501
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Comprehensive Analysis of the Transcriptional and Mutational Landscape of Follicular and Papillary Thyroid Cancers. PLoS Genet 2016; 12:e1006239. [PMID: 27494611 PMCID: PMC4975456 DOI: 10.1371/journal.pgen.1006239] [Citation(s) in RCA: 232] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 07/13/2016] [Indexed: 12/30/2022] Open
Abstract
Follicular thyroid carcinoma (FTC) and benign follicular adenoma (FA) are indistinguishable by preoperative diagnosis due to their similar histological features. Here we report the first RNA sequencing study of these tumors, with data for 30 minimally invasive FTCs (miFTCs) and 25 FAs. We also compared 77 classical papillary thyroid carcinomas (cPTCs) and 48 follicular variant of PTCs (FVPTCs) to observe the differences in their molecular properties. Mutations in H/K/NRAS, DICER1, EIF1AX, IDH1, PTEN, SOS1, and SPOP were identified in miFTC or FA. We identified a low frequency of fusion genes in miFTC (only one, PAX8–PPARG), but a high frequency of that in PTC (17.60%). The frequencies of BRAFV600E and H/K/NRAS mutations were substantially different in miFTC and cPTC, and those of FVPTC were intermediate between miFTC and cPTC. Gene expression analysis demonstrated three molecular subtypes regardless of their histological features, including Non–BRAF–Non–RAS (NBNR), as well as BRAF–like and RAS–like. The novel molecular subtype, NBNR, was associated with DICER1, EIF1AX, IDH1, PTEN, SOS1, SPOP, and PAX8–PPARG. The transcriptome of miFTC or encapsulated FVPTC was indistinguishable from that of FA, providing a molecular explanation for the similarly indolent behavior of these tumors. We identified upregulation of genes that are related to mitochondrial biogenesis including ESRRA and PPARGC1A in oncocytic follicular thyroid neoplasm. Arm-level copy number variations were correlated to histological and molecular characteristics. These results expanded the current molecular understanding of thyroid cancer and may lead to new diagnostic and therapeutic approaches to the disease. Recently, The Cancer Genome Atlas proposed an improved classification of the subtypes of papillary thyroid carcinoma (PTC) based on gene expression profiles, which better represents cell signaling and differentiation. However, a molecular characterization of follicular thyroid carcinoma (FTC), which has a greater tendency for hematogenous spread to lung and bone is not yet fully elucidated. In this study, we describe the first RNA sequencing data of minimally invasive FTC (miFTC) and benign follicular adenoma (FA), which cause diagnostic difficulties due to their similar histological features. Additionally, classical PTC and follicular variant of PTC (FVPTC) were sequenced to compare their transcriptional and mutational landscape. BRAF, H/K/NRAS, fusion genes, and copy number variations were associated with tumor histology. Based on gene expression profiles, thyroid tumors were classified as three molecular subtypes regardless of histological subtypes, BRAF–like, RAS–like, and Non–BRAF–Non–RAS. In particular, we found identical gene expression profiles between miFTC, FA, and encapsulated FVPTC. Oncocytic follicular thyroid tumors have gene expression signatures related to mitochondrial biogenesis including ESRRA and PPARGC1A. These results expanded the current molecular understanding of thyroid cancer to its follicular types.
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502
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Johansson E, Rönö B, Johansson M, Lindgren D, Möller C, Axelson H, Smith EMK. Simultaneous targeted activation of Notch1 and Vhl-disruption in the kidney proximal epithelial tubular cells in mice. Sci Rep 2016; 6:30739. [PMID: 27491826 PMCID: PMC4974510 DOI: 10.1038/srep30739] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 07/07/2016] [Indexed: 01/01/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common subtype of kidney cancer, representing approximately 75% of all renal neoplasms. ccRCC is known to be strongly associated with silencing of the von Hippel Lindau (VHL) tumor suppressor gene, yet VHL deficiency alone does not seem to be sufficient to drive the oncogenic transformation of normal renal epithelium and induce renal tumorigenesis. We, and others, have previously suggested that constitutive activation of the Notch signaling pathway, alongside with VHL loss, contribute to the oncogenic features of ccRCC. Here we report a prevailing hyperactivation of the Notch1 receptor in human ccRCC relative to the healthy counterpart. To explore the consequences of the elevated Notch1 signaling observed in ccRCC patient material, we made use of a conditional mouse model based on concurrent ectopic expression of constitutively active Notch1 (NICD1) and deletion of the Vhl gene. Histological examination of the kidneys of the conditional mice demonstrate the existence of nests of dysplastic cells with a clear cytoplasm as a consequence of lipid accumulation, thus displaying a one important hallmark of human ccRCC.
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Affiliation(s)
- Elinn Johansson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Medicon Village, Building 404 A3, Scheelevägen 8, 404A3, 223 63 Lund, Sweden
| | - Birgitte Rönö
- Division of Translational Cancer Research, Department of Laboratory Medicine, Medicon Village, Building 404 A3, Scheelevägen 8, 404A3, 223 63 Lund, Sweden
| | - Martin Johansson
- Center for Molecular Pathology, Department of Translational Medicine, Skåne University Hospital, 205 02 Malmö, Sweden
| | - David Lindgren
- Division of Translational Cancer Research, Department of Laboratory Medicine, Medicon Village, Building 404 A3, Scheelevägen 8, 404A3, 223 63 Lund, Sweden
| | - Christina Möller
- Division of Translational Cancer Research, Department of Laboratory Medicine, Medicon Village, Building 404 A3, Scheelevägen 8, 404A3, 223 63 Lund, Sweden
| | - Håkan Axelson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Medicon Village, Building 404 A3, Scheelevägen 8, 404A3, 223 63 Lund, Sweden
| | - Emma M K Smith
- Division of Translational Cancer Research, Department of Laboratory Medicine, Medicon Village, Building 404 A3, Scheelevägen 8, 404A3, 223 63 Lund, Sweden
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503
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Unique Transcriptomic Profile of Collecting Duct Carcinomas Relative to Upper Tract Urothelial Carcinomas and other Kidney Carcinomas. Sci Rep 2016; 6:30988. [PMID: 27484008 PMCID: PMC4971524 DOI: 10.1038/srep30988] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 07/11/2016] [Indexed: 01/18/2023] Open
Abstract
Collecting duct carcinoma (CDC) is a kidney cancer subtype that is thought to arise from principal cells in distal parts of the collecting ducts. Some studies suggested an overlap of CDC with upper tract urothelial carcinoma (UTUC), making the pathological diagnosis challenging. Herein, we performed for the first time transcriptome sequencing of CDC and compared them to UTUC and renal cell carcinoma subtypes. We discovered that CDC displays a unique transcriptomic signature among kidney cancer subtypes, with a putative cell of origin in the distal convoluted tubules. Hierarchical unsupervised clustering reveals that the CDC signature is closer to that of other RCC subtypes than to UTUC, which is similar to that of bladder carcinoma. CDC is characterized by a metabolic shift, with impairment of oxidoreductase activity, pyruvate metabolism and the tricarboxlyic acid cycle, as well as an immunogenic response consistent with increased tumor infiltrating lymphocytes, particularly within metastatic cases. In addition, pathways differentially altered between CDC and UTUC point to a basal-like phenotype of CDC in contrast to the luminal-like signature of UTUC. We conclude that CDC harbors a pathognomonic transcriptomic signature characterized by immunogenic and a metabolic aberrations, indicating that targeting these processes might provide therapeutic options for patients.
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504
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Manley BJ, Hsieh JJ. Sarcomatoid renal cell carcinoma: genomic insights from sequencing of matched sarcomatous and carcinomatous components. Transl Cancer Res 2016; 5:S160-S165. [PMID: 29167760 DOI: 10.21037/tcr.2016.07.30] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Brandon J Manley
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James J Hsieh
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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505
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Genomic Characterization of Renal Cell Carcinoma with Sarcomatoid Dedifferentiation Pinpoints Recurrent Genomic Alterations. Eur Urol 2016; 70:348-57. [DOI: 10.1016/j.eururo.2016.01.051] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 01/26/2016] [Indexed: 11/22/2022]
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506
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Scelo G, Hofmann JN, Banks RE, Bigot P, Bhatt RS, Cancel-Tassin G, Chew SK, Creighton CJ, Cussenot O, Davis IJ, Escudier B, Frayling TM, Häggström C, Hildebrandt MAT, Holcatova I, Johansson M, Linehan WM, McDermott DF, Nathanson KL, Ogawa S, Perlman EJ, Purdue MP, Stattin P, Swanton C, Vasudev NS, Wu X, Znaor A, Brennan P, Chanock SJ. International cancer seminars: a focus on kidney cancer. Ann Oncol 2016; 27:1382-5. [PMID: 27130845 PMCID: PMC4959923 DOI: 10.1093/annonc/mdw186] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 04/20/2016] [Indexed: 01/05/2023] Open
Abstract
Recent years have seen important advances in our understanding of the etiology, biology and genetics of kidney cancer. To summarize important achievements and identify prominent research questions that remain, a workshop was organized by IARC and the US NCI. A series of 'difficult questions' were formulated, which should be given future priority in the areas of population, genomic and clinical research.
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Affiliation(s)
- G Scelo
- Section of Genetics, International Agency for Research on Cancer, Lyon, France
| | - J N Hofmann
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Service, National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - R E Banks
- Clinical and Biomedical Proteomics Group, Cancer Research UK Centre, Leeds Institute for Cancer Studies and Pathology, St James' University Hospital, Leeds, UK
| | - P Bigot
- Department of Urology, Centre Hospitalier Universitaire d'Angers, Angers, France
| | - R S Bhatt
- Division of Hematology/Oncology, Beth Israel Deaconess Medical Center, Kidney Cancer Program, Dana-Farber/Harvard Cancer Center, Boston, MA, USA
| | - G Cancel-Tassin
- Groupe de Recherche GRC-UPMC n°5, Centre de Recherche sur les Pathologies Prostatiques et Urologiques (CeRePP), Paris, France
| | - S K Chew
- Translational Cancer Therapeutics Laboratory, UCL Cancer Institute, University College London, London, UK
| | - C J Creighton
- Duncan Cancer Center-Biostatistics, Baylor College of Medicine, Houston
| | - O Cussenot
- Groupe de Recherche GRC-UPMC n°5, Centre de Recherche sur les Pathologies Prostatiques et Urologiques (CeRePP), Paris, France
| | - I J Davis
- Department of Genetics, UNC School of Medicine, Chapel Hill, USA
| | - B Escudier
- Department of Medical Oncology, Institut Gustave Roussy, Villejuif, France
| | | | - C Häggström
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå Department of Biobank Research, Umeå University, Umeå, Sweden
| | - M A T Hildebrandt
- Department of Epidemiology, Division of OVP, Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - I Holcatova
- Institute of Public Health and Preventive Medicine, Charles University, 2nd Faculty of Medicine, Prague, Czech Republic
| | - M Johansson
- Section of Genetics, International Agency for Research on Cancer, Lyon, France
| | - W M Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda
| | - D F McDermott
- Division of Hematology/Oncology, Beth Israel Deaconess Medical Center, Kidney Cancer Program, Dana-Farber/Harvard Cancer Center, Boston, MA, USA
| | - K L Nathanson
- Department of Medicine, University of Pennsylvania, Philadelphia, USA
| | - S Ogawa
- Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - E J Perlman
- Department of Pathology, Northwestern University Feinberg School of Medicine, Robert H. Lurie Comprehensive Cancer Center, Chicago, USA
| | - M P Purdue
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Service, National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - P Stattin
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå
| | - C Swanton
- University College London Hospitals and Cancer Institute, London, UK
| | - N S Vasudev
- Clinical and Biomedical Proteomics Group, Cancer Research UK Centre, Leeds Institute for Cancer Studies and Pathology, St James' University Hospital, Leeds, UK
| | - X Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Znaor
- Section of Genetics, International Agency for Research on Cancer, Lyon, France
| | - P Brennan
- Section of Genetics, International Agency for Research on Cancer, Lyon, France
| | - S J Chanock
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Service, National Cancer Institute, National Institutes of Health, Bethesda, USA
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507
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Ciccarese C, Di Nunno V, Montironi R, Fiorentino M, Brunelli M, Tortora G, Ardizzoni A, Massari F. The role of precision medicine for the treatment of metastatic renal cell carcinoma. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2016. [DOI: 10.1080/23808993.2016.1214057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Chiara Ciccarese
- Medical Oncology, Azienda Ospedaliera Universitaria Integrata, University of Verona, Verona, Italy
| | - Vincenzo Di Nunno
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Sant’Orsola-Malpighi Hospital, Bologna, Italy
| | - Rodolfo Montironi
- Section of Pathological Anatomy, Polytechnic University of the Marche Region, School of Medicine, AOU Ospedali Riuniti, Ancona, Italy
| | - Michelangelo Fiorentino
- Pathology Service, Addarii Institute of Oncology, S-Orsola-Malpighi Hospital, Bologna, Italy
| | - Matteo Brunelli
- Department of Pathology and Diagnostic, Azienda Ospedaliera Universitaria Integrata (AOUI), University of Verona, Verona, Italy
| | - Giampaolo Tortora
- Medical Oncology, Azienda Ospedaliera Universitaria Integrata, University of Verona, Verona, Italy
| | - Andrea Ardizzoni
- Division of Oncology, S.Orsola-Malpighi Hospital, Bologna, Italy
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508
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Abstract
This review provides updated information published in 2014 regarding advances and major achievements in genitourinary cancer. Sections include the best in prostate cancer, renal cancer, bladder cancer, and germ cell tumors. In the field of prostate cancer, data related to treatment approach of hormone-sensitive disease, castrate-resistant prostate cancer, mechanisms of resistance, new drugs, and molecular research are presented. In relation to renal cancer, relevant aspects in the treatment of advanced renal cell carcinoma, immunotherapy, and molecular research, including angiogenesis and von Hippel-Lindau gene, molecular biology of non-clear cell histologies, and epigenetics of clear renal cell cancer are described. New strategies in the management of muscle-invasive localized bladder cancer and metastatic disease are reported as well as salient findings of biomolecular research in urothelial cancer. Some approaches intended to improve outcomes in poor prognosis patients with metastatic germ cell cancer are also reported. Results of clinical trials in these areas are discussed.
