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Salcedo A, Tarabichi M, Buchanan A, Espiritu SMG, Zhang H, Zhu K, Ou Yang TH, Leshchiner I, Anastassiou D, Guan Y, Jang GH, Mootor MFE, Haase K, Deshwar AG, Zou W, Umar I, Dentro S, Wintersinger JA, Chiotti K, Demeulemeester J, Jolly C, Sycza L, Ko M, Wedge DC, Morris QD, Ellrott K, Van Loo P, Boutros PC. Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction. Nat Biotechnol 2024:10.1038/s41587-024-02250-y. [PMID: 38862616 DOI: 10.1038/s41587-024-02250-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 04/17/2024] [Indexed: 06/13/2024]
Abstract
Subclonal reconstruction algorithms use bulk DNA sequencing data to quantify parameters of tumor evolution, allowing an assessment of how cancers initiate, progress and respond to selective pressures. We launched the ICGC-TCGA (International Cancer Genome Consortium-The Cancer Genome Atlas) DREAM Somatic Mutation Calling Tumor Heterogeneity and Evolution Challenge to benchmark existing subclonal reconstruction algorithms. This 7-year community effort used cloud computing to benchmark 31 subclonal reconstruction algorithms on 51 simulated tumors. Algorithms were scored on seven independent tasks, leading to 12,061 total runs. Algorithm choice influenced performance substantially more than tumor features but purity-adjusted read depth, copy-number state and read mappability were associated with the performance of most algorithms on most tasks. No single algorithm was a top performer for all seven tasks and existing ensemble strategies were unable to outperform the best individual methods, highlighting a key research need. All containerized methods, evaluation code and datasets are available to support further assessment of the determinants of subclonal reconstruction accuracy and development of improved methods to understand tumor evolution.
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Affiliation(s)
- Adriana Salcedo
- Department of Human Genetics, University of California, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA.
- Institute for Precision Health, University of California, Los Angeles, CA, USA.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
| | - Maxime Tarabichi
- The Francis Crick Institute, London, UK.
- Wellcome Sanger Institute, Hinxton, UK.
- Institute for Interdisciplinary Research, Université Libre de Bruxelles, Brussels, Belgium.
| | - Alex Buchanan
- Oregon Health and Sciences University, Portland, OR, USA
| | | | - Hongjiu Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Kaiyi Zhu
- Department of Systems Biology, Columbia University, New York, NY, USA
- Center for Cancer Systems Therapeutics, Columbia University, New York, NY, USA
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | - Tai-Hsien Ou Yang
- Department of Systems Biology, Columbia University, New York, NY, USA
- Center for Cancer Systems Therapeutics, Columbia University, New York, NY, USA
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | | | - Dimitris Anastassiou
- Department of Systems Biology, Columbia University, New York, NY, USA
- Center for Cancer Systems Therapeutics, Columbia University, New York, NY, USA
- Department of Electrical Engineering, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Electronic Engineering and Computer Science, University of Michigan, Ann Arbor, MI, USA
| | - Gun Ho Jang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Mohammed F E Mootor
- Department of Human Genetics, University of California, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA
- Institute for Precision Health, University of California, Los Angeles, CA, USA
| | | | - Amit G Deshwar
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - William Zou
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Imaad Umar
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Stefan Dentro
- The Francis Crick Institute, London, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Jeff A Wintersinger
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Kami Chiotti
- Oregon Health and Sciences University, Portland, OR, USA
| | - Jonas Demeulemeester
- The Francis Crick Institute, London, UK
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | | | - Lesia Sycza
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Minjeong Ko
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - David C Wedge
- Big Data Institute, University of Oxford, Oxford, UK
- Manchester Cancer Research Center, University of Manchester, Manchester, UK
| | - Quaid D Morris
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kyle Ellrott
- Oregon Health and Sciences University, Portland, OR, USA.
| | - Peter Van Loo
- The Francis Crick Institute, London, UK.
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Paul C Boutros
- Department of Human Genetics, University of California, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA.
