1
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Hessey S, Fessas P, Zaccaria S, Jamal-Hanjani M, Swanton C. Insights into the metastatic cascade through research autopsies. Trends Cancer 2023; 9:490-502. [PMID: 37059687 DOI: 10.1016/j.trecan.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 04/16/2023]
Abstract
Metastasis is a complex process and the leading cause of cancer-related death globally. Recent studies have demonstrated that genomic sequencing data from paired primary and metastatic tumours can be used to trace the evolutionary origins of cells responsible for metastasis. This approach has yielded new insights into the genomic alterations that engender metastatic potential, and the mechanisms by which cancer spreads. Given that the reliability of these approaches is contingent upon how representative the samples are of primary and metastatic tumour heterogeneity, we review insights from studies that have reconstructed the evolution of metastasis within the context of their cohorts and designs. We discuss the role of research autopsies in achieving the comprehensive sampling necessary to advance the current understanding of metastasis.
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Affiliation(s)
- Sonya Hessey
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK; Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Petros Fessas
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - Simone Zaccaria
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK; Department of Oncology, University College London Hospitals, London, UK.
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Department of Oncology, University College London Hospitals, London, UK; Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
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2
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Huang Y, Wang H, Yue X, Li X. Bone serves as a transfer station for secondary dissemination of breast cancer. Bone Res 2023; 11:21. [PMID: 37085486 PMCID: PMC10121690 DOI: 10.1038/s41413-023-00260-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/28/2023] [Accepted: 03/22/2023] [Indexed: 04/23/2023] Open
Abstract
Metastasis is responsible for the majority of deaths among breast cancer patients. Although parallel polyclonal seeding has been shown to contribute to organ-specific metastasis, in the past decade, horizontal cross-metastatic seeding (metastasis-to-metastasis spreading) has also been demonstrated as a pattern of distant metastasis to multiple sites. Bone, as the most frequent first destination of breast cancer metastasis, has been demonstrated to facilitate the secondary dissemination of breast cancer cells. In this review, we summarize the clinical and experimental evidence that bone is a transfer station for the secondary dissemination of breast cancer. We also discuss the regulatory mechanisms of the bone microenvironment in secondary seeding of breast cancer, focusing on stemness regulation, quiescence-proliferation equilibrium regulation, epigenetic reprogramming and immune escape of cancer cells. Furthermore, we highlight future research perspectives and strategies for preventing secondary dissemination from bone.
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Affiliation(s)
- Yufan Huang
- Department of Biochemistry and Molecular Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin, 300060, China
- Key Laboratory of Breast Cancer Prevention and Treatment of the Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin, 300060, China
| | - Hongli Wang
- Department of Biochemistry and Molecular Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin, 300060, China
- Key Laboratory of Breast Cancer Prevention and Treatment of the Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin, 300060, China
| | - Xiaomin Yue
- Department of Biochemistry and Molecular Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin, 300060, China
- Key Laboratory of Breast Cancer Prevention and Treatment of the Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin, 300060, China
| | - Xiaoqing Li
- Department of Biochemistry and Molecular Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin, 300060, China.
- Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin, 300060, China.
- Key Laboratory of Breast Cancer Prevention and Treatment of the Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin, 300060, China.
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3
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Sommer ER, Napoli GC, Chau CH, Price DK, Figg WD. Targeting the metastatic niche: Single-cell lineage tracing in prime time. iScience 2023; 26:106174. [PMID: 36895653 PMCID: PMC9988656 DOI: 10.1016/j.isci.2023.106174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Abstract
Identification of actionable drug targets remains a rate-limiting step of, and one of the most prominent barriers to successful drug development for metastatic cancers. CRISPR-Cas9, a tool for making targeted genomic edits, has given rise to various novel applications that have greatly accelerated discovery in developmental biology. Recent work has coupled a CRISPR-Cas9-based lineage tracing platform with single-cell transcriptomics in the unexplored context of cancer metastasis. In this perspective, we briefly reflect on the development of these distinct technological advances and the process by which they have become integrated. We also highlight the importance of single-cell lineage tracing in oncology drug development and suggest the profound capacity of a high-resolution, computational approach to reshape cancer drug discovery by enabling identification of novel metastasis-specific drug targets and mechanisms of resistance.
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Affiliation(s)
- Elijah R Sommer
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Giulia C Napoli
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cindy H Chau
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Douglas K Price
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - William D Figg
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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4
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Ring A, Nguyen-Sträuli BD, Wicki A, Aceto N. Biology, vulnerabilities and clinical applications of circulating tumour cells. Nat Rev Cancer 2023; 23:95-111. [PMID: 36494603 PMCID: PMC9734934 DOI: 10.1038/s41568-022-00536-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/07/2022] [Indexed: 12/13/2022]
Abstract
In recent years, exceptional technological advances have enabled the identification and interrogation of rare circulating tumour cells (CTCs) from blood samples of patients, leading to new fields of research and fostering the promise for paradigm-changing, liquid biopsy-based clinical applications. Analysis of CTCs has revealed distinct biological phenotypes, including the presence of CTC clusters and the interaction between CTCs and immune or stromal cells, impacting metastasis formation and providing new insights into cancer vulnerabilities. Here we review the progress made in understanding biological features of CTCs and provide insight into exploiting these developments to design future clinical tools for improving the diagnosis and treatment of cancer.
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Affiliation(s)
- Alexander Ring
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Bich Doan Nguyen-Sträuli
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Department of Gynecology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Andreas Wicki
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Nicola Aceto
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland.
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5
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Sankaran VG, Weissman JS, Zon LI. Cellular barcoding to decipher clonal dynamics in disease. Science 2022; 378:eabm5874. [PMID: 36227997 PMCID: PMC10111813 DOI: 10.1126/science.abm5874] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Cellular barcodes are distinct DNA sequences that enable one to track specific cells across time or space. Recent advances in our ability to detect natural or synthetic cellular barcodes, paired with single-cell readouts of cell state, have markedly increased our knowledge of clonal dynamics and genealogies of the cells that compose a variety of tissues and organs. These advances hold promise to redefine our view of human disease. Here, we provide an overview of cellular barcoding approaches, discuss applications to gain new insights into disease mechanisms, and provide an outlook on future applications. We discuss unanticipated insights gained through barcoding in studies of cancer and blood cell production and describe how barcoding can be applied to a growing array of medical fields, particularly with the increasing recognition of clonal contributions in human diseases.
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Affiliation(s)
- Vijay G Sankaran
- Division of Hematology and Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Leonard I Zon
- Division of Hematology and Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Harvard Stem Cell Institute, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Stem Cell Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
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6
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Chroni A, Miura S, Hamilton L, Vu T, Gaffney SG, Aly V, Karim S, Sanderford M, Townsend JP, Kumar S. Clone Phylogenetics Reveals Metastatic Tumor Migrations, Maps, and Models. Cancers (Basel) 2022; 14:cancers14174326. [PMID: 36077861 PMCID: PMC9454754 DOI: 10.3390/cancers14174326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Metastasis is the spread of cancer cells across organs and is a major cause of cancer mortality. Analysis of tumor sequencing data provides a means toward the reconstruction of routes of metastatic cell migrations. Our reconstructions demonstrated that many metastases were likely seeded from pre-existing metastasis of primary tumors. Additionally, multiple clone exchanges between tumor sites were common. In conclusion, the pattern of cancer cell migrations is often complex and is highly variable among patients. Abstract Dispersal routes of metastatic cells are not medically detected or even visible. A molecular evolutionary analysis of tumor variation provides a way to retrospectively infer metastatic migration histories and answer questions such as whether the majority of metastases are seeded from clones within primary tumors or seeded from clones within pre-existing metastases, as well as whether the evolution of metastases is generally consistent with any proposed models. We seek answers to these fundamental questions through a systematic patient-centric retrospective analysis that maps the dynamic evolutionary history of tumor cell migrations in many cancers. We analyzed tumor genetic heterogeneity in 51 cancer patients and found that most metastatic migration histories were best described by a hybrid of models of metastatic tumor evolution. Synthesizing across metastatic migration histories, we found new tumor seedings arising from clones of pre-existing metastases as often as they arose from clones from primary tumors. There were also many clone exchanges between the source and recipient tumors. Therefore, a molecular phylogenetic analysis of tumor variation provides a retrospective glimpse into general patterns of metastatic migration histories in cancer patients.