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509
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Ciccarese C, Brunelli M, Montironi R, Fiorentino M, Iacovelli R, Heng D, Tortora G, Massari F. The prospect of precision therapy for renal cell carcinoma. Cancer Treat Rev 2016; 49:37-44. [PMID: 27453294 DOI: 10.1016/j.ctrv.2016.07.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/01/2016] [Accepted: 07/04/2016] [Indexed: 02/01/2023]
Abstract
The therapeutic landscape of renal cell carcinoma (RCC) has greatly expanded in the last decade. From being a malignancy orphan of effective therapies, kidney cancer has become today a tumor with several treatment options. Renal cell carcinoma (RCC) is a metabolic disease, being characterized by the dysregulation of metabolic pathways involved in oxygen sensing (VHL/HIF pathway alterations and the subsequent up-regulation of HIF-responsive genes such as VEGF, PDGF, EGF, and glucose transporters GLUT1 and GLUT4, which justify the RCC reliance on aerobic glycolysis), energy sensing (fumarate hydratase-deficient, succinate dehydrogenase-deficient RCC, mutations of HGF/MET pathway resulting in the metabolic Warburg shift marked by RCC increased dependence on aerobic glycolysis and the pentose phosphate shunt, augmented lipogenesis, and reduced AMPK and Krebs cycle activity) and/or nutrient sensing cascade (deregulation of AMPK-TSC1/2-mTOR and PI3K-Akt-mTOR pathways). In this complex scenario it is important to find prognostic and predictive factors that can help in decision making in the treatment of mRCC.
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Affiliation(s)
- Chiara Ciccarese
- Medical Oncology, Azienda Ospedaliera Universitaria Integrata, University of Verona, Verona, Italy
| | - Matteo Brunelli
- Department of Pathology and Diagnostic, Azienda Ospedaliera Universitaria Integrata (AOUI), University of Verona, Verona, Italy
| | - Rodolfo Montironi
- Section of Pathological Anatomy, Polytechnic University of the Marche Region, School of Medicine, AOU Ospedali Riuniti, Ancona, Italy
| | - Michelangelo Fiorentino
- Pathology Service, Addarii Institute of Oncology, S-Orsola-Malpighi Hospital, Bologna, Italy
| | - Roberto Iacovelli
- Medical Oncology, Azienda Ospedaliera Universitaria Integrata, University of Verona, Verona, Italy
| | - Daniel Heng
- Department of Medical Oncology, Tom Baker Cancer Centre, University of Calgary, Calgary, AB, Canada
| | - Giampaolo Tortora
- Medical Oncology, Azienda Ospedaliera Universitaria Integrata, University of Verona, Verona, Italy
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510
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Zhu P, Wang Y, Huang G, Ye B, Liu B, Wu J, Du Y, He L, Fan Z. lnc-β-Catm elicits EZH2-dependent β-catenin stabilization and sustains liver CSC self-renewal. Nat Struct Mol Biol 2016; 23:631-9. [PMID: 27239797 DOI: 10.1038/nsmb.3235] [Citation(s) in RCA: 191] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 04/29/2016] [Indexed: 12/24/2022]
Abstract
Liver cancer stem cells (CSCs) may contribute to the high rate of recurrence and heterogeneity of hepatocellular carcinoma (HCC); however, the molecular mechanisms underlying their self-renewal and differentiation remain largely unknown. Through analysis of transcriptome microarray data, we identified a long noncoding RNA (lncRNA) called lnc-β-Catm, which is highly expressed in human HCC tumors and liver CSCs. We found that lnc-β-Catm is required for self-renewal of liver CSCs and tumor propagation in mice. lnc-β-Catm associates with β-catenin and the methyltransferase EZH2, thereby promoting β-catenin methylation. Methylation suppresses the ubiquitination of β-catenin and promotes its stability, thus leading to activation of Wnt-β-catenin signaling. Accordingly, the expression of lnc-β-Catm, EZH2 and Wnt-β-catenin targets is positively correlated with cancer severity and prognosis of people with HCC.
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MESH Headings
- Animals
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/mortality
- Carcinoma, Hepatocellular/pathology
- Cell Line, Tumor
- Cell Proliferation
- Enhancer of Zeste Homolog 2 Protein/genetics
- Enhancer of Zeste Homolog 2 Protein/metabolism
- Gene Expression Regulation, Neoplastic
- HEK293 Cells
- Hepatocytes/metabolism
- Hepatocytes/pathology
- Humans
- Liver/metabolism
- Liver/pathology
- Liver Neoplasms/genetics
- Liver Neoplasms/metabolism
- Liver Neoplasms/mortality
- Liver Neoplasms/pathology
- Methylation
- Mice
- Mice, Inbred BALB C
- Neoplasm Transplantation
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Prognosis
- Protein Processing, Post-Translational
- Protein Stability
- RNA, Long Noncoding/antagonists & inhibitors
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Survival Analysis
- Transcriptome
- Ubiquitination
- Wnt Signaling Pathway
- beta Catenin/antagonists & inhibitors
- beta Catenin/genetics
- beta Catenin/metabolism
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Affiliation(s)
- Pingping Zhu
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yanying Wang
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Guanling Huang
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Buqing Ye
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Benyu Liu
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiayi Wu
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying Du
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Lei He
- Department of Hepatobiliary Surgery, PLA General Hospital, Beijing, China
| | - Zusen Fan
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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511
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Haake SM, Weyandt JD, Rathmell WK. Insights into the Genetic Basis of the Renal Cell Carcinomas from The Cancer Genome Atlas. Mol Cancer Res 2016; 14:589-98. [PMID: 27330105 PMCID: PMC4955752 DOI: 10.1158/1541-7786.mcr-16-0115] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 04/13/2016] [Indexed: 01/05/2023]
Abstract
The renal cell carcinomas (RCC), clear cell, papillary, and chromophobe, have recently undergone an unmatched genomic characterization by The Cancer Genome Atlas. This analysis has revealed new insights into each of these malignancies and underscores the unique biology of clear cell, papillary, and chromophobe RCC. Themes that have emerged include distinct mechanisms of metabolic dysregulation and common mutations in chromatin modifier genes. Importantly, the papillary RCC classification encompasses a heterogeneous group of diseases, each with highly distinct genetic and molecular features. In conclusion, this review summarizes RCCs that represent a diverse set of malignancies, each with novel biologic programs that define new paradigms for cancer biology. Mol Cancer Res; 14(7); 589-98. ©2016 AACR.
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Affiliation(s)
- Scott M Haake
- Division of Hematology and Oncology, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee
| | - Jamie D Weyandt
- Division of Hematology and Oncology, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee
| | - W Kimryn Rathmell
- Division of Hematology and Oncology, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee.
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512
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Verma M. Genome-wide association studies and epigenome-wide association studies go together in cancer control. Future Oncol 2016; 12:1645-64. [PMID: 27079684 PMCID: PMC5551540 DOI: 10.2217/fon-2015-0035] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/22/2016] [Indexed: 02/07/2023] Open
Abstract
Completion of the human genome a decade ago laid the foundation for: using genetic information in assessing risk to identify individuals and populations that are likely to develop cancer, and designing treatments based on a person's genetic profiling (precision medicine). Genome-wide association studies (GWAS) completed during the past few years have identified risk-associated single nucleotide polymorphisms that can be used as screening tools in epidemiologic studies of a variety of tumor types. This led to the conduct of epigenome-wide association studies (EWAS). This article discusses the current status, challenges and research opportunities in GWAS and EWAS. Information gained from GWAS and EWAS has potential applications in cancer control and treatment.
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Affiliation(s)
- Mukesh Verma
- Methods & Technologies Branch, Epidemiology & Genomics Research Program, Division of Cancer Control & Population Sciences, National Cancer Institute (NCI), NIH, 9609 Medical Center Drive, Suite 4E102, Rockville, MD 20850, USA
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513
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Silva TC, Colaprico A, Olsen C, D'Angelo F, Bontempi G, Ceccarelli M, Noushmehr H. TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages. F1000Res 2016; 5:1542. [PMID: 28232861 PMCID: PMC5302158 DOI: 10.12688/f1000research.8923.2] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/24/2016] [Indexed: 01/09/2023] Open
Abstract
Biotechnological advances in sequencing have led to an explosion of publicly available data via large international consortia such as
The Cancer Genome Atlas (TCGA),
The Encyclopedia of DNA Elements (ENCODE), and
The NIH Roadmap Epigenomics Mapping Consortium (Roadmap). These projects have provided unprecedented opportunities to interrogate the epigenome of cultured cancer cell lines as well as normal and tumor tissues with high genomic resolution. The
Bioconductor project offers more than 1,000 open-source software and statistical packages to analyze high-throughput genomic data. However, most packages are designed for specific data types (e.g. expression, epigenetics, genomics) and there is no one comprehensive tool that provides a complete integrative analysis of the resources and data provided by all three public projects. A need to create an integration of these different analyses was recently proposed. In this workflow, we provide a series of biologically focused integrative analyses of different molecular data. We describe how to download, process and prepare TCGA data and by harnessing several key Bioconductor packages, we describe how to extract biologically meaningful genomic and epigenomic data. Using Roadmap and ENCODE data, we provide a work plan to identify biologically relevant functional epigenomic elements associated with cancer. To illustrate our workflow, we analyzed two types of brain tumors: low-grade glioma (LGG) versus high-grade glioma (glioblastoma multiform or GBM). This workflow introduces the following Bioconductor packages:
AnnotationHub,
ChIPSeeker,
ComplexHeatmap,
pathview,
ELMER,
GAIA,
MINET,
RTCGAToolbox,
TCGAbiolinks.
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Affiliation(s)
- Tiago C Silva
- Department of Genetics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil; Department of Biomedical Sciences, Cedars-Sinai, Los Angeles, CA, USA
| | - Antonio Colaprico
- Interuniversity Institute of Bioinformatics in Brussels, Brussels, Belgium; Machine Learning Group, ULB, Brussels, Belgium
| | - Catharina Olsen
- Interuniversity Institute of Bioinformatics in Brussels, Brussels, Belgium; Machine Learning Group, ULB, Brussels, Belgium
| | - Fulvio D'Angelo
- Department of Science and Technology, University of Sannio, Benevento, Italy; Biogem, Istituto di Ricerche Genetiche Gaetano Salvatore, Avellino, Italy
| | - Gianluca Bontempi
- Interuniversity Institute of Bioinformatics in Brussels, Brussels, Belgium; Machine Learning Group, ULB, Brussels, Belgium; Department of Science and Technology, University of Sannio, Benevento, Italy
| | | | - Houtan Noushmehr
- Department of Genetics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil; Department of Neurosurgery, Henry Ford Hospital, Detroit, MI, USA
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514
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Silva TC, Colaprico A, Olsen C, D'Angelo F, Bontempi G, Ceccarelli M, Noushmehr H. TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages. F1000Res 2016. [PMID: 28232861 DOI: 10.12688/f1000research.8923.1] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Biotechnological advances in sequencing have led to an explosion of publicly available data via large international consortia such as The Cancer Genome Atlas (TCGA), The Encyclopedia of DNA Elements (ENCODE), and The NIH Roadmap Epigenomics Mapping Consortium (Roadmap). These projects have provided unprecedented opportunities to interrogate the epigenome of cultured cancer cell lines as well as normal and tumor tissues with high genomic resolution. The Bioconductor project offers more than 1,000 open-source software and statistical packages to analyze high-throughput genomic data. However, most packages are designed for specific data types (e.g. expression, epigenetics, genomics) and there is no one comprehensive tool that provides a complete integrative analysis of the resources and data provided by all three public projects. A need to create an integration of these different analyses was recently proposed. In this workflow, we provide a series of biologically focused integrative analyses of different molecular data. We describe how to download, process and prepare TCGA data and by harnessing several key Bioconductor packages, we describe how to extract biologically meaningful genomic and epigenomic data. Using Roadmap and ENCODE data, we provide a work plan to identify biologically relevant functional epigenomic elements associated with cancer. To illustrate our workflow, we analyzed two types of brain tumors: low-grade glioma (LGG) versus high-grade glioma (glioblastoma multiform or GBM). This workflow introduces the following Bioconductor packages: AnnotationHub, ChIPSeeker, ComplexHeatmap, pathview, ELMER, GAIA, MINET, RTCGAToolbox, TCGAbiolinks.