- Institute for Precision Health, University of California, Los Angeles, CA, USA.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada.
- Department of Urology, University of California, Los Angeles, CA, USA.
- Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA.
- California NanoSystems Institute, University of California, Los Angeles, CA, USA.
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2
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Murciano-Goroff YR, Uppal M, Chen M, Harada G, Schram AM. Basket Trials: Past, Present, and Future. ANNUAL REVIEW OF CANCER BIOLOGY 2024; 8:59-80. [PMID: 38938274 PMCID: PMC11210107 DOI: 10.1146/annurev-cancerbio-061421-012927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Large-scale tumor molecular profiling has revealed that diverse cancer histologies are driven by common pathways with unifying biomarkers that can be exploited therapeutically. Disease-agnostic basket trials have been increasingly utilized to test biomarker-driven therapies across cancer types. These trials have led to drug approvals and improved the lives of patients while simultaneously advancing our understanding of cancer biology. This review focuses on the practicalities of implementing basket trials, with an emphasis on molecularly targeted trials. We examine the biologic subtleties of genomic biomarker and patient selection, discuss previous successes in drug development facilitated by basket trials, describe certain novel targets and drugs, and emphasize practical considerations for participant recruitment and study design. This review also highlights strategies for aiding patient access to basket trials. As basket trials become more common, steps to ensure equitable implementation of these studies will be critical for molecularly targeted drug development.
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Affiliation(s)
| | - Manik Uppal
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Monica Chen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Guilherme Harada
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alison M Schram
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
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3
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Steinberg PL, Liu LY, Neiman-Golden A, Patel Y, Boutros PC. Quantifying the seed sensitivity of cancer subclonal reconstruction algorithms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.579021. [PMID: 38370678 PMCID: PMC10871259 DOI: 10.1101/2024.02.05.579021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Background Intra-tumoural heterogeneity complicates cancer prognosis and impairs treatment success. One of the ways subclonal reconstruction (SRC) quantifies intra-tumoural heterogeneity is by estimating the number of subclones present in bulk DNA sequencing data. SRC algorithms are probabilistic and need to be initialized by a random seed. However, the seeds used in bioinformatics algorithms are rarely reported in the literature. Thus, the impact of the initializing seed on SRC solutions has not been studied. To address this gap, we generated a set of ten random seeds to systematically benchmark the seed sensitivity of three probabilistic SRC algorithms: PyClone-VI, DPClust, and PhyloWGS. Results We characterized the seed sensitivity of three algorithms across fourteen whole-genome sequences of head and neck squamous cell carcinoma and nine SRC pipelines, each composed of a single nucleotide variant caller, a copy number aberration caller and an SRC algorithm. This led to a total of 1470 subclonal reconstructions, including 1260 single-region and 210 multi-region reconstructions. The number of subclones estimated per patient vary across SRC pipelines, but all three SRC algorithms show substantial seed sensitivity: subclone estimates vary across different seeds for the same set of input using the same SRC algorithm. No seed consistently estimated the mode number of subclones across all patients for any SRC algorithm. Conclusions These findings highlight the variability in quantifying intra-tumoural heterogeneity introduced by the seed sensitivity of probabilistic SRC algorithms. We recommend that authors, reviewers and editors adopt guidelines to both report and randomize seed choices. It may also be valuable to consider seed-sensitivity in the benchmarking of newly developed SRC algorithms. These findings may be of interest in other areas of bioinformatics where seeded probabilistic algorithms are used and suggest consideration of formal seed reporting standards to enhance reproducibility.
