451
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Prognostic factors for the survival of patients with papillary renal cell carcinoma after surgical management. Clin Transl Oncol 2019; 22:725-733. [PMID: 31317521 DOI: 10.1007/s12094-019-02181-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 07/05/2019] [Indexed: 01/14/2023]
Abstract
PURPOSE To examine the possible prognostic factors in patients with type 1 and type 2 papillary renal cell carcinoma (pRCC) after surgical management and to identify the independent predictive factors of the prognosis. METHODS From 2010 to 2017, 1405 patients underwent surgery for renal cell carcinoma, of whom 114 had type 1 or type 2 pRCC and follow-up data were available for 88 patients. Clinicopathological and prognostic parameters were compared between type 1 and type 2 pRCC. Possible prognostic factors were retrospectively analyzed by univariate and multivariate analyses with Cox regression. RESULTS The study included 63 males and 25 females with a mean age of 54.27 ± 12.91. 53 patients were diagnosed by regular physical examination and others presented with hematuria or lumbago. 53 (60.2%) underwent radical nephrectomy and 35 (39.8%) underwent nephron sparing surgery. After a mean follow-up of 46.08 ± 22.65 months, 16 patients died of pRCC metastasis and the 5-year disease-specific survival was 79.3%. The comparison of the 39 (44.3%) type 1 and 49 (55.7%) type 2 pRCCs revealed that type 2 pRCC had significantly higher grade and worse prognosis. Univariate analysis showed that symptomatic diagnosis, type, grade, and tumor stage were prognostic factors. Multivariate analysis identified that type and tumor stage were independent factors of the prognosis. CONCLUSIONS Pathological type and tumor stage could serve as independent factors for the prognosis of patients with pRCC.
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452
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Zhang Z, Luo D, Zhong X, Choi JH, Ma Y, Wang S, Mahrt E, Guo W, Stawiski EW, Modrusan Z, Seshagiri S, Kapur P, Hon GC, Brugarolas J, Wang T. SCINA: A Semi-Supervised Subtyping Algorithm of Single Cells and Bulk Samples. Genes (Basel) 2019; 10:E531. [PMID: 31336988 PMCID: PMC6678337 DOI: 10.3390/genes10070531] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/05/2019] [Accepted: 07/08/2019] [Indexed: 12/30/2022] Open
Abstract
Advances in single-cell RNA sequencing (scRNA-Seq) have allowed for comprehensive analyses of single cell data. However, current analyses of scRNA-Seq data usually start from unsupervised clustering or visualization. These methods ignore prior knowledge of transcriptomes and the probable structures of the data. Moreover, cell identification heavily relies on subjective and possibly inaccurate human inspection afterwards. To address these analytical challenges, we developed SCINA (Semi-supervised Category Identification and Assignment), a semi-supervised model that exploits previously established gene signatures using an expectation-maximization (EM) algorithm. SCINA is applicable to scRNA-Seq and flow cytometry/CyTOF data, as well as other data of similar format. We applied SCINA to a wide range of datasets, and showed its accuracy, stability and efficiency, which exceeded most popular unsupervised approaches. SCINA discovered an intermediate stage of oligodendrocytes from mouse brain scRNA-Seq data. SCINA also detected immune cell population changes in cytometry data in a genetically-engineered mouse model. Furthermore, SCINA performed well with bulk gene expression data. Specifically, we identified a new kidney tumor clade with similarity to FH-deficient tumors (FHD), which we refer to as FHD-like tumors (FHDL). Overall, SCINA provides both methodological advances and biological insights from perspectives different from traditional analytical methods.