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Affiliation(s)
- Tiago C Silva
- Department of Genetics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil; Department of Biomedical Sciences, Cedars-Sinai, Los Angeles, CA, USA
| | - Antonio Colaprico
- Interuniversity Institute of Bioinformatics in Brussels, Brussels, Belgium; Machine Learning Group, ULB, Brussels, Belgium
| | - Catharina Olsen
- Interuniversity Institute of Bioinformatics in Brussels, Brussels, Belgium; Machine Learning Group, ULB, Brussels, Belgium
| | - Fulvio D'Angelo
- Department of Science and Technology, University of Sannio, Benevento, Italy; Biogem, Istituto di Ricerche Genetiche Gaetano Salvatore, Avellino, Italy
| | - Gianluca Bontempi
- Interuniversity Institute of Bioinformatics in Brussels, Brussels, Belgium; Machine Learning Group, ULB, Brussels, Belgium; Department of Science and Technology, University of Sannio, Benevento, Italy
| | | | - Houtan Noushmehr
- Department of Genetics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil; Department of Neurosurgery, Henry Ford Hospital, Detroit, MI, USA
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515
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Poornima P, Kumar JD, Zhao Q, Blunder M, Efferth T. Network pharmacology of cancer: From understanding of complex interactomes to the design of multi-target specific therapeutics from nature. Pharmacol Res 2016; 111:290-302. [PMID: 27329331 DOI: 10.1016/j.phrs.2016.06.018] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 12/14/2022]
Abstract
Despite massive investments in drug research and development, the significant decline in the number of new drugs approved or translated to clinical use raises the question, whether single targeted drug discovery is the right approach. To combat complex systemic diseases that harbour robust biological networks such as cancer, single target intervention is proved to be ineffective. In such cases, network pharmacology approaches are highly useful, because they differ from conventional drug discovery by addressing the ability of drugs to target numerous proteins or networks involved in a disease. Pleiotropic natural products are one of the promising strategies due to their multi-targeting and due to lower side effects. In this review, we discuss the application of network pharmacology for cancer drug discovery. We provide an overview of the current state of knowledge on network pharmacology, focus on different technical approaches and implications for cancer therapy (e.g. polypharmacology and synthetic lethality), and illustrate the therapeutic potential with selected examples green tea polyphenolics, Eleutherococcus senticosus, Rhodiola rosea, and Schisandra chinensis). Finally, we present future perspectives on their plausible applications for diagnosis and therapy of cancer.
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Affiliation(s)
- Paramasivan Poornima
- School of Chemistry, Bangor University, Bangor, Gwynedd LL57 2DG, United Kingdom
| | - Jothi Dinesh Kumar
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - Qiaoli Zhao
- Department of Pharmaceutical Biology, Johannes Gutenberg University, Mainz, Germany
| | - Martina Blunder
- Department of Neuroscience, Biomedical Center, Uppsala University, Uppsala, Sweden and Brain Institute, Federal University of Rio Grande do Norte, UFRN, Natal, Brazil
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Johannes Gutenberg University, Mainz, Germany.
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516
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Shen R, Seshan VE. FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing. Nucleic Acids Res 2016; 44:e131. [PMID: 27270079 PMCID: PMC5027494 DOI: 10.1093/nar/gkw520] [Citation(s) in RCA: 754] [Impact Index Per Article: 94.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/29/2016] [Indexed: 12/02/2022] Open
Abstract
Allele-specific copy number analysis (ASCN) from next generation sequencing (NGS) data can greatly extend the utility of NGS beyond the identification of mutations to precisely annotate the genome for the detection of homozygous/heterozygous deletions, copy-neutral loss-of-heterozygosity (LOH), allele-specific gains/amplifications. In addition, as targeted gene panels are increasingly used in clinical sequencing studies for the detection of ‘actionable’ mutations and copy number alterations to guide treatment decisions, accurate, tumor purity-, ploidy- and clonal heterogeneity-adjusted integer copy number calls are greatly needed to more reliably interpret NGS-based cancer gene copy number data in the context of clinical sequencing. We developed FACETS, an ASCN tool and open-source software with a broad application to whole genome, whole-exome, as well as targeted panel sequencing platforms. It is a fully integrated stand-alone pipeline that includes sequencing BAM file post-processing, joint segmentation of total- and allele-specific read counts, and integer copy number calls corrected for tumor purity, ploidy and clonal heterogeneity, with comprehensive output and integrated visualization. We demonstrate the application of FACETS using The Cancer Genome Atlas (TCGA) whole-exome sequencing of lung adenocarcinoma samples. We also demonstrate its application to a clinical sequencing platform based on a targeted gene panel.
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Affiliation(s)
- Ronglai Shen
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Venkatraman E Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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517
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Malouf GG, Su X, Zhang J, Creighton CJ, Ho TH, Lu Y, Raynal NJM, Karam JA, Tamboli P, Allanick F, Mouawad R, Spano JP, Khayat D, Wood CG, Jelinek J, Tannir NM. DNA Methylation Signature Reveals Cell Ontogeny of Renal Cell Carcinomas. Clin Cancer Res 2016; 22:6236-6246. [PMID: 27256309 DOI: 10.1158/1078-0432.ccr-15-1217] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 04/28/2016] [Accepted: 05/12/2016] [Indexed: 11/16/2022]
Abstract
PURPOSE DNA methylation is a heritable covalent modification that is developmentally regulated and is critical in tissue-type definition. Although genotype-phenotype correlations have been described for different subtypes of renal cell carcinoma (RCC), it is unknown if DNA methylation profiles correlate with morphological or ontology based phenotypes. Here, we test the hypothesis that DNA methylation signatures can discriminate between putative precursor cells in the nephron. EXPERIMENTAL DESIGNS We performed deep profiling of DNA methylation and transcriptome in diverse histopathological RCC subtypes and validated DNA methylation in an independent dataset as well as in The Cancer Genome Atlas Clear Cell and Chromophobe Renal Cell Carcinoma Datasets. RESULTS Our data provide the first mapping of methylome epi-signature and indicate that RCC subtypes can be grouped into two major epi-clusters: C1, which encompasses clear-cell RCC, papillary RCC, mucinous and spindle cell carcinomas and translocation RCC; C2, which comprises oncocytoma and chromophobe RCC. Interestingly, C1 epi-cluster displayed 3-fold more hypermethylation as compared with C2 epi-cluster. Of note, differentially methylated regions between C1 and C2 epi-clusters occur in gene bodies and intergenic regions, instead of gene promoters. Transcriptome analysis of C1 epi-cluster suggests a functional convergence on Polycomb targets, whereas C2 epi-cluster displays DNA methylation defects. Furthermore, we find that our epigenetic ontogeny signature is associated with worse outcomes of patients with clear-cell RCC. CONCLUSIONS Our data define the epi-clusters that can discriminate between distinct RCC subtypes and for the first time define the epigenetic basis for proximal versus distal tubule derived kidney tumors. Clin Cancer Res; 22(24); 6236-46. ©2016 AACR.
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Affiliation(s)
- Gabriel G Malouf
- Department of Medical Oncology, Groupe Hospitalier Pitié-Salpêtrière, University Pierre and Marie Curie (Paris VI), Institut Universitaire de cancérologie, AP-HP, Paris, France.
- AVEC Foundation Laboratory, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Xiaoping Su
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianping Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chad J Creighton
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Thai H Ho
- Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, Arizona
- Center for Individualized Medicine, Epigenomics Group, Mayo Clinic, Rochester, Minnesota
| | - Yue Lu
- Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas
| | - Noël J-M Raynal
- Fels Institute, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Jose A Karam
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Pheroze Tamboli
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Frederick Allanick
- AVEC Foundation Laboratory, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Roger Mouawad
- AVEC Foundation Laboratory, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Jean-Philippe Spano
- Department of Medical Oncology, Groupe Hospitalier Pitié-Salpêtrière, University Pierre and Marie Curie (Paris VI), Institut Universitaire de cancérologie, AP-HP, Paris, France
- AVEC Foundation Laboratory, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - David Khayat
- Department of Medical Oncology, Groupe Hospitalier Pitié-Salpêtrière, University Pierre and Marie Curie (Paris VI), Institut Universitaire de cancérologie, AP-HP, Paris, France
- AVEC Foundation Laboratory, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Christopher G Wood
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jaroslav Jelinek
- Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas
| | - Nizar M Tannir
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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518
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Abstract
Chronic kidney disease (CKD) represents a leading cause of death in the United States. There is no cure for this disease, with current treatment strategies relying on blood pressure control through blockade of the renin-angiotensin system. Such approaches only delay the development of end-stage kidney disease and can be associated with serious side effects. Recent identification of several novel mechanisms contributing to CKD development - including vascular changes, loss of podocytes and renal epithelial cells, matrix deposition, inflammation and metabolic dysregulation - has revealed new potential therapeutic approaches for CKD. This Review assesses emerging strategies and agents for CKD treatment, highlighting the associated challenges in their clinical development.
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519
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Systematic analysis of mutation distribution in three dimensional protein structures identifies cancer driver genes. Sci Rep 2016; 6:26483. [PMID: 27225414 PMCID: PMC4880911 DOI: 10.1038/srep26483] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 05/03/2016] [Indexed: 01/26/2023] Open
Abstract
Protein tertiary structure determines molecular function, interaction, and stability of the protein, therefore distribution of mutation in the tertiary structure can facilitate the identification of new driver genes in cancer. To analyze mutation distribution in protein tertiary structures, we applied a novel three dimensional permutation test to the mutation positions. We analyzed somatic mutation datasets of 21 types of cancers obtained from exome sequencing conducted by the TCGA project. Of the 3,622 genes that had ≥3 mutations in the regions with tertiary structure data, 106 genes showed significant skew in mutation distribution. Known tumor suppressors and oncogenes were significantly enriched in these identified cancer gene sets. Physical distances between mutations in known oncogenes were significantly smaller than those of tumor suppressors. Twenty-three genes were detected in multiple cancers. Candidate genes with significant skew of the 3D mutation distribution included kinases (MAPK1, EPHA5, ERBB3, and ERBB4), an apoptosis related gene (APP), an RNA splicing factor (SF1), a miRNA processing factor (DICER1), an E3 ubiquitin ligase (CUL1) and transcription factors (KLF5 and EEF1B2). Our study suggests that systematic analysis of mutation distribution in the tertiary protein structure can help identify cancer driver genes.
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520
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Colaprico A, Silva TC, Olsen C, Garofano L, Cava C, Garolini D, Sabedot TS, Malta TM, Pagnotta SM, Castiglioni I, Ceccarelli M, Bontempi G, Noushmehr H. TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data. Nucleic Acids Res 2016; 44:e71. [PMID: 26704973 PMCID: PMC4856967 DOI: 10.1093/nar/gkv1507] [Citation(s) in RCA: 2136] [Impact Index Per Article: 267.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/06/2015] [Accepted: 12/10/2015] [Indexed: 12/18/2022] Open
Abstract
The Cancer Genome Atlas (TCGA) research network has made public a large collection of clinical and molecular phenotypes of more than 10 000 tumor patients across 33 different tumor types. Using this cohort, TCGA has published over 20 marker papers detailing the genomic and epigenomic alterations associated with these tumor types. Although many important discoveries have been made by TCGA's research network, opportunities still exist to implement novel methods, thereby elucidating new biological pathways and diagnostic markers. However, mining the TCGA data presents several bioinformatics challenges, such as data retrieval and integration with clinical data and other molecular data types (e.g. RNA and DNA methylation). We developed an R/Bioconductor package called TCGAbiolinks to address these challenges and offer bioinformatics solutions by using a guided workflow to allow users to query, download and perform integrative analyses of TCGA data. We combined methods from computer science and statistics into the pipeline and incorporated methodologies developed in previous TCGA marker studies and in our own group. Using four different TCGA tumor types (Kidney, Brain, Breast and Colon) as examples, we provide case studies to illustrate examples of reproducibility, integrative analysis and utilization of different Bioconductor packages to advance and accelerate novel discoveries.