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Affiliation(s)
- Philippa L. Steinberg
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, CA, 90024, USA
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Lydia Y. Liu
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, CA, 90024, USA
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2C1, Canada
| | - Anna Neiman-Golden
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, CA, 90024, USA
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Yash Patel
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, CA, 90024, USA
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Paul C. Boutros
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, CA, 90024, USA
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Urology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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Xu BL, Wang XM, Chen GY, Yuan P, Han L, Qin P, Li TP, You HQ, Zhang CJ, Fu XM, Yuan L, Wang ZB, Gao QL. In vivo growth of subclones derived from Lewis lung carcinoma is determined by the tumor microenvironment. Am J Cancer Res 2022; 12:5255-5270. [PMID: 36504888 PMCID: PMC9729899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 11/02/2022] [Indexed: 12/15/2022] Open
Abstract
Heterogeneity is a fundamental feature of human tumors and plays a major role in drug resistance and disease progression. In the present study, we selected single-cell-derived cell lines (SCDCLs) derived from Lewis lung carcinoma (LLC1) cells to investigate tumorigenesis and heterogeneity. SCDCLs were generated using limiting dilution. Five SCDCLs were subcutaneously injected into wild-type C57BL/6N mice; however, they displayed significant differences in tumor growth. Subclone SCC1 grew the fastest in vivo, whereas it grew slower in vitro. The growth pattern of SCC2 was the opposite to that of SCC1. Genetic differences in these two subclones showed marked differences in cell adhesion and proliferation. Pathway enrichment results indicate that signal transduction and immune system responses were the most significantly altered functional categories in SCC2 cells compared to those in SCC1 cells in vitro. The number and activation of CD3+ and CD8+ T cells and NK cells in the tumor tissue of tumor-bearing mice inoculated with SCC2 were significantly higher, whereas those of myeloid cells were significantly lower, than those in the SCC1 and LLC1 groups. Our results suggest that the in vivo growth of two subclones derived from LLC1 was determined by the tumor microenvironment rather than their intrinsic proliferative cell characteristics.
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Affiliation(s)
- Ben-Ling Xu
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
| | - Xiao-Ming Wang
- Department of General Surgery, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
| | - Guang-Yu Chen
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
| | - Peng Yuan
- Department of Breast Surgery, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
| | - Lu Han
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
| | - Peng Qin
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
| | - Tie-Peng Li
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
| | - Hong-Qin You
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
| | - Cheng-Juan Zhang
- Center of Bio Repository, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
| | - Xiao-Min Fu
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
| | - Long Yuan
- Department of General Surgery, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
| | - Zi-Bing Wang
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
| | - Quan-Li Gao
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
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Kim HR, Bong JH, Kim TH, Choi KH, Shin SS, Kang MJ, Shim WB, Lee DY, Pyun JC. Homogeneous One-Step Immunoassay Based on Switching Peptides for Detection of the Influenza Virus. Anal Chem 2022; 94:9627-9635. [PMID: 35762898 DOI: 10.1021/acs.analchem.2c00716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In this study, a homogeneous one-step immunoassay based on switching peptides is presented for the detection of influenza viruses A and B (Inf-A and Inf-B, respectively). The one-step immunoassay represents an immunoassay method that does not involve any washing steps, only treatment of the sample. In this method, fluorescence-labeled switching peptides quantitatively dissociate from the antigen-binding site of immunoglobulin G (IgG). In particular, the one-step immunoassay based on soluble detection antibodies with switching peptides is called a homogeneous one-step immunoassay. The immunoassay developed uses switching peptides labeled with two types of fluorescence dyes (FAM and TAMRA) and detection antibodies labeled with two types of fluorescence quenchers (TQ2 for FAM and TQ3 for TAMRA). The optimal switching peptides for the detection of Inf-A and Inf-B have been selected as L1-peptide and H2-peptide. The interactions between the four kinds of switching peptides and IgG have been analyzed using computational docking simulation and SPR biosensor. The location of labeling for the fluorescence quenchers has been determined based on the distance between the fluorescence dyes of the switching peptides and the fluorescence quenchers, calculated on the basis of the efficiency of fluorescence quenching, using the Förster equation. To demonstrate the feasibility of the one-step immunoassay, binding constants (KD) have been calculated for detection antibodies against Inf-A and Inf-B with target antigens (Inf-A and Inf-B) and switching peptides (L1- and H2-peptides), using an isotherm model. The immunoassay has been demonstrated to be feasible using antigens as well as real samples of Inf-A and Inf-B with a critical cycle number (Ct). The immunoassay has also been compared to other commercially available rapid test kits for Inf-A and Inf-B and found to be far more sensitive for detection of Inf-A and Inf-B over the entire detection range.
