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Nauen DW, Guajardo A, Haley L, Powell K, Burger PC, Gocke CD. Chromosomal defects track tumor subpopulations and change in progression in oligodendroglioma. CONVERGENT SCIENCE PHYSICAL ONCOLOGY 2015; 1. [PMID: 31602317 DOI: 10.1088/2057-1739/1/1/015001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
To assess karyotypic changes and tumor subpopulations in progression of oligodendroglioma (ODG) we analyzed histologically diagnosed 1p/19q codeleted cases using single nucleotide polymorphism (SNP) microarray data. We separated cases according to grade, which was assigned blind to karyotype information beyond 1p/19q status. The 51 WHO grade II (O2) and 18 WHO grade III (O3) specimens showed frequent chromosomal locations and patterns of change including loss of heterozygosity (LOH), often copy-neutral, on 9p and LOH on 4p and 4q together. Analysis of co-occurrence indicated that most defects were independent but also suggested increased likelihood of defects on 11q, 13q, and 14q in the presence of defects on 18, 4, and 9, respectively. We used the relative degree of change in B-allele frequency as an indicator of an abnormality's extent, and we present simulated data to clarify how information on subpopulations was thus inferred. Among 9p defects, 89.3% involved the whole tumor, whereas only 47.6% of 4q defects did so. We modeled extent through the tumor as due to a karyotypic change's likelihood of occurring and the fitness it confers on its subpopulation, and used group data to estimate these values. To assess progression directly, we evaluated specimens from six patients who underwent multiple resections since 1996. Four of these patients had received no chemotherapy or radiation, permitting assessment of the natural history of the tumor karyotype in situ. Defects present throughout a tumor at first resection remained so, whereas among subpopulations, some expanded, some remained constant, and some disappeared. The rate of expansion among subpopulations that did so was not uniform, and estimates of fitness predicted subpopulation composition at recurrence. These results extend prior studies of increased karyotypic abnormality in progression of oligodendroglioma and reveal the complex dynamics of subpopulations in the tumor over time.
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Affiliation(s)
- David W Nauen
- Department of Pathology, Johns Hopkins Hospital, Ross 558, 720 Rutland Avenue, Baltimore MD 21205, USA
| | - Andrew Guajardo
- Department of Pathology, Johns Hopkins Hospital, Ross 558, 720 Rutland Avenue, Baltimore MD 21205, USA
| | - Lisa Haley
- Department of Pathology, Johns Hopkins Hospital, Ross 558, 720 Rutland Avenue, Baltimore MD 21205, USA
| | - Kerry Powell
- Department of Pathology, Johns Hopkins Hospital, Ross 558, 720 Rutland Avenue, Baltimore MD 21205, USA
| | - Peter C Burger
- Department of Pathology, Johns Hopkins Hospital, Ross 558, 720 Rutland Avenue, Baltimore MD 21205, USA
| | - Christopher D Gocke
- Department of Pathology, Johns Hopkins Hospital, Ross 558, 720 Rutland Avenue, Baltimore MD 21205, USA
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Sempere LF. Fully automated fluorescence-based four-color multiplex assay for co-detection of microRNA and protein biomarkers in clinical tissue specimens. Methods Mol Biol 2015; 1211:151-70. [PMID: 25218384 DOI: 10.1007/978-1-4939-1459-3_13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The application of locked nucleic acid chemistry for microRNA detection by in situ hybridization, and thereby visualization of microRNA expression at single-cell resolution, has contributed to our understanding of the roles that these short noncoding regulatory RNAs play during development, physiology, and disease. Several groups have implemented chromogenic-based and fluorescence-based protocols to detect microRNA expression in formalin-fixed paraffin-embedded clinical tissue specimens. These emerging robust and reproducible tissue slide-based assays are valid tools to bring about the clinical application of in situ microRNA detection for routine diagnostics. Here, I describe a fully automated fluorescence-based four-color multiplex assay for co-detection of a microRNA (e.g., let-7a, miR-10b, miR-21, miR-34a, miR-126, miR-145, miR-155, miR-205, miR-210), reference RNA (e.g., U6 snRNA, 18S rRNA), and protein markers (e.g., CD11b, CD20, CD45, collagen I, cytokeratin 7, cytokeratin 19, smooth muscle actin, tubulin, vimentin) in FDA-approved Leica Bond-MAX staining station.
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Affiliation(s)
- Lorenzo F Sempere
- Program in Skeletal Disease and Tumor Microenvironment, Laboratory of microRNA Diagnostics and Therapeutics, Center for Cancer and Cell Biology, Van Andel Institute, 333 Bostwick Ave., N.E., Grand Rapids, MI, 49503, USA,
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Gerlinger M, Catto JW, Orntoft TF, Real FX, Zwarthoff EC, Swanton C. Intratumour heterogeneity in urologic cancers: from molecular evidence to clinical implications. Eur Urol 2015; 67:729-37. [PMID: 24836153 DOI: 10.1016/j.eururo.2014.04.014] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 04/21/2014] [Indexed: 02/05/2023]
Abstract
CONTEXT Intratumour heterogeneity (ITH) can impair the precise molecular analysis of tumours and may contribute to difficulties encountered in cancer biomarker qualification and treatment personalisation. OBJECTIVE This review summarises the evidence for genetic ITH in renal, bladder, and prostate carcinomas and potential strategies to address the clinical and translational research challenges arising from ITH. EVIDENCE ACQUISITION Publications that assessed ITH in the relevant urologic cancers were identified in a literature review. EVIDENCE SYNTHESIS ITH with functionally distinct tumour subclones has been identified in all three tumour types. Heterogeneity of actionable genetic changes and of prognostic biomarkers between different tumour regions in the same patient suggests limitations of single biopsy-based molecular analyses for precision medicine approaches. Evolutionary constraints may differ between patients and may allow the prediction of specific evolutionary trajectories. CONCLUSIONS Assessment of multiple tumour regions for precision medicine purposes, monitoring of subclonal dynamics over time, and the preferential targeting of genetic alterations located on the trunk of the phylogenetic tree of individual cancers may accelerate the development of personalised medicine strategies and improve our understanding of treatment failure. PATIENT SUMMARY Genetic alterations can be heterogeneous within urologic tumours, complicating their use as biomarkers for treatment personalisation. We present novel strategies to address these challenges.
