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Li L, Xie W, Zhan L, Wen S, Luo X, Xu S, Cai Y, Tang W, Wang Q, Li M, Xie Z, Deng L, Zhu H, Yu G. Resolving tumor evolution: a phylogenetic approach. JOURNAL OF THE NATIONAL CANCER CENTER 2024; 4:97-106. [PMID: 39282584 PMCID: PMC11390690 DOI: 10.1016/j.jncc.2024.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/28/2024] [Accepted: 03/20/2024] [Indexed: 09/19/2024] Open
Abstract
The evolutionary dynamics of cancer, characterized by its profound heterogeneity, demand sophisticated tools for a holistic understanding. This review delves into tumor phylogenetics, an essential approach bridging evolutionary biology with oncology, offering unparalleled insights into cancer's evolutionary trajectory. We provide an overview of the workflow, encompassing study design, data acquisition, and phylogeny reconstruction. Notably, the integration of diverse data sets emerges as a transformative step, enhancing the depth and breadth of evolutionary insights. With this integrated perspective, tumor phylogenetics stands poised to redefine our understanding of cancer evolution and influence therapeutic strategies.
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Affiliation(s)
- Lin Li
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Wenqin Xie
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Li Zhan
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Shaodi Wen
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Department of Oncology, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital, Nanjing, China
| | - Xiao Luo
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Shuangbin Xu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Division of Laboratory Medicine, Microbiome Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yantong Cai
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Wenli Tang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Qianwen Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Ming Li
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zijing Xie
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Lin Deng
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Hongyuan Zhu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Guangchuang Yu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
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2
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Färber B, Lapshyna O, Künstner A, Kohl M, Sauer T, Bichmann K, Heckelmann B, Watzelt J, Honselmann K, Bolm L, ten Winkel M, Busch H, Ungefroren H, Keck T, Gemoll T, Wellner UF, Braun R. Molecular profiling and specific targeting of gemcitabine-resistant subclones in heterogeneous pancreatic cancer cell populations. Front Oncol 2023; 13:1230382. [PMID: 37719017 PMCID: PMC10502231 DOI: 10.3389/fonc.2023.1230382] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 08/08/2023] [Indexed: 09/19/2023] Open
Abstract
Purpose Chemotherapy is pivotal in the multimodal treatment of pancreatic ductal adenocarcinoma (PDAC). Technical advances unveiled a high degree of inter- and intratumoral heterogeneity. We hypothesized that intratumoral heterogeneity (ITH) impacts response to gemcitabine treatment and demands specific targeting of resistant subclones. Methods Using single cell-derived cell lines (SCDCLs) from the classical cell line BxPC3 and the basal-like cell line Panc-1, we addressed the effect of ITH on response to gemcitabine treatment. Results Individual SCDCLs of both parental tumor cell populations showed considerable heterogeneity in response to gemcitabine. Unsupervised PCA including the 1,000 most variably expressed genes showed a clustering of the SCDCLs according to their respective sensitivity to gemcitabine treatment for BxPC3, while this was less clear for Panc-1. In BxPC3 SCDCLs, enriched signaling pathways EMT, TNF signaling via NfKB, and IL2STAT5 signaling correlated with more resistant behavior to gemcitabine. In Panc-1 SCDCLs MYC targets V1 and V2 as well as E2F targets were associated with stronger resistance. We used recursive feature elimination for Feature Selection in order to compute sets of proteins that showed strong association with the response to gemcitabine. The optimal protein set calculated for Panc-1 comprised fewer proteins in comparison to the protein set determined for BxPC3. Based on molecular profiles, we could show that the gemcitabine-resistant SCDCLs of both BxPC3 and Panc-1 are more sensitive to the BET inhibitor JQ1 compared to the respective gemcitabine-sensitive SCDCLs. Conclusion Our model system of SCDCLs identified gemcitabine-resistant subclones and provides evidence for the critical role of ITH for treatment response in PDAC. We exploited molecular differences as the basis for differential response and used these for more targeted therapy of resistant subclones.
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Affiliation(s)
- Benedikt Färber
- Department of Surgery, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Olga Lapshyna
- Department of Surgery, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Axel Künstner
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
- Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Michael Kohl
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
- Section for Translational Surgical Oncology & Biobanking, Department of Surgery, University Hospital Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Thorben Sauer
- Section for Translational Surgical Oncology & Biobanking, Department of Surgery, University Hospital Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Kira Bichmann
- Department of Surgery, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Benjamin Heckelmann
- Department of Surgery, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Jessica Watzelt
- Department of Surgery, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Kim Honselmann
- Department of Surgery, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Louisa Bolm
- Department of Surgery, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Meike ten Winkel
- Department of Surgery, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Hauke Busch
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
- Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Hendrik Ungefroren
- First Department of Medicine, University Medical Center Schleswig-Holstein, Lübeck, Germany
- Institute of Pathology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Tobias Keck
- Department of Surgery, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Timo Gemoll
- Section for Translational Surgical Oncology & Biobanking, Department of Surgery, University Hospital Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Ulrich F. Wellner
- Department of Surgery, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Rüdiger Braun
- Department of Surgery, University Medical Center Schleswig-Holstein, Lübeck, Germany
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3
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Comaills V, Castellano-Pozo M. Chromosomal Instability in Genome Evolution: From Cancer to Macroevolution. BIOLOGY 2023; 12:671. [PMID: 37237485 PMCID: PMC10215859 DOI: 10.3390/biology12050671] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023]
Abstract
The integrity of the genome is crucial for the survival of all living organisms. However, genomes need to adapt to survive certain pressures, and for this purpose use several mechanisms to diversify. Chromosomal instability (CIN) is one of the main mechanisms leading to the creation of genomic heterogeneity by altering the number of chromosomes and changing their structures. In this review, we will discuss the different chromosomal patterns and changes observed in speciation, in evolutional biology as well as during tumor progression. By nature, the human genome shows an induction of diversity during gametogenesis but as well during tumorigenesis that can conclude in drastic changes such as the whole genome doubling to more discrete changes as the complex chromosomal rearrangement chromothripsis. More importantly, changes observed during speciation are strikingly similar to the genomic evolution observed during tumor progression and resistance to therapy. The different origins of CIN will be treated as the importance of double-strand breaks (DSBs) or the consequences of micronuclei. We will also explain the mechanisms behind the controlled DSBs, and recombination of homologous chromosomes observed during meiosis, to explain how errors lead to similar patterns observed during tumorigenesis. Then, we will also list several diseases associated with CIN, resulting in fertility issues, miscarriage, rare genetic diseases, and cancer. Understanding better chromosomal instability as a whole is primordial for the understanding of mechanisms leading to tumor progression.
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Affiliation(s)
- Valentine Comaills
- Andalusian Center for Molecular Biology and Regenerative Medicine—CABIMER, University of Pablo de Olavide—University of Seville—CSIC, Junta de Andalucía, 41092 Seville, Spain
| | - Maikel Castellano-Pozo
- Andalusian Center for Molecular Biology and Regenerative Medicine—CABIMER, University of Pablo de Olavide—University of Seville—CSIC, Junta de Andalucía, 41092 Seville, Spain
- Genetic Department, Faculty of Biology, University of Seville, 41080 Seville, Spain
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4
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Evaluation of ctDNA in the Prediction of Response to Neoadjuvant Therapy and Prognosis in Locally Advanced Rectal Cancer Patients: A Prospective Study. Pharmaceuticals (Basel) 2023; 16:ph16030427. [PMID: 36986526 PMCID: PMC10057108 DOI: 10.3390/ph16030427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 02/28/2023] [Accepted: 03/03/2023] [Indexed: 03/18/2023] Open
Abstract
“Watch and wait” is becoming a common treatment option for patients with locally advanced rectal cancer (LARC) submitted to neoadjuvant treatment. However, currently, no clinical modality has an acceptable accuracy for predicting pathological complete response (pCR). The aim of this study was to assess the clinical utility of circulating tumor DNA (ctDNA) in predicting the response and prognosis in these patients. We prospectively enrolled a cohort of three Iberian centers between January 2020 and December 2021 and performed an analysis on the association of ctDNA with the main response outcomes and disease-free survival (DFS). The rate of pCR in the total sample was 15.3%. A total of 24 plasma samples from 18 patients were analyzed by next-generation sequencing. At baseline, mutations were detected in 38.9%, with the most common being TP53 and KRAS. Combination of either positive magnetic resonance imaging (MRI) extramural venous invasion (mrEMVI) and ctDNA increased the risk of poor response (p = 0.021). Also, patients with two mutations vs. those with fewer than two mutations had a worse DFS (p = 0.005). Although these results should be read carefully due to sample size, this study suggests that baseline ctDNA combined with mrEMVI could potentially help to predict the response and baseline ctDNA number of mutations might allow the discrimination of groups with different DFS. Further studies are needed to clarify the role of ctDNA as an independent tool in the selection and management of LARC patients.
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5
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Zhu JW, Charkhchi P, Akbari MR. Potential clinical utility of liquid biopsies in ovarian cancer. Mol Cancer 2022; 21:114. [PMID: 35545786 PMCID: PMC9092780 DOI: 10.1186/s12943-022-01588-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/27/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Ovarian cancer (OC) is the most lethal gynecologic malignancy worldwide. One of the main challenges in the management of OC is the late clinical presentation of disease that results in poor survival. Conventional tissue biopsy methods and serological biomarkers such as CA-125 have limited clinical applications. Liquid biopsy is a novel sampling method that analyzes distinctive tumour components released into the peripheral circulation, including circulating tumour DNA (ctDNA), circulating tumour cells (CTCs), cell-free RNA (cfRNA), tumour-educated platelets (TEPs) and exosomes. Increasing evidence suggests that liquid biopsy could enhance the clinical management of OC by improving early diagnosis, predicting prognosis, detecting recurrence, and monitoring response to treatment. Capturing the unique tumour genetic landscape can also guide treatment decisions and the selection of appropriate targeted therapies. Key advantages of liquid biopsy include its non-invasive nature and feasibility, which allow for serial sampling and longitudinal monitoring of dynamic tumour changes over time. In this review, we outline the evidence for the clinical utility of each liquid biopsy component and review the advantages and current limitations of applying liquid biopsy in managing ovarian cancer. We also highlight future directions considering the current challenges and explore areas where more studies are warranted to elucidate its emerging clinical potential.
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Affiliation(s)
- Jie Wei Zhu
- Women's College Research Institute, Women's College Hospital, University of Toronto, 76 Grenville St, Toronto, ON, M5S 1B2, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Parsa Charkhchi
- Women's College Research Institute, Women's College Hospital, University of Toronto, 76 Grenville St, Toronto, ON, M5S 1B2, Canada
| | - Mohammad R Akbari
- Women's College Research Institute, Women's College Hospital, University of Toronto, 76 Grenville St, Toronto, ON, M5S 1B2, Canada.
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
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6
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Tao Y, Rajaraman A, Cui X, Cui Z, Chen H, Zhao Y, Eaton J, Kim H, Ma J, Schwartz R. Assessing the contribution of tumor mutational phenotypes to cancer progression risk. PLoS Comput Biol 2021; 17:e1008777. [PMID: 33711014 PMCID: PMC7990181 DOI: 10.1371/journal.pcbi.1008777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 03/24/2021] [Accepted: 02/06/2021] [Indexed: 01/10/2023] Open
Abstract
Cancer occurs via an accumulation of somatic genomic alterations in a process of clonal evolution. There has been intensive study of potential causal mutations driving cancer development and progression. However, much recent evidence suggests that tumor evolution is normally driven by a variety of mechanisms of somatic hypermutability, which act in different combinations or degrees in different cancers. These variations in mutability phenotypes are predictive of progression outcomes independent of the specific mutations they have produced to date. Here we explore the question of how and to what degree these differences in mutational phenotypes act in a cancer to predict its future progression. We develop a computational paradigm using evolutionary tree inference (tumor phylogeny) algorithms to derive features quantifying single-tumor mutational phenotypes, followed by a machine learning framework to identify key features predictive of progression. Analyses of breast invasive carcinoma and lung carcinoma demonstrate that a large fraction of the risk of future clinical outcomes of cancer progression-overall survival and disease-free survival-can be explained solely from mutational phenotype features derived from the phylogenetic analysis. We further show that mutational phenotypes have additional predictive power even after accounting for traditional clinical and driver gene-centric genomic predictors of progression. These results confirm the importance of mutational phenotypes in contributing to cancer progression risk and suggest strategies for enhancing the predictive power of conventional clinical data or driver-centric biomarkers.