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Affiliation(s)
- Hong-Rae Kim
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-Ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Ji-Hong Bong
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-Ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Tae-Hun Kim
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-Ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Kyung-Hak Choi
- OPTOLANE Technologies Inc., 20 Pangyoyeok-ro 241beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do 13494, Republic of Korea
| | - Seung-Shick Shin
- OPTOLANE Technologies Inc., 20 Pangyoyeok-ro 241beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do 13494, Republic of Korea
| | - Min-Jung Kang
- Korea Institute of Science and Technology (KIST), 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Won-Bo Shim
- Department of Agricultural Chemistry and Food Science & Technology, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Do Young Lee
- OPTOLANE Technologies Inc., 20 Pangyoyeok-ro 241beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do 13494, Republic of Korea
| | - Jae-Chul Pyun
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-Ro, Seodaemun-gu, Seoul 03722, Republic of Korea
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6
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Matsutani T, Hamada M. Clone decomposition based on mutation signatures provides novel insights into mutational processes. NAR Genom Bioinform 2021; 3:lqab093. [PMID: 34734181 PMCID: PMC8559167 DOI: 10.1093/nargab/lqab093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 09/17/2021] [Accepted: 10/19/2021] [Indexed: 11/24/2022] Open
Abstract
Intra-tumor heterogeneity is a phenomenon in which mutation profiles differ from cell to cell within the same tumor and is observed in almost all tumors. Understanding intra-tumor heterogeneity is essential from the clinical perspective. Numerous methods have been developed to predict this phenomenon based on variant allele frequency. Among the methods, CloneSig models the variant allele frequency and mutation signatures simultaneously and provides an accurate clone decomposition. However, this method has limitations in terms of clone number selection and modeling. We propose SigTracer, a novel hierarchical Bayesian approach for analyzing intra-tumor heterogeneity based on mutation signatures to tackle these issues. We show that SigTracer predicts more reasonable clone decompositions than the existing methods against artificial data that mimic cancer genomes. We applied SigTracer to whole-genome sequences of blood cancer samples. The results were consistent with past findings that single base substitutions caused by a specific signature (previously reported as SBS9) related to the activation-induced cytidine deaminase intensively lie within immunoglobulin-coding regions for chronic lymphocytic leukemia samples. Furthermore, we showed that this signature mutates regions responsible for cell-cell adhesion. Accurate assignments of mutations to signatures by SigTracer can provide novel insights into signature origins and mutational processes.
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Affiliation(s)
- Taro Matsutani
- Graduate School of Advanced Science and Engineering, Waseda University, 55N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo 169–8555, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 169–8555, Japan
| | - Michiaki Hamada
- Graduate School of Advanced Science and Engineering, Waseda University, 55N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo 169–8555, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 169–8555, Japan
- Graduate School of Medicine, Nippon Medical School, Sendagi, Bunkyo, Tokyo 113-8602, Japan
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7
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Tang DG. Understanding and targeting prostate cancer cell heterogeneity and plasticity. Semin Cancer Biol 2021; 82:68-93. [PMID: 34844845 PMCID: PMC9106849 DOI: 10.1016/j.semcancer.2021.11.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/01/2021] [Accepted: 11/01/2021] [Indexed: 12/12/2022]
Abstract
Prostate cancer (PCa) is a prevalent malignancy that occurs primarily in old males. Prostate tumors in different patients manifest significant inter-patient heterogeneity with respect to histo-morphological presentations and molecular architecture. An individual patient tumor also harbors genetically distinct clones in which PCa cells display intra-tumor heterogeneity in molecular features and phenotypic marker expression. This inherent PCa cell heterogeneity, e.g., in the expression of androgen receptor (AR), constitutes a barrier to the long-term therapeutic efficacy of AR-targeting therapies. Furthermore, tumor progression as well as therapeutic treatments induce PCa cell plasticity such that AR-positive PCa cells may turn into AR-negative cells and prostate tumors may switch lineage identity from adenocarcinomas to neuroendocrine-like tumors. This induced PCa cell plasticity similarly confers resistance to AR-targeting and other therapies. In this review, I first discuss PCa from the perspective of an abnormal organ development and deregulated cellular differentiation, and discuss the luminal progenitor cells as the likely cells of origin for PCa. I then focus on intrinsic PCa cell heterogeneity in treatment-naïve tumors with the presence of prostate cancer stem cells (PCSCs). I further elaborate on PCa cell plasticity induced by genetic alterations and therapeutic interventions, and present potential strategies to therapeutically tackle PCa cell heterogeneity and plasticity. My discussions will make it clear that, to achieve enduring clinical efficacy, both intrinsic PCa cell heterogeneity and induced PCa cell plasticity need to be targeted with novel combinatorial approaches.