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Affiliation(s)
- Marco Gerlinger
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK; The Royal Marsden Hospital, London, UK.
| | - James W Catto
- Academic Urology Unit, University of Sheffield, Sheffield, South Yorkshire, UK
| | - Torben F Orntoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Molecular Pathology Program, CNIO (Spanish National Cancer Research Centre), Madrid, Spain; Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Charles Swanton
- CR-UK London Research Institute, London, UK; University College London Cancer Institute, London, UK.
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Jia Q, Zhou J, Chen G, Shi Y, Yu H, Guan P, Lin R, Jiang N, Yu P, Li QJ, Wan Y. Diversity index of mucosal resident T lymphocyte repertoire predicts clinical prognosis in gastric cancer. Oncoimmunology 2015; 4:e1001230. [PMID: 26137399 DOI: 10.1080/2162402x.2014.1001230] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 12/16/2014] [Accepted: 12/17/2014] [Indexed: 12/22/2022] Open
Abstract
A characteristic immunopathology of human cancers is the induction of tumor antigen-specific T lymphocyte responses within solid tumor tissues. Current strategies for immune monitoring focus on the quantification of the density and differentiation status of tumor-infiltrating T lymphocytes; however, properties of the TCR repertoire ‒ including antigen specificity, clonality, as well as its prognostic significance ‒ remain elusive. In this study, we enrolled 28 gastric cancer patients and collected tumor tissues, adjacent normal mucosal tissues, and peripheral blood samples to study the landscape and compartmentalization of these patients' TCR β repertoire by deep sequencing analyses. Our results illustrated antigen-driven expansion within the tumor compartment and the contracted size of shared clonotypes in mucosa and peripheral blood. Most importantly, the diversity of mucosal T lymphocytes could independently predict prognosis, which strongly underscores critical roles of resident mucosal T-cells in executing post-surgery immunosurveillance against tumor relapse.
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Affiliation(s)
- Qingzhu Jia
- Department of General Surgery and Center of Minimal Invasive; Southwest Hospital; Third Military Medical University ; Chongqing, China ; Biomedical Analysis Center; Third Military Medical University ; Chongqing, China ; Chongqing Key Laboratory of Cellomics ; Chongqing, China
| | - Junfeng Zhou
- Department of General Surgery and Center of Minimal Invasive; Southwest Hospital; Third Military Medical University ; Chongqing, China
| | - Gang Chen
- Biomedical Analysis Center; Third Military Medical University ; Chongqing, China ; Chongqing Key Laboratory of Cellomics ; Chongqing, China
| | - Yan Shi
- Department of General Surgery and Center of Minimal Invasive; Southwest Hospital; Third Military Medical University ; Chongqing, China
| | - Haili Yu
- Biomedical Analysis Center; Third Military Medical University ; Chongqing, China ; Chongqing Key Laboratory of Cellomics ; Chongqing, China
| | - Peng Guan
- Biomedical Analysis Center; Third Military Medical University ; Chongqing, China ; Chongqing Key Laboratory of Cellomics ; Chongqing, China
| | - Regina Lin
- Department of Immunology; Duke University Medical Center ; Durham, NC USA
| | - Ning Jiang
- Department of Biomedical Engineering; Cockrell School of Engineering; University of Texas at Austin ; Austin, TX USA
| | - Peiwu Yu
- Department of General Surgery and Center of Minimal Invasive; Southwest Hospital; Third Military Medical University ; Chongqing, China
| | - Qi-Jing Li
- Chongqing Key Laboratory of Cellomics ; Chongqing, China ; Department of Immunology; Duke University Medical Center ; Durham, NC USA
| | - Ying Wan
- Biomedical Analysis Center; Third Military Medical University ; Chongqing, China ; Chongqing Key Laboratory of Cellomics ; Chongqing, China
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55
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Sun D, Jonasch E, Lara PN. Genetic Heterogeneity of Kidney Cancer. KIDNEY CANCER 2015. [DOI: 10.1007/978-3-319-17903-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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56
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Favero F, Joshi T, Marquard AM, Birkbak NJ, Krzystanek M, Li Q, Szallasi Z, Eklund AC. Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data. Ann Oncol 2015; 26:64-70. [PMID: 25319062 PMCID: PMC4269342 DOI: 10.1093/annonc/mdu479] [Citation(s) in RCA: 499] [Impact Index Per Article: 55.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 10/08/2014] [Accepted: 10/09/2014] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Exome or whole-genome deep sequencing of tumor DNA along with paired normal DNA can potentially provide a detailed picture of the somatic mutations that characterize the tumor. However, analysis of such sequence data can be complicated by the presence of normal cells in the tumor specimen, by intratumor heterogeneity, and by the sheer size of the raw data. In particular, determination of copy number variations from exome sequencing data alone has proven difficult; thus, single nucleotide polymorphism (SNP) arrays have often been used for this task. Recently, algorithms to estimate absolute, but not allele-specific, copy number profiles from tumor sequencing data have been described. MATERIALS AND METHODS We developed Sequenza, a software package that uses paired tumor-normal DNA sequencing data to estimate tumor cellularity and ploidy, and to calculate allele-specific copy number profiles and mutation profiles. We applied Sequenza, as well as two previously published algorithms, to exome sequence data from 30 tumors from The Cancer Genome Atlas. We assessed the performance of these algorithms by comparing their results with those generated using matched SNP arrays and processed by the allele-specific copy number analysis of tumors (ASCAT) algorithm. RESULTS Comparison between Sequenza/exome and SNP/ASCAT revealed strong correlation in cellularity (Pearson's r = 0.90) and ploidy estimates (r = 0.42, or r = 0.94 after manual inspecting alternative solutions). This performance was noticeably superior to previously published algorithms. In addition, in artificial data simulating normal-tumor admixtures, Sequenza detected the correct ploidy in samples with tumor content as low as 30%. CONCLUSIONS The agreement between Sequenza and SNP array-based copy number profiles suggests that exome sequencing alone is sufficient not only for identifying small scale mutations but also for estimating cellularity and inferring DNA copy number aberrations.