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Affiliation(s)
- Antonia Chroni
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Sayaka Miura
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Lauren Hamilton
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Tracy Vu
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | | | - Vivian Aly
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Sajjad Karim
- Center for Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah 22252, Saudi Arabia
| | - Maxwell Sanderford
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale University, New Haven, CT 06510, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06525, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
- Center for Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah 22252, Saudi Arabia
- Correspondence:
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7
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The Road to Dissemination: The Concept of Oligometastases and the Barriers for Widespread Disease. Cancers (Basel) 2022; 14:cancers14082046. [PMID: 35454951 PMCID: PMC9033015 DOI: 10.3390/cancers14082046] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/02/2022] [Accepted: 04/13/2022] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Oligometastatic disease is an intermediate state of metastatic dissemination with a limited number of metastatic sites and extent of disease. Tumor cells need multiple capabilities in order to migrate, survive and evolve to macroscopic metastases. These capabilities are acquired by evolutionary mechanisms and are associated with several clinical factors and biomarkers. Better understanding of these properties and biomarkers may help to select patients that can benefit from local ablative therapies, which have shown to be a promising approach in recent clinical evidence. Abstract Over the last years, the oligometastatic disease state has gained more and more interest, and randomized trials are now suggesting an added value of stereotactic radiotherapy on all macroscopic disease in oligometastatic patients; but what barriers could impede widespread disease in some patients? In this review, we first discuss the concept of oligometastatic disease and some examples of clinical evidence. We then explore the route to dissemination: the hurdles a tumoral clone has to overtake before it can produce efficient and widespread dissemination. The spectrum theory argues that the range of metastatic patterns encountered in the clinic is the consequence of gradually obtained metastatic abilities of the tumor cells. Tumor clones can obtain these capabilities by Darwinian evolution, hence early in their genetic progression tumors might produce only a limited number of metastases. We illustrate selective dissemination by discussing organ tropism, the preference of different cancer (sub)types to metastasize to certain organs. Finally we discuss biomarkers that may help to distinguish the oligometastatic state.
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8
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Kozlov A, Alves JM, Stamatakis A, Posada D. CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data. Genome Biol 2022; 23:37. [PMID: 35081992 PMCID: PMC8790911 DOI: 10.1186/s13059-021-02583-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 12/20/2021] [Indexed: 01/15/2023] Open
Abstract
We introduce CellPhy, a maximum likelihood framework for inferring phylogenetic trees from somatic single-cell single-nucleotide variants. CellPhy leverages a finite-site Markov genotype model with 16 diploid states and considers amplification error and allelic dropout. We implement CellPhy into RAxML-NG, a widely used phylogenetic inference package that provides statistical confidence measurements and scales well on large datasets with hundreds or thousands of cells. Comprehensive simulations suggest that CellPhy is more robust to single-cell genomics errors and outperforms state-of-the-art methods under realistic scenarios, both in accuracy and speed. CellPhy is freely available at https://github.com/amkozlov/cellphy .
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Affiliation(s)
- Alexey Kozlov
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany
| | - Joao M. Alves
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
| | - David Posada
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
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9
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Fan B, Xu X, Wang X. Mutational landscape of paired primary and synchronous metastatic lymph node in chemotherapy naive gallbladder cancer. Mol Biol Rep 2022; 49:1295-1301. [PMID: 34988893 DOI: 10.1007/s11033-021-06957-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 11/11/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Comprehensive genomic analysis of paired primary tumors and their metastatic lesions may provide new insights into the biology of metastatic processes and therefore guide the development of novel strategies for intervention. To date, our knowledge of the genetic divergence and phylogenetic relationships in gallbladder cancer (GBC) is limited. METHODS We performed whole exome sequencing for 5 patients with primary tumor, metastatic lymph node (LNM) and corresponding normal tissue. Mutations, mutation signatures and copy number variations were analyzed with state-of-art bioinformatics methods. Phylogenetic tree was also generated to infer metastatic pattern. RESULTS Five driver mutations were detected in these patients. Among which, TP53 was the only shared mutation between primary tumor and LNM. Although tumor mutational burden was comparable between primary tumor and LNM, higher mutation burden was observed in LNM of one patient. Copy number variations (CNVs) burden was higher in LNM than their primary tumor. Phylogenetic analysis indicated both linear and parallel progression of metastasis exist in these patients. TP53 mutation and CNVs were homogenously between primary tumor and LNM. CONCLUSIONS High consistence of genetic landscape were shown between primary tumor and LNM in GBC. However, heterogenicity still exist between primary tumor and LNM in particular patients in term of driver mutation, TMB and CNV burden. Phylogenetic analysis indicated both Linear and parallel progression of metastasis were exist among these patients.
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Affiliation(s)
- Boqiang Fan
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, No. 300, Guangzhou Road, Nanjing, Jiangsu Province, China
| | - Xianfeng Xu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xuehao Wang
- Key Laboratory of Liver Transplantation, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Chinese Academy of Medical Sciences, Nanjing, Jiangsu Province, China.
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10
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Quinn JJ, Jones MG, Okimoto RA, Nanjo S, Chan MM, Yosef N, Bivona TG, Weissman JS. Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts. Science 2021; 371:eabc1944. [PMID: 33479121 PMCID: PMC7983364 DOI: 10.1126/science.abc1944] [Citation(s) in RCA: 135] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 09/23/2020] [Accepted: 12/17/2020] [Indexed: 12/11/2022]
Abstract
Detailed phylogenies of tumor populations can recount the history and chronology of critical events during cancer progression, such as metastatic dissemination. We applied a Cas9-based, single-cell lineage tracer to study the rates, routes, and drivers of metastasis in a lung cancer xenograft mouse model. We report deeply resolved phylogenies for tens of thousands of cancer cells traced over months of growth and dissemination. This revealed stark heterogeneity in metastatic capacity, arising from preexisting and heritable differences in gene expression. We demonstrate that these identified genes can drive invasiveness and uncovered an unanticipated suppressive role for KRT17 We also show that metastases disseminated via multidirectional tissue routes and complex seeding topologies. Overall, we demonstrate the power of tracing cancer progression at subclonal resolution and vast scale.
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Affiliation(s)
- Jeffrey J Quinn
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- Inscripta, Inc., Boulder, CO, USA
| | - Matthew G Jones
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Integrative Program in Quantitative Biology, University of California, San Francisco, San Francisco, CA, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ross A Okimoto
- UCSF Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Shigeki Nanjo
- UCSF Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Michelle M Chan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Nir Yosef
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub Investigator, San Francisco, CA, USA
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA, USA
| | - Trever G Bivona
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
- UCSF Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- Whitehead Institute, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
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11
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Stadler T, Pybus OG, Stumpf MPH. Phylodynamics for cell biologists. Science 2021; 371:371/6526/eaah6266. [PMID: 33446527 DOI: 10.1126/science.aah6266] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/13/2020] [Indexed: 12/12/2022]
Abstract
Multicellular organisms are composed of cells connected by ancestry and descent from progenitor cells. The dynamics of cell birth, death, and inheritance within an organism give rise to the fundamental processes of development, differentiation, and cancer. Technical advances in molecular biology now allow us to study cellular composition, ancestry, and evolution at the resolution of individual cells within an organism or tissue. Here, we take a phylogenetic and phylodynamic approach to single-cell biology. We explain how "tree thinking" is important to the interpretation of the growing body of cell-level data and how ecological null models can benefit statistical hypothesis testing. Experimental progress in cell biology should be accompanied by theoretical developments if we are to exploit fully the dynamical information in single-cell data.
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Affiliation(s)
- T Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - O G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.
| | - M P H Stumpf
- Melbourne Integrative Genomics, School of BioSciences and School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia.
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12
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Bonneville R, Paruchuri A, Wing MR, Krook MA, Reeser JW, Chen HZ, Dao T, Samorodnitsky E, Smith AM, Yu L, Nowacki N, Chen W, Roychowdhury S. Characterization of Clonal Evolution in Microsatellite Unstable Metastatic Cancers through Multiregional Tumor Sequencing. Mol Cancer Res 2020; 19:465-474. [PMID: 33229401 DOI: 10.1158/1541-7786.mcr-19-0955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 07/10/2020] [Accepted: 11/18/2020] [Indexed: 11/16/2022]
Abstract
Microsatellites are short, repetitive segments of DNA, which are dysregulated in mismatch repair-deficient (MMRd) tumors resulting in microsatellite instability (MSI). MSI has been identified in many human cancer types with varying incidence, and microsatellite instability-high (MSI-H) tumors often exhibit increased sensitivity to immune-enhancing therapies such as PD-1/PD-L1 inhibition. Next-generation sequencing (NGS) has permitted advancements in MSI detection, and recent computational advances have enabled characterization of tumor heterogeneity via NGS. However, the evolution and heterogeneity of microsatellite changes in MSI-positive tumors remains poorly described. We determined MSI status in 6 patients using our previously published algorithm, MANTIS, and inferred subclonal composition and phylogeny with Canopy and SuperFreq. We developed a simulated annealing-based method to characterize microsatellite length distributions in specific subclones and assessed the evolution of MSI in the context of tumor heterogeneity. We identified three to eight tumor subclones per patient, and each subclone exhibited MMRd-associated base substitution signatures. We noted that microsatellites tend to shorten over time, and that MMRd fosters heterogeneity by introducing novel mutations throughout the disease course. Some microsatellites are altered among all subclones in a patient, whereas other loci are only altered in particular subclones corresponding to subclonal phylogenetic relationships. Overall, our results indicate that MMRd is a substantial driver of heterogeneity, leading to both MSI and subclonal divergence. IMPLICATIONS: We leveraged subclonal inference to assess clonal evolution based on somatic mutations and microsatellites, which provides insight into MMRd as a dynamic mutagenic process in MSI-H malignancies.
