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Vera J, Lai X, Baur A, Erdmann M, Gupta S, Guttà C, Heinzerling L, Heppt MV, Kazmierczak PM, Kunz M, Lischer C, Pützer BM, Rehm M, Ostalecki C, Retzlaff J, Witt S, Wolkenhauer O, Berking C. Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence. Brief Bioinform 2022; 23:6761961. [PMID: 36252807 DOI: 10.1093/bib/bbac433] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/28/2022] [Accepted: 09/08/2022] [Indexed: 12/19/2022] Open
Abstract
We live in an unprecedented time in oncology. We have accumulated samples and cases in cohorts larger and more complex than ever before. New technologies are available for quantifying solid or liquid samples at the molecular level. At the same time, we are now equipped with the computational power necessary to handle this enormous amount of quantitative data. Computational models are widely used helping us to substantiate and interpret data. Under the label of systems and precision medicine, we are putting all these developments together to improve and personalize the therapy of cancer. In this review, we use melanoma as a paradigm to present the successful application of these technologies but also to discuss possible future developments in patient care linked to them. Melanoma is a paradigmatic case for disruptive improvements in therapies, with a considerable number of metastatic melanoma patients benefiting from novel therapies. Nevertheless, a large proportion of patients does not respond to therapy or suffers from adverse events. Melanoma is an ideal case study to deploy advanced technologies not only due to the medical need but also to some intrinsic features of melanoma as a disease and the skin as an organ. From the perspective of data acquisition, the skin is the ideal organ due to its accessibility and suitability for many kinds of advanced imaging techniques. We put special emphasis on the necessity of computational strategies to integrate multiple sources of quantitative data describing the tumour at different scales and levels.
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Affiliation(s)
- Julio Vera
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | - Xin Lai
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | - Andreas Baur
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | - Michael Erdmann
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock 18051, Germany
| | - Cristiano Guttà
- Institute of Cell Biology and Immunology, University of Stuttgart, 70569 Stuttgart, Germany
| | - Lucie Heinzerling
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany.,Department of Dermatology, LMU University Hospital, Munich, Germany
| | - Markus V Heppt
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | | | - Manfred Kunz
- Department of Dermatology, Venereology and Allergology, University of Leipzig, 04103 Leipzig, Germany
| | - Christopher Lischer
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | - Brigitte M Pützer
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, 18057 Rostock, Germany
| | - Markus Rehm
- Institute of Cell Biology and Immunology, University of Stuttgart, 70569 Stuttgart, Germany.,Stuttgart Research Center Systems Biology, University of Stuttgart, 70569 Stuttgart, Germany
| | - Christian Ostalecki
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | - Jimmy Retzlaff
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | | | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock 18051, Germany
| | - Carola Berking
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
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Coope RJ, Schlosser C, Corbett RD, Pleasance S, Tessier-Cloutier B, Pandoh P, Kirk H, Haile S, Zhao Y, Mungall AJ, Marra MA. Whole-slide laser microdissection for tumour enrichment. J Pathol 2020; 253:225-233. [PMID: 33135777 DOI: 10.1002/path.5575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 10/24/2020] [Accepted: 10/26/2020] [Indexed: 12/30/2022]
Abstract
The practical application of genome-scale technologies to precision oncology research requires flexible tissue processing strategies that can be used to differentially select both tumour and normal cell populations from formalin-fixed, paraffin-embedded tissues. As tumour sequencing scales towards clinical implementation, practical difficulties in scheduling and obtaining fresh tissue biopsies at scale, including blood samples as surrogates for matched 'normal' DNA, have focused attention on the use of formalin-preserved clinical samples collected routinely for diagnostic purposes. In practice, such samples often contain both tumour and normal cells which, if correctly partitioned, could be used to profile both tumour and normal genomes, thus identifying somatic alterations. Here we report a semi-automated method for laser microdissecting entire slide-mounted tissue sections to enrich for cells of interest with sufficient yield for whole genome and transcriptome sequencing. Using this method, we demonstrated enrichment of tumour material from mixed tumour-normal samples by up to 67%. Leveraging new methods that allow for the extraction of high-quality nucleic acids from small amounts of formalin-fixed tissues, we further showed that the method was successful in yielding sequence data of sufficient quality for use in BC Cancer's Personalized OncoGenomics (POG) program. © 2020 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Robin Jn Coope
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Colin Schlosser
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Richard D Corbett
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Stephen Pleasance
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Pawan Pandoh
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Heather Kirk
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Simon Haile
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
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