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Affiliation(s)
- F Favero
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - T Joshi
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - A M Marquard
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - N J Birkbak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - M Krzystanek
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Q Li
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark; Medical School, Xiamen University, Xiamen, China
| | - Z Szallasi
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark; Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology (CHIP@HST), Harvard Medical School, Boston, USA
| | - A C Eklund
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
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57
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Li SC, Tachiki LML, Kabeer MH, Dethlefs BA, Anthony MJ, Loudon WG. Cancer genomic research at the crossroads: realizing the changing genetic landscape as intratumoral spatial and temporal heterogeneity becomes a confounding factor. Cancer Cell Int 2014; 14:115. [PMID: 25411563 PMCID: PMC4236490 DOI: 10.1186/s12935-014-0115-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 10/24/2014] [Indexed: 02/06/2023] Open
Abstract
The US National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI) created the Cancer Genome Atlas (TCGA) Project in 2006. The TCGA’s goal was to sequence the genomes of 10,000 tumors to identify common genetic changes among different types of tumors for developing genetic-based treatments. TCGA offered great potential for cancer patients, but in reality has little impact on clinical applications. Recent reports place the past TCGA approach of testing a small tumor mass at a single time-point at a crossroads. This crossroads presents us with the conundrum of whether we should sequence more tumors or obtain multiple biopsies from each individual tumor at different time points. Sequencing more tumors with the past TCGA approach of single time-point sampling can neither capture the heterogeneity between different parts of the same tumor nor catch the heterogeneity that occurs as a function of time, error rates, and random drift. Obtaining multiple biopsies from each individual tumor presents multiple logistical and financial challenges. Here, we review current literature and rethink the utility and application of the TCGA approach. We discuss that the TCGA-led catalogue may provide insights into studying the functional significance of oncogenic genes in reference to non-cancer genetic background. Different methods to enhance identifying cancer targets, such as single cell technology, real time imaging of cancer cells with a biological global positioning system, and cross-referencing big data sets, are offered as ways to address sampling discrepancies in the face of tumor heterogeneity. We predict that TCGA landmarks may prove far more useful for cancer prevention than for cancer diagnosis and treatment when considering the effect of non-cancer genes and the normal genetic background on tumor microenvironment. Cancer prevention can be better realized once we understand how therapy affects the genetic makeup of cancer over time in a clinical setting. This may help create novel therapies for gene mutations that arise during a tumor’s evolution from the selection pressure of treatment.
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Affiliation(s)
- Shengwen Calvin Li
- CHOC Children's Hospital Research Institute, University of California Irvine, 1201 West La Veta Ave, Orange, CA 92868 USA ; Department of Neurology, University of California Irvine School of Medicine, Irvine, CA 92697-4292 USA ; Department of Biological Science, California State University, Fullerton, CA 92834 USA
| | - Lisa May Ling Tachiki
- CHOC Children's Hospital Research Institute, University of California Irvine, 1201 West La Veta Ave, Orange, CA 92868 USA ; University of California Irvine School of Medicine, Irvine, CA 92697 USA
| | - Mustafa H Kabeer
- CHOC Children's Hospital Research Institute, University of California Irvine, 1201 West La Veta Ave, Orange, CA 92868 USA ; Department of Pediatric Surgery, CHOC Children's Hospital, 1201 West La Veta Ave, Orange, CA 92868 USA ; Department of Surgery, University of California Irvine School of Medicine, 333 City Blvd. West, Suite 700, Orange, CA 92868 USA
| | - Brent A Dethlefs
- CHOC Children's Hospital Research Institute, University of California Irvine, 1201 West La Veta Ave, Orange, CA 92868 USA
| | | | - William G Loudon
- CHOC Children's Hospital Research Institute, University of California Irvine, 1201 West La Veta Ave, Orange, CA 92868 USA ; Department of Neurological Surgery, Saint Joseph Hospital, Orange, CA 92868 USA ; Department of Neurological Surgery, University of California Irvine School of Medicine, Orange, CA 92862 USA ; Department of Biological Science, California State University, Fullerton, CA 92834 USA
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58
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Zhang J, Fujimoto J, Zhang J, Wedge DC, Song X, Zhang J, Seth S, Chow CW, Cao Y, Gumbs C, Gold KA, Kalhor N, Little L, Mahadeshwar H, Moran C, Protopopov A, Sun H, Tang J, Wu X, Ye Y, William WN, Lee JJ, Heymach JV, Hong WK, Swisher S, Wistuba II, Futreal PA. Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing. Science 2014; 346:256-9. [PMID: 25301631 DOI: 10.1126/science.1256930] [Citation(s) in RCA: 726] [Impact Index Per Article: 72.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cancers are composed of populations of cells with distinct molecular and phenotypic features, a phenomenon termed intratumor heterogeneity (ITH). ITH in lung cancers has not been well studied. We applied multiregion whole-exome sequencing (WES) on 11 localized lung adenocarcinomas. All tumors showed clear evidence of ITH. On average, 76% of all mutations and 20 out of 21 known cancer gene mutations were identified in all regions of individual tumors, which suggested that single-region sequencing may be adequate to identify the majority of known cancer gene mutations in localized lung adenocarcinomas. With a median follow-up of 21 months after surgery, three patients have relapsed, and all three patients had significantly larger fractions of subclonal mutations in their primary tumors than patients without relapse. These data indicate that a larger subclonal mutation fraction may be associated with increased likelihood of postsurgical relapse in patients with localized lung adenocarcinomas.
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Affiliation(s)
- Jianjun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA. Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Jianhua Zhang
- Applied Cancer Science Institute, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - David C Wedge
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Xingzhi Song
- Applied Cancer Science Institute, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Jiexin Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Sahil Seth
- Applied Cancer Science Institute, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Chi-Wan Chow
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Yu Cao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Curtis Gumbs
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Kathryn A Gold
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Neda Kalhor
- Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Latasha Little
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Harshad Mahadeshwar
- Applied Cancer Science Institute, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Cesar Moran
- Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Alexei Protopopov
- Applied Cancer Science Institute, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Huandong Sun
- Applied Cancer Science Institute, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Jiabin Tang
- Applied Cancer Science Institute, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Yuanqing Ye
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - William N William
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA. Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Waun Ki Hong
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Stephen Swisher
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA. Honorary Faculty, Wellcome Trust Sanger Institute, Hinxton, UK CB10 1SA.