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Affiliation(s)
- Ze Zhang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Danni Luo
- Bioinformatics Core Facility, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xue Zhong
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yuanqing Ma
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, TX 75390, USA
| | - Stacy Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Elena Mahrt
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wei Guo
- BioHPC, University of Texas Southwestern Medical Center, Dallas, Texas, TX 75390, USA
| | - Eric W Stawiski
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA 94080, USA
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Zora Modrusan
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Somasekar Seshagiri
- Molecular Biology Department, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Payal Kapur
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gary C Hon
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - James Brugarolas
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, TX 75390, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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453
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Sun Y, Sun Z, Jiang Y, Li Y, Ma S. An integrative sparse boosting analysis of cancer genomic commonality and difference. Stat Methods Med Res 2019; 29:1325-1337. [PMID: 31282286 DOI: 10.1177/0962280219859026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In cancer research, high-throughput profiling has been extensively conducted. In recent studies, the integrative analysis of data on multiple cancer patient groups/subgroups has been conducted. Such analysis has the potential to reveal the genomic commonality as well as difference across groups/subgroups. However, in the existing literature, methods with a special attention to the genomic commonality and difference are very limited. In this study, a novel estimation and marker selection method based on the sparse boosting technique is developed to address the commonality/difference problem. In terms of technical innovation, a new penalty and computation of increments are introduced. The proposed method can also effectively accommodate the grouping structure of covariates. Simulation shows that it can outperform direct competitors under a wide spectrum of settings. The analysis of two TCGA (The Cancer Genome Atlas) datasets is conducted, showing that the proposed analysis can identify markers with important biological implications and have satisfactory prediction and stability.
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Affiliation(s)
- Yifan Sun
- Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing, China
| | - Zhengyang Sun
- Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing, China
| | - Yu Jiang
- School of Public Health, University of Memphis, Tennessee, USA
| | - Yang Li
- Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing, China
| | - Shuangge Ma
- Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing, China.,Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
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454
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The Cancer Genome Atlas of renal cell carcinoma: findings and clinical implications. Nat Rev Urol 2019; 16:539-552. [DOI: 10.1038/s41585-019-0211-5] [Citation(s) in RCA: 213] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2019] [Indexed: 11/09/2022]
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455
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Zhang Y, Earp HS, Liu P. Beyond growth signaling: apoptotic sensor MERTK activates AKT by a novel mechanism. Mol Cell Oncol 2019; 6:1611161. [PMID: 31211243 DOI: 10.1080/23723556.2019.1611161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 04/18/2019] [Accepted: 04/22/2019] [Indexed: 01/11/2023]
Abstract
Canonically the oncogenic kinase AKT is activated by growth signals. Our work suggests apoptotic materials, abundant in tumors, also contribute to AKT activation by stimulating MERTK that in turn phosphorylates Y26 in the AKT PH domain. pY26 reverses binding of an AKT endogenous, WW-domain containing inhibitor, SAV1, allowing AKT responsiveness to classic growth signals. This novel mechanism may contribute to drug resistance.
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Affiliation(s)
- Yanqiong Zhang
- UNC Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biochemistry and Biophysics, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - H Shelton Earp
- UNC Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Medicine and Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Pengda Liu
- UNC Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biochemistry and Biophysics, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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456
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Heidegger I, Pircher A, Pichler R. Targeting the Tumor Microenvironment in Renal Cell Cancer Biology and Therapy. Front Oncol 2019; 9:490. [PMID: 31259150 PMCID: PMC6587703 DOI: 10.3389/fonc.2019.00490] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/23/2019] [Indexed: 12/17/2022] Open
Abstract
Renal cell cancer (RCC) is a highly vascularized and immunogenic tumor type. The inhibition of vessel formation by anti-angiogenic therapies, as well as the stimulation of the immune system by immunotherapy has revolutionized the therapeutic landscape of RCC in recent years. Nevertheless, both therapies are associated with therapy resistance due to a highly dynamic, adaptive and heterogeneous tumor microenvironment (TME). The aim of this short review article is to provide an overview of the components of the RCC TME as well as to discuss their contribution to disease progression. In addition, we report on preclinical and clinical findings and how the different TME components can be modulated to impede treatment progression as well as to overcome therapy resistance to anti-angiogenic or immunomodulating therapy concepts. Furthermore, we discuss the predictive and prognostic role of the TME in RCC therapy. We also report on the concept of combinational targeting of anti-angiogenic therapies and immune checkpoint inhibitor therapy, also including the latest results of clinical studies discussed at recent oncological meetings. Finally, promising new therapeutic targets within the TME are mentioned.
