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Chuang YM, Tzeng SF, Ho PC, Tsai CH. Immunosurveillance encounters cancer metabolism. EMBO Rep 2024; 25:471-488. [PMID: 38216787 PMCID: PMC10897436 DOI: 10.1038/s44319-023-00038-w] [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: 02/10/2023] [Revised: 12/02/2023] [Accepted: 12/12/2023] [Indexed: 01/14/2024] Open
Abstract
Tumor cells reprogram nutrient acquisition and metabolic pathways to meet their energetic, biosynthetic, and redox demands. Similarly, metabolic processes in immune cells support host immunity against cancer and determine differentiation and fate of leukocytes. Thus, metabolic deregulation and imbalance in immune cells within the tumor microenvironment have been reported to drive immune evasion and to compromise therapeutic outcomes. Interestingly, emerging evidence indicates that anti-tumor immunity could modulate tumor heterogeneity, aggressiveness, and metabolic reprogramming, suggesting that immunosurveillance can instruct cancer progression in multiple dimensions. This review summarizes our current understanding of how metabolic crosstalk within tumors affects immunogenicity of tumor cells and promotes cancer progression. Furthermore, we explain how defects in the metabolic cascade can contribute to developing dysfunctional immune responses against cancers and discuss the contribution of immunosurveillance to these defects as a feedback mechanism. Finally, we highlight ongoing clinical trials and new therapeutic strategies targeting cellular metabolism in cancer.
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Affiliation(s)
- Yu-Ming Chuang
- Department of Fundamental Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Sheue-Fen Tzeng
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Ping-Chih Ho
- Department of Fundamental Oncology, University of Lausanne, Lausanne, Switzerland.
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.
| | - Chin-Hsien Tsai
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan.
- Department and Graduate Institute of Biochemistry, National Defense Medical Center, Taipei, Taiwan.
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Angaroni F, Guidi A, Ascolani G, d'Onofrio A, Antoniotti M, Graudenzi A. J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments. BMC Bioinformatics 2022; 23:269. [PMID: 35804300 PMCID: PMC9270769 DOI: 10.1186/s12859-022-04779-8] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/09/2022] [Indexed: 11/15/2022] Open
Abstract
Background The combined effects of biological variability and measurement-related errors on cancer sequencing data remain largely unexplored. However, the spatio-temporal simulation of multi-cellular systems provides a powerful instrument to address this issue. In particular, efficient algorithmic frameworks are needed to overcome the harsh trade-off between scalability and expressivity, so to allow one to simulate both realistic cancer evolution scenarios and the related sequencing experiments, which can then be used to benchmark downstream bioinformatics methods. Result We introduce a Julia package for SPAtial Cancer Evolution (J-SPACE), which allows one to model and simulate a broad set of experimental scenarios, phenomenological rules and sequencing settings.Specifically, J-SPACE simulates the spatial dynamics of cells as a continuous-time multi-type birth-death stochastic process on a arbitrary graph, employing different rules of interaction and an optimised Gillespie algorithm. The evolutionary dynamics of genomic alterations (single-nucleotide variants and indels) is simulated either under the Infinite Sites Assumption or several different substitution models, including one based on mutational signatures. After mimicking the spatial sampling of tumour cells, J-SPACE returns the related phylogenetic model, and allows one to generate synthetic reads from several Next-Generation Sequencing (NGS) platforms, via the ART read simulator. The results are finally returned in standard FASTA, FASTQ, SAM, ALN and Newick file formats. Conclusion J-SPACE is designed to efficiently simulate the heterogeneous behaviour of a large number of cancer cells and produces a rich set of outputs. Our framework is useful to investigate the emergent spatial dynamics of cancer subpopulations, as well as to assess the impact of incomplete sampling and of experiment-specific errors. Importantly, the output of J-SPACE is designed to allow the performance assessment of downstream bioinformatics pipelines processing NGS data. J-SPACE is freely available at: https://github.com/BIMIB-DISCo/J-Space.jl.