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Affiliation(s)
- Antonio Colaprico
- Interuniversity Institute of Bioinformatics in Brussels (IB), Brussels, Belgium Machine Learning Group (MLG), Department d'Informatique, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Tiago C Silva
- Department of Genetics Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, São Paulo, Brazil
| | - Catharina Olsen
- Interuniversity Institute of Bioinformatics in Brussels (IB), Brussels, Belgium Machine Learning Group (MLG), Department d'Informatique, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Luciano Garofano
- Department of Science and Technology, University of Sannio, Benevento, Italy Unlimited Software srl, Naples, Italy
| | - Claudia Cava
- Institute of Molecular Bioimaging and Physiology of the National Research Council (IBFM-CNR), Milan, Italy
| | - Davide Garolini
- Physics for Complex Systems, Department of Physics, University of Turin, Italy
| | - Thais S Sabedot
- Department of Genetics Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, São Paulo, Brazil
| | - Tathiane M Malta
- Department of Genetics Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, São Paulo, Brazil
| | - Stefano M Pagnotta
- Department of Science and Technology, University of Sannio, Benevento, Italy Bioinformatics Laboratory, BIOGEM, Ariano Irpino, Avellino, Italy
| | - Isabella Castiglioni
- Institute of Molecular Bioimaging and Physiology of the National Research Council (IBFM-CNR), Milan, Italy
| | | | - Gianluca Bontempi
- Interuniversity Institute of Bioinformatics in Brussels (IB), Brussels, Belgium Machine Learning Group (MLG), Department d'Informatique, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Houtan Noushmehr
- Department of Genetics Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, São Paulo, Brazil
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521
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Albiges L, Escudier B. Current and future strategies in nonclear-cell metastatic renal cell carcinoma. Curr Opin Urol 2016; 25:367-73. [PMID: 26153638 DOI: 10.1097/mou.0000000000000197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW Therapeutic options for patients with metastatic nonclear-cell renal cell carcinoma (non-ccRCC) are limited and display minimum benefit. Conducting clinical trials in these rare and heterogeneous diseases without identified key biological drivers is a challenge for drug development. A growing body of prospective dedicated clinical trials and large molecular characterization initiatives are raising new expectations in non-ccRCC. RECENT FINDINGS The first randomized phase II study in non-ccRCC failed to demonstrate the benefit of everolimus over sunitinib in first-line setting, although this study was small and was not supposed to draw final conclusions. Single-arm phase II trials have reported the results of sunitinib or everolimus in the papillary. The potential role of a sunitinib-gemcitabine combination has been investigated in RCC with sarcomatoid features. In parallel, the molecular characterization of non-ccRCC has been initiated, highlighting the heterogeneity of the distinct subtypes. SUMMARY Current efforts to develop clinical trials in non-ccRCC have provided preliminary results with approved agents. The molecular characterization programs have not yet translated into clinical meaningful results, but MET proto-oncogene inhibition holds promises in the population of papillary RCC. Non-ccRCC management raises the challenge of structuring networks to optimize pathological diagnosis, target identification, and for dedicated clinical trials design.
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522
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Du Z, Li L, Huang X, Jin J, Huang S, Zhang Q, Tao Q. The epigenetic modifier CHD5 functions as a novel tumor suppressor for renal cell carcinoma and is predominantly inactivated by promoter CpG methylation. Oncotarget 2016; 7:21618-30. [PMID: 26943038 PMCID: PMC5008310 DOI: 10.18632/oncotarget.7822] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/29/2016] [Indexed: 12/31/2022] Open
Abstract
Renal cell carcinoma (RCC) is the most common urological cancer with steadily increasing incidence. A series of tumor suppressor genes (TSGs) have been identified methylated in RCC as potential epigenetic biomarkers. We identified a 1p36.3 TSG candidate CHD5 as a methylated target in RCC through epigenome study. As the role of CHD5 in RCC pathogenesis remains elusive, we further studied its expression and molecular functions in RCC cells. We found that CHD5 was broadly expressed in most normal genitourinary tissues including kidney, but frequently silenced or downregulated by promoter CpG methylation in 78% of RCC cell lines and 44% (24/55) of primary tumors. In addition, CHD5 mutations appear to be rare in RCC tumors through genome database mining. In methylated/silenced RCC cell lines, CHD5 expression could be restored with azacytidine demethylation treatment. Ectopic expression of CHD5 in RCC cells significantly inhibited their clonogenicity, migration and invasion. Moreover, we found that CHD5, as a chromatin remodeling factor, suppressed the expression of multiple targets including oncogenes (MYC, MDM2, STAT3, CCND1, YAP1), epigenetic master genes (Bmi-1, EZH2, JMJD2C), as well as epithelial-mesenchymal transition and stem cell markers (SNAI1, FN1, OCT4). Further chromatin immunoprecipitation (ChIP) assays confirmed the binding of CHD5 to target gene promoters. Thus, we demonstrate that CHD5 functions as a novel TSG for RCC, but is predominantly inactivated by promoter methylation in primary tumors.
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Affiliation(s)
- Zhenfang Du
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong and CUHK-Shenzhen Research Institute, Shatin, Hong Kong
| | - Lili Li
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong and CUHK-Shenzhen Research Institute, Shatin, Hong Kong
| | - Xin Huang
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong and CUHK-Shenzhen Research Institute, Shatin, Hong Kong
| | - Jie Jin
- Department of Urology, Peking University First Hospital and Institute of Urology, National Research Center for Genitourinary Oncology, Beijing, China
| | - Suming Huang
- Departments of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Qian Zhang
- Department of Urology, Peking University First Hospital and Institute of Urology, National Research Center for Genitourinary Oncology, Beijing, China
| | - Qian Tao
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong and CUHK-Shenzhen Research Institute, Shatin, Hong Kong
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523
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Seles M, Hutterer GC, Kiesslich T, Pummer K, Berindan-Neagoe I, Perakis S, Schwarzenbacher D, Stotz M, Gerger A, Pichler M. Current Insights into Long Non-Coding RNAs in Renal Cell Carcinoma. Int J Mol Sci 2016; 17:573. [PMID: 27092491 PMCID: PMC4849029 DOI: 10.3390/ijms17040573] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/08/2016] [Accepted: 04/12/2016] [Indexed: 02/07/2023] Open
Abstract
Renal cell carcinoma (RCC) represents a deadly disease with rising mortality despite intensive therapeutic efforts. It comprises several subtypes in terms of distinct histopathological features and different clinical presentations. Long non-coding RNAs (lncRNAs) are non-protein-coding transcripts in the genome which vary in expression levels and length and perform diverse functions. They are involved in the inititation, evolution and progression of primary cancer, as well as in the development and spread of metastases. Recently, several lncRNAs were described in RCC. This review emphasises the rising importance of lncRNAs in RCC. Moreover, it provides an outlook on their therapeutic potential in the future.
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Affiliation(s)
- Maximilian Seles
- Department of Urology, Medical University of Graz, A-8036 Graz, Austria.
| | - Georg C Hutterer
- Department of Urology, Medical University of Graz, A-8036 Graz, Austria.
| | - Tobias Kiesslich
- Department of Internal Medicine I, Salzburger Landeskliniken (SALK), Paracelsus Medical University, A-5020 Salzburg, Austria.
- Laboratory for Tumour Biology and Experimental Therapies, Institute of Physiology and Pathophysiology, Paracelsus Medical University, A-5020 Salzburg, Austria.
| | - Karl Pummer
- Department of Urology, Medical University of Graz, A-8036 Graz, Austria.
| | - Ioana Berindan-Neagoe
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
- Research Center of Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania.
- Department of Experimental Pathology, The Oncology Institute Ion Chiricuta, 400015 Cluj-Napoca, Romania.
| | - Samantha Perakis
- Institute of Human Genetics, Medical University of Graz, A-8036 Graz, Austria.
| | - Daniela Schwarzenbacher
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, A-8036 Graz, Austria.
| | - Michael Stotz
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, A-8036 Graz, Austria.
| | - Armin Gerger
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, A-8036 Graz, Austria.
- Center for Biomarker Research in Medicine, Medical University of Graz, A-8036 Graz, Austria.
| | - Martin Pichler
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, A-8036 Graz, Austria.
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524
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Abstract
Disruptions in 3D genomic architecture allow cancer genes to evade transcriptional silencing
[Also see Report by
Hnisz
et al.
]
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Affiliation(s)
- Jeremiah Wala
- Departments of Medical Oncology and Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA, and Broad Institute, Cambridge, MA 02142, USA
| | - Rameen Beroukhim
- Departments of Medical Oncology and Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA, and Broad Institute, Cambridge, MA 02142, USA.
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525
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Chen F, Zhang Y, Şenbabaoğlu Y, Ciriello G, Yang L, Reznik E, Shuch B, Micevic G, De Velasco G, Shinbrot E, Noble MS, Lu Y, Covington KR, Xi L, Drummond JA, Muzny D, Kang H, Lee J, Tamboli P, Reuter V, Shelley CS, Kaipparettu BA, Bottaro DP, Godwin AK, Gibbs RA, Getz G, Kucherlapati R, Park PJ, Sander C, Henske EP, Zhou JH, Kwiatkowski DJ, Ho TH, Choueiri TK, Hsieh JJ, Akbani R, Mills GB, Hakimi AA, Wheeler DA, Creighton CJ. Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma. Cell Rep 2016; 14:2476-89. [PMID: 26947078 DOI: 10.1016/j.celrep.2016.02.024] [Citation(s) in RCA: 261] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 12/22/2015] [Accepted: 02/01/2016] [Indexed: 12/25/2022] Open
Abstract
On the basis of multidimensional and comprehensive molecular characterization (including DNA methalylation and copy number, RNA, and protein expression), we classified 894 renal cell carcinomas (RCCs) of various histologic types into nine major genomic subtypes. Site of origin within the nephron was one major determinant in the classification, reflecting differences among clear cell, chromophobe, and papillary RCC. Widespread molecular changes associated with TFE3 gene fusion or chromatin modifier genes were present within a specific subtype and spanned multiple subtypes. Differences in patient survival and in alteration of specific pathways (including hypoxia, metabolism, MAP kinase, NRF2-ARE, Hippo, immune checkpoint, and PI3K/AKT/mTOR) could further distinguish the subtypes. Immune checkpoint markers and molecular signatures of T cell infiltrates were both highest in the subtype associated with aggressive clear cell RCC. Differences between the genomic subtypes suggest that therapeutic strategies could be tailored to each RCC disease subset.
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Affiliation(s)
- Fengju Chen
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yasin Şenbabaoğlu
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Lixing Yang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Ed Reznik
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Brian Shuch
- Department of Urology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Goran Micevic
- Department of Dermatology, Yale University, New Haven, CT 06510, USA; Department of Pathology, Yale University, New Haven, CT 06510, USA
| | - Guillermo De Velasco
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Eve Shinbrot
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael S Noble
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Yiling Lu
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Kyle R Covington
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Liu Xi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer A Drummond
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hyojin Kang
- Department of Convergence Technology Research, Korea Institute of Science and Technology Information (KAIST), Daejeon 305-806, Korea
| | - Junehawk Lee
- Department of Convergence Technology Research, Korea Institute of Science and Technology Information (KAIST), Daejeon 305-806, Korea; Department of Bio and Brain Engineering, KAIST, Daejeon 305-806, Korea
| | - Pheroze Tamboli
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Victor Reuter
- Department of Pathology, Memorial Sloan-Kettering Cancer, New York, NY 10065, USA
| | - Carl Simon Shelley
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53726, USA
| | - Benny A Kaipparettu
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donald P Bottaro
- Urologic Oncology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gad Getz
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Raju Kucherlapati
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Chris Sander
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elizabeth P Henske
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Jane H Zhou
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Tufts University School of Medicine, Boston, MA 02111, USA
| | - David J Kwiatkowski
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Thai H Ho
- Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, AZ 85054, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - James J Hsieh
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Rehan Akbani
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gordon B Mills
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - A Ari Hakimi
- Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA.
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526
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Buti S, Bersanelli M. Non-clear-cell renal carcinoma therapy: handle with care. Lancet Oncol 2016; 17:270-271. [PMID: 26972852 DOI: 10.1016/s1470-2045(16)00013-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 01/06/2016] [Indexed: 02/05/2023]
Affiliation(s)
- Sebastiano Buti
- Medical Oncology Unit, University Hospital of Parma, 43125 Parma, Italy.