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Affiliation(s)
- Isabel Heidegger
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Andreas Pircher
- Department of Internal Medicine, Hematology and Oncology, Medical University of Innsbruck, Innsbruck, Austria
| | - Renate Pichler
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
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457
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Di Nunno V, Frega G, Santoni M, Gatto L, Fiorentino M, Montironi R, Battelli N, Brandi G, Massari F. BAP1 in solid tumors. Future Oncol 2019; 15:2151-2162. [PMID: 31159579 DOI: 10.2217/fon-2018-0915] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
One of the most attractive cancer-related genes under investigation is BAP1. Reasons of this growing interest are related to the wide spectrum of pathways directly or indirectly modulated by this gene and shared by several solid tumors. Programmed cell-death, cell metabolisms, immune cells development, ferroptosis and defects in DNA damage response are only some of the multitude of processes depending on BAP1. Loss of this gene seems to occur in different times of tumor history. Moreover, times of BAP1 loss strongly diverge among primary tumors suggesting the presence of several and different triggering factors. Regardless of when it happens, BAP1 loss usually results in prognosis worsening and in the acquisition of more aggressive clinical features by cancer cells.
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Affiliation(s)
| | - Giorgio Frega
- Oncology Unit, Department of Experimental, Diagnostic & Specialty Medicine, Sant'Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Matteo Santoni
- Department of Oncology, Macerata Hospital, Macerata, Italy
| | - Lidia Gatto
- Oncology Unit, Department of Experimental, Diagnostic & Specialty Medicine, Sant'Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Michelangelo Fiorentino
- Pathology Service, Addarii Institute of Oncology, S-Orsola-Malpighi Hospital, Bologna, Italy
| | - Rodolfo Montironi
- Section of Pathological Anatomy, Polytechnic University of the Marche Region, School of Medicine, United Hospitals, Ancona, Italy
| | | | - Giovanni Brandi
- Oncology Unit, Department of Experimental, Diagnostic & Specialty Medicine, Sant'Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
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458
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Shiomi E, Sugai T, Ishida K, Osakabe M, Tsuyukubo T, Kato Y, Takata R, Obara W. Analysis of Expression Patterns of MicroRNAs That Are Closely Associated With Renal Carcinogenesis. Front Oncol 2019; 9:431. [PMID: 31214494 PMCID: PMC6555129 DOI: 10.3389/fonc.2019.00431] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/07/2019] [Indexed: 12/28/2022] Open
Abstract
Background: MicroRNAs (miRNA) are frequently dysregulated in clear cell renal cell carcinoma (ccRCC). Objective: This study aimed to elucidate the role of miRNA expression patterns in renal carcinogenesis and to identify the specific miRNAs that exhibit expression patterns closely associated with patient outcomes. Methods: We examined the expression patterns of selected miRNAs, including miRNA-155-5p, miRNA-122-5p, miRNA-21-5p, miRNA-185-5p, miRNA-106a-5p, miRNA-106b-3p, miRNA-34b-3p, miRNA-210-3p, miRNA-141-3p, miRNA-200c-3p, miRNA-135a-5p, miRNA-30a-5p, miRNA-218-5p, miRNA-429, miRNA-200a-3p and miRNA-200b-3p, in 96 samples of ccRCCs using the TaqMan real-time PCR method. In addition, cluster analysis was performed to stratify expression patterns of multiple miRNAs. Results: In the present study, three distinct subgroups could be clearly stratified in ccRCCs. Subgroup 1 was characterized by upregulation of miRNA-155-5p, miRNA-122-5p, miRNA-21-5p, miRNA-185-5p, miRNA-106a-5p, miRNA-106b-3p, miRNA-34b-3p and miRNA-210-3p. Subgroup 2 was closely associated with downregulation of miRNA-141-3p, miRNA200c-3p, miRNA-30a-5p, miRNA-218-5p, miRNA-429, miRNA-200a-3p and miRNA-200b-3p. Moreover, significant lower expression of miRNA-135a-5p was a distinctive feature of subgroup 3, which was correlated with metachronous metastasis. Among the individual markers in subgroup 3, miRNA-135a-5p was retained in multivariate analysis. The cutoff value of miRNA-135a-5p expression to identify the association of an altered level of miRNA-135a-5p with metachronous metastasis in ccRCCs was determined and showed excellent specificity. Conclusion: We suggest that the expression pattern of the chosen miRNAs is useful to identify renal carcinogenesis and to help identify the association of such expression patterns with metachronous metastasis in ccRCCs. In addition, miRNA-135a-5p was an excellent marker for prediction of metachronous metastasis.