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Gulati S, Martinez P, Joshi T, Birkbak NJ, Santos CR, Rowan AJ, Pickering L, Gore M, Larkin J, Szallasi Z, Bates PA, Swanton C, Gerlinger M. Systematic evaluation of the prognostic impact and intratumour heterogeneity of clear cell renal cell carcinoma biomarkers. Eur Urol 2014; 66:936-48. [PMID: 25047176 PMCID: PMC4410302 DOI: 10.1016/j.eururo.2014.06.053] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/30/2014] [Indexed: 12/23/2022]
Abstract
BACKGROUND Candidate biomarkers have been identified for clear cell renal cell carcinoma (ccRCC) patients, but most have not been validated. OBJECTIVE To validate published ccRCC prognostic biomarkers in an independent patient cohort and to assess intratumour heterogeneity (ITH) of the most promising markers to guide biomarker optimisation. DESIGN, SETTING, AND PARTICIPANTS Cancer-specific survival (CSS) for each of 28 identified genetic or transcriptomic biomarkers was assessed in 350 ccRCC patients. ITH was interrogated in a multiregion biopsy data set of 10 ccRCCs. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Biomarker association with CSS was analysed by univariate and multivariate analyses. RESULTS AND LIMITATIONS A total of 17 of 28 biomarkers (TP53 mutations; amplifications of chromosomes 8q, 12, 20q11.21q13.32, and 20 and deletions of 4p, 9p, 9p21.3p24.1, and 22q; low EDNRB and TSPAN7 expression and six gene expression signatures) were validated as predictors of poor CSS in univariate analysis. Tumour stage and the ccB expression signature were the only independent predictors in multivariate analysis. ITH of the ccB signature was identified in 8 of 10 tumours. Several genetic alterations that were significant in univariate analysis were enriched, and chromosomal instability indices were increased in samples expressing the ccB signature. The study may be underpowered to validate low-prevalence biomarkers. CONCLUSIONS The ccB signature was the only independent prognostic biomarker. Enrichment of multiple poor prognosis genetic alterations in ccB samples indicated that several events may be required to establish this aggressive phenotype, catalysed in some tumours by chromosomal instability. Multiregion assessment may improve the precision of this biomarker. PATIENT SUMMARY We evaluated the ability of published biomarkers to predict the survival of patients with clear cell kidney cancer in an independent patient cohort. Only one molecular test adds prognostic information to routine clinical assessments. This marker showed good and poor prognosis results within most individual cancers. Future biomarkers need to consider variation within tumours to improve accuracy.
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Affiliation(s)
- Sakshi Gulati
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Pierre Martinez
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Tejal Joshi
- Centre for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Nicolai Juul Birkbak
- Centre for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Claudio R Santos
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Andrew J Rowan
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK
| | | | | | | | - Zoltan Szallasi
- Centre for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark; Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, USA
| | - Paul A Bates
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, London, UK.
| | - Charles Swanton
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK; UCL Cancer Institute, London, UK.
| | - Marco Gerlinger
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK; Present address: Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
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60
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Wright CM, Yang IA, Bowman RV, Fong KM. The potential of genome-wide analyses to improve non-small-cell lung cancer care. Lung Cancer Manag 2014. [DOI: 10.2217/lmt.14.31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
SUMMARY Genomic technologies have revolutionized the way we study and understand cancer. The advent of next-generation sequencing technology in particular is now starting to change the clinical management of non-small-cell lung cancer. These technologies have helped us to refine prognostication and identify new driver mutations that can allow subselection of patients for therapeutic intervention. However, several limitations and challenges must be overcome before these technologies are widely accepted in diagnostic laboratories. It will be important for clinicians and diagnostic laboratories to consider sample type, analytical platform, cost, data security and ethics, and the bioinformatics challenges associated with 'big data', before widespread integration to the clinic. If these challenges can be overcome, then genomics has the potential to change clinical management of lung cancer.
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Affiliation(s)
- Casey M Wright
- Asbestos Diseases Research Institute, Sydney, NSW, Australia
| | - Ian A Yang
- Department of Thoracic Medicine, The Prince Charles Hospital, 627 Rode Road, Chermside, QLD 4032, Australia
- University of Queensland Thoracic Research Centre, School of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Rayleen V Bowman
- Department of Thoracic Medicine, The Prince Charles Hospital, 627 Rode Road, Chermside, QLD 4032, Australia
- University of Queensland Thoracic Research Centre, School of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Kwun M Fong
- Department of Thoracic Medicine, The Prince Charles Hospital, 627 Rode Road, Chermside, QLD 4032, Australia
- University of Queensland Thoracic Research Centre, School of Medicine, The University of Queensland, Brisbane, QLD, Australia
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Sempere LF. Tissue slide-based microRNA characterization of tumors: how detailed could diagnosis become for cancer medicine? Expert Rev Mol Diagn 2014; 14:853-69. [PMID: 25090088 PMCID: PMC4364265 DOI: 10.1586/14737159.2014.944507] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
miRNAs are short, non-coding, regulatory RNAs that exert cell type-dependent, context-dependent, transcriptome-wide gene expression control under physiological and pathological conditions. Tissue slide-based assays provide qualitative (tumor compartment) and semi-quantitative (expression levels) information about altered miRNA expression at single-cell resolution in clinical tumor specimens. Reviewed here are key technological advances in the last 5 years that have led to implementation of fully automated, robust and reproducible tissue slide-based assays for in situ miRNA detection on US FDA-approved instruments; recent tissue slide-based discovery studies that suggest potential clinical applications of specific miRNAs in cancer medicine are highlighted; and the challenges in bringing tissue slide-based miRNA assays into the clinic are discussed, including clinical validation, biomarker performance, biomarker space and integration with other biomarkers.