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527
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Kou T, Kanai M, Matsumoto S, Okuno Y, Muto M. The possibility of clinical sequencing in the management of cancer. Jpn J Clin Oncol 2016; 46:399-406. [PMID: 26917600 DOI: 10.1093/jjco/hyw018] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 01/31/2016] [Indexed: 02/07/2023] Open
Abstract
Comprehensive genomic profiling using next-generation sequencing technologies provides insights into understanding the genomic architecture of human cancer. This new understanding of the cancer genome allows us to identify many more genomic alterations occurring within tumors than before, some of which could be potential therapeutic targets through molecular targeted agents. Currently, a large number of molecular targeted agents are being developed, and consequently, cancer treatment is rapidly shifting from empiric therapy employing cytotoxic anticancer drugs to genotype-directed therapy using molecular targeted agents. In current daily clinical practice, hotspot-based single-gene assays that detect RAS mutations in colorectal cancer or EGFR mutations in non-small cell lung cancer are widely used to identify variants. However, it is becoming evident that more comprehensive genomic analysis is crucial in identifying the patient population that may benefit from molecular targeted therapy and the accelerated development of novel drugs for early clinical trials. For these purposes, an increasing number of gene panel-based targeted sequencing is commercially available in clinical practice from sequencing companies. Despite several challenges in implementing this approach, comprehensive genomic profiling and identification of actionable mutations is likely to become one of the standard options in the management of cancer in the near future. The use of clinical sequencing has the potential to usher a new era in precision medicine for cancer diagnosis and treatment. In this review, we discuss the application of comprehensive genomic profiling using next-generation sequencing technologies in clinical oncology and address the current challenges for its implementation.
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Affiliation(s)
- Tadayuki Kou
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto Department of Clinical Oncology, Kyoto University Hospital Cancer Center, Kyoto
| | - Masashi Kanai
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto Department of Clinical Oncology, Kyoto University Hospital Cancer Center, Kyoto
| | - Shigemi Matsumoto
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto Department of Clinical Oncology, Kyoto University Hospital Cancer Center, Kyoto
| | - Yasushi Okuno
- Department of Clinical System Onco-Informatics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Manabu Muto
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto Department of Clinical Oncology, Kyoto University Hospital Cancer Center, Kyoto
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528
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Reznik E, Miller ML, Şenbabaoğlu Y, Riaz N, Sarungbam J, Tickoo SK, Al-Ahmadie HA, Lee W, Seshan VE, Hakimi AA, Sander C. Mitochondrial DNA copy number variation across human cancers. eLife 2016; 5:e10769. [PMID: 26901439 PMCID: PMC4775221 DOI: 10.7554/elife.10769] [Citation(s) in RCA: 345] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 01/08/2016] [Indexed: 12/18/2022] Open
Abstract
Mutations, deletions, and changes in copy number of mitochondrial DNA (mtDNA), are observed throughout cancers. Here, we survey mtDNA copy number variation across 22 tumor types profiled by The Cancer Genome Atlas project. We observe a tendency for some cancers, especially of the bladder, breast, and kidney, to be depleted of mtDNA, relative to matched normal tissue. Analysis of genetic context reveals an association between incidence of several somatic alterations, including IDH1 mutations in gliomas, and mtDNA content. In some but not all cancer types, mtDNA content is correlated with the expression of respiratory genes, and anti-correlated to the expression of immune response and cell-cycle genes. In tandem with immunohistochemical evidence, we find that some tumors may compensate for mtDNA depletion to sustain levels of respiratory proteins. Our results highlight the extent of mtDNA copy number variation in tumors and point to related therapeutic opportunities.
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Affiliation(s)
- Ed Reznik
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Martin L Miller
- Cancer Research UK, Cambridge Institute, Cambridge, United Kingdom
| | - Yasin Şenbabaoğlu
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Judy Sarungbam
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Satish K Tickoo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Hikmat A Al-Ahmadie
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, United States
| | - William Lee
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Venkatraman E Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - A Ari Hakimi
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Chris Sander
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
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529
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Genomic characterization of sarcomatoid transformation in clear cell renal cell carcinoma. Proc Natl Acad Sci U S A 2016; 113:2170-5. [PMID: 26864202 DOI: 10.1073/pnas.1525735113] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The presence of sarcomatoid features in clear cell renal cell carcinoma (ccRCC) confers a poor prognosis and is of unknown pathogenesis. We performed exome sequencing of matched normal-carcinomatous-sarcomatoid specimens from 21 subjects. Two tumors had hypermutation consistent with mismatch repair deficiency. In the remainder, sarcomatoid and carcinomatous elements shared 42% of somatic single-nucleotide variants (SSNVs). Sarcomatoid elements had a higher overall SSNV burden (mean 90 vs. 63 SSNVs, P = 4.0 × 10(-4)), increased frequency of nonsynonymous SSNVs in Pan-Cancer genes (mean 1.4 vs. 0.26, P = 0.002), and increased frequency of loss of heterozygosity (LOH) across the genome (median 913 vs. 460 Mb in LOH, P < 0.05), with significant recurrent LOH on chromosomes 1p, 9, 10, 14, 17p, 18, and 22. The most frequent SSNVs shared by carcinomatous and sarcomatoid elements were in known ccRCC genes including von Hippel-Lindau tumor suppressor (VHL), polybromo 1 (PBRM1), SET domain containing 2 (SETD2), phosphatase and tensin homolog (PTEN). Most interestingly, sarcomatoid elements acquired biallelic tumor protein p53 (TP53) mutations in 32% of tumors (P = 5.47 × 10(-17)); TP53 mutations were absent in carcinomatous elements in nonhypermutated tumors and rare in previously studied ccRCCs. Mutations in known cancer drivers AT-rich interaction domain 1A (ARID1A) and BRCA1 associated protein 1 (BAP1) were significantly mutated in sarcomatoid elements and were mutually exclusive with TP53 and each other. These findings provide evidence that sarcomatoid elements arise from dedifferentiation of carcinomatous ccRCCs and implicate specific genes in this process. These findings have implications for the treatment of patients with these poor-prognosis cancers.
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530
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Abstract
Molecular informatics (MI) is an evolving discipline that will support the dynamic landscape of molecular pathology and personalized medicine. MI provides a fertile ground for development of clinical solutions to bridge the gap between clinical informatics and bioinformatics. Rapid adoption of next generation sequencing (NGS) in the clinical arena has triggered major endeavors in MI that are expected to bring a paradigm shift in the practice of pathology. This brief review presents a broad overview of various aspects of MI, particularly in the context of NGS based testing.
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Affiliation(s)
- Somak Roy
- Department of Pathology, Molecular and Genomic Pathology, University of Pittsburgh Medical Center, 3477 Euler way, Pittsburgh, PA 15213, USA.
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531
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Kato I, Iribe Y, Nagashima Y, Kuroda N, Tanaka R, Nakatani Y, Hasumi H, Yao M, Furuya M. Fluorescent and chromogenic in situ hybridization of CEN17q as a potent useful diagnostic marker for Birt-Hogg-Dubé syndrome-associated chromophobe renal cell carcinomas. Hum Pathol 2016; 52:74-82. [PMID: 26980015 DOI: 10.1016/j.humpath.2016.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 01/14/2016] [Accepted: 01/15/2016] [Indexed: 12/20/2022]
Abstract
Birt-Hogg-Dubé syndrome (BHD) is a familial disorder associated with a germline mutation of FLCN that is a tumor suppressor gene. Patients with BHD have high risks for developing multiple renal cell carcinomas (RCCs). The frequent histological types are hybrid oncocytic/chromophobe tumors (HOCTs) and chromophobe RCCs. The morphology of HOCTs could alert pathologists to the possibility of BHD. On the other hand, chromophobe RCCs occurring in BHD patients demonstrate positive immunostaining for cytokeratin-7, CD82, and Ksp-cadherin similar to their sporadic counterparts. Highly reliable markers for BHD-associated chromophobe RCCs have not been identified. In the present study, we analyzed the state of chromosome 17 in 18 renal tumors composed of 8 chromophobe RCCs, 7 HOCTs, and 3 papillary RCCs obtained from BHD patients using fluorescent and chromogenic in situ hybridization probes for the centromeric region of chromosome 17 long arm. All chromophobe RCCs and HOCTs were disomic except for 1 chromophobe RCC that showed monosomy. On the other hand, 12 of 14 sporadic chromophobe RCCs were monosomic (P = .0008). The state of chromosomes 2 and 6 were also statistically different (P = .0074 and P = .0007, respectively). Three BHD-associated papillary RCCs demonstrated either trisomy (n = 2) or disomy (n = 1). Three of 5 sporadic papillary RCCs showed trisomy. The results indicate that fluorescent and chromogenic in situ hybridization of the centromeric region of chromosome 17 long arm should be a potent useful marker for chromophobe RCCs in patients who have not been diagnosed with BHD and thereby help to determine whether the cases should be considered for genetic testing.
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Affiliation(s)
- Ikuma Kato
- Department of Molecular Pathology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Yasuhiro Iribe
- Department of Molecular Pathology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Yoji Nagashima
- Department of Surgical Pathology, Tokyo Women's Medical University, Tokyo 162-8666, Japan
| | - Naoto Kuroda
- Department of Diagnostic Pathology, Kochi Red Cross Hospital, Kochi 780-8562, Japan
| | - Reiko Tanaka
- Medical Mycology Research Center, Chiba University, Chiba 260-8677, Japan
| | - Yukio Nakatani
- Department of Diagnostic Pathology, Chiba University Graduate School of Medicine, Chiba 260-8677, Japan
| | - Hisashi Hasumi
- Department of Urology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Masahiro Yao
- Department of Urology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Mitsuko Furuya
- Department of Molecular Pathology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan.
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532
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Genome-Wide Uniparental Disomy and Copy Number Variations in Renal Cell Carcinomas Associated with Birt-Hogg-Dubé Syndrome. THE AMERICAN JOURNAL OF PATHOLOGY 2016; 186:337-46. [DOI: 10.1016/j.ajpath.2015.10.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 09/11/2015] [Accepted: 10/07/2015] [Indexed: 11/24/2022]
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533
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Zhao H, Leppert JT, Peehl DM. A Protective Role for Androgen Receptor in Clear Cell Renal Cell Carcinoma Based on Mining TCGA Data. PLoS One 2016; 11:e0146505. [PMID: 26814892 PMCID: PMC4729482 DOI: 10.1371/journal.pone.0146505] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/17/2015] [Indexed: 12/11/2022] Open
Abstract
Androgen receptor (AR) is expressed in normal murine and human kidneys of both genders, but its physiologic role is uncertain. Several studies showed loss of AR in renal cell carcinoma (RCC) in conjunction with increasing clinical stage and pathological grade, but others found that higher AR expression correlated with worse outcomes. Limited functional studies with renal cell lines suggested tumor-promoting activity of AR. In this study, we queried transcriptomic, proteomic, epigenetic and survival data from The Cancer Genome Atlas (TCGA) to evaluate AR expression and its association with overall survival in three subtypes of RCC (clear cell [ccRCC], papillary [pRCC], and chromophobe [chRCC]). We found that although there was no significant difference in AR mRNA expression in ccRCC of males vs. females, AR protein expression in ccRCC was significantly higher in male compared to female patients. More importantly, higher expression of AR at both transcript and protein levels was associated with improved overall survival in both genders with ccRCC, but did not predict survival of either gender with pRCC or chRCC. Genes whose transcript levels were associated with AR mRNA levels significantly overlapped between ccRCC and pRCC, but not with chRCC, suggesting a similar transcriptional program mediated by AR in ccRCC and pRCC. Ingenuity pathway analysis also identified overlapping pathways and upstream regulators enriched in AR-associated genes in ccRCC and pRCC. Hypermethylation of CpG sites located in the promoter and first exon of AR was associated with loss of AR expression and poor overall survival. Our findings support a tumor suppressor role for AR in both genders that might be exploited to decrease the incidence or progression of ccRCC.
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MESH Headings
- Carcinoma, Papillary/metabolism
- Carcinoma, Papillary/mortality
- Carcinoma, Papillary/pathology
- Carcinoma, Renal Cell/metabolism
- Carcinoma, Renal Cell/mortality
- Carcinoma, Renal Cell/pathology
- Cluster Analysis
- Cohort Studies
- CpG Islands
- DNA Methylation
- Databases, Genetic
- Female
- Humans
- Kaplan-Meier Estimate
- Kidney Neoplasms/metabolism
- Kidney Neoplasms/mortality
- Kidney Neoplasms/pathology
- Male
- Prognosis
- Promoter Regions, Genetic
- RNA, Messenger/metabolism
- RNA, Neoplasm/chemistry
- RNA, Neoplasm/metabolism
- Receptors, Androgen/genetics
- Receptors, Androgen/metabolism
- Sequence Analysis, RNA
- Sex Factors
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Affiliation(s)
- Hongjuan Zhao
- Department of Urology, Stanford University School of Medicine, Stanford, California, United States of America
| | - John T. Leppert
- Department of Urology, Stanford University School of Medicine, Stanford, California, United States of America
- Veterans Affairs Palo Alto Health Care System, Palo Alto, California, United States of America
| | - Donna M. Peehl
- Department of Urology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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534
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Brooks SA, Khandani AH, Fielding JR, Lin W, Sills T, Lee Y, Arreola A, Milowsky MI, Wallen EM, Woods ME, Smith AB, Nielsen ME, Parker JS, Lalush DS, Rathmell WK. Alternate Metabolic Programs Define Regional Variation of Relevant Biological Features in Renal Cell Carcinoma Progression. Clin Cancer Res 2016; 22:2950-9. [PMID: 26787754 DOI: 10.1158/1078-0432.ccr-15-2115] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 12/13/2015] [Indexed: 01/18/2023]
Abstract
PURPOSE Clear cell renal cell carcinoma (ccRCC) has recently been redefined as a highly heterogeneous disease. In addition to genetic heterogeneity, the tumor displays risk variability for developing metastatic disease, therefore underscoring the urgent need for tissue-based prognostic strategies applicable to the clinical setting. We have recently employed the novel PET/magnetic resonance (MR) image modality to enrich our understanding of how tumor heterogeneity can relate to gene expression and tumor biology to assist in defining individualized treatment plans. EXPERIMENTAL DESIGN ccRCC patients underwent PET/MR imaging, and these images subsequently used to identify areas of varied intensity for sampling. Samples from 8 patients were subjected to histologic, immunohistochemical, and microarray analysis. RESULTS Tumor subsamples displayed a range of heterogeneity for common features of hypoxia-inducible factor expression and microvessel density, as well as for features closely linked to metabolic processes, such as GLUT1 and FBP1. In addition, gene signatures linked with disease risk (ccA and ccB) also demonstrated variable heterogeneity, with most tumors displaying a dominant panel of features across the sampled regions. Intriguingly, the ccA- and ccB-classified samples corresponded with metabolic features and functional imaging levels. These correlations further linked a variety of metabolic pathways (i.e., the pentose phosphate and mTOR pathways) with the more aggressive, and glucose avid ccB subtype. CONCLUSIONS Higher tumor dependency on exogenous glucose accompanies the development of features associated with the poor risk ccB subgroup. Linking these panels of features may provide the opportunity to create functional maps to enable enhanced visualization of the heterogeneous biologic processes of an individual's disease. Clin Cancer Res; 22(12); 2950-9. ©2016 AACR.