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Affiliation(s)
- Ei Shiomi
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan.,Department of Urology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Tamotsu Sugai
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Kazuyuki Ishida
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Mitsumasa Osakabe
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Takashi Tsuyukubo
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan.,Department of Urology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Yoichiro Kato
- Department of Urology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Ryo Takata
- Department of Urology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Wataru Obara
- Department of Urology, School of Medicine, Iwate Medical University, Morioka, Japan
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459
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DiNatale RG, Sanchez A, Hakimi AA, Reznik E. Metabolomics informs common patterns of molecular dysfunction across histologies of renal cell carcinoma. Urol Oncol 2019; 38:755-762. [PMID: 31155438 DOI: 10.1016/j.urolonc.2019.04.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/16/2019] [Accepted: 04/24/2019] [Indexed: 02/07/2023]
Abstract
The last 30 years of research in renal cell carcinoma (RCC) has revealed that the vast majority of RCC histologies share a recurrent pattern of mutations to metabolic genes, including VHL, MTOR, ELOC, TSC1/2, FH, SDH, and mitochondrial DNA. This has prompted intense study of the consequences of these mutations on cellular metabolism and physiology in vivo by leveraging high-throughput technologies to measure small-molecule metabolites (i.e., metabolomics). The purpose of this review is to give a broad and integrated view on the discoveries made in RCC with metabolomics, and to give a basic understanding of the experimental design of metabolomic studies. Our discussion is organized around five concepts which synthesize discoveries from genomics and metabolomics into the molecular basis of RCC and transcend the different RCC histologies: (1) metabolic phenotypes unique to certain genotypes, (2) mitochondrial dysfunction, (3) the oxidative stress response, (4) epigenetics, and (5) therapy targeted to metabolism. We conclude by proposing several promising lines of investigation that intersect metabolism with emerging ideas in RCC biology.
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Affiliation(s)
- Renzo G DiNatale
- Urology Department, Memorial Sloan Kettering Cancer Center, New York, NY; Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alejandro Sanchez
- Urology Department, Memorial Sloan Kettering Cancer Center, New York, NY
| | - A Ari Hakimi
- Urology Department, Memorial Sloan Kettering Cancer Center, New York, NY; Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ed Reznik
- Computational Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY; Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY.
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460
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Fumarate hydratase in cancer: A multifaceted tumour suppressor. Semin Cell Dev Biol 2019; 98:15-25. [PMID: 31085323 DOI: 10.1016/j.semcdb.2019.05.002] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 02/07/2023]
Abstract
Cancer is now considered a multifactorial disorder with different aetiologies and outcomes. Yet, all cancers share some common molecular features. Among these, the reprogramming of cellular metabolism has emerged as a key player in tumour initiation and progression. The finding that metabolic enzymes such as fumarate hydratase (FH), succinate dehydrogenase (SDH) and isocitrate dehydrogenase (IDH), when mutated, cause cancer suggested that metabolic dysregulation is not only a consequence of oncogenic transformation but that it can act as cancer driver. However, the mechanisms underpinning the link between metabolic dysregulation and cancer remain only partially understood. In this review we discuss the role of FH loss in tumorigenesis, focusing on the role of fumarate as a key activator of a variety of oncogenic cascades. We also discuss how these alterations are integrated and converge towards common biological processes. This review highlights the complexity of the signals elicited by FH loss, describes that fumarate can act as a bona fide oncogenic event, and provides a compelling hypothesis of the stepwise neoplastic progression after FH loss.