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Affiliation(s)
- Lorenzo F Sempere
- Laboratory of microRNA Diagnostics and Therapeutics, Van Andel Research Institute, 333 Bostwick Ave, N.E, Grand Rapids, MI 49503, USA
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62
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Fisher R, Horswell S, Rowan A, Salm MP, de Bruin EC, Gulati S, McGranahan N, Stares M, Gerlinger M, Varela I, Crockford A, Favero F, Quidville V, André F, Navas C, Grönroos E, Nicol D, Hazell S, Hrouda D, O’Brien T, Matthews N, Phillimore B, Begum S, Rabinowitz A, Biggs J, Bates PA, McDonald NQ, Stamp G, Spencer-Dene B, Hsieh JJ, Xu J, Pickering L, Gore M, Larkin J, Swanton C. Development of synchronous VHL syndrome tumors reveals contingencies and constraints to tumor evolution. Genome Biol 2014; 15:433. [PMID: 25159823 PMCID: PMC4166471 DOI: 10.1186/s13059-014-0433-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 08/08/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Genomic analysis of multi-focal renal cell carcinomas from an individual with a germline VHL mutation offers a unique opportunity to study tumor evolution. RESULTS We perform whole exome sequencing on four clear cell renal cell carcinomas removed from both kidneys of a patient with a germline VHL mutation. We report that tumors arising in this context are clonally independent and harbour distinct secondary events exemplified by loss of chromosome 3p, despite an identical genetic background and tissue microenvironment. We propose that divergent mutational and copy number anomalies are contingent upon the nature of 3p loss of heterozygosity occurring early in tumorigenesis. However, despite distinct 3p events, genomic, proteomic and immunohistochemical analyses reveal evidence for convergence upon the PI3K-AKT-mTOR signaling pathway. Four germline tumors in this young patient, and in a second, older patient with VHL syndrome demonstrate minimal intra-tumor heterogeneity and mutational burden, and evaluable tumors appear to follow a linear evolutionary route, compared to tumors from patients with sporadic clear cell renal cell carcinoma. CONCLUSIONS In tumors developing from a germline VHL mutation, the evolutionary principles of contingency and convergence in tumor development are complementary. In this small set of patients with early stage VHL-associated tumors, there is reduced mutation burden and limited evidence of intra-tumor heterogeneity.
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Affiliation(s)
- Rosalie Fisher
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
- />Royal Marsden NHS Foundation Trust, London, SW3 6JJ UK
| | - Stuart Horswell
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | - Andrew Rowan
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | | | - Elza C de Bruin
- />University College London Cancer Institute, London, WC1E 6DD UK
| | - Sakshi Gulati
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | - Nicholas McGranahan
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
- />Centre for Mathematics & Physics in the Life Science & Experimental Biology (CoMPLEX), University College London, London, WC1E 6BT UK
| | - Mark Stares
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
- />Royal Marsden NHS Foundation Trust, London, SW3 6JJ UK
| | - Marco Gerlinger
- />Centre for Evolution and Cancer, Institute of Cancer Research, London, SW7 3RP UK
| | - Ignacio Varela
- />Instituto de Biomedicina y Biotecnología de Cantabria (CSIC-UC-Sodercan), Departamento de Biología Molecular, Universidad de Cantabria, Santander, 39011 Spain
| | - Andrew Crockford
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | - Francesco Favero
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
- />Cancer System Biology, Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, DK-2800 Denmark
| | | | | | - Carolina Navas
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | - Eva Grönroos
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | - David Nicol
- />Royal Marsden NHS Foundation Trust, London, SW3 6JJ UK
| | - Steve Hazell
- />Royal Marsden NHS Foundation Trust, London, SW3 6JJ UK
| | - David Hrouda
- />Imperial College Healthcare NHS Trust, London, W6 8RF UK
| | - Tim O’Brien
- />Guy’s and St Thomas’ NHS Foundation Trust, London, SE1 9RT UK
| | - Nik Matthews
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | - Ben Phillimore
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | - Sharmin Begum
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | - Adam Rabinowitz
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | - Jennifer Biggs
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | - Paul A Bates
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | - Neil Q McDonald
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | - Gordon Stamp
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | | | - James J Hsieh
- />Department of Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, 10065 USA
| | - Jianing Xu
- />Department of Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, 10065 USA
| | - Lisa Pickering
- />Royal Marsden NHS Foundation Trust, London, SW3 6JJ UK
| | - Martin Gore
- />Royal Marsden NHS Foundation Trust, London, SW3 6JJ UK
| | - James Larkin
- />Royal Marsden NHS Foundation Trust, London, SW3 6JJ UK
| | - Charles Swanton
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
- />University College London Cancer Institute, London, WC1E 6DD UK
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63
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El-Mokadem I, Fitzpatrick J, Bondad J, Rauchhaus P, Cunningham J, Pratt N, Fleming S, Nabi G. Chromosome 9p deletion in clear cell renal cell carcinoma predicts recurrence and survival following surgery. Br J Cancer 2014; 111:1381-90. [PMID: 25137021 PMCID: PMC4183850 DOI: 10.1038/bjc.2014.420] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/25/2014] [Accepted: 07/01/2014] [Indexed: 11/23/2022] Open
Abstract
Background: Wider clinical applications of 9p status in clear cell renal cell carcinoma (ccRCC) are limited owing to the lack of validation and consensus for interphase fluorescent in situ hybridisation (I-FISH) scoring technique. The aim of this study was to analytically validate the applicability of I-FISH in assessing 9p deletion in ccRCC and to clinically assess its long-term prognostic impact following surgical excision of ccRCC. Methods: Tissue microarrays were constructed from 108 renal cell carcinoma (RCC) tumour paraffin blocks. Interphase fluorescent in situ hybridisation analysis was undertaken based on preset criteria by two independent observers to assess interobserver variability. 9p status in ccRCC tumours was determined and correlated to clinicopathological variables, recurrence-free survival and disease-specific survival. Results: There were 80 ccRCCs with valid 9p scoring and a median follow-up of 95 months. Kappa statistic for interobserver variability was 0.71 (good agreement). 9p deletion was detected in 44% of ccRCCs. 9p loss was associated with higher stage, larger tumours, necrosis, microvascular and renal vein invasion, and higher SSIGN (stage, size, grade and necrosis) score. Patients with 9p-deleted ccRCC were at a higher risk of recurrence (P=0.008) and RCC-specific mortality (P=0.001). On multivariate analysis, 9p deletion was an independent predictor of recurrence (hazard ratio 4.323; P=0.021) and RCC-specific mortality (hazard ratio 4.603; P=0.007). The predictive accuracy of SSIGN score improved from 87.7% to 93.1% by integrating 9p status to the model (P=0.001). Conclusions: Loss of 9p is associated with aggressive ccRCC and worse prognosis in patients following surgery. Our findings independently confirm the findings of previous reports relying on I-FISH to detect 9p (CDKN2A) deletion.