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Affiliation(s)
- Dean G Tang
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; Experimental Therapeutics (ET) Graduate Program, The University at Buffalo & Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.
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8
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Benchmarking pipelines for subclonal deconvolution of bulk tumour sequencing data. Nat Commun 2021; 12:6396. [PMID: 34737285 PMCID: PMC8569188 DOI: 10.1038/s41467-021-26698-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 10/20/2021] [Indexed: 11/09/2022] Open
Abstract
Intratumour heterogeneity provides tumours with the ability to adapt and acquire treatment resistance. The development of more effective and personalised treatments for cancers, therefore, requires accurate characterisation of the clonal architecture of tumours, enabling evolutionary dynamics to be tracked. Many methods exist for achieving this from bulk tumour sequencing data, involving identifying mutations and performing subclonal deconvolution, but there is a lack of systematic benchmarking to inform researchers on which are most accurate, and how dataset characteristics impact performance. To address this, we use the most comprehensive tumour genome simulation tool available for such purposes to create 80 bulk tumour whole exome sequencing datasets of differing depths, tumour complexities, and purities, and use these to benchmark subclonal deconvolution pipelines. We conclude that i) tumour complexity does not impact accuracy, ii) increasing either purity or purity-corrected sequencing depth improves accuracy, and iii) the optimal pipeline consists of Mutect2, FACETS and PyClone-VI. We have made our benchmarking datasets publicly available for future use.
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9
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Fraser M, Livingstone J, Wrana JL, Finelli A, He HH, van der Kwast T, Zlotta AR, Bristow RG, Boutros PC. Somatic driver mutation prevalence in 1844 prostate cancers identifies ZNRF3 loss as a predictor of metastatic relapse. Nat Commun 2021; 12:6248. [PMID: 34716314 PMCID: PMC8556363 DOI: 10.1038/s41467-021-26489-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/08/2021] [Indexed: 12/13/2022] Open
Abstract
Driver gene mutations that are more prevalent in metastatic, castration-resistant prostate cancer (mCRPC) than localized disease represent candidate prognostic biomarkers. We analyze 1,844 localized (1,289) or mCRPC (555) tumors and quantify the prevalence of 113 somatic driver single nucleotide variants (SNVs), copy number aberrations (CNAs), and structural variants (SVs) in each state. One-third are significantly more prevalent in mCRPC than expected while a quarter are less prevalent. Mutations in AR and its enhancer are more prevalent in mCRPC, as are those in TP53, MYC, ZNRF3 and PRKDC. ZNRF3 loss is associated with decreased ZNRF3 mRNA abundance, WNT, cell cycle & PRC1/2 activity, and genomic instability. ZNRF3 loss, RNA downregulation and hypermethylation are prognostic of metastasis and overall survival, independent of clinical and pathologic indices. These data demonstrate a strategy for identifying biomarkers of localized cancer aggression, with ZNRF3 loss as a predictor of metastasis in prostate cancer.