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461
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Linehan WM, Schmidt LS, Crooks DR, Wei D, Srinivasan R, Lang M, Ricketts CJ. The Metabolic Basis of Kidney Cancer. Cancer Discov 2019; 9:1006-1021. [PMID: 31088840 DOI: 10.1158/2159-8290.cd-18-1354] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/19/2019] [Accepted: 03/22/2019] [Indexed: 01/27/2023]
Abstract
Kidney cancer is not a single disease but represents several distinct types of cancer that have defining histologies and genetic alterations and that follow different clinical courses and have different responses to therapy. Mutation of genes associated with kidney cancer, such as VHL, FLCN, TFE3, FH, or SDHB, dysregulates the tumor's responses to changes in oxygen, iron, nutrient, or energy levels. The identification of these varying genetic bases of kidney cancer has increased our understanding of the biology of this cancer, allowing the development of targeted therapies and the appreciation that it is a cancer driven by metabolic alterations. SIGNIFICANCE: Kidney cancer is a complex disease composed of different types of cancer that present with different histologies, clinical courses, genetic changes, and responses to therapy. This review describes the known genetic changes within kidney cancer, how they alter tumor metabolism, and how these metabolic changes can be therapeutically targeted.
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Affiliation(s)
- W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
| | - Laura S Schmidt
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,Basic Science Program, Frederick Laboratory for Cancer Research, Frederick, Maryland
| | - Daniel R Crooks
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Darmood Wei
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Ramaprasad Srinivasan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Martin Lang
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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462
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Wang Y, Tanaka H, Ye Y, Ding X, Ward RD, Campbell RA, DeWitt-Foy ME, Suk-Ouichai C, Remer EM, Campbell SC. The Complete Spectrum of Infiltrative Renal Masses: Clinical Characteristics and Prognostic Implications. Urology 2019; 130:86-92. [PMID: 31075276 DOI: 10.1016/j.urology.2019.04.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/23/2019] [Accepted: 04/27/2019] [Indexed: 12/17/2022]
Abstract
OBJECTIVE To analyze the full spectrum of patients presenting with radiologically-identified infiltrative renal masses (IRMs), including those managed surgically or otherwise, with focus on clinical presentation/prognosis. METHODS All 280 patients presenting with radiologically-identified renal mass with infiltrative features (2008-2017) were retrospectively reviewed. Poorly-defined interface between tumor and parenchyma and irregular shape (nonelliptical) in one or more distinct/unequivocal areas were required for classification as IRM. IRM was confirmed in 265 and clinical characteristics and outcomes were assessed. RESULTS Median age/tumor size were 65-years/6.9 cm, respectively, and 225 patients (85%) were R.E.N.A.L. = 10-12. Overall, 181 patients (68%) presented symptomatically, locally-advanced cancer (cT3-T4) was observed in 176 (66%) and disseminated disease and/or lymphadenopathy (>2 cm) in 181(68%). Clinical/radiographic findings were suggestive of etiology and could direct evaluation, but were nonspecific for definitive diagnosis. Renal-mass biopsy was performed in 103 patients and diagnostic in 97 (94%). Renal surgery was only performed in 82 patients (31%) and partial nephrectomy in 3 (1.1%). Overall, 72 patients (27%) received systemic chemotherapy and 59 (22%) targeted therapy. Final-diagnosis was renal cell carcinoma in 94 patients (35%), including 49 with highly-aggressive histology (sarcomatoid/rhabdoid/collecting-duct/medullary/unclassified). High-grade urothelial-carcinoma was found in 70 (26%), and lymphoma/metastatic cancer in 26 (10%)/25 (9%), respectively. Overall, 153 patients (58%) died; 138 (52%) cancer-related at median of 5 months. The majority of patients with renal cell carcinoma, urothelial-carcinoma, and renal metastasis died, almost exclusively cancer-related, at medians of 8, 3, and 2 months, respectively. CONCLUSION Our series includes the full spectrum of IRMs and confirms predominance of symptomatic, poorly-differentiated, highly-lethal malignancies. Our study highlights the overriding importance of identifying infiltrative features, a simple radiologic diagnosis, during assessment of renal masses.