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Affiliation(s)
- Yifeng Tao
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Joint Carnegie Mellon-University of Pittsburgh Ph.D. Program in Computational Biology, Pittsburgh, Pennsylvania, United States of America
| | - Ashok Rajaraman
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Xiaoyue Cui
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Joint Carnegie Mellon-University of Pittsburgh Ph.D. Program in Computational Biology, Pittsburgh, Pennsylvania, United States of America
| | - Ziyi Cui
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Haoran Chen
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Joint Carnegie Mellon-University of Pittsburgh Ph.D. Program in Computational Biology, Pittsburgh, Pennsylvania, United States of America
| | - Yuanqi Zhao
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Jesse Eaton
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Hannah Kim
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Russell Schwartz
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
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7
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Rapsomaniki MA, Maxouri S, Nathanailidou P, Garrastacho MR, Giakoumakis NN, Taraviras S, Lygeros J, Lygerou Z. In silico analysis of DNA re-replication across a complete genome reveals cell-to-cell heterogeneity and genome plasticity. NAR Genom Bioinform 2021; 3:lqaa112. [PMID: 33554116 PMCID: PMC7846089 DOI: 10.1093/nargab/lqaa112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/15/2020] [Accepted: 01/20/2021] [Indexed: 01/06/2023] Open
Abstract
DNA replication is a complex and remarkably robust process: despite its inherent uncertainty, manifested through stochastic replication timing at a single-cell level, multiple control mechanisms ensure its accurate and timely completion across a population. Disruptions in these mechanisms lead to DNA re-replication, closely connected to genomic instability and oncogenesis. Here, we present a stochastic hybrid model of DNA re-replication that accurately portrays the interplay between discrete dynamics, continuous dynamics and uncertainty. Using experimental data on the fission yeast genome, model simulations show how different regions respond to re-replication and permit insight into the key mechanisms affecting re-replication dynamics. Simulated and experimental population-level profiles exhibit a good correlation along the genome, robust to model parameters, validating our approach. At a single-cell level, copy numbers of individual loci are affected by intrinsic properties of each locus, in cis effects from adjoining loci and in trans effects from distant loci. In silico analysis and single-cell imaging reveal that cell-to-cell heterogeneity is inherent in re-replication and can lead to genome plasticity and a plethora of genotypic variations.
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Affiliation(s)
- Maria Anna Rapsomaniki
- Department of Biology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
| | - Stella Maxouri
- Department of Biology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
| | - Patroula Nathanailidou
- Department of Biology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
| | | | | | - Stavros Taraviras
- Department of Physiology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
| | - John Lygeros
- Automatic Control Laboratory, ETH Zurich, 8092 Zurich, Switzerland
| | - Zoi Lygerou
- Department of Biology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
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8
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Li S, Sun Y, Huang J, Wang B, Gong Y, Fang Y, Liu Y, Wang S, Guo Y, Wang H, Xu Z, Guo Y. Anti-tumor effects and mechanisms of Astragalus membranaceus (AM) and its specific immunopotentiation: Status and prospect. JOURNAL OF ETHNOPHARMACOLOGY 2020; 258:112797. [PMID: 32243990 DOI: 10.1016/j.jep.2020.112797] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/10/2020] [Accepted: 03/23/2020] [Indexed: 06/11/2023]
Abstract
With cancer deaths increasing, the initiation, pathophysiology and curative management of cancer is receiving increasing attention. Traditional therapies such as surgery and chemoradiotherapy are often accompanied by suppression of host immunity, which increase the risk of metastasis. Astragalus membranceus (AM) is commonly utilized as one herbal medicine of traditional Chinese medicines (TCMs) with a variety of biological activities. Studies have shown that the active ingredients of AM and AM-based TCMs, combined with chemotherapy, can enhance anti-tumor efficacy in cancer patients, in addition to reduce complications and avoid side effects induced by chemotherapy. By using various cancer models and cell lines, AM has been found to be capable of shrinking or stabilizing tumors by direct anti-proliferation or pro-apoptosis effect on tumor cells. Further, AM ameliorates immunosuppression by activating M1 macrophages and T cells tumor-kill function in tumor microenvironment (TME). AM is also found to improve systemic immunity which may help promoting efficacy of chemotherapy and preventing metastasis. Thereby this review contributes to an understanding of AM as an adjunctive therapy in the whole course of cancer treatment, at the same time providing useful information for development of more effective anti-tumor medication. The combination of AM and immune checkpoint therapies has a promising therapeutic prospect, and the observation of direct efficacy and mechanisms on tumor growth and metastasis of AM combined with chemotherapies or other therapies require more in vivo validations and further clinical investigation as well.
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Affiliation(s)
- Shanshan Li
- Acupuncture Research Center, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Yi Sun
- Nephropathy and Rheumatology Department, Second Affiliated Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, 300250, China
| | - Jin Huang
- Acupuncture Research Center, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Bin Wang
- Tianjin Medical University Cancer Institute of Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Yinan Gong
- Acupuncture Research Center, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Yuxin Fang
- Acupuncture Research Center, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; Acu-moxibustion and Tuina Department, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Yangyang Liu
- Acupuncture Research Center, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; Acu-moxibustion and Tuina Department, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Shenjun Wang
- Acupuncture Research Center, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; Acu-moxibustion and Tuina Department, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Yi Guo
- Acupuncture Research Center, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; College of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Hong Wang
- Acu-moxibustion and Tuina Department, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Zhifang Xu
- Acupuncture Research Center, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; Acu-moxibustion and Tuina Department, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
| | - Yongming Guo
- Acupuncture Research Center, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; Acu-moxibustion and Tuina Department, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
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9
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Commander R, Wei C, Sharma A, Mouw JK, Burton LJ, Summerbell E, Mahboubi D, Peterson RJ, Konen J, Zhou W, Du Y, Fu H, Shanmugam M, Marcus AI. Subpopulation targeting of pyruvate dehydrogenase and GLUT1 decouples metabolic heterogeneity during collective cancer cell invasion. Nat Commun 2020; 11:1533. [PMID: 32210228 PMCID: PMC7093428 DOI: 10.1038/s41467-020-15219-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 02/24/2020] [Indexed: 12/21/2022] Open
Abstract
Phenotypic heterogeneity exists within collectively invading packs of tumor cells, suggesting that cellular subtypes cooperate to drive invasion and metastasis. Here, we take a chemical biology approach to probe cell:cell cooperation within the collective invasion pack. These data reveal metabolic heterogeneity within invasive chains, in which leader cells preferentially utilize mitochondrial respiration and trailing follower cells rely on elevated glucose uptake. We define a pyruvate dehydrogenase (PDH) dependency in leader cells that can be therapeutically exploited with the mitochondria-targeting compound alexidine dihydrochloride. In contrast, follower cells highly express glucose transporter 1 (GLUT1), which sustains an elevated level of glucose uptake required to maintain proliferation. Co-targeting of both leader and follower cells with PDH and GLUT1 inhibitors, respectively, inhibits cell growth and collective invasion. Taken together, our work reveals metabolic heterogeneity within the lung cancer collective invasion pack and provides rationale for co-targeting PDH and GLUT1 to inhibit collective invasion. The presence of phenotypic heterogeneity in collectively invading cells suggests cooperation amongst distinct subtypes of cells to promote invasion and metastasis. Here, the authors use chemical biology tools and report metabolic heterogeneity within the lung cancer collective invasion pack.
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Affiliation(s)
- R Commander
- Graduate Program in Cancer Biology, Emory University, Atlanta, GA, USA
| | - C Wei
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - A Sharma
- Winship Cancer Institute, Emory University, Atlanta, GA, USA.,Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA
| | - J K Mouw
- Winship Cancer Institute, Emory University, Atlanta, GA, USA.,Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA
| | - L J Burton
- Winship Cancer Institute, Emory University, Atlanta, GA, USA.,Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA
| | - E Summerbell
- Graduate Program in Cancer Biology, Emory University, Atlanta, GA, USA
| | - D Mahboubi
- Graduate Program in Molecular Systems Pharmacology, Emory University, Atlanta, GA, USA
| | - R J Peterson
- Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, GA, USA
| | - J Konen
- Department of Thoracic/Head & Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - W Zhou
- Winship Cancer Institute, Emory University, Atlanta, GA, USA.,Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA
| | - Y Du
- Winship Cancer Institute, Emory University, Atlanta, GA, USA.,Department of Pharmacology and Chemical Biology, Emory University, Atlanta, GA, USA.,Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA, USA
| | - H Fu
- Winship Cancer Institute, Emory University, Atlanta, GA, USA.,Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA.,Department of Pharmacology and Chemical Biology, Emory University, Atlanta, GA, USA.,Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA, USA
| | - M Shanmugam
- Winship Cancer Institute, Emory University, Atlanta, GA, USA. .,Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA.
| | - A I Marcus
- Winship Cancer Institute, Emory University, Atlanta, GA, USA. .,Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA.
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10
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Dzobo K, Senthebane DA, Thomford NE, Rowe A, Dandara C, Parker MI. Not Everyone Fits the Mold: Intratumor and Intertumor Heterogeneity and Innovative Cancer Drug Design and Development. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2019; 22:17-34. [PMID: 29356626 DOI: 10.1089/omi.2017.0174] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Disruptive innovations in medicine are game-changing in nature and bring about radical shifts in the way we understand human diseases, their treatment, and/or prevention. Yet, disruptive innovations in cancer drug design and development are still limited. Therapies that cure all cancer patients are in short supply or do not exist at all. Chief among the causes of this predicament is drug resistance, a mechanism that is much more dynamic than previously understood. Drug resistance has limited the initial success experienced with biomarker-guided targeted therapies as well. A major contributor to drug resistance is intratumor heterogeneity. For example, within solid tumors, there are distinct subclones of cancer cells, presenting profound complexity to cancer treatment. Well-known contributors to intratumor heterogeneity are genomic instability, the microenvironment, cellular genotype, cell plasticity, and stochastic processes. This expert review explains that for oncology drug design and development to be more innovative, we need to take into account intratumor heterogeneity. Initially thought to be the preserve of cancer cells, recent evidence points to the highly heterogeneous nature and diverse locations of stromal cells, such as cancer-associated fibroblasts (CAFs) and cancer-associated macrophages (CAMs). Distinct subpopulations of CAFs and CAMs are now known to be located immediately adjacent and distant from cancer cells, with different subpopulations exerting different effects on cancer cells. Disruptive innovation and precision medicine in clinical oncology do not have to be a distant reality, but can potentially be achieved by targeting these spatially separated and exclusive cancer cell subclones and CAF subtypes. Finally, we emphasize that disruptive innovations in drug discovery and development will likely come from drugs whose effect is not necessarily tumor shrinkage.
