU - Jespersen, Henrik

AU - Ny, Lars

AU - Lindnér, Per

AU - Larsson, Erik

AU - Olofsson Bagge, Roger

AU - Nilsson, Jonas A.

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N2 - Metastatic uveal melanoma is less well understood than its primary counterpart, has a distinct biology compared to skin melanoma, and lacks effective treatments. Here we genomically profile metastatic tumors and infiltrating lymphocytes. BAP1 alterations are overrepresented and found in 29/32 of cases. Reintroducing a functional BAP1 allele into a deficient patient-derived cell line, reveals a broad shift towards a transcriptomic subtype previously associated with better prognosis of the primary disease. One outlier tumor has a high mutational burden associated with UV-damage. CDKN2A deletions also occur, which are rarely present in primaries. A focused knockdown screen is used to investigate overexpressed genes associated withcopy number gains. Tumor-infiltrating lymphocytes are in several cases found tumor-reactive, but expression of the immune checkpoint receptors TIM-3, TIGIT and LAG3 is also abundant. This study represents the largest whole-genome analysis of uveal melanoma to date, and presents an updated view of the metastatic disease.

AB - Metastatic uveal melanoma is less well understood than its primary counterpart, has a distinct biology compared to skin melanoma, and lacks effective treatments. Here we genomically profile metastatic tumors and infiltrating lymphocytes. BAP1 alterations are overrepresented and found in 29/32 of cases. Reintroducing a functional BAP1 allele into a deficient patient-derived cell line, reveals a broad shift towards a transcriptomic subtype previously associated with better prognosis of the primary disease. One outlier tumor has a high mutational burden associated with UV-damage. CDKN2A deletions also occur, which are rarely present in primaries. A focused knockdown screen is used to investigate overexpressed genes associated withcopy number gains. Tumor-infiltrating lymphocytes are in several cases found tumor-reactive, but expression of the immune checkpoint receptors TIM-3, TIGIT and LAG3 is also abundant. This study represents the largest whole-genome analysis of uveal melanoma to date, and presents an updated view of the metastatic disease.

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Molecular profiling of driver events in metastatic uveal melanoma

Abstract

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