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Affiliation(s)
- Michael Fraser
- grid.17063.330000 0001 2157 2938Department of Surgery, Division of Urology, University of Toronto, Toronto, ON Canada ,grid.415224.40000 0001 2150 066XDepartment of Surgical Oncology, Genitourinary Site Group, Princess Margaret Cancer Centre, Toronto, ON Canada ,grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, ON Canada
| | - Julie Livingstone
- grid.19006.3e0000 0000 9632 6718Department of Human Genetics, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Urology, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Institute for Precision Health, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, CA USA
| | - Jeffrey L. Wrana
- grid.416166.20000 0004 0473 9881Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON Canada ,grid.492573.eMount Sinai Hospital, Sinai Health System, Toronto, Canada
| | - Antonio Finelli
- grid.17063.330000 0001 2157 2938Department of Surgery, Division of Urology, University of Toronto, Toronto, ON Canada ,grid.415224.40000 0001 2150 066XDepartment of Surgical Oncology, Genitourinary Site Group, Princess Margaret Cancer Centre, Toronto, ON Canada ,grid.415224.40000 0001 2150 066XPrincess Margaret Cancer Centre, Toronto, ON Canada
| | - Housheng Hansen He
- grid.415224.40000 0001 2150 066XPrincess Margaret Cancer Centre, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Medical Biophysics, University of Toronto, Toronto, ON Canada
| | - Theodorus van der Kwast
- grid.17063.330000 0001 2157 2938Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada ,grid.231844.80000 0004 0474 0428Laboratory Medicine Program, University Health Network, Toronto, ON Canada
| | - Alexandre R. Zlotta
- grid.17063.330000 0001 2157 2938Department of Surgery, Division of Urology, University of Toronto, Toronto, ON Canada ,grid.415224.40000 0001 2150 066XDepartment of Surgical Oncology, Genitourinary Site Group, Princess Margaret Cancer Centre, Toronto, ON Canada ,grid.416166.20000 0004 0473 9881Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON Canada ,grid.492573.eMount Sinai Hospital, Sinai Health System, Toronto, Canada
| | - Robert G. Bristow
- grid.17063.330000 0001 2157 2938Department of Medical Biophysics, University of Toronto, Toronto, ON Canada ,Manchester Cancer Research Centre, Manchester, UK ,grid.5379.80000000121662407University of Manchester, Manchester, UK
| | - Paul C. Boutros
- grid.19006.3e0000 0000 9632 6718Department of Human Genetics, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Urology, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Institute for Precision Health, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, CA USA ,grid.17063.330000 0001 2157 2938Department of Medical Biophysics, University of Toronto, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON Canada
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Freeland J, Crowell PD, Giafaglione JM, Boutros PC, Goldstein AS. Aging of the progenitor cells that initiate prostate cancer. Cancer Lett 2021; 515:28-35. [PMID: 34052326 PMCID: PMC8494000 DOI: 10.1016/j.canlet.2021.05.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 12/18/2022]
Abstract
Many organs experience a loss of tissue mass and a decline in regenerative capacity during aging. In contrast, the prostate continues to grow in volume. In fact, age is the most important risk factor for prostate cancer. However, the age-related factors that influence the composition, morphology and molecular features of prostate epithelial progenitor cells, the cells-of-origin for prostate cancer, are poorly understood. Here, we review the evidence that prostate luminal progenitor cells are expanded with age. We explore the age-related changes to the microenvironment that may influence prostate epithelial cells and risk of transformation. Finally, we raise a series of questions about models of aging and regulators of prostate aging which need to be addressed. A fundamental understanding of aging in the prostate will yield critical insights into mechanisms that promote the development of age-related prostatic disease.
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Affiliation(s)
- Jack Freeland
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, USA
| | - Preston D Crowell
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, USA
| | - Jenna M Giafaglione
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, USA
| | - Paul C Boutros
- Departments of Human Genetics & Urology, Jonsson Comprehensive Cancer Center and Institute for Precision Health, University of California, Los Angeles, USA
| | - Andrew S Goldstein
- Departments of Molecular, Cell and Developmental Biology & Urology, Broad Stem Cell Research Center and Jonsson Comprehensive Cancer Center, University of California, Los Angeles, USA.