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Affiliation(s)
- Kevin Dzobo
- 1 International Centre for Genetic Engineering and Biotechnology (ICGEB) , Cape Town, South Africa .,2 Division of Medical Biochemistry, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town , Cape Town, South Africa
| | - Dimakatso Alice Senthebane
- 1 International Centre for Genetic Engineering and Biotechnology (ICGEB) , Cape Town, South Africa .,2 Division of Medical Biochemistry, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town , Cape Town, South Africa
| | - Nicholas Ekow Thomford
- 3 Pharmacogenetics Research Group, Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town , Cape Town, South Africa
| | - Arielle Rowe
- 1 International Centre for Genetic Engineering and Biotechnology (ICGEB) , Cape Town, South Africa
| | - Collet Dandara
- 3 Pharmacogenetics Research Group, Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town , Cape Town, South Africa
| | - M Iqbal Parker
- 2 Division of Medical Biochemistry, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town , Cape Town, South Africa
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11
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Abstract
Cancer is an evolutionary process. Recent advances in sequencing technologies have allowed us to investigate intratumor heterogeneity at the single nucleotide level. Here, we describe computational methods that use sequencing data to identify genetically distinct tumor subclones and reconstruct tumor evolutionary histories.
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12
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Fiedler D, Heselmeyer-Haddad K, Hirsch D, Hernandez LS, Torres I, Wangsa D, Hu Y, Zapata L, Rueschoff J, Belle S, Ried T, Gaiser T. Single-cell genetic analysis of clonal dynamics in colorectal adenomas indicates CDX2 gain as a predictor of recurrence. Int J Cancer 2018; 144:1561-1573. [PMID: 30229897 DOI: 10.1002/ijc.31869] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/11/2018] [Accepted: 08/13/2018] [Indexed: 12/19/2022]
Abstract
Colorectal adenomas are common precancerous lesions with the potential for malignant transformation to colorectal adenocarcinoma. Endoscopic polypectomy provides an opportunity for cancer prevention; however, recurrence rates are high. We collected formalin-fixed paraffin-embedded tissue of 15 primary adenomas with recurrence, 15 adenomas without recurrence, and 14 matched pair samples (primary adenoma and the corresponding recurrent adenoma). The samples were analysed by array-comparative genomic hybridisation (aCGH) and single-cell multiplex interphase fluorescence in situ hybridisation (miFISH) to understand clonal evolution, to examine the dynamics of copy number alterations (CNAs) and to identify molecular markers for recurrence prediction. The miFISH probe panel consisted of 14 colorectal carcinogenesis-relevant genes (COX2, PIK3CA, APC, CLIC1, EGFR, MYC, CCND1, CDX2, CDH1, TP53, HER2, SMAD7, SMAD4 and ZNF217), and a centromere probe (CEP10). The aCGH analysis confirmed the genetic landscape typical for colorectal tumorigenesis, that is, CNAs of chromosomes 7, 13q, 18 and 20q. Focal aberrations (≤10 Mbp) were mapped to chromosome bands 6p22.1-p21.33 (33.3%), 7q22.1 (31.4%) and 16q21 (29.4%). MiFISH detected gains of EGFR (23.6%), CDX2 (21.8%) and ZNF217 (18.2%). Most adenomas exhibited a major clone population which was accompanied by multiple smaller clone populations. Gains of CDX2 were exclusively seen in primary adenomas with recurrence (25%) compared to primary adenomas without recurrence (0%). Generation of phylogenetic trees for matched pair samples revealed four distinct patterns of clonal dynamics. In conclusion, adenoma development and recurrence are complex genetic processes driven by multiple CNAs whose evaluations by miFISH, with emphasis on CDX2, might serve as a predictor of recurrence.
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Affiliation(s)
- David Fiedler
- Institute of Pathology, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Kerstin Heselmeyer-Haddad
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Daniela Hirsch
- Institute of Pathology, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Leanora S Hernandez
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Irianna Torres
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Darawalee Wangsa
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Yue Hu
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Luis Zapata
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom.,Genomic and Epigenomic Variation in Disease Group, Centre for Genomic Regulation (CGR), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Sebastian Belle
- Department of Internal Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Central Interdisciplinary Endoscopy Unit, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Timo Gaiser
- Institute of Pathology, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
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13
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Subclonal evolution of pulmonary adenocarcinomas delineated by spatially distributed somatic mitochondrial mutations. Lung Cancer 2018; 126:80-88. [PMID: 30527196 DOI: 10.1016/j.lungcan.2018.10.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 02/06/2023]
Abstract
OBJECTIVES The potential role of cancer associated somatic mutations of the mitochondrial genome (mtDNA) is controversial and still poorly understood. Our group and others recently challenged a direct tumorigenic impact and suggested a passenger-like character. In combination with the known increased mutation rate, somatic mtDNA mutations account for an interesting tool to delineate tumor evolution. Here, we comprehensively analyzed the spatial distribution of somatic mtDNA mutations throughout whole tumor sections of pulmonary adenocarcinoma (ADC). MATERIALS AND METHODS Central sections of 19 ADC were analyzed in a segmented manner (11-34 segments/tumor) together with non-neoplastic tissue samples and lymph node metastasis, if present. We performed whole mtDNA sequencing and real-time PCR based quantification of mtDNA copy numbers for all samples. Further, histological growth patterns were determined on H&E sections and the tumor cell content was quantified by digital pathology analyses. RESULTS Somatic mtDNA mutations were present in 96% (18/19) of the analyzed tumors, either ubiquitously or restricted to specific tumor regions. Spatial and histological mapping of the mutations enabled the identification of subclonal structures and phylogenetic relations within a tumor section indicating different progression levels. In this regard, lymph node metastases seem to be related to early events in ADC development. There was no concurrence between histological and mtDNA mutation based clusters. However, micropapillary patterns occurred only in tumors with ubiquitous mutations. ADC with more than two ubiquitous mutations were associated with shorter disease-free survival (p < 0.01). CONCLUSION Cancer related mtDNA mutations are interesting candidates for the understanding of subclonal ADC evolution and perspectively for monitoring tumor progression. Our data reveal a potential prognostic relevance of somatic mtDNA mutations.
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14
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Jing A, Vizeacoumar FS, Parameswaran S, Haave B, Cunningham CE, Wu Y, Arnold R, Bonham K, Freywald A, Han J, Vizeacoumar FJ. Expression-based analyses indicate a central role for hypoxia in driving tumor plasticity through microenvironment remodeling and chromosomal instability. NPJ Syst Biol Appl 2018; 4:38. [PMID: 30374409 PMCID: PMC6200725 DOI: 10.1038/s41540-018-0074-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 09/25/2018] [Accepted: 09/27/2018] [Indexed: 12/27/2022] Open
Abstract
Can transcriptomic alterations drive the evolution of tumors? We asked if changes in gene expression found in all patients arise earlier in tumor development and can be relevant to tumor progression. Our analyses of non-mutated genes from the non-amplified regions of the genome of 158 triple-negative breast cancer (TNBC) cases identified 219 exclusively expression-altered (EEA) genes that may play important role in TNBC. Phylogenetic analyses of these genes predict a "punctuated burst" of multiple gene upregulation events occurring at early stages of tumor development, followed by minimal subsequent changes later in tumor progression. Remarkably, this punctuated burst of expressional changes is instigated by hypoxia-related molecular events, predominantly in two groups of genes that control chromosomal instability (CIN) and those that remodel tumor microenvironment (TME). We conclude that alterations in the transcriptome are not stochastic and that early-stage hypoxia induces CIN and TME remodeling to permit further tumor evolution.
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Affiliation(s)
- Anqi Jing
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G2R3 Canada
| | - Frederick S. Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
| | - Sreejit Parameswaran
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
| | - Bjorn Haave
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
| | - Chelsea E. Cunningham
- Department of Biochemistry, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
| | - Yuliang Wu
- Department of Biochemistry, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
| | - Roland Arnold
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Keith Bonham
- Department of Biochemistry, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
- Cancer Research, Saskatchewan Cancer Agency, Saskatoon, SK S7N 5E5 Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
- Department of Biochemistry, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
| | - Jie Han
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G2R3 Canada
| | - Franco J. Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
- Department of Biochemistry, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5 Canada
- Cancer Research, Saskatchewan Cancer Agency, Saskatoon, SK S7N 5E5 Canada
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15
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Araldi RP, Sant’Ana TA, Módolo DG, de Melo TC, Spadacci-Morena DD, de Cassia Stocco R, Cerutti JM, de Souza EB. The human papillomavirus (HPV)-related cancer biology: An overview. Biomed Pharmacother 2018; 106:1537-1556. [DOI: 10.1016/j.biopha.2018.06.149] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/24/2018] [Accepted: 06/27/2018] [Indexed: 02/07/2023] Open
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16
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Paz MFCJ, Sobral ALP, Picada JN, Grivicich I, Júnior ALG, da Mata AMOF, de Alencar MVOB, de Carvalho RM, da Conceição Machado K, Islam MT, de Carvalho Melo Cavalcante AA, da Silva J. Persistent Increased Frequency of Genomic Instability in Women Diagnosed with Breast Cancer: Before, during, and after Treatments. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:2846819. [PMID: 30013718 PMCID: PMC6022262 DOI: 10.1155/2018/2846819] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 02/13/2018] [Indexed: 12/12/2022]
Abstract
This study aimed to evaluate DNA damage in patients with breast cancer before treatment (background) and after chemotherapy (QT) and radiotherapy (RT) treatment using the Comet assay in peripheral blood and the micronucleus test in buccal cells. We also evaluated repair of DNA damage after the end of RT, as well as the response of patient's cells before treatment with an oxidizing agent (H2O2; challenge assay). Fifty women with a mammographic diagnosis negative for cancer (control group) and 100 women with a diagnosis of breast cancer (followed up during the treatment) were involved in this study. The significant DNA damage was observed by increasing in the index and frequency of damage along with the increasing of the frequency of micronuclei in peripheral blood and cells of the buccal mucosa, respectively. Despite the variability of the responses of breast cancer patients, the individuals presented lesions on the DNA, detected by the Comet assay and micronucleus Test, from the diagnosis until the end of the oncological treatment and were more susceptible to oxidative stress. We can conclude that the damages were due to clastogenic and/or aneugenic effects related to the neoplasia itself and that they increased, especially after RT.