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Affiliation(s)
- Russell Bonneville
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio.,Biomedical Sciences Graduate Program, The Ohio State University, Columbus, Ohio
| | - Anoosha Paruchuri
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Michele R Wing
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Melanie A Krook
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Julie W Reeser
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Hui-Zi Chen
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio.,Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
| | - Thuy Dao
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | | | - Amy M Smith
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Lianbo Yu
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
| | - Nicholas Nowacki
- Department of Pathology, The Ohio State University, Columbus, Ohio
| | - Wei Chen
- Department of Pathology, The Ohio State University, Columbus, Ohio
| | - Sameek Roychowdhury
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio. .,Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
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13
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Miura S, Vu T, Deng J, Buturla T, Oladeinde O, Choi J, Kumar S. Power and pitfalls of computational methods for inferring clone phylogenies and mutation orders from bulk sequencing data. Sci Rep 2020; 10:3498. [PMID: 32103044 PMCID: PMC7044161 DOI: 10.1038/s41598-020-59006-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 01/23/2020] [Indexed: 12/13/2022] Open
Abstract
Tumors harbor extensive genetic heterogeneity in the form of distinct clone genotypes that arise over time and across different tissues and regions in cancer. Many computational methods produce clone phylogenies from population bulk sequencing data collected from multiple tumor samples from a patient. These clone phylogenies are used to infer mutation order and clone origins during tumor progression, rendering the selection of the appropriate clonal deconvolution method critical. Surprisingly, absolute and relative accuracies of these methods in correctly inferring clone phylogenies are yet to consistently assessed. Therefore, we evaluated the performance of seven computational methods. The accuracy of the reconstructed mutation order and inferred clone groupings varied extensively among methods. All the tested methods showed limited ability to identify ancestral clone sequences present in tumor samples correctly. The presence of copy number alterations, the occurrence of multiple seeding events among tumor sites during metastatic tumor evolution, and extensive intermixture of cancer cells among tumors hindered the detection of clones and the inference of clone phylogenies for all methods tested. Overall, CloneFinder, MACHINA, and LICHeE showed the highest overall accuracy, but none of the methods performed well for all simulated datasets. So, we present guidelines for selecting methods for data analysis.
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Affiliation(s)
- Sayaka Miura
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, 19122, USA.,Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Tracy Vu
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, 19122, USA.,Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Jiamin Deng
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, 19122, USA.,Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Tiffany Buturla
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, 19122, USA.,Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Olumide Oladeinde
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, 19122, USA.,Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Jiyeong Choi
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, 19122, USA.,Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, 19122, USA. .,Department of Biology, Temple University, Philadelphia, PA, 19122, USA. .,Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia.
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14
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Is the Recommendation of a Pelvic Lymphadenectomy in Conjunction with Radical Prostatectomy in Prostate Cancer Patients Justified? Report from a Multidisciplinary Expert Panel Meeting. Adv Ther 2020; 37:213-224. [PMID: 31679107 DOI: 10.1007/s12325-019-01133-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Indexed: 01/04/2023]
Abstract
INTRODUCTION Pelvic lymphadenectomy (pLA) in prostate cancer (PCa) is one of the most common uro-oncologic surgical procedures. An increased complication rate is accompanied by unproven oncologic benefit. Extent of pLA and mechanisms of metastasis are discussed controversially. We aimed to explore evidence and knowledge gaps in pLA and mechanisms of metastasis in PCa and to develop further steps to clarify oncologic benefits through an expert panel. METHODS A multidisciplinary expert meeting was initiated, compiling available facts on pLA and mechanisms of metastasis in PCa. Questions and hypotheses were formulated. The resulting protocol was modeled on priority and consistency in four anonymized voting rounds using the Delphi method (March 2018-June 2018). RESULTS The oncologic benefit of pLA in PCa is still unclear. Results of randomized trials (RCTs) are pending. Extent and techniques of pLA are differently applied and inconsistently recommended by the guidelines as well as the indication for pLA. Different growth rates for the primaries and metastases and different survival curves for lymph node and organ metastasis at diagnosis argue against metastasis originating from positive nodes. However, results from clinical and basic research support this opportunity in PCa. CONCLUSIONS The RCTs required to clarify the estimated low oncologic benefit of pLA prove to be difficult because of the great effort (e.g., high case number). Establishing a network of treatment centers for implementation of high-quality cohort studies could be an alternative approach. Future studies with larger panels and international participants based on the presented feasibility should be launched to set this process in motion. Until valid data are available, benefits and harms of pLA should be weighted under consideration of low-invasive techniques (e.g., sentinel pLA).
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15
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Miura S, Gomez K, Murillo O, Huuki LA, Vu T, Buturla T, Kumar S. Predicting clone genotypes from tumor bulk sequencing of multiple samples. Bioinformatics 2019; 34:4017-4026. [PMID: 29931046 DOI: 10.1093/bioinformatics/bty469] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 06/12/2018] [Indexed: 12/25/2022] Open
Abstract
Motivation Analyses of data generated from bulk sequencing of tumors have revealed extensive genomic heterogeneity within patients. Many computational methods have been developed to enable the inference of genotypes of tumor cell populations (clones) from bulk sequencing data. However, the relative and absolute accuracy of available computational methods in estimating clone counts and clone genotypes is not yet known. Results We have assessed the performance of nine methods, including eight previously-published and one new method (CloneFinder), by analyzing computer simulated datasets. CloneFinder, LICHeE, CITUP and cloneHD inferred clone genotypes with low error (<5% per clone) for a majority of datasets in which the tumor samples contained evolutionarily-related clones. Computational methods did not perform well for datasets in which tumor samples contained mixtures of clones from different clonal lineages. Generally, the number of clones was underestimated by cloneHD and overestimated by PhyloWGS, and BayClone2, Canopy and Clomial required prior information regarding the number of clones. AncesTree and Canopy did not produce results for a large number of datasets. Overall, the deconvolution of clone genotypes from single nucleotide variant (SNV) frequency differences among tumor samples remains challenging, so there is a need to develop more accurate computational methods and robust software for clone genotype inference. Availability and implementation CloneFinder is implemented in Python and is available from https://github.com/gstecher/CloneFinderAPI. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sayaka Miura
- Institute for Genomics and Evolutionary Medicine.,Department of Biology, Temple University, Philadelphia, PA, USA
| | - Karen Gomez
- Institute for Genomics and Evolutionary Medicine.,Department of Biology, Temple University, Philadelphia, PA, USA.,College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Oscar Murillo
- Institute for Genomics and Evolutionary Medicine.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Louise A Huuki
- Institute for Genomics and Evolutionary Medicine.,Department of Biology, Temple University, Philadelphia, PA, USA
| | - Tracy Vu
- Institute for Genomics and Evolutionary Medicine.,Department of Biology, Temple University, Philadelphia, PA, USA
| | - Tiffany Buturla
- Institute for Genomics and Evolutionary Medicine.,Department of Biology, Temple University, Philadelphia, PA, USA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine.,Department of Biology, Temple University, Philadelphia, PA, USA.,Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
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16
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Hu Z, Ding J, Ma Z, Sun R, Seoane JA, Scott Shaffer J, Suarez CJ, Berghoff AS, Cremolini C, Falcone A, Loupakis F, Birner P, Preusser M, Lenz HJ, Curtis C. Quantitative evidence for early metastatic seeding in colorectal cancer. Nat Genet 2019; 51:1113-1122. [PMID: 31209394 PMCID: PMC6982526 DOI: 10.1038/s41588-019-0423-x] [Citation(s) in RCA: 272] [Impact Index Per Article: 54.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/18/2019] [Indexed: 02/07/2023]
Abstract
Both the timing and molecular determinants of metastasis are unknown, hindering treatment and prevention efforts. Here we characterize the evolutionary dynamics of this lethal process by analyzing exome-sequencing data from 118 biopsies from 23 patients with colorectal cancer with metastases to the liver or brain. The data show that the genomic divergence between the primary tumor and metastasis is low and that canonical driver genes were acquired early. Analysis within a spatial tumor growth model and statistical inference framework indicates that early disseminated cells commonly (81%, 17 out of 21 evaluable patients) seed metastases while the carcinoma is clinically undetectable (typically, less than 0.01 cm3). We validated the association between early drivers and metastasis in an independent cohort of 2,751 colorectal cancers, demonstrating their utility as biomarkers of metastasis. This conceptual and analytical framework provides quantitative in vivo evidence that systemic spread can occur early in colorectal cancer and illuminates strategies for patient stratification and therapeutic targeting of the canonical drivers of tumorigenesis.