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11
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Technical and biological constraints on ctDNA-based genotyping. Trends Cancer 2021; 7:995-1009. [PMID: 34219051 DOI: 10.1016/j.trecan.2021.06.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 12/18/2022]
Abstract
Circulating tumor DNA (ctDNA) enables real-time genomic profiling of cancer without the need for tissue biopsy. ctDNA-based technology is seeing rapid uptake in clinical practice due to the potential to inform patient management from diagnosis to advanced disease. In metastatic disease, ctDNA can identify somatic mutations, copy-number variants (CNVs), and structural rearrangements that are predictive of therapy response. However, the ctDNA fraction (ctDNA%) is unpredictable and confounds variant detection strategies, undermining confidence in liquid biopsy results. Assay design also influences which types of genomic alterations are identifiable. Here, we describe the relationships between ctDNA%, methodology, and sensitivity-specificity for major classes of genomic alterations in prostate cancer. We provide recommendations to navigate the technical complexities that constrain the detection of clinically relevant genomic alterations in ctDNA.
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12
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Cmero M, Yuan K, Ong CS, Schröder J, Corcoran NM, Papenfuss T, Hovens CM, Markowetz F, Macintyre G. Inferring structural variant cancer cell fraction. Nat Commun 2020; 11:730. [PMID: 32024845 PMCID: PMC7002525 DOI: 10.1038/s41467-020-14351-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 12/16/2019] [Indexed: 12/14/2022] Open
Abstract
We present SVclone, a computational method for inferring the cancer cell fraction of structural variant (SV) breakpoints from whole-genome sequencing data. SVclone accurately determines the variant allele frequencies of both SV breakends, then simultaneously estimates the cancer cell fraction and SV copy number. We assess performance using in silico mixtures of real samples, at known proportions, created from two clonal metastases from the same patient. We find that SVclone's performance is comparable to single-nucleotide variant-based methods, despite having an order of magnitude fewer data points. As part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) consortium, which aggregated whole-genome sequencing data from 2658 cancers across 38 tumour types, we use SVclone to reveal a subset of liver, ovarian and pancreatic cancers with subclonally enriched copy-number neutral rearrangements that show decreased overall survival. SVclone enables improved characterisation of SV intra-tumour heterogeneity.
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Affiliation(s)
- Marek Cmero
- Department of Surgery, Division of Urology, Royal Melbourne Hospital and University of Melbourne, Parkville, VIC, 3050, Australia.
- The Epworth Prostate Centre, Epworth Hospital, Richmond, VIC, 3121, Australia.
- Department of Computing and Information Systems, University of Melbourne, Parkville, VIC, 3010, Australia.
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
- Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia.
| | - Ke Yuan
- School of Computing Science, University of Glasgow, Sir Alwyn Williams Building, Glasgow, G12 8RZ, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Cheng Soon Ong
- Electrical and Electronic Engineering, University of Melbourne, Parkville, VIC, 3010, Australia
- Machine Learning Research Group, Data61, Canberra, ACT, 2601, Australia
- Research School of Computer Science, Australian National University, Canberra, ACT, 2601, Australia
| | - Jan Schröder
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Niall M Corcoran
- Department of Surgery, Division of Urology, Royal Melbourne Hospital and University of Melbourne, Parkville, VIC, 3050, Australia
- The Epworth Prostate Centre, Epworth Hospital, Richmond, VIC, 3121, Australia
| | - Tony Papenfuss
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Christopher M Hovens
- Department of Surgery, Division of Urology, Royal Melbourne Hospital and University of Melbourne, Parkville, VIC, 3050, Australia
- The Epworth Prostate Centre, Epworth Hospital, Richmond, VIC, 3121, Australia
| | - Florian Markowetz
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Geoff Macintyre
- Department of Computing and Information Systems, University of Melbourne, Parkville, VIC, 3010, Australia.
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK.
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