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Affiliation(s)
- I El-Mokadem
- Academic section of Urology, Medical Research Institute, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - J Fitzpatrick
- Academic section of Urology, Medical Research Institute, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - J Bondad
- Academic section of Urology, Medical Research Institute, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - P Rauchhaus
- Division of Population Sciences, Medical Research Institute, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - J Cunningham
- Department of Clinical Genetics, NHS Tayside Health Board, Dundee DD1 9SY, UK
| | - N Pratt
- Department of Clinical Genetics, NHS Tayside Health Board, Dundee DD1 9SY, UK
| | - S Fleming
- Department of Pathology, Medical Research Institute, School of Medicine, Dundee DD1 9SY, UK
| | - G Nabi
- Academic section of Urology, Medical Research Institute, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
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64
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Sankin A, Hakimi AA, Mikkilineni N, Ostrovnaya I, Silk MT, Liang Y, Mano R, Chevinsky M, Motzer RJ, Solomon SB, Cheng EH, Durack JC, Coleman JA, Russo P, Hsieh JJ. The impact of genetic heterogeneity on biomarker development in kidney cancer assessed by multiregional sampling. Cancer Med 2014; 3:1485-92. [PMID: 25124064 PMCID: PMC4298374 DOI: 10.1002/cam4.293] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 05/22/2014] [Accepted: 06/06/2014] [Indexed: 12/12/2022] Open
Abstract
Primary clear cell renal cell carcinoma (ccRCC) genetic heterogeneity may lead to an underestimation of the mutational burden detected from a single site evaluation. We sought to characterize the extent of clonal branching involving key tumor suppressor mutations in primary ccRCC and determine if genetic heterogeneity could limit the mutation profiling from a single region assessment. Ex vivo core needle biopsies were obtained from three to five different regions of resected renal tumors at a single institution from 2012 to 2013. DNA was extracted and targeted sequencing was performed on five genes associated with ccRCC (von-Hippel Lindau [VHL], PBRM1, SETD2, BAP1, and KDM5C). We constructed phylogenetic trees by inferring clonal evolution based on the mutations present within each core and estimated the predictive power of detecting a mutation for each successive tumor region sampled. We obtained 47 ex vivo biopsy cores from 14 primary ccRCC's (median tumor size 4.5 cm, IQR 4.0–5.9 cm). Branching patterns of various complexities were observed in tumors with three or more mutations. A VHL mutation was detected in nine tumors (64%), each time being present ubiquitously throughout the tumor. Other genes had various degrees of regional mutational variation. Based on the mutations' prevalence we estimated that three different tumor regions should be sampled to detect mutations in PBRM1, SETD2, BAP1, and/or KDM5C with 90% certainty. The mutational burden of renal tumors varies by region sampled. Single site assessment of key tumor suppressor mutations in primary ccRCC may not adequately capture the genetic predictors of tumor behavior.
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Affiliation(s)
- Alexander Sankin
- Urology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York City, New York
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65
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Hodgkinson CL, Morrow CJ, Li Y, Metcalf RL, Rothwell DG, Trapani F, Polanski R, Burt DJ, Simpson KL, Morris K, Pepper SD, Nonaka D, Greystoke A, Kelly P, Bola B, Krebs MG, Antonello J, Ayub M, Faulkner S, Priest L, Carter L, Tate C, Miller CJ, Blackhall F, Brady G, Dive C. Tumorigenicity and genetic profiling of circulating tumor cells in small-cell lung cancer. Nat Med 2014; 20:897-903. [PMID: 24880617 DOI: 10.1038/nm.3600] [Citation(s) in RCA: 518] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 05/16/2014] [Indexed: 12/11/2022]
Abstract
Small-cell lung cancer (SCLC), an aggressive neuroendocrine tumor with early dissemination and dismal prognosis, accounts for 15-20% of lung cancer cases and ∼200,000 deaths each year. Most cases are inoperable, and biopsies to investigate SCLC biology are rarely obtainable. Circulating tumor cells (CTCs), which are prevalent in SCLC, present a readily accessible 'liquid biopsy'. Here we show that CTCs from patients with either chemosensitive or chemorefractory SCLC are tumorigenic in immune-compromised mice, and the resultant CTC-derived explants (CDXs) mirror the donor patient's response to platinum and etoposide chemotherapy. Genomic analysis of isolated CTCs revealed considerable similarity to the corresponding CDX. Most marked differences were observed between CDXs from patients with different clinical outcomes. These data demonstrate that CTC molecular analysis via serial blood sampling could facilitate delivery of personalized medicine for SCLC. CDXs are readily passaged, and these unique mouse models provide tractable systems for therapy testing and understanding drug resistance mechanisms.