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Affiliation(s)
- Zheng Hu
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jie Ding
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Veracyte Inc, South San Francisco, CA, USA
| | - Zhicheng Ma
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ruping Sun
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jose A Seoane
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - J Scott Shaffer
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Carlos J Suarez
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Anna S Berghoff
- Comprehensive Cancer Center CNS Tumor Unit, Medical University of Vienna, Vienna, Austria
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
- Institute of Neurology, Medical University of Vienna, Vienna, Austria
| | - Chiara Cremolini
- Department of Oncology, University Hospital of Pisa, Pisa, Italy
| | - Alfredo Falcone
- Department of Oncology, University Hospital of Pisa, Pisa, Italy
| | - Fotios Loupakis
- Unit of Medical Oncology 1, Department of Clinical and Experimental Oncology, Istituto Oncologico Veneto, IRCCS, Padua, Italy
| | - Peter Birner
- Comprehensive Cancer Center CNS Tumor Unit, Medical University of Vienna, Vienna, Austria
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Matthias Preusser
- Comprehensive Cancer Center CNS Tumor Unit, Medical University of Vienna, Vienna, Austria
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Heinz-Josef Lenz
- Department of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christina Curtis
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
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17
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Su Z, Wang Z, Ni X, Duan J, Gao Y, Zhuo M, Li R, Zhao J, Ma Q, Bai H, Chen H, Wang S, Chen X, An T, Wang Y, Tian Y, Yu J, Wang D, Xie XS, Bai F, Wang J. Inferring the Evolution and Progression of Small-Cell Lung Cancer by Single-Cell Sequencing of Circulating Tumor Cells. Clin Cancer Res 2019; 25:5049-5060. [PMID: 31113842 DOI: 10.1158/1078-0432.ccr-18-3571] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 03/18/2019] [Accepted: 05/15/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Genomic analyses of small-cell lung cancer (SCLC) are limited by the availability of tumor specimens. This study aimed to investigate the suitability of single-cell sequencing of circulating tumor cells (CTC) as a method of inferring the evolution and progression of SCLCs. EXPERIMENTAL DESIGN Between July 1, 2011, and July 28, 2014, 48 consecutively diagnosed patients with SCLC were recruited for this study. CTCs were captured from each patient with CellSearch system. Somatic mutations and copy number alterations (CNA) were monitored by single-cell sequencing of CTCs during chemotherapy. RESULTS Single-cell sequencing of CTCs can provide a mutational atlas for SCLC. A 10-CNA score based on single CTCs was established as a classifier for outcomes of initial chemotherapy in patients with SCLC. The survival analyses demonstrated that patients with low CNA scores (<0) had significantly prolonged progression-free survival (PFS) and overall survival (OS) after first-line chemotherapy in comparison with those with high scores (≥0; PFS: 212 days vs. 110.5 days, P = 0.0042; and OS: 223.5 days vs. 424 days, P = 0.0006). The positive predictive value and negative predictive value of the CNA score for clinical subtype (refractory vs. sensitive) were 80.0% and 93.7%, respectively. By tracing allele-specific CNAs in CTCs isolated at different time points during chemotherapy, we showed that CNA heterogeneity might result from allelic losses of initially consistent CNAs. CONCLUSIONS Single CTC-based sequencing can be utilized to depict the genomic profiles and evolutionary history of SCLC, thus offering the potential for clinical stratification of patients with SCLC.
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Affiliation(s)
- Zhe Su
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Zhijie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiaohui Ni
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Jianchun Duan
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yan Gao
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Minglei Zhuo
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Ruoyan Li
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Jun Zhao
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Qi Ma
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Hua Bai
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hengyu Chen
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Shuhang Wang
- Clinical Trial Center, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xixi Chen
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Tongtong An
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Yuyan Wang
- Department of Thoracic Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Yanhua Tian
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Jiangyong Yu
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Di Wang
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xiaoliang Sunney Xie
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China. .,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Fan Bai
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China.
| | - Jie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
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18
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Abstract
This paper surveys some of the important insights that molecular evolution has contributed to evolutionary medicine; they include phage therapy, cancer biology, helminth manipulation of the host immune system, quality control of gametes, and pathogen outbreaks. Molecular evolution has helped to revolutionize our understanding of cancer, of autoimmune disease, and of the origin, spread, and pathogenesis of emerging diseases, where it has suggested new therapies, illuminated mechanisms, and revealed historical processes: all have practical therapeutic implications. While much has been accomplished, much remains to be done.
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Affiliation(s)
- Stephen C Stearns
- Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, New Haven, CT, 06520-8106, USA.
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19
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Niida A, Iwasaki WM, Innan H. Neutral Theory in Cancer Cell Population Genetics. Mol Biol Evol 2019; 35:1316-1321. [PMID: 29718454 DOI: 10.1093/molbev/msy091] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Kimura's neutral theory provides the whole theoretical basis of the behavior of mutations in a Wright-Fisher population. We here discuss how it can be applied to a cancer cell population, in which there is an increasing interest in genetic variation within a tumor. We explain a couple of fundamental differences between cancer cell populations and asexual organismal populations. Once these differences are taken into account, a number of powerful theoretical tools developed for a Wright-Fisher population could be readily contribute to our deeper understanding of the evolutionary dynamics of cancer cell population.
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Affiliation(s)
- Atsushi Niida
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Watal M Iwasaki
- Department of Evolutionary Studies of Biosystems, SOKENDAI, The Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
| | - Hideki Innan
- Department of Evolutionary Studies of Biosystems, SOKENDAI, The Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
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20
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Barry P, Vatsiou A, Spiteri I, Nichol D, Cresswell GD, Acar A, Trahearn N, Hrebien S, Garcia-Murillas I, Chkhaidze K, Ermini L, Huntingford IS, Cottom H, Zabaglo L, Koelble K, Khalique S, Rusby JE, Muscara F, Dowsett M, Maley CC, Natrajan R, Yuan Y, Schiavon G, Turner N, Sottoriva A. The Spatiotemporal Evolution of Lymph Node Spread in Early Breast Cancer. Clin Cancer Res 2018; 24:4763-4770. [PMID: 29891724 PMCID: PMC6296441 DOI: 10.1158/1078-0432.ccr-17-3374] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/11/2018] [Accepted: 06/05/2018] [Indexed: 01/13/2023]
Abstract
Purpose: The most significant prognostic factor in early breast cancer is lymph node involvement. This stage between localized and systemic disease is key to understanding breast cancer progression; however, our knowledge of the evolution of lymph node malignant invasion remains limited, as most currently available data are derived from primary tumors.Experimental Design: In 11 patients with treatment-naïve node-positive early breast cancer without clinical evidence of distant metastasis, we investigated lymph node evolution using spatial multiregion sequencing (n = 78 samples) of primary and lymph node deposits and genomic profiling of matched longitudinal circulating tumor DNA (ctDNA).Results: Linear evolution from primary to lymph node was rare (1/11), whereas the majority of cases displayed either early divergence between primary and nodes (4/11) or no detectable divergence (6/11), where both primary and nodal cells belonged to a single recent expansion of a metastatic clone. Divergence of metastatic subclones was driven in part by APOBEC. Longitudinal ctDNA samples from 2 of 7 subjects with evaluable plasma taken perioperatively reflected the two major evolutionary patterns and demonstrate that private mutations can be detected even from early metastatic nodal deposits. Moreover, node removal resulted in disappearance of private lymph node mutations in ctDNA.Conclusions: This study sheds new light on a crucial evolutionary step in the natural history of breast cancer, demonstrating early establishment of axillary lymph node metastasis in a substantial proportion of patients. Clin Cancer Res; 24(19); 4763-70. ©2018 AACR.