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Affiliation(s)
- Yanbo Wang
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH; Department of Urology, First Hospital of Jilin University, Changchun, China
| | - Hajime Tanaka
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH; Department of Urology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yunlin Ye
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH; Department of Urology Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Xiaobo Ding
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH; Department of Radiology, First Hospital of Jilin University, Changchun, China; Imaging Institute, Cleveland Clinic, Cleveland, OH
| | - Ryan D Ward
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH; Imaging Institute, Cleveland Clinic, Cleveland, OH
| | - Rebecca A Campbell
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH
| | - Molly E DeWitt-Foy
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH
| | - Chalairat Suk-Ouichai
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH; Division of Urology, Department of Surgery, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Erick M Remer
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH; Imaging Institute, Cleveland Clinic, Cleveland, OH
| | - Steven C Campbell
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH.
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463
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Lucarelli G, Loizzo D, Franzin R, Battaglia S, Ferro M, Cantiello F, Castellano G, Bettocchi C, Ditonno P, Battaglia M. Metabolomic insights into pathophysiological mechanisms and biomarker discovery in clear cell renal cell carcinoma. Expert Rev Mol Diagn 2019; 19:397-407. [PMID: 30983433 DOI: 10.1080/14737159.2019.1607729] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Clear cell renal cell carcinoma (ccRCC) is a metabolic disease, of which the incidence rate is increasing worldwide. Renal carcinoma is characterized by mutations in target genes involved in metabolic pathways. Metabolic reprogramming covers different processes such as aerobic glycolysis, fatty acid metabolism, and the utilization of tryptophan, glutamine, and arginine. In the era of the multi-omics approach (with integrated transcriptomics, proteomics, and metabolomics), discovering biomarkers for early diagnosis is gaining renewed importance. Areas covered: In this review, we discuss the pathophysiological mechanisms underlying ccRCC metabolic reprogramming. In addition, we describe the emerging metabolomics-based biomarkers differentially expressed in ccRCC and the rationale for the recently developed drugs specifically targeting the ccRCC metabolome. Expert opinion: A number of metabolic pathways will be explored in future years, and many of these pathways are potential therapeutic targets and may serve as diagnostic and prognostic biomarkers of ccRCC.