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Affiliation(s)
- Márcia Fernanda Correia Jardim Paz
- Laboratory of Genetic Toxicology, PPGBioSaúde and PPGGTA, Lutheran University of Brazil (ULBRA), Av. Farroupilha 8001, Prédio 22, Sala 22 (4° Andar), 92425-900 Canoas, RS, Brazil
- Laboratory of Genetic Toxicology, PPGCF, Federal University of Piauí, Av. Universitária S/N, Ininga, 64049-550 Teresina, PI, Brazil
- Post-Graduation Program in Biotechnology, RENORBIO, Federal University of Piauí, Av. Universitária, S/N, Ininga, 64049-550 Teresina, PI, Brazil
| | - André Luiz Pinho Sobral
- University Hospital of Piauí, Av. Universitária, S/N, Ininga, 64049-550 Teresina, PI, Brazil
| | - Jaqueline Nascimento Picada
- Laboratory of Genetic Toxicology, PPGBioSaúde and PPGGTA, Lutheran University of Brazil (ULBRA), Av. Farroupilha 8001, Prédio 22, Sala 22 (4° Andar), 92425-900 Canoas, RS, Brazil
| | - Ivana Grivicich
- Laboratory of Cancer Biology, PPGBioSaúde and PPGGTA, Lutheran University of Brazil (ULBRA), Av. Farroupilha 8001, Prédio 22, Sala 22 (4° Andar), 92425-900 Canoas, RS, Brazil
| | - Antonio Luiz Gomes Júnior
- Laboratory of Genetic Toxicology, PPGCF, Federal University of Piauí, Av. Universitária S/N, Ininga, 64049-550 Teresina, PI, Brazil
- Post-Graduation Program in Biotechnology, RENORBIO, Federal University of Piauí, Av. Universitária, S/N, Ininga, 64049-550 Teresina, PI, Brazil
- Biomedicine Department, UNINOVAFAPI University, Teresina, Brazil
| | - Ana Maria Oliveira Ferreira da Mata
- Laboratory of Genetic Toxicology, PPGCF, Federal University of Piauí, Av. Universitária S/N, Ininga, 64049-550 Teresina, PI, Brazil
- Post-Graduation Program in Biotechnology, RENORBIO, Federal University of Piauí, Av. Universitária, S/N, Ininga, 64049-550 Teresina, PI, Brazil
| | - Marcus Vinícius Oliveira Barros de Alencar
- Laboratory of Genetic Toxicology, PPGCF, Federal University of Piauí, Av. Universitária S/N, Ininga, 64049-550 Teresina, PI, Brazil
- Department of Biochemistry and Pharmacology, Federal University of Piauí, Av. Universitária, S/N, Ininga, 64049-550 Teresina, PI, Brazil
| | - Rodrigo Mendes de Carvalho
- Central Laboratory of Public Health of Piauí, Rua Dezenove de Novembro 1945, Bairro Primavera, 64002-570 Teresina, PI, Brazil
| | - Kátia da Conceição Machado
- Laboratory of Genetic Toxicology, PPGCF, Federal University of Piauí, Av. Universitária S/N, Ininga, 64049-550 Teresina, PI, Brazil
- Post-Graduation Program in Biotechnology, RENORBIO, Federal University of Piauí, Av. Universitária, S/N, Ininga, 64049-550 Teresina, PI, Brazil
| | - Muhammad Torequl Islam
- Department for Management of Science and Technology Development, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
| | - Ana Amélia de Carvalho Melo Cavalcante
- Laboratory of Genetic Toxicology, PPGCF, Federal University of Piauí, Av. Universitária S/N, Ininga, 64049-550 Teresina, PI, Brazil
- Post-Graduation Program in Biotechnology, RENORBIO, Federal University of Piauí, Av. Universitária, S/N, Ininga, 64049-550 Teresina, PI, Brazil
| | - Juliana da Silva
- Laboratory of Genetic Toxicology, PPGBioSaúde and PPGGTA, Lutheran University of Brazil (ULBRA), Av. Farroupilha 8001, Prédio 22, Sala 22 (4° Andar), 92425-900 Canoas, RS, Brazil
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17
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Simon E, Bick T, Sarji S, Shentzer T, Prinz E, Yehiam L, Sabo E, Ben-Izhak O, Hershkovitz D. Clinically significant sub-clonality for common drivers can be detected in 26% of KRAS/EGFR mutated lung adenocarcinomas. Oncotarget 2018; 8:45736-45749. [PMID: 28501852 PMCID: PMC5542222 DOI: 10.18632/oncotarget.17399] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/05/2017] [Indexed: 12/30/2022] Open
Abstract
Genetic sub-clonality has been described in multiple malignancies, however the presence of sub-clonality for major drivers in lung adenocarcinoma and its clinical significance is a subject under debate. Using molecular and morphometric approach, 347 lung adenocarcinoma samples were analyzed for KRAS and EGFR sub-clonality, which was further correlated with clinical and pathological variables.KRAS and EGFR mutations were identified in 100 (29%) and 82 (23%) cases, respectively. One hundred and forty four KRAS or EGFR positive cases were also available for morphometric analysis, among which 37 (26%) were defined as sub-clonal. The presence of sub-clonality was associated with shorter survival time (p=0.02). Interestingly, cases with sub-clonality were also associated with earlier disease stage (89% vs 66% stage I disease in sub-clonal vs clonal cases, respectively, p=0.01) and less lymph node involvement (8% vs 25% in sub-clonal vs clonal cases, respectively, p=0.02). Our findings demonstrate the presence of sub-clonality for mutations in common drivers in lung adenocarcinoma and link it both to earlier disease stage and to poor survival. These findings are in line with the different evolutionary models that can present with genetic sub-clonality.
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Affiliation(s)
- Einav Simon
- Institute of Pathology, Rambam Health Care Campus, Haifa, Israel
| | - Tova Bick
- Institute of Pathology, Rambam Health Care Campus, Haifa, Israel
| | - Shada Sarji
- Institute of Pathology, Rambam Health Care Campus, Haifa, Israel
| | - Talia Shentzer
- Institute of Oncology, Rambam Health Care Campus, Haifa, Israel
| | - Elad Prinz
- The Technion Integrated Cancer Center, B. Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Liza Yehiam
- The Technion Integrated Cancer Center, B. Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Edmond Sabo
- Institute of Pathology, Rambam Health Care Campus, Haifa, Israel.,The Technion Integrated Cancer Center, B. Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ofer Ben-Izhak
- Institute of Pathology, Rambam Health Care Campus, Haifa, Israel.,The Technion Integrated Cancer Center, B. Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Dov Hershkovitz
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel.,Department of Pathology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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18
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Román M, Baraibar I, López I, Nadal E, Rolfo C, Vicent S, Gil-Bazo I. KRAS oncogene in non-small cell lung cancer: clinical perspectives on the treatment of an old target. Mol Cancer 2018; 17:33. [PMID: 29455666 PMCID: PMC5817724 DOI: 10.1186/s12943-018-0789-x] [Citation(s) in RCA: 202] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 02/01/2018] [Indexed: 12/14/2022] Open
Abstract
Lung neoplasms are the leading cause of death by cancer worldwide. Non-small cell lung cancer (NSCLC) constitutes more than 80% of all lung malignancies and the majority of patients present advanced disease at onset. However, in the last decade, multiple oncogenic driver alterations have been discovered and each of them represents a potential therapeutic target. Although KRAS mutations are the most frequently oncogene aberrations in lung adenocarcinoma patients, effective therapies targeting KRAS have yet to be developed. Moreover, the role of KRAS oncogene in NSCLC remains unclear and its predictive and prognostic impact remains controversial. The study of the underlying biology of KRAS in NSCLC patients could help to determine potential candidates to evaluate novel targeted agents and combinations that may allow a tailored treatment for these patients. The aim of this review is to update the current knowledge about KRAS-mutated lung adenocarcinoma, including a historical overview, the biology of the molecular pathways involved, the clinical relevance of KRAS mutations as a prognostic and predictive marker and the potential therapeutic approaches for a personalized treatment of KRAS-mutated NSCLC patients.
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Affiliation(s)
- Marta Román
- Department of Oncology, Clínica Universidad de Navarra, 31008, Pamplona, Spain.,Program of Solid Tumors and Biomarkers, Center for Applied Medical Research, Pamplona, Spain
| | - Iosune Baraibar
- Department of Oncology, Clínica Universidad de Navarra, 31008, Pamplona, Spain.,Program of Solid Tumors and Biomarkers, Center for Applied Medical Research, Pamplona, Spain
| | - Inés López
- Program of Solid Tumors and Biomarkers, Center for Applied Medical Research, Pamplona, Spain
| | - Ernest Nadal
- Thoracic Oncology Unit, Department of Medical Oncology, Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, Barcelona, Spain
| | - Christian Rolfo
- Phase I-Early Clinical Phase I-Early Clinical Trials Unit, Oncology Department, Antwerp University Hospital, Edegem, Belgium
| | - Silvestre Vicent
- Program of Solid Tumors and Biomarkers, Center for Applied Medical Research, Pamplona, Spain.,Navarra Health Research Institute (IDISNA), Pamplona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Ignacio Gil-Bazo
- Department of Oncology, Clínica Universidad de Navarra, 31008, Pamplona, Spain. .,Program of Solid Tumors and Biomarkers, Center for Applied Medical Research, Pamplona, Spain. .,Navarra Health Research Institute (IDISNA), Pamplona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
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19
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Wang ZF, Ma DG, Zhu Z, Mu YP, Yang YY, Feng L, Yang H, Liang JQ, Liu YY, Liu L, Lu HW. Astragaloside IV inhibits pathological functions of gastric cancer-associated fibroblasts. World J Gastroenterol 2017; 23:8512-8525. [PMID: 29358859 PMCID: PMC5752711 DOI: 10.3748/wjg.v23.i48.8512] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/29/2017] [Accepted: 11/22/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To investigate the inhibitory effect of astragaloside IV on the pathological functions of cancer-associated fibroblasts, and to explore the underlying mechanism. METHODS Paired gastric normal fibroblast (GNF) and gastric cancer-associated fibroblast (GCAF) cultures were established from resected tissues. GCAFs were treated with vehicle control or different concentrations of astragaloside IV. Conditioned media were prepared from GNFs, GCAFs, control-treated GCAFs, and astragaloside IV-treated GCAFs, and used to culture BGC-823 human gastric cancer cells. Proliferation, migration and invasion capacities of BGC-823 cells were determined by MTT, wound healing, and Transwell invasion assays, respectively. The action mechanism of astragaloside IV was investigated by detecting the expression of microRNAs and the expression and secretion of the oncogenic factor, macrophage colony-stimulating factor (M-CSF), and the tumor suppressive factor, tissue inhibitor of metalloproteinase 2 (TIMP2), in different groups of GCAFs. The expression of the oncogenic pluripotency factors SOX2 and NANOG in BGC-823 cells cultured with different conditioned media was also examined. RESULTS GCAFs displayed higher capacities to induce BGC-823 cell proliferation, migration, and invasion than GNFs (P < 0.01). Astragaloside IV treatment strongly inhibited the proliferation-, migration- and invasion-promoting capacities of GCAFs (P < 0.05 for 10 μmol/L, P < 0.01 for 20 μmol/L and 40 μmol/L). Compared with GNFs, GCAFs expressed a lower level of microRNA-214 (P < 0.01) and a higher level of microRNA-301a (P < 0.01). Astragaloside IV treatment significantly up-regulated microRNA-214 expression (P < 0.01) and down-regulated microRNA-301a expression (P < 0.01) in GCAFs. Reestablishing the microRNA expression balance subsequently suppressed M-CSF production (P < 0.01) and secretion (P < 0.05), and elevated TIMP2 production (P < 0.01) and secretion (P < 0.05). Consequently, the ability of GCAFs to increase SOX2 and NANOG expression in BGC-823 cells was abolished by astragaloside IV. CONCLUSION Astragaloside IV can inhibit the pathological functions of GCAFs by correcting their dysregulation of microRNA expression, and it is promisingly a potent therapeutic agent regulating tumor microenvironment.