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Affiliation(s)
- Samira A Brooks
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina. Curriculum in Toxicology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Amir H Khandani
- Department of Radiology, University of North Carolina, Chapel Hill, North Carolina. Department of Radiology, Nuclear Medicine, University of North Carolina at Chapel Hill, North Carolina.
| | - Julia R Fielding
- Department of Radiology, University of North Carolina, Chapel Hill, North Carolina
| | - Weili Lin
- Department of Radiology, University of North Carolina, Chapel Hill, North Carolina
| | - Tiffany Sills
- Department of Urology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Yueh Lee
- Department of Radiology, University of North Carolina, Chapel Hill, North Carolina
| | - Alexandra Arreola
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina
| | - Mathew I Milowsky
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina. Department of Urology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Eric M Wallen
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina. Department of Urology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Michael E Woods
- Department of Radiology, University of North Carolina, Chapel Hill, North Carolina
| | - Angie B Smith
- Department of Urology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Mathew E Nielsen
- Department of Urology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Joel S Parker
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina. Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - David S Lalush
- Department of Radiology, Nuclear Medicine, University of North Carolina at Chapel Hill, North Carolina. Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, Raleigh, North Carolina
| | - W Kimryn Rathmell
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina. Department of Urology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina. Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
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535
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Everolimus versus sunitinib for patients with metastatic non-clear cell renal cell carcinoma (ASPEN): a multicentre, open-label, randomised phase 2 trial. Lancet Oncol 2016; 17:378-388. [PMID: 26794930 DOI: 10.1016/s1470-2045(15)00515-x] [Citation(s) in RCA: 302] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/11/2015] [Accepted: 11/11/2015] [Indexed: 12/28/2022]
Abstract
BACKGROUND Non-clear cell renal cell carcinomas are histologically and genetically diverse kidney cancers with variable prognoses, and their optimum initial treatment is unknown. We aimed to compare the mTOR inhibitor everolimus and the VEGF receptor inhibitor sunitinib in patients with non-clear cell renal cell carcinoma. METHODS We enrolled patients with metastatic papillary, chromophobe, or unclassified non-clear cell renal cell carcinoma with no history of previous systemic treatment. Patients were randomly assigned (1:1) to receive everolimus (10 mg/day) or sunitinib (50 mg/day; 6-week cycles of 4 weeks with treatment followed by 2 weeks without treatment) administered orally until disease progression or unacceptable toxicity. Randomisation was stratified by Memorial Sloan Kettering Cancer Center risk group and papillary histology. The primary endpoint was progression-free survival in the intention-to-treat population using the RECIST 1.1 criteria. Safety was assessed in all patients who were randomly assigned to treatment. This study is registered with ClinicalTrials.gov, number NCT01108445. FINDINGS Between Sept 23, 2010, and Oct 28, 2013, 108 patients were randomly assigned to receive either sunitinib (n=51) or everolimus (n=57). As of December, 2014, 87 progression-free survival events had occurred with two remaining active patients, and the trial was closed for the primary analysis. Sunitinib significantly increased progression-free survival compared with everolimus (8·3 months [80% CI 5·8-11·4] vs 5·6 months [5·5-6·0]; hazard ratio 1·41 [80% CI 1·03-1·92]; p=0·16), although heterogeneity of the treatment effect was noted on the basis of histological subtypes and prognostic risk groups. No unexpected toxic effects were reported, and the most common grade 3-4 adverse events were hypertension (12 [24%] of 51 patients in the sunitinib group vs one [2%] of 57 patients in the everolimus group), infection (six [12%] vs four [7%]), diarrhoea (five [10%] vs one [2%]), pneumonitis (none vs five [9%]), stomatitis (none vs five [9%]), and hand-foot syndrome (four [8%] vs none). INTERPRETATION In patients with metastatic non-clear cell renal cell carcinoma, sunitinib improved progression-free survival compared with everolimus. Future trials of novel agents should account for heterogeneity in disease outcomes based on genetic, histological, and prognostic factors. FUNDING Novartis and Pfizer.
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536
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Piggin CL, Roden DL, Gallego-Ortega D, Lee HJ, Oakes SR, Ormandy CJ. ELF5 isoform expression is tissue-specific and significantly altered in cancer. Breast Cancer Res 2016; 18:4. [PMID: 26738740 PMCID: PMC4704400 DOI: 10.1186/s13058-015-0666-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 12/16/2015] [Indexed: 12/14/2022] Open
Abstract
Background E74-like factor 5 (ELF5) is an epithelial-specific member of the E26 transforming sequence (ETS) transcription factor family and a critical regulator of cell fate in the placenta, pulmonary bronchi, and milk-producing alveoli of the mammary gland. ELF5 also plays key roles in malignancy, particularly in basal-like and endocrine-resistant forms of breast cancer. Almost all genes undergo alternative transcription or splicing, which increases the diversity of protein structure and function. Although ELF5 has multiple isoforms, this has not been considered in previous studies of ELF5 function. Methods RNA-sequencing data for 6757 samples from The Cancer Genome Atlas were analyzed to characterize ELF5 isoform expression in multiple normal tissues and cancers. Extensive in vitro analysis of ELF5 isoforms, including a 116-gene quantitative polymerase chain reaction panel, was performed in breast cancer cell lines. Results ELF5 isoform expression was found to be tissue-specific due to alternative promoter use but altered in multiple cancer types. The normal breast expressed one main isoform, while in breast cancer there were subtype-specific alterations in expression. Expression of other ETS factors was also significantly altered in breast cancer, with the basal-like subtype demonstrating a distinct ETS expression profile. In vitro inducible expression of the full-length isoforms 1 and 2, as well as isoform 3 (lacking the Pointed domain) had similar phenotypic and transcriptional effects. Conclusions Alternative promoter use, conferring differential regulatory responses, is the main mechanism governing ELF5 action rather than differential transcriptional activity of the isoforms. This understanding of expression and function at the isoform level is a vital first step in realizing the potential of transcription factors such as ELF5 as prognostic markers or therapeutic targets in cancer. Electronic supplementary material The online version of this article (doi:10.1186/s13058-015-0666-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Catherine L Piggin
- Cancer Division, Garvan Institute of Medical Research/The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia.
| | - Daniel L Roden
- Cancer Division, Garvan Institute of Medical Research/The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia.
| | - David Gallego-Ortega
- Cancer Division, Garvan Institute of Medical Research/The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia.
| | - Heather J Lee
- Cancer Division, Garvan Institute of Medical Research/The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia. .,Babraham Institute, Cambridge, CB22 3AT, UK.
| | - Samantha R Oakes
- Cancer Division, Garvan Institute of Medical Research/The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia.
| | - Christopher J Ormandy
- Cancer Division, Garvan Institute of Medical Research/The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia.
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537
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Albiges L, Fay AP, McKay RR, Kaymakcalan MD, Choueiri TK. Diagnosis of Renal Cell Carcinoma: A Clinician's Perspective. Surg Pathol Clin 2015; 8:657-662. [PMID: 26612219 DOI: 10.1016/j.path.2015.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Renal cell carcinoma (RCC) is a heterogeneous disease. A rigorous diagnostic assessment by a pathologist with close communication with the clinician provides more accurate prognostication and informed treatment decisions. In the localized setting, an accurate prognostic assessment directs patients to potential adjuvant clinical trials. For patients with advanced disease, the pathologic assessment may have a direct impact on the systemic therapy algorithm. Additionally, it provides the basis for continuous efforts in biomarker development. In rare histologic subtypes, the interaction between clinicians and pathologists provides an opportunity to offer patients specific clinical trials. Molecular characterization platforms may identify targets for therapeutic intervention.
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Affiliation(s)
- Laurence Albiges
- Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue (DANA 1230), Boston, MA 02215, USA
| | - André P Fay
- Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue (DANA 1230), Boston, MA 02215, USA
| | - Rana R McKay
- Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue (DANA 1230), Boston, MA 02215, USA; Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Marina D Kaymakcalan
- Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue (DANA 1230), Boston, MA 02215, USA
| | - Toni K Choueiri
- Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue (DANA 1230), Boston, MA 02215, USA; Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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538
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Joshi S, Tolkunov D, Aviv H, Hakimi AA, Yao M, Hsieh JJ, Ganesan S, Chan CS, White E. The Genomic Landscape of Renal Oncocytoma Identifies a Metabolic Barrier to Tumorigenesis. Cell Rep 2015; 13:1895-908. [PMID: 26655904 PMCID: PMC4779191 DOI: 10.1016/j.celrep.2015.10.059] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/28/2015] [Accepted: 10/19/2015] [Indexed: 12/26/2022] Open
Abstract
Oncocytomas are predominantly benign neoplasms possessing pathogenic mitochondrial mutations and accumulation of respiration-defective mitochondria, characteristics of unknown significance. Using exome and transcriptome sequencing, we identified two main subtypes of renal oncocytoma. Type 1 is diploid with CCND1 rearrangements, whereas type 2 is aneuploid with recurrent loss of chromosome 1, X or Y, and/or 14 and 21, which may proceed to more aggressive eosinophilic chromophobe renal cell carcinoma (ChRCC). Oncocytomas activate 5' adenosine monophosphate-activated protein kinase (AMPK) and Tp53 (p53) and display disruption of Golgi and autophagy/lysosome trafficking, events attributed to defective mitochondrial function. This suggests that the genetic defects in mitochondria activate a metabolic checkpoint, producing autophagy impairment and mitochondrial accumulation that limit tumor progression, revealing a novel tumor-suppressive mechanism for mitochondrial inhibition with metformin. Alleviation of this metabolic checkpoint in type 2 by p53 mutations may allow progression to eosinophilic ChRCC, indicating that they represent higher risk.
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Affiliation(s)
- Shilpy Joshi
- Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Denis Tolkunov
- Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Hana Aviv
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, One Robert Wood Johnson Place, MEB 212, New Brunswick, NJ 08901, USA
| | - Abraham A Hakimi
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Ming Yao
- Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - James J Hsieh
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Shridar Ganesan
- Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA; Department of Medicine, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, 1 Robert Wood Johnson Place, New Brunswick, NJ 08901, USA
| | - Chang S Chan
- Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA; Department of Medicine, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, 1 Robert Wood Johnson Place, New Brunswick, NJ 08901, USA.
| | - Eileen White
- Rutgers Cancer Institute of New Jersey (CINJ), 195 Little Albany Street, New Brunswick, NJ 08903, USA; Department of Molecular Biology and Biochemistry, Rutgers University, 604 Allison Road, Piscataway, NJ 08854, USA.
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539
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Alexandrov LB, Jones PH, Wedge DC, Sale JE, Campbell PJ, Nik-Zainal S, Stratton MR. Clock-like mutational processes in human somatic cells. Nat Genet 2015; 47:1402-7. [PMID: 26551669 PMCID: PMC4783858 DOI: 10.1038/ng.3441] [Citation(s) in RCA: 647] [Impact Index Per Article: 71.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 10/14/2015] [Indexed: 12/16/2022]
Abstract
During the course of a lifetime, somatic cells acquire mutations. Different mutational processes may contribute to the mutations accumulated in a cell, with each imprinting a mutational signature on the cell's genome. Some processes generate mutations throughout life at a constant rate in all individuals, and the number of mutations in a cell attributable to these processes will be proportional to the chronological age of the person. Using mutations from 10,250 cancer genomes across 36 cancer types, we investigated clock-like mutational processes that have been operating in normal human cells. Two mutational signatures show clock-like properties. Both exhibit different mutation rates in different tissues. However, their mutation rates are not correlated, indicating that the underlying processes are subject to different biological influences. For one signature, the rate of cell division may influence its mutation rate. This study provides the first survey of clock-like mutational processes operating in human somatic cells.