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Affiliation(s)
- Cassandra L Hodgkinson
- 1] Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK. [2]
| | - Christopher J Morrow
- 1] Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK. [2]
| | - Yaoyong Li
- Computational Biology Support Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Robert L Metcalf
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Dominic G Rothwell
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Francesca Trapani
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Radoslaw Polanski
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Deborah J Burt
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Kathryn L Simpson
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Karen Morris
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Stuart D Pepper
- Molecular Biology Core Facility, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | | | - Alastair Greystoke
- 1] Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK. [2] The Christie NHS Foundation Trust, Manchester, UK. [3] Institute of Cancer Sciences, University of Manchester, Manchester, UK
| | - Paul Kelly
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Becky Bola
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Matthew G Krebs
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Jenny Antonello
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Mahmood Ayub
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Suzanne Faulkner
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Lynsey Priest
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Louise Carter
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Catriona Tate
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Crispin J Miller
- 1] Computational Biology Support Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK. [2] RNA Biology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Fiona Blackhall
- 1] The Christie NHS Foundation Trust, Manchester, UK. [2] Institute of Cancer Sciences, University of Manchester, Manchester, UK. [3]
| | - Ged Brady
- 1] Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK. [2]
| | - Caroline Dive
- 1] Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK. [2]
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66
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Abstract
Pancreatic cancer is one of the worst prognostic cancers because of the late diagnosis and the absence of effective treatment. Within all subtypes of this disease, ductal adenocarcinoma has the shortest survival time. In recent years, global genomics profiling allowed the identification of hundreds of genes that are perturbed in pancreatic cancer. The integration of different omics sources in the study of pancreatic cancer has revealed several molecular mechanisms, indicating the complex history of its development. However, validation of these genes as biomarkers for early diagnosis, prognosis or treatment efficacy is still incomplete but should lead to new approaches for the treatment of the disease in the future.
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Affiliation(s)
- Christian Pilarsky
- Department of Vascular-, Thoracic and Visceral Surgery, University Hospital Dresden, Technische Universit?t Dresden, Fetscherstr. 74, Dresden 01307, Germany.
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67
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Renovanz M, Kim EL. Intratumoral heterogeneity, its contribution to therapy resistance and methodological caveats to assessment. Front Oncol 2014; 4:142. [PMID: 24959421 PMCID: PMC4050363 DOI: 10.3389/fonc.2014.00142] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 05/27/2014] [Indexed: 12/16/2022] Open
Affiliation(s)
- Mirjam Renovanz
- The Translational Neurooncology Research Group, Department of Neurosurgery, Johannes Gutenberg University Medical Centre , Mainz , Germany
| | - Ella L Kim
- The Translational Neurooncology Research Group, Department of Neurosurgery, Johannes Gutenberg University Medical Centre , Mainz , Germany
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68
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Gerlinger M, Quezada SA, Peggs KS, Furness AJS, Fisher R, Marafioti T, Shende VH, McGranahan N, Rowan AJ, Hazell S, Hamm D, Robins HS, Pickering L, Gore M, Nicol DL, Larkin J, Swanton C. Ultra-deep T cell receptor sequencing reveals the complexity and intratumour heterogeneity of T cell clones in renal cell carcinomas. J Pathol 2014; 231:424-32. [PMID: 24122851 PMCID: PMC4241038 DOI: 10.1002/path.4284] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/24/2013] [Accepted: 09/25/2013] [Indexed: 12/31/2022]
Abstract
The recognition of cancer cells by T cells can impact upon prognosis and be exploited for immunotherapeutic approaches. This recognition depends on the specific interaction between antigens displayed on the surface of cancer cells and the T cell receptor (TCR), which is generated by somatic rearrangements of TCR α- and β-chains (TCRb). Our aim was to assess whether ultra-deep sequencing of the rearranged TCRb in DNA extracted from unfractionated clear cell renal cell carcinoma (ccRCC) samples can provide insights into the clonality and heterogeneity of intratumoural T cells in ccRCCs, a tumour type that can display extensive genetic intratumour heterogeneity (ITH). For this purpose, DNA was extracted from two to four tumour regions from each of four primary ccRCCs and was analysed by ultra-deep TCR sequencing. In parallel, tumour infiltration by CD4, CD8 and Foxp3 regulatory T cells was evaluated by immunohistochemistry and correlated with TCR-sequencing data. A polyclonal T cell repertoire with 367-16 289 (median 2394) unique TCRb sequences was identified per tumour region. The frequencies of the 100 most abundant T cell clones/tumour were poorly correlated between most regions (Pearson correlation coefficient, -0.218 to 0.465). 3-93% of these T cell clones were not detectable across all regions. Thus, the clonal composition of T cell populations can be heterogeneous across different regions of the same ccRCC. T cell ITH was higher in tumours pretreated with an mTOR inhibitor, which could suggest that therapy can influence adaptive tumour immunity. These data show that ultra-deep TCR-sequencing technology can be applied directly to DNA extracted from unfractionated tumour samples, allowing novel insights into the clonality of T cell populations in cancers. These were polyclonal and displayed ITH in ccRCC. TCRb sequencing may shed light on mechanisms of cancer immunity and the efficacy of immunotherapy approaches.
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Affiliation(s)
- Marco Gerlinger
- Cancer Research UK, London Research Institute, UK; Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, London, UK
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69
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Abstract
This editorial will review our current understanding of intratumour heterogeneity and cancer evolution and its potential impact on patient outcome and biomarker validation.
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Affiliation(s)
- Charles Swanton
- Cancer Research UK London Research Institute, London; UCL Cancer Institute and Hospitals, London, UK.
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70
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Gerlinger M, Horswell S, Larkin J, Rowan AJ, Salm MP, Varela I, Fisher R, McGranahan N, Matthews N, Santos CR, Martinez P, Phillimore B, Begum S, Rabinowitz A, Spencer-Dene B, Gulati S, Bates PA, Stamp G, Pickering L, Gore M, Nicol DL, Hazell S, Futreal PA, Stewart A, Swanton C. Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing. Nat Genet 2014; 46:225-233. [PMID: 24487277 PMCID: PMC4636053 DOI: 10.1038/ng.2891] [Citation(s) in RCA: 948] [Impact Index Per Article: 94.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 01/13/2014] [Indexed: 02/08/2023]
Abstract
Clear cell renal carcinomas (ccRCCs) can display intratumor heterogeneity (ITH). We applied multiregion exome sequencing (M-seq) to resolve the genetic architecture and evolutionary histories of ten ccRCCs. Ultra-deep sequencing identified ITH in all cases. We found that 73-75% of identified ccRCC driver aberrations were subclonal, confounding estimates of driver mutation prevalence. ITH increased with the number of biopsies analyzed, without evidence of saturation in most tumors. Chromosome 3p loss and VHL aberrations were the only ubiquitous events. The proportion of C>T transitions at CpG sites increased during tumor progression. M-seq permits the temporal resolution of ccRCC evolution and refines mutational signatures occurring during tumor development.