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Affiliation(s)
- Zhen-Fei Wang
- Laboratory for Tumor Molecular Diagnosis, Affiliated People’s Hospital of Inner Mongolia Medical University, Huhhot 010020, Inner Mongolia Autonomous Region, China
| | - Da-Guang Ma
- Laboratory for Tumor Molecular Diagnosis, Affiliated People’s Hospital of Inner Mongolia Medical University, Huhhot 010020, Inner Mongolia Autonomous Region, China
| | - Zhe Zhu
- Department of cytotherapy for tumors, Affiliated People’s Hospital of Inner Mongolia Medical University, Huhhot 010020, Inner Mongolia Autonomous Region, China
| | - Yong-Ping Mu
- Laboratory for Tumor Molecular Diagnosis, Affiliated People’s Hospital of Inner Mongolia Medical University, Huhhot 010020, Inner Mongolia Autonomous Region, China
| | - Yong-Yan Yang
- Laboratory for Tumor Molecular Diagnosis, Affiliated People’s Hospital of Inner Mongolia Medical University, Huhhot 010020, Inner Mongolia Autonomous Region, China
| | - Li Feng
- Department of Abdominal Tumor Surgery, Affiliated People’s Hospital of Inner Mongolia Medical University, Huhhot 010020, Inner Mongolia Autonomous Region, China
| | - Hao Yang
- Department of Radiotherapy, Affiliated People’s Hospital of Inner Mongolia Medical University, Huhhot 010020, Inner Mongolia Autonomous Region, China
| | - Jun-Qing Liang
- Department of cytotherapy for tumors, Affiliated People’s Hospital of Inner Mongolia Medical University, Huhhot 010020, Inner Mongolia Autonomous Region, China
| | - Yong-Yan Liu
- Department of cytotherapy for tumors, Affiliated People’s Hospital of Inner Mongolia Medical University, Huhhot 010020, Inner Mongolia Autonomous Region, China
| | - Li Liu
- Central Laboratory, People’s Hospital of Wuhai City, Wuhai 016000, Inner Mongolia Autonomous Region, China
| | - Hai-Wen Lu
- Laboratory for Tumor Molecular Diagnosis, Affiliated People’s Hospital of Inner Mongolia Medical University, Huhhot 010020, Inner Mongolia Autonomous Region, China
- Affiliated Hospital of Inner Mongolia Medical University, Huhhot 010050, Inner Mongolia Autonomous Region, China
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20
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Yang B, Yan T, Cui H, Xu E, Ma Y, Cheng C, Zhang L, Kong P, Wang F, Qian Y, Yang J, Li Y, Li H, Bi Y, Hu X, Wang J, Song B, Yang J, Gao W, Liu J, Zou B, Shi R, Zhang Y, Liu H, Liu Y, Zhai Y, Chang L, Wang Y, Zhang Y, Jia Z, Chen X, Xi Y, Li G, Liang J, Guo J, Guo S, Zhang R, Cheng X, Cui Y. The macro-evolutionary events in esophageal squamous cell carcinoma. Oncotarget 2017; 8:112770-112782. [PMID: 29348864 PMCID: PMC5762549 DOI: 10.18632/oncotarget.22625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/28/2017] [Indexed: 11/25/2022] Open
Abstract
Understanding the evolutionary processes operative in cancer genome may provide insights into clinical outcome and drug-resistance. However, studies focus on genomic signatures, especially for macro-evolutionary events, in esophageal squamous cell carcinoma (ESCC) are limited. Here, we integrated published genomic sequencing data to investigate underlying evolutionary characteristics in ESCC. We found most of ESCC genomes were polyploidy with high genomic instability. Whole genome doubling that acts as one of mechanisms for polyploidy was predicted as a late event in the majority of ESCC genome. Moreover, loss of heterozygosity events were more likely to occur in chromosomes harboring tumor suppressor genes in ESCC. The 40% of neutral loss of heterozygosity events was not a result of genome doubling, suggesting an alternative mechanism for neutral loss of heterozygosity formation. Importantly, deconstruction of copy number alterations extending to telomere revealed that telomere-bounded copy number alterations play a critical role for amplification/deletion of oncogenes/suppressor genes. For well-known genes SOX2, PIK3CA and TERT, nearly all of their amplifications were telomere bounded, which was further confirmed in a Japanese ESCC cohort. Furthermore, we provide evidence that karyotype evolution was mostly punctuated in ESCC. Collectively, our data reveal the potential biological role of whole genome doubling, neutral loss of heterozygosity and telomere-bounded copy number alterations, and highlight mecro-evolution in ESCC tumorigenesis.
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Affiliation(s)
- Bin Yang
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China.,Department of Tumor Surgery, Shanxi Cancer Hospital, Taiyuan, Shanxi, China
| | - Ting Yan
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Heyang Cui
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Enwei Xu
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China.,Department of Pathology, Shanxi Cancer Hospital, Taiyuan, Shanxi, China
| | - Yanchun Ma
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Caixia Cheng
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China.,Department of Pathology, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Ling Zhang
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Pengzhou Kong
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Fang Wang
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yu Qian
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jian Yang
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yaoping Li
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China.,Department of Colorectal & Anal Surgery, Shanxi Provincial People's Hospital, Taiyuan, Shanxi, China
| | - Hongyi Li
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yanghui Bi
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiaoling Hu
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Juan Wang
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Bin Song
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jie Yang
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Wei Gao
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jing Liu
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Department of General Surgery, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Binbin Zou
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Ruyi Shi
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yanyan Zhang
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Department of General Surgery, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Haiyan Liu
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yiqian Liu
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yuanfang Zhai
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Lu Chang
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yi Wang
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yingchun Zhang
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Zhiwu Jia
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xing Chen
- Department of Endoscopy, Shanxi Cancer Hospital, Taiyuan, Shanxi, China
| | - Yanfeng Xi
- Department of Pathology, Shanxi Cancer Hospital, Taiyuan, Shanxi, China
| | - Guodong Li
- Department of Pathology, Shanxi Cancer Hospital, Taiyuan, Shanxi, China
| | - Jianfang Liang
- Department of Pathology, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jiansheng Guo
- Department of General Surgery, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Shiping Guo
- Department of Tumor Surgery, Shanxi Cancer Hospital, Taiyuan, Shanxi, China
| | - Rongsheng Zhang
- Department of Tumor Surgery, Shanxi Cancer Hospital, Taiyuan, Shanxi, China
| | - Xiaolong Cheng
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yongping Cui
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Shanxi Key Laboratory of Carcinogenesis and Translational Research on Esophageal Cancer, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
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21
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Abstract
PURPOSE OF REVIEW Perturbation of the epigenome is emerging as a central driving force in the pathogenesis of diffuse large B-cell lymphomas (DLBCL) and follicular lymphoma. The purpose of this review is to explain how alteration of different layers of the epigenome contributes to the biology and clinical features of these tumors. RECENT FINDINGS Key new findings implicate DNA methylation heterogeneity as a core feature of DLBCL. Epigenetic diversity is linked to unfavorable clinical outcomes, clonal selection at relapse, and is driven at least in part because of the actions of activation-induced cytosine deaminase, which is a unique feature of B-cell lymphomas. Somatic mutations in histone modifier genes drive lymphomagenesis through the establishment of aberrant gene-specific histone modification signatures. For example, EZH2 somatic mutations drive silencing of bivalent gene promoters through histone 3 lysine 27 trimethylation, whereas KMT2D (MLL2) mutations disrupt specific sets of enhancers through depletion of histone 3 lysine 4 mono and dimethylation (H3K4me1/me2). SUMMARY Appreciation of the epigenome in determining lymphoma clonal heterogeneity and in driving lymphoma phenotypes through altered promoter and enhancer histone modification profiles is leading to a paradigm shift in how we understand and design therapies for DLBCL and follicular lymphoma.
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22
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Shagin DA, Turchaninova MA, Shagina IA, Shugay M, Zaretsky AR, Zueva OI, Bolotin DA, Lukyanov S, Chudakov DM. Application of nonsense-mediated primer exclusion (NOPE) for preparation of unique molecular barcoded libraries. BMC Genomics 2017; 18:440. [PMID: 28583065 PMCID: PMC5460480 DOI: 10.1186/s12864-017-3815-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 05/24/2017] [Indexed: 12/18/2022] Open
Abstract
Background Recently we proposed efficient method to exclude undesirable primers at any stage of amplification reaction, here termed NOPE (NOnsense-mediated Primer Exclusion). According to this method, added oligonucleotide overlapping with the 3′-end of unwanted amplification primer (NOPE oligo) simultaneously provides a template for its elongation. This elongation disrupts specificity of unwanted primer, preventing its further participation in PCR. The suggested approach allows to rationally manage the course of PCR reactions in order to facilitate analysis of complex DNA mixtures as well as to perform multistage PCR bypassing intermediate purification steps. Results Here we apply NOPE method to DNA library preparation for the high-throughput sequencing (HTS) with the PCR-based introduction of unique molecular identifiers (UMI). We show that NOPE oligo efficiently neutralizes UMI-containing oligonucleotides after introduction of UMI into sample DNA molecules, thus allowing to proceed with further amplification steps without purification and associated loss of starting material. At the same time, NOPE oligo does not affect the efficiency of target PCR amplification. Conclusion We describe a simple, robust and cheap modification of UMI-labeled HTS libraries preparation procedure, that allows to bypass purification step and thus to preserve starting material which may be limited, e.g. circulating tumor DNA, circulating fetal DNA, or small amounts of isolated cells of interest. Furthermore, demonstrated simplicity and robustness of NOPE method should make it popular in various PCR protocols.
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Affiliation(s)
- Dmitriy A Shagin
- Pirogov Russian National Research Medical University, Moscow, Russia.,Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Maria A Turchaninova
- Pirogov Russian National Research Medical University, Moscow, Russia.,Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Irina A Shagina
- Pirogov Russian National Research Medical University, Moscow, Russia.,Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Mikhail Shugay
- Pirogov Russian National Research Medical University, Moscow, Russia.,Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Andrew R Zaretsky
- Pirogov Russian National Research Medical University, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - Olga I Zueva
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Dmitriy A Bolotin
- Pirogov Russian National Research Medical University, Moscow, Russia.,Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Sergey Lukyanov
- Pirogov Russian National Research Medical University, Moscow, Russia.,Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Dmitriy M Chudakov
- Pirogov Russian National Research Medical University, Moscow, Russia. .,Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia. .,Central European Institute of Technology, Masaryk University, Brno, Czech Republic. .,Skolkovo Institute of Science and Technology, Moscow, Russia.
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23
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MAGERI: Computational pipeline for molecular-barcoded targeted resequencing. PLoS Comput Biol 2017; 13:e1005480. [PMID: 28475621 PMCID: PMC5419444 DOI: 10.1371/journal.pcbi.1005480] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 03/24/2017] [Indexed: 12/16/2022] Open
Abstract
Unique molecular identifiers (UMIs) show outstanding performance in targeted high-throughput resequencing, being the most promising approach for the accurate identification of rare variants in complex DNA samples. This approach has application in multiple areas, including cancer diagnostics, thus demanding dedicated software and algorithms. Here we introduce MAGERI, a computational pipeline that efficiently handles all caveats of UMI-based analysis to obtain high-fidelity mutation profiles and call ultra-rare variants. Using an extensive set of benchmark datasets including gold-standard biological samples with known variant frequencies, cell-free DNA from tumor patient blood samples and publicly available UMI-encoded datasets we demonstrate that our method is both robust and efficient in calling rare variants. The versatility of our software is supported by accurate results obtained for both tumor DNA and viral RNA samples in datasets prepared using three different UMI-based protocols.
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24
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Foijer F, Albacker LA, Bakker B, Spierings DC, Yue Y, Xie SZ, Davis S, Lutum-Jehle A, Takemoto D, Hare B, Furey B, Bronson RT, Lansdorp PM, Bradley A, Sorger PK. Deletion of the MAD2L1 spindle assembly checkpoint gene is tolerated in mouse models of acute T-cell lymphoma and hepatocellular carcinoma. eLife 2017; 6. [PMID: 28318489 PMCID: PMC5400506 DOI: 10.7554/elife.20873] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 03/18/2017] [Indexed: 12/17/2022] Open
Abstract
Chromosome instability (CIN) is deleterious to normal cells because of the burden of aneuploidy. However, most human solid tumors have an abnormal karyotype implying that gain and loss of chromosomes by cancer cells confers a selective advantage. CIN can be induced in the mouse by inactivating the spindle assembly checkpoint. This is lethal in the germline but we show here that adult T cells and hepatocytes can survive conditional inactivation of the Mad2l1 SAC gene and resulting CIN. This causes rapid onset of acute lymphoblastic leukemia (T-ALL) and progressive development of hepatocellular carcinoma (HCC), both lethal diseases. The resulting DNA copy number variation and patterns of chromosome loss and gain are tumor-type specific, suggesting differential selective pressures on the two tumor cell types.