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Affiliation(s)
- Ludmil B Alexandrov
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico, USA
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Philip H Jones
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Medical Research Council (MRC) Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, UK
| | - David C Wedge
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Serena Nik-Zainal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Medical Genetics, Addenbrooke's Hospital National Health Service (NHS) Trust, Cambridge, UK
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540
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Tannir NM, Jonasch E, Albiges L, Altinmakas E, Ng CS, Matin SF, Wang X, Qiao W, Dubauskas Lim Z, Tamboli P, Rao P, Sircar K, Karam JA, McDermott DF, Wood CG, Choueiri TK. Everolimus Versus Sunitinib Prospective Evaluation in Metastatic Non-Clear Cell Renal Cell Carcinoma (ESPN): A Randomized Multicenter Phase 2 Trial. Eur Urol 2015; 69:866-74. [PMID: 26626617 DOI: 10.1016/j.eururo.2015.10.049] [Citation(s) in RCA: 256] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 10/27/2015] [Indexed: 01/11/2023]
Abstract
BACKGROUND Sunitinib and everolimus are standard first-line and second-line therapies, respectively, in clear cell renal cell carcinoma (ccRCC). OBJECTIVE To conduct a randomized phase 2 trial comparing sunitinib and everolimus in non-clear cell RCC (non-ccRCC). DESIGN, SETTING, AND PARTICIPANTS Patients with metastatic, non-ccRCC, or ccRCC with >20% sarcomatoid features (ccSRCC) were randomized to receive sunitinib or everolimus with crossover at disease progression. OUTCOME MEASUREMENT AND STATISTICAL ANALYSIS Primary end point was progression-free survival (PFS) in first-line therapy; 108 patients were needed to show improvement in median PFS (mPFS) from 12 wk with sunitinib to 20 wk with everolimus. RESULTS AND LIMITATIONS Interim analysis of 68 patients (papillary [27], chromophobe [12], unclassified [10], translocation [7], ccSRCC [12]) prompted early trial closure. The mPFS in first-line therapy was 6.1 mo with sunitinib and 4.1 mo with everolimus (p=0.6); median overall survival (mOS) was not reached with sunitinib and was 10.5 mo with everolimus, respectively (p=0.014). At final analysis, mOS was 16.2 and 14.9 mo with sunitinib and everolimus, respectively (p=0.18). There were four partial responses (PRs) in first-line therapy (sunitinib: 3 of 33 [9%]; everolimus, 1 of 35 [2.8%]) and four PRs in second-line therapy (sunitinib: 2 of 21 [9.5%]; everolimus, 2 of 23 [8.6%]), with mPFS of 1.8 mo and 2.8 mo, respectively. In patients without sarcomatoid features in their tumors (n=49), mOS was 31.6 mo with sunitinib and 10.5 mo with everolimus (p=0.075). Genomic profiling of a chromophobe RCC from a patient with a PR to first-line everolimus revealed a somatic TSC2 mutation. CONCLUSIONS In this trial, everolimus was not superior to sunitinib. Both agents demonstrated modest efficacy, underscoring the need for better therapies in non-ccRCC. PATIENT SUMMARY This randomized phase 2 trial provides the first head-to-head comparison of everolimus and sunitinib in patients with metastatic non-clear cell renal cell carcinoma (non-ccRCC). The observed very modest efficacy underscores the need to develop more effective therapies for non-ccRCC.
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Affiliation(s)
- Nizar M Tannir
- Department of Genitourinary Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Eric Jonasch
- Department of Genitourinary Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Laurence Albiges
- Dana-Farber Cancer Institute/Harvard Medical School, Boston, MA, USA
| | - Emre Altinmakas
- Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chaan S Ng
- Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Surena F Matin
- Department of Urology, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xuemei Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wei Qiao
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zita Dubauskas Lim
- Department of Genitourinary Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pheroze Tamboli
- Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Priya Rao
- Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kanishka Sircar
- Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jose A Karam
- Department of Urology, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Christopher G Wood
- Department of Urology, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Toni K Choueiri
- Dana-Farber Cancer Institute/Harvard Medical School, Boston, MA, USA
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541
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Leibowitz ML, Zhang CZ, Pellman D. Chromothripsis: A New Mechanism for Rapid Karyotype Evolution. Annu Rev Genet 2015; 49:183-211. [DOI: 10.1146/annurev-genet-120213-092228] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mitchell L. Leibowitz
- Department of Pediatric Oncology,
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115;
| | - Cheng-Zhong Zhang
- Department of Pediatric Oncology,
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215;
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115;
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
| | - David Pellman
- Department of Pediatric Oncology,
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115;
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
- Howard Hughes Medical Institute, Boston, Massachusetts 02115
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542
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Hascoet P, Chesnel F, Le Goff C, Le Goff X, Arlot-Bonnemains Y. Unconventional Functions of Mitotic Kinases in Kidney Tumorigenesis. Front Oncol 2015; 5:241. [PMID: 26579493 PMCID: PMC4621426 DOI: 10.3389/fonc.2015.00241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/12/2015] [Indexed: 01/25/2023] Open
Abstract
Human tumors exhibit a variety of genetic alterations, including point mutations, translocations, gene amplifications and deletions, as well as aneuploid chromosome numbers. For carcinomas, aneuploidy is associated with poor patient outcome for a large variety of tumor types, including breast, colon, and renal cell carcinoma. The Renal cell carcinoma (RCC) is a heterogeneous carcinoma consisting of different histologic types. The clear renal cell carcinoma (ccRCC) is the most common subtype and represents 85% of the RCC. Central to the biology of the ccRCC is the loss of function of the Von Hippel–Lindau gene, but is also associated with genetic instability that could be caused by abrogation of the cell cycle mitotic spindle checkpoint and may involve the Aurora kinases, which regulate centrosome maturation. Aneuploidy can also result from the loss of cell–cell adhesion and apical–basal cell polarity that also may be regulated by the mitotic kinases (polo-like kinase 1, casein kinase 2, doublecortin-like kinase 1, and Aurora kinases). In this review, we describe the “non-mitotic” unconventional functions of these kinases in renal tumorigenesis.
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Affiliation(s)
- Pauline Hascoet
- UMR 6290 (IGDR), CNRS, University Rennes-1 , Rennes , France
| | - Franck Chesnel
- UMR 6290 (IGDR), CNRS, University Rennes-1 , Rennes , France
| | - Cathy Le Goff
- UMR 6290 (IGDR), CNRS, University Rennes-1 , Rennes , France
| | - Xavier Le Goff
- UMR 6290 (IGDR), CNRS, University Rennes-1 , Rennes , France
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543
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Ito T, Pei J, Dulaimi E, Menges C, Abbosh PH, Smaldone MC, Chen DYT, Greenberg RE, Kutikov A, Viterbo R, Uzzo RG, Testa JR. Genomic Copy Number Alterations in Renal Cell Carcinoma with Sarcomatoid Features. J Urol 2015; 195:852-8. [PMID: 26602888 DOI: 10.1016/j.juro.2015.10.180] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2015] [Indexed: 01/31/2023]
Abstract
PURPOSE Sarcomatoid changes in renal cell carcinoma are associated with a poor prognosis. The identification of genetic alterations that drive this aggressive phenotype could aid in the development of more effective targeted therapies. In this study we aimed to pinpoint unique copy number alterations in sarcomatoid renal cell carcinoma compared to classical renal cell carcinoma subtypes. MATERIALS AND METHODS Genomic copy number analysis was performed using single nucleotide polymorphism based microarrays on tissue extracted from the tumors of 81 patients who underwent renal mass excision, including 17 with sarcomatoid renal cell carcinoma. RESULTS Sarcomatoid renal cell carcinoma showed a significantly higher number of copy number alterations than clear cell, papillary and chromophobe renal cell carcinoma (mean 18.0 vs 5.8, 6.5 and 7.2, respectively, p <0.0001). Copy number losses of chromosome arms 9q, 15q, 18p/q and 22q, and gains of 1q and 8q occurred in a significantly higher proportion of sarcomatoid renal cell carcinomas than in the other 3 histologies. Patients with sarcomatoid renal cell carcinoma demonstrated significantly worse overall survival compared to those without that condition on Kaplan-Meier analysis (p = 0.0001). Patients with 9 or more copy number alterations also demonstrated significantly worse overall survival than those with fewer than 9 copy number alterations (p = 0.004). CONCLUSIONS Sarcomatoid changes in renal cell carcinoma are associated with a high rate of chromosomal imbalances with losses of 9q, 15q, 18p/q and 22q, and gains of 1q and 8q occurring at significantly higher frequencies in comparison to nonsarcomatoid renal cell carcinoma. Identifying candidate driver genes or tumor suppressor loci in these chromosomal regions may help identify targets for future therapies.
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Affiliation(s)
- Timothy Ito
- Cancer Biology Program and Blood Cell Development and Function Program (ED), Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Jianming Pei
- Cancer Biology Program and Blood Cell Development and Function Program (ED), Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Essel Dulaimi
- Cancer Biology Program and Blood Cell Development and Function Program (ED), Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Craig Menges
- Cancer Biology Program and Blood Cell Development and Function Program (ED), Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Philip H Abbosh
- Cancer Biology Program and Blood Cell Development and Function Program (ED), Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Marc C Smaldone
- Cancer Biology Program and Blood Cell Development and Function Program (ED), Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - David Y T Chen
- Cancer Biology Program and Blood Cell Development and Function Program (ED), Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Richard E Greenberg
- Cancer Biology Program and Blood Cell Development and Function Program (ED), Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Alexander Kutikov
- Cancer Biology Program and Blood Cell Development and Function Program (ED), Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Rosalia Viterbo
- Cancer Biology Program and Blood Cell Development and Function Program (ED), Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Robert G Uzzo
- Cancer Biology Program and Blood Cell Development and Function Program (ED), Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Joseph R Testa
- Cancer Biology Program and Blood Cell Development and Function Program (ED), Fox Chase Cancer Center, Philadelphia, Pennsylvania.
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544
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Ren Y, Liu K, Kang X, Pang L, Qi Y, Hu Z, Jia W, Zhang H, Li L, Hu J, Liang W, Zhao J, Zou H, Yuan X, Li F. Chromophobe renal cell carcinoma with and without sarcomatoid change: a clinicopathological, comparative genomic hybridization, and whole-exome sequencing study. Am J Transl Res 2015; 7:2482-2499. [PMID: 26807193 PMCID: PMC4697725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 10/13/2015] [Indexed: 06/05/2023]
Abstract
Chromophobe renal cell carcinomas (CRCC) with and without sarcomatoid change have different outcomes; however, fewstudies have compared their genetic profiles. Therefore, we identified the genomic alterationsin CRCC common type (CRCC C) (n=8) and CRCC with sarcomatoid change (CRCC S) (n=4) using comparative genomic hybridization (CGH) and whole-exome sequencing. The CGH profiles showed that the CRCC C group had more chromosomal losses (72 vs. 18) but fewer chromosomal gains (23 vs. 57) than the CRCC S group. Losses of chromosomes 1p, 8p21-23, 10p16-20, 10p12-ter, 13p20-30, and 17p13 and gains of chromosomes 1q11, 1q21-23, 1p13-15, 2p23-24, and 3p21-ter differed between the groups. Whole-exome sequencing showed that the mutational status of 270 genes differed between CRCC (n=12) and normal renal tissues (n=18). In the functional enrichment analysis, the missense-mutated genes were classified into 6 biological processes (38 functions) and 5 pathways. The biological processes included cell adhesion, cell motility, ATP metabolism, sensory perception, carbohydrate and lipid metabolism and transport. The pathways included ATP-binding cassette transporter, extracellular matrix-receptor interaction, olfactory transduction, chondroitin sulfate biosynthesis, and hypertrophic cardiomyopathy. Whole-exome sequencing analysis revealed that the missense mutation statuses of 49 genes differed between the CRCC C and CRCC S groups. Furthermore, genetic alterations in metastasis suppressor 1, serine peptidase inhibitor Kazal type 8, transient receptor potential cation channel super family M member 6, Rh family B glycoprotein, and mannose receptor C type 1 were located in different chromosomal regions. These alterations may provide clues regarding CRCC tumorigenesis and provide a basis for future targeted therapies.