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Affiliation(s)
- Peter Barry
- Department of Surgery, Breast Unit, Royal Marsden Hospital, London, United Kingdom
| | - Alexandra Vatsiou
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Inmaculada Spiteri
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Daniel Nichol
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - George D Cresswell
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Ahmet Acar
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Nicholas Trahearn
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Sarah Hrebien
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Isaac Garcia-Murillas
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Kate Chkhaidze
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Luca Ermini
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | | | - Hannah Cottom
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Lila Zabaglo
- Ralph Lauren Breast Cancer Research Centre, Royal Marsden Hospital, London, United Kingdom
| | - Konrad Koelble
- Ralph Lauren Breast Cancer Research Centre, Royal Marsden Hospital, London, United Kingdom
| | - Saira Khalique
- Ralph Lauren Breast Cancer Research Centre, Royal Marsden Hospital, London, United Kingdom
| | - Jennifer E Rusby
- Department of Surgery, Breast Unit, Royal Marsden Hospital, London, United Kingdom
| | - Francesca Muscara
- Department of Surgery, Breast Unit, Royal Marsden Hospital, London, United Kingdom
| | - Mitch Dowsett
- Ralph Lauren Breast Cancer Research Centre, Royal Marsden Hospital, London, United Kingdom
| | - Carlo C Maley
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
- Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Rachael Natrajan
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Yinyin Yuan
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Gaia Schiavon
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Nicholas Turner
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom.
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21
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Environmental Carcinogenesis and Transgenerational Transmission of Carcinogenic Risk: From Genetics to Epigenetics. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15081791. [PMID: 30127322 PMCID: PMC6121489 DOI: 10.3390/ijerph15081791] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 08/09/2018] [Indexed: 12/12/2022]
Abstract
The dominant pathogenic model, somatic mutation theory (SMT), considers carcinogenesis as a ‘genetic accident’ due to the accumulation of ‘stochastic’ DNA mutations. This model was proposed and accepted by the scientific community when cancer mainly affected the elderly, but it does not explain the epidemiological observation of the continuous increase in cancer incidence among children and young adults. Somatic mutation theory has been proposed for a revision based on the emerging experimental evidence, as it does not fully address some issues that have proven to be crucial for carcinogenesis, namely: the inflammatory context of cancer; the key role played by the stroma, microenvironment, endothelial cells, activated macrophages, and surrounding tissues; and the distorted developmental course followed by the neoplastic tissue. Furthermore, SMT is often not able to consider either the existence of specific mutations resulting in a well-defined cancer type, or a clear relationship between mutations and tumor progression. Moreover, it does not explain the mechanism of action of the non-mutagenic and environmental carcinogens. In the last decade, cancer research has highlighted the prominent role of an altered regulation of gene expression, suggesting that cancer should be considered as a result of a polyclonal epigenetic disruption of stem/progenitor cells, mediated by tumour-inducing genes. The maternal and fetal exposure to a wide range of chemicals and environmental contaminants is raising the attention of the scientific community. Indeed, the most powerful procarcinogenic mechanisms of endocrine disruptors and other pollutants is linked to their potential to interfere epigenetically with the embryo-fetal programming of tissues and organs, altering the regulation of the genes involved in the cell cycle, cell proliferation, apoptosis, and other key signaling pathways. The embryo-fetal exposure to environmental, stressful, and proinflammatory triggers (first hit), seems to act as a ‘disease primer’, making fetal cells and tissues more susceptible to the subsequent environmental exposures (second hit), triggering the carcinogenic pathways. Furthermore, even at the molecular level, in carcinogenesis, ‘epigenetics precedes genetics’ as global DNA hypomethylation, and the hypermethylation of tumor suppressor genes are common both in cancerous and in precancerous cells, and generally precede mutations. These epigenetic models may better explain the increase of cancer and chronic/degenerative diseases in the last decades and could be useful to adopt appropriate primary prevention measures, essentially based on the reduction of maternal-fetal and child exposure to several procarcinogenic agents and factors dispersed in the environment and in the food-chains, as recently suggested by the World Health Organization.
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22
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Abstract
Kimura's neutral theory argued that positive selection was not responsible for an appreciable fraction of molecular substitutions. Correspondingly, quantitative analysis reveals that the vast majority of substitutions in cancer genomes are not detectably under selection. Insights from the somatic evolution of cancer reveal that beneficial substitutions in cancer constitute a small but important fraction of the molecular variants. The molecular evolution of cancer community will benefit by incorporating the neutral theory of molecular evolution into their understanding and analysis of cancer evolution-and accepting the use of tractable, predictive models, even when there is some evidence that they are not perfect.
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Affiliation(s)
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale University, New Haven, CT
- Program in Computational Biology and Bioinformatics
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
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23
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Barradas-Bautista D, Alvarado-Mentado M, Agostino M, Cocho G. Cancer growth and metastasis as a metaphor of Go gaming: An Ising model approach. PLoS One 2018; 13:e0195654. [PMID: 29718932 PMCID: PMC5931478 DOI: 10.1371/journal.pone.0195654] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 03/27/2018] [Indexed: 01/03/2023] Open
Abstract
This work aims for modeling and simulating the metastasis of cancer, via the analogy between the cancer process and the board game Go. In the game of Go, black stones that play first could correspond to a metaphor of the birth, growth, and metastasis of cancer. Moreover, playing white stones on the second turn could correspond the inhibition of cancer invasion. Mathematical modeling and algorithmic simulation of Go may therefore benefit the efforts to deploy therapies to surpass cancer illness by providing insight into the cellular growth and expansion over a tissue area. We use the Ising Hamiltonian, that models the energy exchange in interacting particles, for modeling the cancer dynamics. Parameters in the energy function refer the biochemical elements that induce cancer birth, growth, and metastasis; as well as the biochemical immune system process of defense.
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Affiliation(s)
| | | | - Mark Agostino
- Curtin Health Innovation Research Institute and Curtin Institute Computation, Curtin University, Perth, Australia
| | - Germinal Cocho
- Complex Sciences Center, UNAM, Mexico City, Mexico.,Physics Institute, UNAM, Mexico City, Mexico
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24
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El-Kebir M, Satas G, Raphael BJ. Inferring parsimonious migration histories for metastatic cancers. Nat Genet 2018; 50:718-726. [PMID: 29700472 PMCID: PMC6103651 DOI: 10.1038/s41588-018-0106-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 03/09/2018] [Indexed: 01/29/2023]
Abstract
Metastasis is the migration of cancerous cells from a primary tumor to other anatomical sites. Although metastasis was long thought to result from monoclonal seeding, or single cellular migrations, recent phylogenetic analyses of metastatic cancers have reported complex patterns of cellular migrations between sites, including polyclonal migrations and reseeding. However, accurate determination of migration patterns from somatic mutation data is complicated by intratumor heterogeneity and discordance between clonal lineage and cellular migration. We introduce MACHINA, a multi-objective optimization algorithm that jointly infers clonal lineages and parsimonious migration histories of metastatic cancers from DNA sequencing data. MACHINA analysis of data from multiple cancers shows that migration patterns are often not uniquely determined from sequencing data alone and that complicated migration patterns among primary tumors and metastases may be less prevalent than previously reported. MACHINA's rigorous analysis of migration histories will aid in studies of the drivers of metastasis.
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Affiliation(s)
- Mohammed El-Kebir
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gryte Satas
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Department of Computer Science, Brown University, Providence, RI, USA
| | - Benjamin J Raphael
- Department of Computer Science, Princeton University, Princeton, NJ, USA.
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25
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Watkins TBK, Schwarz RF. Phylogenetic Quantification of Intratumor Heterogeneity. Cold Spring Harb Perspect Med 2018; 8:cshperspect.a028316. [PMID: 28710259 DOI: 10.1101/cshperspect.a028316] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
As sequencing efforts continue to reveal the extent of the intratumor heterogeneity (ITH) present in human cancers, the importance of evolutionary studies attempting to trace its etiology has increased. Sequencing multiple samples or tumor regions from the same patient has become affordable and is an effective way of tracing these evolutionary pathways, understanding selection, and detecting clonal expansions in ways impractical with single samples alone. In this article, we discuss and show the benefits of such multisample studies. We describe how multiple samples can guide tree inference through accurate phasing of germline variants and copy-number profiles. We show their relevance in detecting clonal expansions and deriving summary statistics quantifying the overall degree of ITH, and discuss how the relationship of metastatic clades might give us insight into the dominant mode of cancer progression. We further outline how multisample studies might help us better understand selective processes acting on cancer genomes and help to detect neutral evolution and mutator phenotypes.