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Affiliation(s)
- Fabrizio Angaroni
- Dept. of Informatics, Systems and Communication, Univ. of Milan-Bicocca, Milan, Italy.
| | - Alessandro Guidi
- Dept. of Informatics, Systems and Communication, Univ. of Milan-Bicocca, Milan, Italy
| | - Gianluca Ascolani
- Dept. of Informatics, Systems and Communication, Univ. of Milan-Bicocca, Milan, Italy
| | - Alberto d'Onofrio
- Department of Mathematics and Geosciences, Univ. of Trieste, Trieste, Italy
| | - Marco Antoniotti
- Dept. of Informatics, Systems and Communication, Univ. of Milan-Bicocca, Milan, Italy.,Bicocca Bioinformatics, Biostatistics and Bioimaging Centre (B4), Milan, Italy
| | - Alex Graudenzi
- Dept. of Informatics, Systems and Communication, Univ. of Milan-Bicocca, Milan, Italy.,Bicocca Bioinformatics, Biostatistics and Bioimaging Centre (B4), Milan, Italy.,Inst. of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Segrate, Italy
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Al-Rawi DH, Bakhoum SF. Chromosomal instability as a source of genomic plasticity. Curr Opin Genet Dev 2022; 74:101913. [PMID: 35526333 DOI: 10.1016/j.gde.2022.101913] [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: 01/10/2022] [Revised: 02/27/2022] [Accepted: 03/31/2022] [Indexed: 11/03/2022]
Abstract
Chromosomal instability (CIN) is a hallmark of the most aggressive malignancies. Features of these tumors include complex genomic rearrangements, the presence of mis-segregated chromosomes in micronuclei, and extrachromosomal DNA (ecDNA) formation. Here, we review the development of CIN, and examine CIN in the context of cancer evolution, tumor genomic evolution, and therapeutic resistance. We also discuss the role of whole-genome duplications, breakage-fusion-bridge cycles, ecDNA or double minutes in gene amplification promoting tumor evolution.
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Affiliation(s)
- Duaa H Al-Rawi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Li G, Yang Z, Wu D, Liu S, Li X, Li T, Li Y, Liang L, Zou W, Wu CI, Wang HY, Lu X. Evolution under spatially heterogeneous selection in solid tumors. Mol Biol Evol 2021; 39:6440067. [PMID: 34850073 PMCID: PMC8788224 DOI: 10.1093/molbev/msab335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Spatial genetic and phenotypic diversity within solid tumors has been well documented. Nevertheless, how this heterogeneity affects temporal dynamics of tumorigenesis has not been rigorously examined because solid tumors do not evolve as the standard population genetic model due to the spatial constraint. We therefore, propose a neutral spatial (NS) model whereby the mutation accumulation increases toward the periphery; the genealogical relationship is spatially determined and the selection efficacy is blunted (due to kin competition). In this model, neutral mutations are accrued and spatially distributed in manners different from those of advantageous mutations. Importantly, the distinctions could be blurred in the conventional model. To test the NS model, we performed a three-dimensional multiple microsampling of two hepatocellular carcinomas. Whole-genome sequencing (WGS) revealed a 2-fold increase in mutations going from the center to the periphery. The operation of natural selection can then be tested by examining the spatially determined clonal relationships and the clonal sizes. Due to limited migration, only the expansion of highly advantageous clones can sweep through a large part of the tumor to reveal the selective advantages. Hence, even multiregional sampling can only reveal a fraction of fitness differences in solid tumors. Our results suggest that the NS patterns are crucial for testing the influence of natural selection during tumorigenesis, especially for small solid tumors.
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Affiliation(s)
- Guanghao Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,China National Center for Bioinformation, Beijing, 100101, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zuyu Yang
- China National Center for Bioinformation, Beijing, 100101, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,Institute of Environmental Science and Research, Porirua, New Zealand
| | - Dafei Wu
- China National Center for Bioinformation, Beijing, 100101, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Sixue Liu
- China National Center for Bioinformation, Beijing, 100101, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuening Li
- China National Center for Bioinformation, Beijing, 100101, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Li
- China National Center for Bioinformation, Beijing, 100101, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yawei Li
- China National Center for Bioinformation, Beijing, 100101, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liji Liang
- China National Center for Bioinformation, Beijing, 100101, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Weilong Zou
- Surgery of Liver Transplant, The Third Medical Center of Chinese PLA General Hospital, Beijing, 100039, China.,Surgery of Hepatopancreatobiliary, Peking University Shougang Hospital, Beijing, 100144, China
| | - Chung-I Wu
- China National Center for Bioinformation, Beijing, 100101, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,State Key Laboratory of Biocontrol, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Hurng-Yi Wang
- Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, 11031, Taiwan.,Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 106, Taiwan
| | - Xuemei Lu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,China National Center for Bioinformation, Beijing, 100101, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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