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Affiliation(s)
- Marco Gerlinger
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Stuart Horswell
- Bioinformatics and Biostatistics, Cancer Research UK London Research Institute, London, UK
| | - James Larkin
- Department of Medicine, Royal Marsden Hospital, London, UK
| | - Andrew J Rowan
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Max P Salm
- Bioinformatics and Biostatistics, Cancer Research UK London Research Institute, London, UK
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria (CSIC-UC-Sodercan), Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Rosalie Fisher
- Department of Medicine, Royal Marsden Hospital, London, UK
| | - Nicholas McGranahan
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Nicholas Matthews
- Advanced Sequencing Facility, Cancer Research UK London Research Institute, London, UK
| | - Claudio R Santos
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Pierre Martinez
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Benjamin Phillimore
- Advanced Sequencing Facility, Cancer Research UK London Research Institute, London, UK
| | - Sharmin Begum
- Advanced Sequencing Facility, Cancer Research UK London Research Institute, London, UK
| | - Adam Rabinowitz
- Advanced Sequencing Facility, Cancer Research UK London Research Institute, London, UK
| | - Bradley Spencer-Dene
- Experimental Histopathology, Cancer Research UK London Research Institute, London, UK
| | - Sakshi Gulati
- Biomolecular Modelling, Cancer Research UK London Research Institute, London, UK
| | - Paul A Bates
- Biomolecular Modelling, Cancer Research UK London Research Institute, London, UK
| | - Gordon Stamp
- Experimental Histopathology, Cancer Research UK London Research Institute, London, UK
| | - Lisa Pickering
- Department of Medicine, Royal Marsden Hospital, London, UK
| | - Martin Gore
- Department of Medicine, Royal Marsden Hospital, London, UK
| | - David L Nicol
- Department of Urology, Royal Marsden Hospital, London, UK
| | - Steven Hazell
- Department of Pathology, Royal Marsden Hospital, London, UK
| | - P Andrew Futreal
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, Texas, USA
| | - Aengus Stewart
- Bioinformatics and Biostatistics, Cancer Research UK London Research Institute, London, UK
| | - Charles Swanton
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK
- University College London Cancer Institute, University College London, London, UK
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71
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Crockford A, Jamal-Hanjani M, Hicks J, Swanton C. Implications of intratumour heterogeneity for treatment stratification. J Pathol 2014; 232:264-73. [PMID: 24115146 DOI: 10.1002/path.4270] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 09/17/2013] [Accepted: 09/18/2013] [Indexed: 12/23/2022]
Abstract
Despite advances in the diagnosis and treatment of cancer, the majority of advanced metastatic solid tumours remain incurable. Differential gene expression, somatic mutational status, tumour-specific genetic signatures and micro-environmental selection pressures within individual tumours have implications for the success of predictive assays to guide therapeutic intervention. In this review we discuss the evidence for genetic and phenotypic heterogeneity and its potential implications for clinical decision making. We highlight areas of research that could be improved in order to better stratify patient treatment. We also discuss the predictive potential of patient-derived models of tumour response, including xenograft and cell line-based systems within the context of intratumour heterogeneity.
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Affiliation(s)
- Andrew Crockford
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, WC2A 3LY, UK
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72
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Martinez P, McGranahan N, Birkbak NJ, Gerlinger M, Swanton C. Computational optimisation of targeted DNA sequencing for cancer detection. Sci Rep 2013; 3:3309. [PMID: 24296834 PMCID: PMC6506443 DOI: 10.1038/srep03309] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 11/06/2013] [Indexed: 12/13/2022] Open
Abstract
Despite recent progress thanks to next-generation sequencing technologies, personalised cancer medicine is still hampered by intra-tumour heterogeneity and drug resistance. As most patients with advanced metastatic disease face poor survival, there is need to improve early diagnosis. Analysing circulating tumour DNA (ctDNA) might represent a non-invasive method to detect mutations in patients, facilitating early detection. In this article, we define reduced gene panels from publicly available datasets as a first step to assess and optimise the potential of targeted ctDNA scans for early tumour detection. Dividing 4,467 samples into one discovery and two independent validation cohorts, we show that up to 76% of 10 cancer types harbour at least one mutation in a panel of only 25 genes, with high sensitivity across most tumour types. Our analyses demonstrate that targeting “hotspot” regions would introduce biases towards in-frame mutations and would compromise the reproducibility of tumour detection.
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Affiliation(s)
- Pierre Martinez
- Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
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The causes and consequences of genetic heterogeneity in cancer evolution. Nature 2013; 501:338-45. [PMID: 24048066 DOI: 10.1038/nature12625] [Citation(s) in RCA: 1547] [Impact Index Per Article: 140.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 07/13/2013] [Indexed: 02/06/2023]
Abstract
Recent studies have revealed extensive genetic diversity both between and within tumours. This heterogeneity affects key cancer pathways, driving phenotypic variation, and poses a significant challenge to personalized cancer medicine. A major cause of genetic heterogeneity in cancer is genomic instability. This instability leads to an increased mutation rate and can shape the evolution of the cancer genome through a plethora of mechanisms. By understanding these mechanisms we can gain insight into the common pathways of tumour evolution that could support the development of future therapeutic strategies.
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Ow TJ, Sandulache VC, Skinner HD, Myers JN. Integration of cancer genomics with treatment selection: from the genome to predictive biomarkers. Cancer 2013; 119:3914-28. [PMID: 24037788 DOI: 10.1002/cncr.28304] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 07/02/2013] [Accepted: 07/02/2013] [Indexed: 12/11/2022]
Abstract
The field of cancer genomics is rapidly advancing as new technology provides detailed genetic and epigenetic profiling of human cancers. The amount of new data available describing the genetic make-up of tumors is paralleled by rapid advances in drug discovery and molecular therapy currently under investigation to treat these diseases. This review summarizes the challenges and approaches associated with the integration of genomic data into the development of new biomarkers in the management of cancer.
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Affiliation(s)
- Thomas J Ow
- Department of Otorhinolaryngology-Head and Neck Surgery, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, New York; Department of Pathology, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, New York
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