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Affiliation(s)
| | - Roland F Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
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26
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Gomez K, Miura S, Huuki LA, Spell BS, Townsend JP, Kumar S. Somatic evolutionary timings of driver mutations. BMC Cancer 2018; 18:85. [PMID: 29347918 PMCID: PMC5774140 DOI: 10.1186/s12885-017-3977-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 12/21/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND A unified analysis of DNA sequences from hundreds of tumors concluded that the driver mutations primarily occur in the earliest stages of cancer formation, with relatively few driver mutation events detected in the late-arising subclones. However, emerging evidence from the sequencing of multiple tumors and tumor regions per individual suggests that late-arising subclones with additional driver mutations are underestimated in single-sample analyses. METHODS To test whether driver mutations generally map to early tumor development, we examined multi-regional tumor sequencing data from 101 individuals reported in 11 published studies. Following previous studies, we annotated mutations as early-arising when all tumors/regions had those mutations (ubiquitous). We then inferred the fraction of mutations occurring early and compared it with late-arising mutations that were found in only single tumors/regions. RESULTS While a large fraction of driver mutations in tumors occurred relatively early in cancers, later driver mutations occurred at least as frequently as the early drivers in a substantial number of patients. This result was robust to many different approaches to annotate driver mutations. The relative frequency of early and late driver mutations varied among patients of the same cancer type and in different cancer types. We found that previous reports of the preponderance of early driver mutations were primarily informed by analysis of single tumor variant allele profiles, with which it is challenging to clearly distinguish between early and late drivers. CONCLUSIONS The origin and preponderance of new driver mutations are not limited to early stages of tumor evolution, with different tumors and regions showing distinct driver mutations and, consequently, distinct characteristics. Therefore, tumors with extensive intratumor heterogeneity appear to have many newly acquired drivers.
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Affiliation(s)
- Karen Gomez
- Institute for Genomics and Evolutionary Medicine, Sudhir Kumar, SERC 602A, 1925 N. 12th Street, Philadelphia, PA 19122 USA
- Department of Biology, Temple University, Philadelphia, PA 19122 USA
| | - Sayaka Miura
- Institute for Genomics and Evolutionary Medicine, Sudhir Kumar, SERC 602A, 1925 N. 12th Street, Philadelphia, PA 19122 USA
- Department of Biology, Temple University, Philadelphia, PA 19122 USA
| | - Louise A. Huuki
- Institute for Genomics and Evolutionary Medicine, Sudhir Kumar, SERC 602A, 1925 N. 12th Street, Philadelphia, PA 19122 USA
| | - Brianna S. Spell
- Institute for Genomics and Evolutionary Medicine, Sudhir Kumar, SERC 602A, 1925 N. 12th Street, Philadelphia, PA 19122 USA
- Department of Biology, Temple University, Philadelphia, PA 19122 USA
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut 06510 USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511 USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511 USA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Sudhir Kumar, SERC 602A, 1925 N. 12th Street, Philadelphia, PA 19122 USA
- Department of Biology, Temple University, Philadelphia, PA 19122 USA
- Center for Genomic Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
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27
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Liu B, Mitani Y, Rao X, Zafereo M, Zhang J, Zhang J, Futreal PA, Lozano G, El-Naggar AK. Spatio-Temporal Genomic Heterogeneity, Phylogeny, and Metastatic Evolution in Salivary Adenoid Cystic Carcinoma. J Natl Cancer Inst 2017; 109:3855145. [PMID: 29117356 DOI: 10.1093/jnci/djx033] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 02/13/2017] [Indexed: 12/24/2022] Open
Abstract
Background Adenoid cystic carcinoma (ACC), an uncommon and indolent salivary gland malignancy, is characterized by varied morphologic and clinical manifestations. Molecular genetic studies of ACC identified certain structural and mutational alterations that may play a driver role in tumor development. The evolution and regional consistency of these events in ACC development progression are uncertain. Methods To investigate the spatial and temporal clonal landscape of ACC, whole-genome sequencing and variant analyses were performed on 34 regionally sampled primary tumors and their concurrent and metachronous metastatic deposits from eight patients. Results The average mutation rate per case (primary and metastasis) was 0.32 per million base pairs, and the average incidence of shared mutations in primary and metastatic specimens in each case was 21.9% (range = 0%-44.4%). The analyses revealed considerable spatial clonal differences within and between primary tumors and metastatic disease. Phylogeny formation displayed branching evolution with a main trunk and two distinct mono-splits in all cases. One of the main branches represented intratumor subclonal diversity, and the other delineated metastatic departure and progression. All metastatic tumors shared clonal linkage to their matching primary in concordance with parallel dissemination of metastasis. Synchronous metastases were genomically more similar to their primary than metachronous metastatic disease. Truncal genetic alterations included somatic mutations in the NOTCH pathway genes (NOTCH1 and SPEN) and t(6;9) associated gene fusions. Conclusions Our study delineated clonal and subclonal phylogeny for primary and metastatic ACC, defined early genetic drivers, and provides a conceptual framework for a rational strategy to integrate heterogeneity in clinical assessment.
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Affiliation(s)
- Bin Liu
- Affiliations of authors: Departments of Genetics and The Center for Genetics and Genomics (BL, XR, GL), Pathology (YM, AKEN), Head and Neck Surgery (MZ), Thoracic/Head and Neck Medical Oncology (JianjZ), and Genomic Medicine (JianjZ, JianhZ, PAF), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yoshitsugu Mitani
- Affiliations of authors: Departments of Genetics and The Center for Genetics and Genomics (BL, XR, GL), Pathology (YM, AKEN), Head and Neck Surgery (MZ), Thoracic/Head and Neck Medical Oncology (JianjZ), and Genomic Medicine (JianjZ, JianhZ, PAF), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Xiayu Rao
- Affiliations of authors: Departments of Genetics and The Center for Genetics and Genomics (BL, XR, GL), Pathology (YM, AKEN), Head and Neck Surgery (MZ), Thoracic/Head and Neck Medical Oncology (JianjZ), and Genomic Medicine (JianjZ, JianhZ, PAF), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Mark Zafereo
- Affiliations of authors: Departments of Genetics and The Center for Genetics and Genomics (BL, XR, GL), Pathology (YM, AKEN), Head and Neck Surgery (MZ), Thoracic/Head and Neck Medical Oncology (JianjZ), and Genomic Medicine (JianjZ, JianhZ, PAF), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jianjun Zhang
- Affiliations of authors: Departments of Genetics and The Center for Genetics and Genomics (BL, XR, GL), Pathology (YM, AKEN), Head and Neck Surgery (MZ), Thoracic/Head and Neck Medical Oncology (JianjZ), and Genomic Medicine (JianjZ, JianhZ, PAF), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jianhua Zhang
- Affiliations of authors: Departments of Genetics and The Center for Genetics and Genomics (BL, XR, GL), Pathology (YM, AKEN), Head and Neck Surgery (MZ), Thoracic/Head and Neck Medical Oncology (JianjZ), and Genomic Medicine (JianjZ, JianhZ, PAF), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - P Andrew Futreal
- Affiliations of authors: Departments of Genetics and The Center for Genetics and Genomics (BL, XR, GL), Pathology (YM, AKEN), Head and Neck Surgery (MZ), Thoracic/Head and Neck Medical Oncology (JianjZ), and Genomic Medicine (JianjZ, JianhZ, PAF), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Guillermina Lozano
- Affiliations of authors: Departments of Genetics and The Center for Genetics and Genomics (BL, XR, GL), Pathology (YM, AKEN), Head and Neck Surgery (MZ), Thoracic/Head and Neck Medical Oncology (JianjZ), and Genomic Medicine (JianjZ, JianhZ, PAF), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Adel K El-Naggar
- Affiliations of authors: Departments of Genetics and The Center for Genetics and Genomics (BL, XR, GL), Pathology (YM, AKEN), Head and Neck Surgery (MZ), Thoracic/Head and Neck Medical Oncology (JianjZ), and Genomic Medicine (JianjZ, JianhZ, PAF), The University of Texas MD Anderson Cancer Center, Houston, TX
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28
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Maley CC, Aktipis A, Graham TA, Sottoriva A, Boddy AM, Janiszewska M, Silva AS, Gerlinger M, Yuan Y, Pienta KJ, Anderson KS, Gatenby R, Swanton C, Posada D, Wu CI, Schiffman JD, Hwang ES, Polyak K, Anderson ARA, Brown JS, Greaves M, Shibata D. Classifying the evolutionary and ecological features of neoplasms. Nat Rev Cancer 2017; 17:605-619. [PMID: 28912577 PMCID: PMC5811185 DOI: 10.1038/nrc.2017.69] [Citation(s) in RCA: 243] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neoplasms change over time through a process of cell-level evolution, driven by genetic and epigenetic alterations. However, the ecology of the microenvironment of a neoplastic cell determines which changes provide adaptive benefits. There is widespread recognition of the importance of these evolutionary and ecological processes in cancer, but to date, no system has been proposed for drawing clinically relevant distinctions between how different tumours are evolving. On the basis of a consensus conference of experts in the fields of cancer evolution and cancer ecology, we propose a framework for classifying tumours that is based on four relevant components. These are the diversity of neoplastic cells (intratumoural heterogeneity) and changes over time in that diversity, which make up an evolutionary index (Evo-index), as well as the hazards to neoplastic cell survival and the resources available to neoplastic cells, which make up an ecological index (Eco-index). We review evidence demonstrating the importance of each of these factors and describe multiple methods that can be used to measure them. Development of this classification system holds promise for enabling clinicians to personalize optimal interventions based on the evolvability of the patient's tumour. The Evo- and Eco-indices provide a common lexicon for communicating about how neoplasms change in response to interventions, with potential implications for clinical trials, personalized medicine and basic cancer research.