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Affiliation(s)
- Yuan Ren
- Department of Pathology, School of Medicine, First Affiliated Hospital, Shihezi University, Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education of ChinaShihezi, China
| | - Kunpeng Liu
- Department of Pathology, School of Medicine, First Affiliated Hospital, Shihezi University, Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education of ChinaShihezi, China
| | - Xueling Kang
- Department of Pathology, Shanghai General HospitalShanghai, China
| | - Lijuan Pang
- Department of Pathology, School of Medicine, First Affiliated Hospital, Shihezi University, Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education of ChinaShihezi, China
| | - Yan Qi
- Department of Pathology, School of Medicine, First Affiliated Hospital, Shihezi University, Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education of ChinaShihezi, China
| | - Zhenyan Hu
- Department of Pathology, School of Medicine, First Affiliated Hospital, Shihezi University, Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education of ChinaShihezi, China
| | - Wei Jia
- Department of Pathology, School of Medicine, First Affiliated Hospital, Shihezi University, Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education of ChinaShihezi, China
| | - Haijun Zhang
- Department of Pathology, School of Medicine, First Affiliated Hospital, Shihezi University, Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education of ChinaShihezi, China
| | - Li Li
- Department of Pathology, School of Medicine, First Affiliated Hospital, Shihezi University, Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education of ChinaShihezi, China
| | - Jianming Hu
- Department of Pathology, School of Medicine, First Affiliated Hospital, Shihezi University, Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education of ChinaShihezi, China
| | - Weihua Liang
- Department of Pathology, School of Medicine, First Affiliated Hospital, Shihezi University, Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education of ChinaShihezi, China
| | - Jin Zhao
- Department of Pathology, School of Medicine, First Affiliated Hospital, Shihezi University, Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education of ChinaShihezi, China
| | - Hong Zou
- Department of Pathology, School of Medicine, First Affiliated Hospital, Shihezi University, Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education of ChinaShihezi, China
| | - Xianglin Yuan
- Tongji Hospital Cancer Center, Tongji Medical College, Huazhong University of Science and TechnologyWuhan, China
| | - Feng Li
- Department of Pathology, School of Medicine, First Affiliated Hospital, Shihezi University, Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education of ChinaShihezi, China
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545
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Maiti A, Brown RE, Corn PG, Murthy R, Ganeshan DM, Tsimberidou AM, Subbiah V. Antitumor Response to Combined Antiangiogenic and Cytotoxic Chemotherapy in Recurrent Metastatic Chromophobe Renal Cell Carcinoma: Response Signatures and Proteomic Correlates. Clin Genitourin Cancer 2015; 14:e187-93. [PMID: 26684814 DOI: 10.1016/j.clgc.2015.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 11/03/2015] [Indexed: 01/04/2023]
Affiliation(s)
- Abhishek Maiti
- Department of Internal Medicine, University of Texas Health Sciences Center at Houston, Houston, TX
| | - Robert E Brown
- Department of Pathology and Laboratory Medicine, University of Texas Health Sciences Center at Houston, Houston, TX
| | - Paul G Corn
- Division of Cancer Medicine, Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ravi Murthy
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Apostolia M Tsimberidou
- Division of Cancer Medicine, Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Vivek Subbiah
- Division of Cancer Medicine, Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX.
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546
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Clinicopathological and Targeted Exome Gene Features of a Patient with Metastatic Acinic Cell Carcinoma of the Parotid Gland Harboring an ARID2 Nonsense Mutation and CDKN2A/B Deletion. Case Rep Oncol Med 2015; 2015:893694. [PMID: 26634163 PMCID: PMC4655020 DOI: 10.1155/2015/893694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/18/2015] [Indexed: 01/16/2023] Open
Abstract
We describe the presentation, treatment, clinical outcome, and targeted genome analysis of a metastatic salivary acinic cell carcinoma (AciCC). A 71-year-old male presented with a 3 cm right tail of a parotid lesion, first detected as a nodule by the patient seven months earlier. He had a right total parotidectomy with cranial nerve VII resection, right facial nerve resection and grafting, resection of the right conchal cartilage, and right modified radical neck dissection. The primary tumor revealed AciCC with two distinct areas: a well-differentiated component with glandular architecture and a dedifferentiated component with infiltrative growth pattern associated with prominent stromal response, necrosis, perineural invasion, and cellular pleomorphism. Tumor staging was pT4 N0 MX. Immunohistochemistry staining showed pankeratin (+), CD56 (−), and a Ki67 proliferation index of 15%. Upon microscopic inspection, 49 local lymph nodes resected during parotidectomy were negative for cancer cells. Targeted sequencing of the primary tumor revealed deletions of CDKN2A and CDKN2B, a nonsense mutation in ARID2, and single missense mutations of unknown significance in nine other genes. Despite postoperative localized radiation treatment, follow-up whole body PET/CT scan showed lung, soft tissue, bone, and liver metastases. The patient expired 9 months after resection of the primary tumor.
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547
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Valentijn LJ, Koster J, Zwijnenburg DA, Hasselt NE, van Sluis P, Volckmann R, van Noesel MM, George RE, Tytgat GAM, Molenaar JJ, Versteeg R. TERT rearrangements are frequent in neuroblastoma and identify aggressive tumors. Nat Genet 2015; 47:1411-4. [PMID: 26523776 DOI: 10.1038/ng.3438] [Citation(s) in RCA: 261] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 10/09/2015] [Indexed: 12/13/2022]
Abstract
Whole-genome sequencing detected structural rearrangements of TERT in 17 of 75 high-stage neuroblastomas, with five cases resulting from chromothripsis. Rearrangements were associated with increased TERT expression and targeted regions immediately up- and downstream of TERT, positioning a super-enhancer close to the breakpoints in seven cases. TERT rearrangements (23%), ATRX deletions (11%) and MYCN amplifications (37%) identify three almost non-overlapping groups of high-stage neuroblastoma, each associated with very poor prognosis.
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Affiliation(s)
- Linda J Valentijn
- Department of Oncogenomics, Academic Medical Center, Amsterdam, the Netherlands
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center, Amsterdam, the Netherlands
| | - Danny A Zwijnenburg
- Department of Oncogenomics, Academic Medical Center, Amsterdam, the Netherlands
| | - Nancy E Hasselt
- Department of Oncogenomics, Academic Medical Center, Amsterdam, the Netherlands
| | - Peter van Sluis
- Department of Oncogenomics, Academic Medical Center, Amsterdam, the Netherlands
| | - Richard Volckmann
- Department of Oncogenomics, Academic Medical Center, Amsterdam, the Netherlands
| | - Max M van Noesel
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Rani E George
- Department of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Godelieve A M Tytgat
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Department of Pediatric Oncology, Academic Medical Center, Amsterdam, the Netherlands
| | - Jan J Molenaar
- Department of Oncogenomics, Academic Medical Center, Amsterdam, the Netherlands
| | - Rogier Versteeg
- Department of Oncogenomics, Academic Medical Center, Amsterdam, the Netherlands
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548
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Lang M, Vocke CD, Merino MJ, Schmidt LS, Linehan WM. Mitochondrial DNA mutations distinguish bilateral multifocal renal oncocytomas from familial Birt-Hogg-Dubé tumors. Mod Pathol 2015; 28:1458-69. [PMID: 26428318 PMCID: PMC4628590 DOI: 10.1038/modpathol.2015.101] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 04/10/2015] [Accepted: 07/08/2015] [Indexed: 01/06/2023]
Abstract
Oncocytomas are mostly benign tumors characterized by accumulation of defective mitochondria, and in sporadic cases, are associated with disruptive mitochondrial DNA (mtDNA) mutations. However, the role mtDNA mutations have in renal tumors of Birt-Hogg-Dubé (BHD) patients and other renal oncocytomas with an apparent genetic component has not been investigated to date. Here we characterize the mitochondrial genome in different renal tumors and investigate the possibility of employing mtDNA sequencing analyses of biopsy specimens to aid in the differential diagnosis of oncocytomas. The entire mitochondrial genome was sequenced in 25 samples of bilateral and multifocal (BMF) renal oncocytomas, 30 renal tumors from BHD patients and 36 non-oncocytic renal tumors of different histologies as well as in biopsy samples of kidney tumors. mtDNA sequencing in BMF oncocytomas revealed that all tumors carry disruptive mutations, which impair the assembly of the NADH-ubiquinone oxidoreductase. Multiple tumors from a given BMF oncocytoma patient mainly harbor the same somatic mutation and the kidneys of these patients display diffuse oncocytosis. In contrast, renal oncocytomas of patients with BHD syndrome and renal tumors with different histologies do not show disruptive mtDNA mutations. Moreover, we demonstrate that it is feasible to amplify and sequence the entire mtDNA in biopsy specimens, and that these sequences are representative of the tumor DNA. These results show that pathogenic mtDNA mutations affecting complex I of the respiratory chain are strongly correlated with the oncocytoma phenotype in non-BHD-related renal tumors and that mtDNA sequences from biopsies are predictive of the tumor genotype. This work supports a role for mtDNA mutations in respiratory chain complexes as diagnostic markers for renal oncocytomas.
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Affiliation(s)
- Martin Lang
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Cathy D. Vocke
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Maria J. Merino
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Laura S. Schmidt
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - W. Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
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549
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Hamilton HH, McDermott A, Smith MT, Savage SJ, Wolff DJ. Clinical utility of concurrent single-nucleotide polymorphism microarray on fresh tissue as a supplementary test in the diagnosis of renal epithelial neoplasms. Am J Clin Pathol 2015; 144:731-7. [PMID: 26486737 DOI: 10.1309/ajcpjt7f5vnrxxpf] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
OBJECTIVES The histologic and immunohistochemical variability of renal epithelial tumors makes classification difficult; with significant clinical implications, efforts to make the proper diagnoses are necessary. Single-nucleotide polymorphism (SNP) microarray analysis has been proposed as a supplementary study for the classification of renal epithelial neoplasms; however, its practical use in the routine clinical setting has not been explored. METHODS Surgical pathology cases that were classified histologically as renal epithelial tumor subtypes and had concurrent SNP microarray were retrospectively reviewed to correlate tumor morphology and SNP microarray results. RESULTS Of the 99 cases reviewed, 88 (89%) had concordant histologic and microarray results. Four (4%) cases were unclassifiable by microarray due to uncharacteristic chromosomal abnormalities. Seven (7%) of the 99 cases had discordant microarray and histologic diagnoses, and following review of the histology, the diagnoses in two of these cases were subsequently changed. CONCLUSIONS For most cases, concurrent SNP microarray confirmed the histologic diagnosis. However, discrepant microarray results prompted review of morphology and further ancillary studies, resulting in amendment of the final diagnosis in 29% of discrepant cases. SNP microarray analysis can be used to assist with the diagnosis of renal epithelial tumors, particularly those with atypical morphologic features.
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550
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Porta-Pardo E, Garcia-Alonso L, Hrabe T, Dopazo J, Godzik A. A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces. PLoS Comput Biol 2015; 11:e1004518. [PMID: 26485003 PMCID: PMC4616621 DOI: 10.1371/journal.pcbi.1004518] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 08/21/2015] [Indexed: 12/19/2022] Open
Abstract
Despite their importance in maintaining the integrity of all cellular pathways, the role of mutations on protein-protein interaction (PPI) interfaces as cancer drivers has not been systematically studied. Here we analyzed the mutation patterns of the PPI interfaces from 10,028 proteins in a pan-cancer cohort of 5,989 tumors from 23 projects of The Cancer Genome Atlas (TCGA) to find interfaces enriched in somatic missense mutations. To that end we use e-Driver, an algorithm to analyze the mutation distribution of specific protein functional regions. We identified 103 PPI interfaces enriched in somatic cancer mutations. 32 of these interfaces are found in proteins coded by known cancer driver genes. The remaining 71 interfaces are found in proteins that have not been previously identified as cancer drivers even that, in most cases, there is an extensive literature suggesting they play an important role in cancer. Finally, we integrate these findings with clinical information to show how tumors apparently driven by the same gene have different behaviors, including patient outcomes, depending on which specific interfaces are mutated. Until now, most efforts in cancer genomics have focused on identifying genes and pathways driving tumor development. Although this has been unquestionably a success, as evidenced by the fact that we now have an extensive catalogue of cancer driver genes and pathways, there is still a poor understanding of why patients with the same affected driver genes may have different disease outcomes or drug responses. This is precisely the aim of this work-to show how by considering proteins as multifunctional factories instead of monolithic black boxes, it is possible to identify novel cancer driver genes and propose molecular hypotheses to explain such heterogeneity. To that end we have mapped the mutation profiles of 5,989 cancer patients from TCGA to more than 10,000 protein structures, leading us to identify 103 protein interaction interfaces enriched in somatic mutations. Finally, we have integrated clinical annotations as well as proteomics data to show how tumors apparently driven by the same gene can display different behaviors, including patient outcomes, depending on which specific interfaces are mutated.
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Affiliation(s)
- Eduard Porta-Pardo
- Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Luz Garcia-Alonso
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Thomas Hrabe
- Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Joaquin Dopazo
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
- Functional Genomics Node, (INB) at CIPF, Valencia, Spain
- Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
- * E-mail: (JD); (AG)
| | - Adam Godzik
- Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
- * E-mail: (JD); (AG)
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