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Affiliation(s)
- Floris Foijer
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Lee A Albacker
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Bjorn Bakker
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Diana C Spierings
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Ying Yue
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Stephanie Z Xie
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Stephanie Davis
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | | | - Darin Takemoto
- Vertex Pharmaceuticals Incorporated, Cambridge, United States
| | - Brian Hare
- Vertex Pharmaceuticals Incorporated, Cambridge, United States
| | - Brinley Furey
- Vertex Pharmaceuticals Incorporated, Cambridge, United States
| | - Roderick T Bronson
- Rodent Histopathology Core, Dana-Farber/Harvard Cancer Center, Harvard Medical School, Boston, United States
| | | | - Allan Bradley
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Peter K Sorger
- Department of Systems Biology, Harvard Medical School, Boston, United States
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25
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Hu Z, Sun R, Curtis C. A population genetics perspective on the determinants of intra-tumor heterogeneity. Biochim Biophys Acta Rev Cancer 2017; 1867:109-126. [PMID: 28274726 DOI: 10.1016/j.bbcan.2017.03.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/01/2017] [Accepted: 03/02/2017] [Indexed: 12/17/2022]
Abstract
Cancer results from the acquisition of somatic alterations in a microevolutionary process that typically occurs over many years, much of which is occult. Understanding the evolutionary dynamics that are operative at different stages of progression in individual tumors might inform the earlier detection, diagnosis, and treatment of cancer. Although these processes cannot be directly observed, the resultant spatiotemporal patterns of genetic variation amongst tumor cells encode their evolutionary histories. Such intra-tumor heterogeneity is pervasive not only at the genomic level, but also at the transcriptomic, phenotypic, and cellular levels. Given the implications for precision medicine, the accurate quantification of heterogeneity within and between tumors has become a major focus of current research. In this review, we provide a population genetics perspective on the determinants of intra-tumor heterogeneity and approaches to quantify genetic diversity. We summarize evidence for different modes of evolution based on recent cancer genome sequencing studies and discuss emerging evolutionary strategies to therapeutically exploit tumor heterogeneity. 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)
- Zheng Hu
- Departments of Medicine and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ruping Sun
- Departments of Medicine and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Christina Curtis
- Departments of Medicine and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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26
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Vallejo A, Perurena N, Guruceaga E, Mazur PK, Martinez-Canarias S, Zandueta C, Valencia K, Arricibita A, Gwinn D, Sayles LC, Chuang CH, Guembe L, Bailey P, Chang DK, Biankin A, Ponz-Sarvise M, Andersen JB, Khatri P, Bozec A, Sweet-Cordero EA, Sage J, Lecanda F, Vicent S. An integrative approach unveils FOSL1 as an oncogene vulnerability in KRAS-driven lung and pancreatic cancer. Nat Commun 2017; 8:14294. [PMID: 28220783 PMCID: PMC5321758 DOI: 10.1038/ncomms14294] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 12/16/2016] [Indexed: 12/28/2022] Open
Abstract
KRAS mutated tumours represent a large fraction of human cancers, but the vast majority remains refractory to current clinical therapies. Thus, a deeper understanding of the molecular mechanisms triggered by KRAS oncogene may yield alternative therapeutic strategies. Here we report the identification of a common transcriptional signature across mutant KRAS cancers of distinct tissue origin that includes the transcription factor FOSL1. High FOSL1 expression identifies mutant KRAS lung and pancreatic cancer patients with the worst survival outcome. Furthermore, FOSL1 genetic inhibition is detrimental to both KRAS-driven tumour types. Mechanistically, FOSL1 links the KRAS oncogene to components of the mitotic machinery, a pathway previously postulated to function orthogonally to oncogenic KRAS. FOSL1 targets include AURKA, whose inhibition impairs viability of mutant KRAS cells. Lastly, combination of AURKA and MEK inhibitors induces a deleterious effect on mutant KRAS cells. Our findings unveil KRAS downstream effectors that provide opportunities to treat KRAS-driven cancers.
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Affiliation(s)
- Adrian Vallejo
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors and Biomarkers, Pamplona 31010, Spain
| | - Naiara Perurena
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors and Biomarkers, Pamplona 31010, Spain
| | - Elisabet Guruceaga
- University of Navarra, Center for Applied Medical Research, Proteomics, Genomics and Bioinformatics Core Facility, Pamplona 31010, Spain
| | - Pawel K. Mazur
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Susana Martinez-Canarias
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors and Biomarkers, Pamplona 31010, Spain
| | - Carolina Zandueta
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors and Biomarkers, Pamplona 31010, Spain
| | - Karmele Valencia
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors and Biomarkers, Pamplona 31010, Spain
| | - Andrea Arricibita
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors and Biomarkers, Pamplona 31010, Spain
| | - Dana Gwinn
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Leanne C. Sayles
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Chen-Hua Chuang
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Laura Guembe
- University of Navarra, Center for Applied Medical Research, Morphology Unit, Pamplona 31010, Spain
| | - Peter Bailey
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - David K. Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
- Department of Surgery, Bankstown Hospital, Eldridge Road, Bankstown, Sydney, New South Wales 2200, Australia
- South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, New South Wales 2170, Australia
| | - Andrew Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
- Department of Surgery, Bankstown Hospital, Eldridge Road, Bankstown, Sydney, New South Wales 2200, Australia
- South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, New South Wales 2170, Australia
| | - Mariano Ponz-Sarvise
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors and Biomarkers, Pamplona 31010, Spain
- Clínica Universidad de Navarra, Department of Medical Oncology, Pamplona 31008, Spain
| | - Jesper B. Andersen
- Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Purvesh Khatri
- Stanford Institute for Immunity, Transplantation and Infection, Stanford, California 94305, USA
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California 94305, USA
| | - Aline Bozec
- Department of Internal Medicine 3 and Institute of Clinical Immunology, University of Erlangen-Nuremberg, 91054 Erlangen, Germany
| | | | - Julien Sage
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Fernando Lecanda
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors and Biomarkers, Pamplona 31010, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona 31008, Spain
- University of Navarra, Department of Histology and Pathology, Pamplona 31008, Spain
| | - Silve Vicent
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors and Biomarkers, Pamplona 31010, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona 31008, Spain
- University of Navarra, Department of Histology and Pathology, Pamplona 31008, Spain
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Cell-Free DNA Provides a Good Representation of the Tumor Genome Despite Its Biased Fragmentation Patterns. PLoS One 2017; 12:e0169231. [PMID: 28046008 PMCID: PMC5207727 DOI: 10.1371/journal.pone.0169231] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/13/2016] [Indexed: 12/17/2022] Open
Abstract
Cell-free DNA (cfDNA) is short, extracellular, fragmented double-stranded DNA found in plasma. Plasma of patients with solid tumor has been found to show significantly increased quantities of cfDNA. Although currently poorly understood, the mechanism of cfDNA generation is speculated to be a product of genomic DNA fragmentation during cellular apoptosis and necrosis. Sequencing of cfDNA with tumor origin has identified tumor biomarkers, elucidating molecular pathology and assisting in accurate diagnosis. In this study, we performed whole-genome sequencing ofcfDNA samples with matching tumor and whole blood samples from five patients diagnosed with stage IV gastric or lung cancer. We analyzed the coverage spectrum of the human genome in our cfDNA samples. cfDNA exhibited no large regions with significant under-coverage, although we observed unbalanced coverage depth in cfDNA at transcription start sites and exon boundaries as a consequence of biased fragmentation due to ordered nucleosome positioning. We also analyzed the copy number variant status based on the whole-genome sequencing results and found high similarity between copy number profile constructed from tumor samples and cfDNA samples. Overall, we conclude that cfDNA comprises a good representation of the tumor genome in late stage gastric and lung cancer.
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28
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Ambrogio C, Nadal E, Villanueva A, Gómez-López G, Cash TP, Barbacid M, Santamaría D. KRAS-driven lung adenocarcinoma: combined DDR1/Notch inhibition as an effective therapy. ESMO Open 2016; 1:e000076. [PMID: 27843638 PMCID: PMC5070278 DOI: 10.1136/esmoopen-2016-000076] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/25/2016] [Accepted: 07/29/2016] [Indexed: 12/28/2022] Open
Abstract
Understanding the early evolution of cancer heterogeneity during the initial steps of tumorigenesis can uncover vulnerabilities of cancer cells that may be masked at later stages. We describe a comprehensive approach employing gene expression analysis in early lesions to identify novel therapeutic targets and the use of mouse models to test synthetic lethal drug combinations to treat human Kirsten rat sarcoma viral oncogene homologue (KRAS)-driven lung adenocarcinoma.
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Affiliation(s)
- Chiara Ambrogio
- Experimental Oncology, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain; Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Ernest Nadal
- Department of Medical Oncology, Multidisciplinary Thoracic Oncology Unit , Catalan Institute of Oncology , Barcelona , Spain
| | - Alberto Villanueva
- Xenopat S.L., Business Bioincubator, Bellvitge Health Science Campus, Barcelona, Spain; Chemoresistance and Predictive Factors Group, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - Gonzalo Gómez-López
- Bioinformatics Unit , Structural Biology and Biocomputing Programme, Centro Nacional de Investigaciones Oncológicas (CNIO) , Madrid , Spain
| | - Timothy P Cash
- Tumour Suppression, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO) , Madrid , Spain
| | - Mariano Barbacid
- Experimental Oncology, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO) , Madrid , Spain
| | - David Santamaría
- Experimental Oncology, Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO) , Madrid , Spain
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29
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Koren E, Fuchs Y. The bad seed: Cancer stem cells in tumor development and resistance. Drug Resist Updat 2016; 28:1-12. [DOI: 10.1016/j.drup.2016.06.006] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 06/11/2016] [Accepted: 06/19/2016] [Indexed: 12/17/2022]
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30
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Alekseenko IV, Pleshkan VV, Monastyrskaya GS, Kuzmich AI, Snezhkov EV, Didych DA, Sverdlov ED. Fundamentally low reproducibility in molecular genetic cancer research. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416070036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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Yant L, Bomblies K. Genome management and mismanagement--cell-level opportunities and challenges of whole-genome duplication. Genes Dev 2016; 29:2405-19. [PMID: 26637526 PMCID: PMC4691946 DOI: 10.1101/gad.271072.115] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Whole-genome duplication (WGD) doubles the DNA content in the nucleus and leads to polyploidy. In this review, Yant and Bomblies discuss both the adaptive potential and problems associated with WGD, focusing primarily on cellular effects. Whole-genome duplication (WGD) doubles the DNA content in the nucleus and leads to polyploidy. In whole-organism polyploids, WGD has been implicated in adaptability and the evolution of increased genome complexity, but polyploidy can also arise in somatic cells of otherwise diploid plants and animals, where it plays important roles in development and likely environmental responses. As with whole organisms, WGD can also promote adaptability and diversity in proliferating cell lineages, although whether WGD is beneficial is clearly context-dependent. WGD is also sometimes associated with aging and disease and may be a facilitator of dangerous genetic and karyotypic diversity in tumorigenesis. Scaling changes can affect cell physiology, but problems associated with WGD in large part seem to arise from problems with chromosome segregation in polyploid cells. Here we discuss both the adaptive potential and problems associated with WGD, focusing primarily on cellular effects. We see value in recognizing polyploidy as a key player in generating diversity in development and cell lineage evolution, with intriguing parallels across kingdoms.
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Affiliation(s)
- Levi Yant
- John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom
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32
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Structural variation discovery in the cancer genome using next generation sequencing: computational solutions and perspectives. Oncotarget 2016; 6:5477-89. [PMID: 25849937 PMCID: PMC4467381 DOI: 10.18632/oncotarget.3491] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/04/2015] [Indexed: 01/03/2023] Open
Abstract
Somatic Structural Variations (SVs) are a complex collection of chromosomal mutations that could directly contribute to carcinogenesis. Next Generation Sequencing (NGS) technology has emerged as the primary means of interrogating the SVs of the cancer genome in recent investigations. Sophisticated computational methods are required to accurately identify the SV events and delineate their breakpoints from the massive amounts of reads generated by a NGS experiment. In this review, we provide an overview of current analytic tools used for SV detection in NGS-based cancer studies. We summarize the features of common SV groups and the primary types of NGS signatures that can be used in SV detection methods. We discuss the principles and key similarities and differences of existing computational programs and comment on unresolved issues related to this research field. The aim of this article is to provide a practical guide of relevant concepts, computational methods, software tools and important factors for analyzing and interpreting NGS data for the detection of SVs in the cancer genome.