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Affiliation(s)
- Carlo C Maley
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave, Tempe, Arizona 85287, USA
| | - Athena Aktipis
- Department of Psychology, Center for Evolution and Medicine, Arizona State University, 651 E. University Drive, Tempe, Arizona 85287, USA
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Amy M Boddy
- Department of Anthropology, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Michalina Janiszewska
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue D740C, Boston, Massachusetts 02215, USA
| | - Ariosto S Silva
- Department of Cancer Imaging and Metabolism, Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, USA
| | - Marco Gerlinger
- Centre for Evolution and Cancer, Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Yinyin Yuan
- Centre for Evolution and Cancer, The Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Kenneth J Pienta
- Brady Urological Institute, The Johns Hopkins School of Medicine, 600 N. Wolfe Street, Baltimore, Maryland 21287, USA
| | - Karen S Anderson
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave, Tempe, Arizona 85287, USA
| | - Robert Gatenby
- Cancer Biology and Evolution Program, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, Florida 33612, USA
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - David Posada
- Department of Biochemistry, Genetics and Immunology and Biomedical Research Center (CINBIO), University of Vigo, Spain; Galicia Sur Health Research Institute, Vigo, 36310, Spain
| | - Chung-I Wu
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
| | - Joshua D Schiffman
- Departments of Pediatrics and Oncological Sciences, Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, Utah 84108, USA
| | - E Shelley Hwang
- Department of Surgery, Duke University and Duke Cancer Institute, 465 Seeley Mudd Building, Durham, North Carolina 27710, USA
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue D740C, Boston, Massachusetts 02215, USA
| | - Alexander R A Anderson
- Integrated Mathematical Oncology Department, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, Florida 33612, USA
| | - Joel S Brown
- Integrated Mathematical Oncology Department, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, Florida 33612, USA
| | - Mel Greaves
- Centre for Evolution and Cancer, The Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Darryl Shibata
- Department of Pathology, Norris Comprehensive Cancer Center, University of Southern California, 1441 Eastlake Avenue, NOR2424, Los Angeles, California 90033, USA
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29
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Abstract
Rapid advances in high-throughput sequencing and a growing realization of the importance of evolutionary theory to cancer genomics have led to a proliferation of phylogenetic studies of tumour progression. These studies have yielded not only new insights but also a plethora of experimental approaches, sometimes reaching conflicting or poorly supported conclusions. Here, we consider this body of work in light of the key computational principles underpinning phylogenetic inference, with the goal of providing practical guidance on the design and analysis of scientifically rigorous tumour phylogeny studies. We survey the range of methods and tools available to the researcher, their key applications, and the various unsolved problems, closing with a perspective on the prospects and broader implications of this field.
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Affiliation(s)
- Russell Schwartz
- Department of Biological Sciences and Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15217, USA
| | - Alejandro A Schäffer
- Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20892, USA
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30
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Reiter JG, Makohon-Moore AP, Gerold JM, Bozic I, Chatterjee K, Iacobuzio-Donahue CA, Vogelstein B, Nowak MA. Reconstructing metastatic seeding patterns of human cancers. Nat Commun 2017; 8:14114. [PMID: 28139641 PMCID: PMC5290319 DOI: 10.1038/ncomms14114] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 11/24/2016] [Indexed: 12/12/2022] Open
Abstract
Reconstructing the evolutionary history of metastases is critical for understanding their basic biological principles and has profound clinical implications. Genome-wide sequencing data has enabled modern phylogenomic methods to accurately dissect subclones and their phylogenies from noisy and impure bulk tumour samples at unprecedented depth. However, existing methods are not designed to infer metastatic seeding patterns. Here we develop a tool, called Treeomics, to reconstruct the phylogeny of metastases and map subclones to their anatomic locations. Treeomics infers comprehensive seeding patterns for pancreatic, ovarian, and prostate cancers. Moreover, Treeomics correctly disambiguates true seeding patterns from sequencing artifacts; 7% of variants were misclassified by conventional statistical methods. These artifacts can skew phylogenies by creating illusory tumour heterogeneity among distinct samples. In silico benchmarking on simulated tumour phylogenies across a wide range of sample purities (15–95%) and sequencing depths (25-800 × ) demonstrates the accuracy of Treeomics compared with existing methods. Tumours frequently metastasize to multiple anatomical sites and understanding how these different metastases evolve may be important for therapy. Here, the authors develop a method—Treeomics—that can construct phylogenies from multiple metastases from next-generation sequencing data.
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Affiliation(s)
- Johannes G Reiter
- Program for Evolutionary Dynamics, Harvard University, Cambridge, Massachusetts 02138, USA.,IST (Institute of Science and Technology) Austria, Klosterneuburg 3400, Austria
| | - Alvin P Makohon-Moore
- The David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Jeffrey M Gerold
- Program for Evolutionary Dynamics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Ivana Bozic
- Program for Evolutionary Dynamics, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Mathematics, Harvard University, Cambridge, Massachusetts 02138, USA
| | | | - Christine A Iacobuzio-Donahue
- The David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Bert Vogelstein
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,The Ludwig Center and Howard Hughes Medical Institute at The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Martin A Nowak
- Program for Evolutionary Dynamics, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Mathematics, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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31
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Salazar BM, Balczewski EA, Ung CY, Zhu S. Neuroblastoma, a Paradigm for Big Data Science in Pediatric Oncology. Int J Mol Sci 2016; 18:E37. [PMID: 28035989 PMCID: PMC5297672 DOI: 10.3390/ijms18010037] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/14/2016] [Accepted: 12/17/2016] [Indexed: 12/13/2022] Open
Abstract
Pediatric cancers rarely exhibit recurrent mutational events when compared to most adult cancers. This poses a challenge in understanding how cancers initiate, progress, and metastasize in early childhood. Also, due to limited detected driver mutations, it is difficult to benchmark key genes for drug development. In this review, we use neuroblastoma, a pediatric solid tumor of neural crest origin, as a paradigm for exploring "big data" applications in pediatric oncology. Computational strategies derived from big data science-network- and machine learning-based modeling and drug repositioning-hold the promise of shedding new light on the molecular mechanisms driving neuroblastoma pathogenesis and identifying potential therapeutics to combat this devastating disease. These strategies integrate robust data input, from genomic and transcriptomic studies, clinical data, and in vivo and in vitro experimental models specific to neuroblastoma and other types of cancers that closely mimic its biological characteristics. We discuss contexts in which "big data" and computational approaches, especially network-based modeling, may advance neuroblastoma research, describe currently available data and resources, and propose future models of strategic data collection and analyses for neuroblastoma and other related diseases.
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Affiliation(s)
- Brittany M Salazar
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55902, USA.
| | - Emily A Balczewski
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
| | - Choong Yong Ung
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55902, USA.