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33
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Combined inhibition of DDR1 and Notch signaling is a therapeutic strategy for KRAS-driven lung adenocarcinoma. Nat Med 2016; 22:270-7. [PMID: 26855149 DOI: 10.1038/nm.4041] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 12/29/2015] [Indexed: 12/11/2022]
Abstract
Patients with advanced Kirsten rat sarcoma viral oncogene homolog (KRAS)-mutant lung adenocarcinoma are currently treated with standard chemotherapy because of a lack of efficacious targeted therapies. We reasoned that the identification of mediators of Kras signaling in early mouse lung hyperplasias might bypass the difficulties that are imposed by intratumor heterogeneity in advanced tumors, and that it might unveil relevant therapeutic targets. Transcriptional profiling of Kras(G12V)-driven mouse hyperplasias revealed intertumor diversity with a subset that exhibited an aggressive transcriptional profile analogous to that of advanced human adenocarcinomas. The top-scoring gene in this profile encodes the tyrosine kinase receptor DDR1. The genetic and pharmacological inhibition of DDR1 blocked tumor initiation and tumor progression, respectively. The concomitant inhibition of both DDR1 and Notch signaling induced the regression of KRAS;TP53-mutant patient-derived lung xenografts (PDX) with a therapeutic efficacy that was at least comparable to that of standard chemotherapy. Our data indicate that the combined inhibition of DDR1 and Notch signaling could be an effective targeted therapy for patients with KRAS-mutant lung adenocarcinoma.
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Abstract
The past several years can be considered a renaissance era in the treatment of metastatic melanoma. Following a 30-year stretch in which oncologists barely put a dent in a very grim overall survival (OS) rate for these patients, things have rapidly changed course with the recent approval of three new melanoma drugs by the FDA. Both oncogene-targeted therapy and immune checkpoint blockade approaches have shown remarkable efficacy in a subset of melanoma patients and have clearly been game-changers in terms of clinical impact. However, most patients still succumb to their disease, and thus, there remains an urgent need to improve upon current therapies. Fortunately, innovations in molecular medicine have led to many silent gains that have greatly increased our understanding of the nature of cancer biology as well as the complex interactions between tumors and the immune system. They have also allowed for the first time a detailed understanding of an individual patient's cancer at the genomic and proteomic level. This information is now starting to be employed at all stages of cancer treatment, including diagnosis, choice of drug therapy, treatment monitoring, and analysis of resistance mechanisms upon recurrence. This new era of personalized medicine will foreseeably lead to paradigm shifts in immunotherapeutic treatment approaches such as individualized cancer vaccines and adoptive transfer of genetically modified T cells. Advances in xenograft technology will also allow for the testing of drug combinations using in vivo models, a truly necessary development as the number of new drugs needing to be tested is predicted to skyrocket in the coming years. This chapter will provide an overview of recent technological developments in cancer research, and how they are expected to impact future diagnosis, monitoring, and development of novel treatments for metastatic melanoma.
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Affiliation(s)
| | | | | | - Patrick Hwu
- University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Gregory Lizée
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Abstract
The incidence of esophageal adenocarcinoma (EAC), a debilitating and highly lethal malignancy, has risen dramatically over the past 40 years in the United States and other Western countries. To reverse this trend, EAC prevention and early detection efforts by clinicians, academic researchers and endoscope manufacturers have targeted Barrett's esophagus (BE), the widely accepted EAC precursor lesion. Data from surgical, endoscopic and pre-clinical investigations strongly support the malignant potential of BE. For patients with BE, the risk of developing EAC has been estimated at 11- to 125-fold greater than that of the individual at average risk. Nevertheless, screening for BE in symptomatic patients (ie, with symptoms of reflux) and surveillance in patients diagnosed with BE have not had a substantial impact on the incidence, morbidity or mortality of EAC; the overwhelming majority of EAC patients are diagnosed without a pre-operative diagnosis of BE. This article will discuss the current state of the science of esophageal adenocarcinoma prevention, including ideas about carcinogenesis and its underlying genomic and molecular level mechanisms, and suggest strategies for a systems approach to targeted preventive management.
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Affiliation(s)
- Ellen Richmond
- Division of Cancer Prevention, National Cancer Institute, Rockville, MD, USA.
| | - Asad Umar
- Division of Cancer Prevention, National Cancer Institute, Rockville, MD, USA
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36
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Kryukova E, Kryukov F, Hajek R. Centrosome amplification and clonal evolution in multiple myeloma: Short review. Crit Rev Oncol Hematol 2015; 98:116-21. [PMID: 26589397 DOI: 10.1016/j.critrevonc.2015.10.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 09/14/2015] [Accepted: 10/28/2015] [Indexed: 12/11/2022] Open
Abstract
Multiple myeloma (MM) is composed of an array of multiple clones, each potentially associated with different clinical behavior. Previous studies focused on clinical implication of centrosome amplification (CA) in MM show contradictory results. It seems that the role of CA as well as CA formation in MM differ from other malignancies. This has brought about a question about the role of CA positive clone which is--is it going to be a more aggressive clone evolutionally arising under pressure of negative conditions or can CA serve as a marker of cell abnormality and lead to cell death and further elimination of this damaged subpopulation? This current review is devoted to the discussion of the existence of MM subclones with centrosome amplification (CA), its evolutionary behaviour within intraclonal heterogeneity as well as its potential impact on the disease progression and MM treatment.
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Affiliation(s)
- Elena Kryukova
- Department of Haematooncology, Faculty of Medicine, University of Ostrava, Czech Republic; Department of Haematooncology, University Hospital Ostrava, Czech Republic
| | - Fedor Kryukov
- Department of Haematooncology, Faculty of Medicine, University of Ostrava, Czech Republic; Department of Haematooncology, University Hospital Ostrava, Czech Republic.
| | - Roman Hajek
- Department of Haematooncology, Faculty of Medicine, University of Ostrava, Czech Republic; Department of Haematooncology, University Hospital Ostrava, Czech Republic
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37
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Polivka J, Pesta M, Janku F. Testing for oncogenic molecular aberrations in cell-free DNA-based liquid biopsies in the clinic: are we there yet? Expert Rev Mol Diagn 2015; 15:1631-44. [PMID: 26559503 DOI: 10.1586/14737159.2015.1110021] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The optimal choice of cancer therapy depends upon analysis of the tumor genome for druggable molecular alterations. The spatial and temporal intratumor heterogeneity of cancers creates substantial challenges, as molecular profile depends on time and site of tumor tissue collection. To capture the entire molecular profile, multiple biopsies from primary and metastatic sites at different time points would be required, which is not feasible for ethical or economic reasons. Molecular analysis of circulating cell-free DNA offers a novel, minimally invasive method that can be performed at multiple time-points and plausibly better represents the prevailing molecular profile of the cancer. Molecular analysis of this cell-free DNA offers multiple clinically useful applications, such as identification of molecular targets for cancer therapy, monitoring of tumor molecular profile in real time, detection of emerging molecular aberrations associated with resistance to particular therapy, determination of cancer prognosis and diagnosis of cancer recurrence or progression.
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Affiliation(s)
- Jiri Polivka
- a Department of Histology and Embryology and Biomedical Centre, Faculty of Medicine in Plzen , Charles University in Prague , Plzen , Czech Republic.,b Department of Neurology , Faculty Hospital Plzen , Plzen , Czech Republic
| | - Martin Pesta
- c Department of Biology, Faculty of Medicine in Plzen , Charles University in Prague , Plzen , Czech Republic
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38
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Rovigatti U. Cancer modelling in the NGS era - Part I: Emerging technology and initial modelling. Crit Rev Oncol Hematol 2015; 96:274-307. [PMID: 26427785 DOI: 10.1016/j.critrevonc.2015.05.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 04/14/2015] [Accepted: 05/19/2015] [Indexed: 02/07/2023] Open
Abstract
It is today indisputable that great progresses have been made in our molecular understanding of cancer cells, but an effective implementation of such knowledge into dramatic cancer-cures is still belated and yet desperately needed. This review gives a snapshot at where we stand today in this search for cancer understanding and definitive treatments, how far we have progressed and what are the major obstacles we will have to overcome both technologically and for disease modelling. In the first part, promising 3rd/4th Generation Sequencing Technologies will be summarized (particularly IonTorrent and OxfordNanopore technologies). Cancer modelling will be then reviewed from its origin in XIX Century Germany to today's NGS applications for cancer understanding and therapeutic interventions. Developments after Molecular Biology revolution (1953) are discussed as successions of three phases. The first, PH1, labelled "Clonal Outgrowth" (from 1960s to mid 1980s) was characterized by discoveries in cytogenetics (Nowell, Rowley) and viral oncology (Dulbecco, Bishop, Varmus), which demonstrated clonality. Treatments were consequently dominated by a "cytotoxic eradication" strategy with chemotherapeutic agents. In PH2, (from the mid 1980s to our days) the description of cancer as "Gene Networks" led to targeted-gene-therapies (TGTs). TGTs are the focus of Section 3: in view of their apparent failing (Ephemeral Therapies), alternative strategies will be discussed in review part II (particularly cancer immunotherapy, CIT). Additional Pitfalls impinge on the concepts of tumour heterogeneity (inter/intra; ITH). The described pitfalls set the basis for a new phase, PH3, which is called "NGS Era" and will be also discussed with ten emerging cancer models in the Review 2nd part.
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Affiliation(s)
- Ugo Rovigatti
- University of Pisa Medical School, Oncology Department, via Roma 55, 56127 Pisa, Italy.
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39
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Turning the headlights on novel cancer biomarkers: Inspection of mechanics underlying intratumor heterogeneity. Mol Aspects Med 2015; 45:3-13. [PMID: 26024970 DOI: 10.1016/j.mam.2015.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/20/2015] [Indexed: 01/20/2023]
Abstract
Although the existence of intratumoral heterogeneity (ITH) in the expression of common biomarkers has been described by pathologists since the late 1890s, we have only recently begun to fathom the staggering extent and near ubiquity of this phenomenon. From the tumor's perspective, ITH provides a stabilizing diversity that allows for the evolution of aggressive cancer phenotypes. As the weight of the evidence correlating ITH to poor prognosis burgeons, it has become increasingly important to determine the mechanisms by which a tumor acquires ITH, find clinically-adaptable means to quantify ITH and design strategies to deal with the numerous profound clinical ramifications that ITH forces upon us. Elucidation of the drivers of ITH could enable development of novel biomarkers whose interrogation might permit quantitative evaluation of the ITH inherent in a tumor in order to predict the poor prognosis risk associated with that tumor. This review proposes centrosome amplification (CA), aided and abetted by centrosome clustering mechanisms, as a critical driver of chromosomal instability (CIN) that makes a key contribution to ITH generation. Herein we also evaluate how a tumor's inherent mitotic propensity, which reflects the cell cycling kinetics within the tumor's proliferative cells, functions as the indispensable engine underpinning CIN, and determines the rate of CIN. We thus expound how the forces of centrosome amplification and mitotic propensity collaborate to sculpt the genetic landscape of a tumor and spawn extensive subclonal diversity. As such, centrosome amplification and mitotic propensity profiles could serve as clinically facile and powerful prognostic biomarkers that would enable more accurate risk segmentation of patients and design of individualized therapies.