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
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32
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Somarelli JA, Ware KE, Kostadinov R, Robinson JM, Amri H, Abu-Asab M, Fourie N, Diogo R, Swofford D, Townsend JP. PhyloOncology: Understanding cancer through phylogenetic analysis. Biochim Biophys Acta Rev Cancer 2016; 1867:101-108. [PMID: 27810337 DOI: 10.1016/j.bbcan.2016.10.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 10/14/2016] [Accepted: 10/26/2016] [Indexed: 11/30/2022]
Abstract
Despite decades of research and an enormity of resultant data, cancer remains a significant public health problem. New tools and fresh perspectives are needed to obtain fundamental insights, to develop better prognostic and predictive tools, and to identify improved therapeutic interventions. With increasingly common genome-scale data, one suite of algorithms and concepts with potential to shed light on cancer biology is phylogenetics, a scientific discipline used in diverse fields. From grouping subsets of cancer samples to tracing subclonal evolution during cancer progression and metastasis, the use of phylogenetics is a powerful systems biology approach. Well-developed phylogenetic applications provide fast, robust approaches to analyze high-dimensional, heterogeneous cancer data sets. This article is part of a Special Issue entitled: Evolutionary principles - heterogeneity in cancer?, edited by Dr. Robert A. Gatenby.
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Affiliation(s)
- Jason A Somarelli
- Duke Cancer Institute and the Department of Medicine, Duke University Medical Center, Durham, NC 27710, United States.
| | - Kathryn E Ware
- Duke Cancer Institute and the Department of Medicine, Duke University Medical Center, Durham, NC 27710, United States
| | - Rumen Kostadinov
- Pediatric Oncology, School of Medicine, Johns Hopkins University, United States
| | - Jeffrey M Robinson
- Anatomy Department, College of Medicine, Howard University, Washington, DC 20059, United States; Digestive Disorders Unit, National Institute of Nursing Research, NIH, Bethesda, MD 20892, United States
| | - Hakima Amri
- Department of Biochemistry and Cellular and Molecular Biology, Georgetown University Medical Center, Washington, DC 20007, United States
| | - Mones Abu-Asab
- Section of Ultrastructural Biology, National Eye Institute, NIH, Bethesda, MD 20892, United States
| | - Nicolaas Fourie
- Digestive Disorders Unit, National Institute of Nursing Research, NIH, Bethesda, MD 20892, United States
| | - Rui Diogo
- Anatomy Department, College of Medicine, Howard University, Washington, DC 20059, United States
| | - David Swofford
- Department of Biology, Duke University Trinity College of Arts and Sciences, Durham, NC 27710, United States
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale University, United States; Department of Ecology and Evolutionary Biology, Yale University, United States; Department of Program in Computational Biology and Bioinformatics, Yale University, United States.
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33
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Mangiola S, Hong MKH, Cmero M, Kurganovs N, Ryan A, Costello AJ, Corcoran NM, Macintyre G, Hovens CM. Comparing nodal versus bony metastatic spread using tumour phylogenies. Sci Rep 2016; 6:33918. [PMID: 27653089 PMCID: PMC5031992 DOI: 10.1038/srep33918] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/31/2016] [Indexed: 02/07/2023] Open
Abstract
The role of lymph node metastases in distant prostate cancer dissemination and lethality is ill defined. Patients with metastases restricted to lymph nodes have a better prognosis than those with distant metastatic spread, suggesting the possibility of distinct aetiologies. To explore this, we traced patterns of cancer dissemination using tumour phylogenies inferred from genome-wide copy-number profiling of 48 samples across 3 patients with lymph node metastatic disease and 3 patients with osseous metastatic disease. Our results show that metastatic cells in regional lymph nodes originate from evolutionary advanced extraprostatic tumour cells rather than less advanced central tumour cell populations. In contrast, osseous metastases do not exhibit such a constrained developmental lineage, arising from either intra or extraprostatic tumour cell populations, at early and late stages in the evolution of the primary. Collectively, this comparison suggests that lymph node metastases may not be an intermediate developmental step for distant osseous metastases, but rather represent a distinct metastatic lineage.
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Affiliation(s)
- Stefano Mangiola
- Departments of Urology and Surgery, Royal Melbourne Hospital and University of Melbourne, Parkville 3050 Victoria, Australia.,Centre for Neural Engineering, 203 Bouverie St, Carlton 3053, Victoria, Australia
| | - Matthew K H Hong
- Departments of Urology and Surgery, Royal Melbourne Hospital and University of Melbourne, Parkville 3050 Victoria, Australia
| | - Marek Cmero
- Departments of Urology and Surgery, Royal Melbourne Hospital and University of Melbourne, Parkville 3050 Victoria, Australia.,Centre for Neural Engineering, 203 Bouverie St, Carlton 3053, Victoria, Australia
| | - Natalie Kurganovs
- Departments of Urology and Surgery, Royal Melbourne Hospital and University of Melbourne, Parkville 3050 Victoria, Australia
| | - Andrew Ryan
- TissuPath Specialist Pathology, Mount Waverley 3149, Victoria, Australia
| | - Anthony J Costello
- Departments of Urology and Surgery, Royal Melbourne Hospital and University of Melbourne, Parkville 3050 Victoria, Australia.,The Epworth Prostate Centre, Epworth Hospital, Richmond 3121, Victoria, Australia
| | - Niall M Corcoran
- Departments of Urology and Surgery, Royal Melbourne Hospital and University of Melbourne, Parkville 3050 Victoria, Australia.,The Epworth Prostate Centre, Epworth Hospital, Richmond 3121, Victoria, Australia
| | - Geoff Macintyre
- Centre for Neural Engineering, 203 Bouverie St, Carlton 3053, Victoria, Australia.,Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Christopher M Hovens
- Departments of Urology and Surgery, Royal Melbourne Hospital and University of Melbourne, Parkville 3050 Victoria, Australia.,The Epworth Prostate Centre, Epworth Hospital, Richmond 3121, Victoria, Australia
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34
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Grizzi F. Cancer heterogeneity and drug metabolism: what we know and what we need to know. Future Oncol 2016; 12:1317-9. [PMID: 27182685 DOI: 10.2217/fon-2015-0039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Fabio Grizzi
- Department of Immunology & Inflammation Humanitas Clinical & Research Center, 20089 Rozzano, Milan, Italy
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Abstract
Many aspects of the evolutionary process of tumorigenesis that are fundamental to cancer biology and targeted treatment have been challenging to reveal, such as the divergence times and genetic clonality of metastatic lineages. To address these challenges, we performed tumor phylogenetics using molecular evolutionary models, reconstructed ancestral states of somatic mutations, and inferred cancer chronograms to yield three conclusions. First, in contrast to a linear model of cancer progression, metastases can originate from divergent lineages within primary tumors. Evolved genetic changes in cancer lineages likely affect only the proclivity toward metastasis. Single genetic changes are unlikely to be necessary or sufficient for metastasis. Second, metastatic lineages can arise early in tumor development, sometimes long before diagnosis. The early genetic divergence of some metastatic lineages directs attention toward research on driver genes that are mutated early in cancer evolution. Last, the temporal order of occurrence of driver mutations can be inferred from phylogenetic analysis of cancer chronograms, guiding development of targeted therapeutics effective against primary tumors and metastases.
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36
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Cancer classification in the genomic era: five contemporary problems. Hum Genomics 2015; 9:27. [PMID: 26481255 PMCID: PMC4612488 DOI: 10.1186/s40246-015-0049-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 10/06/2015] [Indexed: 12/20/2022] Open
Abstract
Classification is an everyday instinct as well as a full-fledged scientific discipline. Throughout the history of medicine, disease classification is central to how we develop knowledge, make diagnosis, and assign treatment. Here, we discuss the classification of cancer and the process of categorizing cancer subtypes based on their observed clinical and biological features. Traditionally, cancer nomenclature is primarily based on organ location, e.g., “lung cancer” designates a tumor originating in lung structures. Within each organ-specific major type, finer subgroups can be defined based on patient age, cell type, histological grades, and sometimes molecular markers, e.g., hormonal receptor status in breast cancer or microsatellite instability in colorectal cancer. In the past 15+ years, high-throughput technologies have generated rich new data regarding somatic variations in DNA, RNA, protein, or epigenomic features for many cancers. These data, collected for increasingly large tumor cohorts, have provided not only new insights into the biological diversity of human cancers but also exciting opportunities to discover previously unrecognized cancer subtypes. Meanwhile, the unprecedented volume and complexity of these data pose significant challenges for biostatisticians, cancer biologists, and clinicians alike. Here, we review five related issues that represent contemporary problems in cancer taxonomy and interpretation. (1) How many cancer subtypes are there? (2) How can we evaluate the robustness of a new classification system? (3) How are classification systems affected by intratumor heterogeneity and tumor evolution? (4) How should we interpret cancer subtypes? (5) Can multiple classification systems co-exist? While related issues have existed for a long time, we will focus on those aspects that have been magnified by the recent influx of complex multi-omics data. Exploration of these problems is essential for data-driven refinement of cancer classification and the successful application of these concepts in precision medicine.
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