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40
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Modelska A, Quattrone A, Re A. Molecular portraits: the evolution of the concept of transcriptome-based cancer signatures. Brief Bioinform 2015; 16:1000-7. [PMID: 25832647 PMCID: PMC4652618 DOI: 10.1093/bib/bbv013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Indexed: 12/13/2022] Open
Abstract
Cancer results from dysregulation of multiple steps of gene expression programs. We review how transcriptome profiling has been widely explored for cancer classification and biomarker discovery but resulted in limited clinical impact. Therefore, we discuss alternative and complementary omics approaches.
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41
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Ilyas AM, Ahmad S, Faheem M, Naseer MI, Kumosani TA, Al-Qahtani MH, Gari M, Ahmed F. Next generation sequencing of acute myeloid leukemia: influencing prognosis. BMC Genomics 2015; 16 Suppl 1:S5. [PMID: 25924101 PMCID: PMC4315161 DOI: 10.1186/1471-2164-16-s1-s5] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Acute myeloid leukemia (AML) is a clonal disorder of the blood forming cells characterized by accumulation of immature blast cells in the bone marrow and peripheral blood. Being a heterogeneous disease, AML has been the subject of numerous studies that focus on unraveling the clinical, cellular and molecular variations with the aim to better understand and treat the disease. Cytogenetic-risk stratification of AML is well established and commonly used by clinicians in therapeutic management of cases with chromosomal abnormalities. Successive inclusion of novel molecular abnormalities has substantially modified the classification and understanding of AML in the past decade. With the advent of next generation sequencing (NGS) technologies the discovery of novel molecular abnormalities has accelerated. NGS has been successfully used in several studies and has provided an unprecedented overview of molecular aberrations as well as the underlying clonal evolution in AML. The extended spectrum of abnormalities discovered by NGS is currently under extensive validation for their prognostic and therapeutic values. In this review we highlight the recent advances in the understanding of AML in the NGS era.
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42
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Stepanenko A, Andreieva S, Korets K, Mykytenko D, Huleyuk N, Vassetzky Y, Kavsan V. Step-wise and punctuated genome evolution drive phenotype changes of tumor cells. Mutat Res 2015; 771:56-69. [PMID: 25771981 DOI: 10.1016/j.mrfmmm.2014.12.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 12/14/2014] [Accepted: 12/18/2014] [Indexed: 06/04/2023]
Abstract
The pattern of genome evolution can be divided into two phases: the step-wise continuous phase (step-wise clonal evolution, stable dominant clonal chromosome aberrations (CCAs), and low frequency of non-CCAs, NCCAs) and punctuated phase (marked by elevated NCCAs and transitional CCAs). Depending on the phase, system stresses (the diverse CIN promoting factors) may lead to the very different phenotype responses. To address the contribution of chromosome instability (CIN) to phenotype changes of tumor cells, we characterized CCAs/NCCAs of HeLa and HEK293 cells, and their derivatives after genotoxic stresses (a stable plasmid transfection, ectopic expression of cancer-associated CHI3L1 gene or treatment with temozolomide) by conventional cytogenetics, copy number alterations (CNAs) by array comparative genome hybridization, and phenotype changes by cell viability and soft agar assays. Transfection of either the empty vector pcDNA3.1 or pcDNA3.1_CHI3L1 into 293 cells initiated the punctuated genome changes. In contrast, HeLa_CHI3L1 cells demonstrated the step-wise genome changes. Increased CIN correlated with lower viability of 293_pcDNA3.1 cells but higher colony formation efficiency (CFE). Artificial CHI3L1 production in 293_CHI3L1 cells increased viability and further contributed to CFE. The opposite growth characteristics of 293_CHI3L1 and HeLa_CHI3L1 cells were revealed. The effect and function of a (trans)gene can be opposite and versatile in cells with different genetic network, which is defined by genome context. Temozolomide treatment of 293_pcDNA3.1 cells intensified the stochastic punctuated genome changes and CNAs, and significantly reduced viability and CFE. In contrast, temozolomide treatment of HeLa_CHI3L1 cells promoted the step-wise genome changes, CNAs, and increased viability and CFE, which did not correlate with the ectopic CHI3L1 production. Thus, consistent coevolution of karyotypes and phenotypes was observed. CIN as a driving force of genome evolution significantly influences growth characteristics of tumor cells and should be always taken into consideration during the different experimental manipulations.
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Affiliation(s)
- Aleksei Stepanenko
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv 03680, Ukraine.
| | - Svitlana Andreieva
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv 03680, Ukraine
| | - Kateryna Korets
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv 03680, Ukraine
| | - Dmytro Mykytenko
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv 03680, Ukraine
| | - Nataliya Huleyuk
- Institute of Hereditary Pathology, National Academy of Medical Sciences of Ukraine, Lviv 79008, Ukraine
| | - Yegor Vassetzky
- CNRS UMR8126, Université Paris-Sud 11, Institut de Cancérologie Gustave Roussy, Villejuif 94805, France
| | - Vadym Kavsan
- Department of Biosynthesis of Nucleic Acids, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv 03680, Ukraine
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Abstract
A role for somatic mutations in carcinogenesis is well accepted, but the degree to which mutation rates influence cancer initiation and development is under continuous debate. Recently accumulated genomic data have revealed that thousands of tumour samples are riddled by hypermutation, broadening support for the idea that many cancers acquire a mutator phenotype. This major expansion of cancer mutation data sets has provided unprecedented statistical power for the analysis of mutation spectra, which has confirmed several classical sources of mutation in cancer, highlighted new prominent mutation sources (such as apolipoprotein B mRNA editing enzyme catalytic polypeptide-like (APOBEC) enzymes) and empowered the search for cancer drivers. The confluence of cancer mutation genomics and mechanistic insight provides great promise for understanding the basic development of cancer through mutations.
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44
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Brown R, Curry E, Magnani L, Wilhelm-Benartzi CS, Borley J. Poised epigenetic states and acquired drug resistance in cancer. Nat Rev Cancer 2014; 14:747-53. [PMID: 25253389 DOI: 10.1038/nrc3819] [Citation(s) in RCA: 218] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Epigenetic events, which are somatically inherited through cell division, are potential drivers of acquired drug resistance in cancer. The high rate of epigenetic change in tumours generates diversity in gene expression patterns that can rapidly evolve through drug selection during treatment, leading to the development of acquired resistance. This will potentially confound stratified chemotherapy decisions that are solely based on mutation biomarkers. Poised epigenetic states in tumour cells may drive multistep epigenetic fixation of gene expression during the acquisition of drug resistance, which has implications for clinical strategies to prevent the emergence of drug resistance.
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Affiliation(s)
- Robert Brown
- Department of Surgery &Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Edward Curry
- Department of Surgery &Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Luca Magnani
- Department of Surgery &Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | | | - Jane Borley
- Department of Surgery &Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
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45
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Burrell RA, Swanton C. Tumour heterogeneity and the evolution of polyclonal drug resistance. Mol Oncol 2014; 8:1095-111. [PMID: 25087573 PMCID: PMC5528620 DOI: 10.1016/j.molonc.2014.06.005] [Citation(s) in RCA: 282] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 06/09/2014] [Indexed: 12/15/2022] Open
Abstract
Cancer drug resistance is a major problem, with the majority of patients with metastatic disease ultimately developing multidrug resistance and succumbing to their disease. Our understanding of molecular events underpinning treatment failure has been enhanced by new genomic technologies and pre-clinical studies. Intratumour genetic heterogeneity (ITH) is a prominent contributor to therapeutic failure, and it is becoming increasingly apparent that individual tumours may achieve resistance via multiple routes simultaneously - termed polyclonal resistance. Efforts to target single resistance mechanisms to overcome therapeutic failure may therefore yield only limited success. Clinical studies with sequential analysis of tumour material are needed to enhance our understanding of inter-clonal functional relationships and tumour evolution during therapy, and to improve drug development strategies in cancer medicine.
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Affiliation(s)
- Rebecca A Burrell
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3L7, UK; UCL Cancer Institute, Paul O'Gorman Building University College London, 72 Huntley Street, London WC1E 6DD, UK.
| | - Charles Swanton
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3L7, UK; UCL Cancer Institute, Paul O'Gorman Building University College London, 72 Huntley Street, London WC1E 6DD, UK.
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Ciardiello F, Arnold D, Casali PG, Cervantes A, Douillard JY, Eggermont A, Eniu A, McGregor K, Peters S, Piccart M, Popescu R, Van Cutsem E, Zielinski C, Stahel R. Delivering precision medicine in oncology today and in future-the promise and challenges of personalised cancer medicine: a position paper by the European Society for Medical Oncology (ESMO). Ann Oncol 2014; 25:1673-1678. [PMID: 24950979 DOI: 10.1093/annonc/mdu217] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023] Open
Affiliation(s)
- F Ciardiello
- Department of Experimental and Clinical Medicine and Surgery 'F. Magrassi and A. Lanzara', Second University of Naples, Naples, Italy.
| | - D Arnold
- Klinik für Internistische Onkologie, Klinik für Tumorbiologie, Freiburg, Germany
| | - P G Casali
- Department of Cancer Medicine, Adult Mesenchymal Tumor Medical Oncology Unit, Fondazione IRCCS-Istituto Nazionale dei Tumori, Milan, Italy
| | - A Cervantes
- Department of Hematology and Medical Oncology, Institute of Heath Research INCLIVA, University Hospital of Valencia, Valencia, Spain
| | - J-Y Douillard
- Department of Medical Oncology, Centre René Gauducheau, Institut de Cancérologie de L'Ouest, St Herblain
| | - A Eggermont
- Institute Gustave Roussy, Villejuif/Paris-Sud, France
| | - A Eniu
- Cancer Institute Ion Chiricuta, Cluj-Napoca, Romania
| | - K McGregor
- European Society for Medical Oncology, Lugano
| | - S Peters
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - M Piccart
- Department of Medicine, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - R Popescu
- Department of Medical Oncology, Hirslanden Medical Center, Aarau, Switzerland
| | - E Van Cutsem
- Department of Digestive Oncology, University Hospitals Leuven and KULeuven, Leuven, Belgium
| | - C Zielinski
- Clinical Division of Oncology, Comprehensive Cancer Center, Medical University Vienna-General Hospital, Vienna, Austria
| | - R Stahel
- Clinic of Oncology, UniversitätsSpital Zürich, Zurich, Switzerland
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47
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Horne SD, Pollick SA, Heng HHQ. Evolutionary mechanism unifies the hallmarks of cancer. Int J Cancer 2014; 136:2012-21. [PMID: 24957955 DOI: 10.1002/ijc.29031] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 06/13/2014] [Indexed: 12/15/2022]
Abstract
The basis for the gene mutation theory of cancer that dominates current molecular cancer research consists of: the belief that gene-level aberrations such as mutations are the main cause of cancers, the concept that stepwise gene mutation accumulation drives cancer progression, and the hallmarks of cancer. The research community swiftly embraced the hallmarks of cancer, as such synthesis has supported the notions that common cancer genes are responsible for the majority of cancers and the complexity of cancer can be dissected into simplified molecular principles. The gene/pathway classification based on individual hallmarks provides explanation for the large number of diverse gene mutations, which is in contrast to the original estimation that only a handful of gene mutations would be discovered. Further, these hallmarks have been highly influential as they also provide the rationale and research direction for continued gene-based cancer research. While the molecular knowledge of these hallmarks is drastically increasing, the clinical implication remains limited, as cancer dynamics cannot be summarized by a few isolated/fixed molecular principles. Furthermore, the highly heterogeneous genetic signature of cancers, including massive stochastic genome alterations, challenges the utility of continuously studying each individual gene mutation under the framework of these hallmarks. It is therefore necessary to re-evaluate the concept of cancer hallmarks through the lens of cancer evolution. In this analysis, the evolutionary basis for the hallmarks of cancer will be discussed and the evolutionary mechanism of cancer suggested by the genome theory will be employed to unify the diverse molecular mechanisms of cancer.
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Affiliation(s)
- Steven D Horne
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI
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