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Affiliation(s)
- Giuseppe Lucarelli
- a Department of Emergency and Organ Transplantation - Urology, Andrology and Kidney Transplantation Unit , University of Bari , Bari , Italy
| | - Davide Loizzo
- a Department of Emergency and Organ Transplantation - Urology, Andrology and Kidney Transplantation Unit , University of Bari , Bari , Italy
| | - Rossana Franzin
- a Department of Emergency and Organ Transplantation - Urology, Andrology and Kidney Transplantation Unit , University of Bari , Bari , Italy
| | - Stefano Battaglia
- a Department of Emergency and Organ Transplantation - Urology, Andrology and Kidney Transplantation Unit , University of Bari , Bari , Italy
| | - Matteo Ferro
- b Division of Urology , European Institute of Oncology , Milan , Italy
| | - Francesco Cantiello
- c Department of Urology , Magna Graecia University of Catanzaro , Catanzaro , Italy
| | - Giuseppe Castellano
- d Department of Emergency and Organ Transplantation - Nephrology and Dialysis Unit , University of Bari , Bari , Italy
| | - Carlo Bettocchi
- a Department of Emergency and Organ Transplantation - Urology, Andrology and Kidney Transplantation Unit , University of Bari , Bari , Italy
| | - Pasquale Ditonno
- a Department of Emergency and Organ Transplantation - Urology, Andrology and Kidney Transplantation Unit , University of Bari , Bari , Italy
| | - Michele Battaglia
- a Department of Emergency and Organ Transplantation - Urology, Andrology and Kidney Transplantation Unit , University of Bari , Bari , Italy
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Bowen L, Xiaojing L. Radiogenomics of Clear Cell Renal Cell Carcinoma: Associations Between mRNA-Based Subtyping and CT Imaging Features. Acad Radiol 2019; 26:e32-e37. [PMID: 30064916 DOI: 10.1016/j.acra.2018.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 12/11/2022]
Abstract
PURPOSE To investigate associations between clear-cell renal cell carcinoma mRNA-based subtyping and CT features. MATERIALS AND METHODS The CT data from 177 patients generated with The Cancer Imaging Archive were reviewed. The correlation was analyzed using chi-square test and univariate regression analysis. RESULTS Identified were 124 (53.2%) m1, 67 (28.8%) m2, 17 (7.3%) m3, and 14 (8.7%) m4 subtypes. m1-subtype rates were significantly higher in well-defined margin lesions (p = 0.041). m3-subtype rates were significantly higher in ill-defined margin lesions (p = 0.012), in collecting system invasion lesions (p = 0.028) and collecting system invasion lesions (p = 0.026).On univariate logistic regression analysis, tumor margin (well-defined margin vs ill-defined margin, OR: 2.104; p = 0.041; 95% CI: 1.024-4.322) was associated with m1-subtype. Tumor margin (well-defined margin vs ill-defined margin, OR: 2.104; p = 0.012; 95% CI: 0.212-0.834) and collecting system invasion (yes vs no, OR: 0.421; p = 0.028; 95% CI: 0.212-0.834) and renal vein invasion (yes vs no, OR: 2.164; p = 0.026; 95% CI: 1.090-4.294) were associated with m3-subtype. There was no significant difference between mRNA-based subtyping (m2 vs other; m4 vs other) and the CT features. CONCLUSIONS This preliminary radiogenomics analysis of clear-cell renal cell carcinoma revealed associations between CT features and mRNA-based subtyping which warrant further investigation and validation.
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465
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Zhang Y, Chen J, Wang Y, Wang D, Cong W, Lai BS, Zhao Y. Multilayer network analysis of miRNA and protein expression profiles in breast cancer patients. PLoS One 2019; 14:e0202311. [PMID: 30946749 PMCID: PMC6448837 DOI: 10.1371/journal.pone.0202311] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 03/19/2019] [Indexed: 12/21/2022] Open
Abstract
MiRNAs and proteins play important roles in different stages of breast tumor development and serve as biomarkers for the early diagnosis of breast cancer. A new algorithm that combines machine learning algorithms and multilayer complex network analysis is hereby proposed to explore the potential diagnostic values of miRNAs and proteins. XGBoost and random forest algorithms were employed to screen the most important miRNAs and proteins. Maximal information coefficient was applied to assess intralayer and interlayer connection. A multilayer complex network was constructed to identify miRNAs and proteins that could serve as biomarkers for breast cancer. Proteins and miRNAs that are nodes in the network were subsequently categorized into two network layers considering their distinct functions. The betweenness centrality was used as the first measurement of the importance of the nodes within each single layer. The degree of the nodes was chosen as the second measurement to map their signalling pathways. By combining these two measurements into one score and comparing the difference of the same candidate between normal tissue and cancer tissue, this novel multilayer network analysis could be applied to successfully identify molecules associated with breast cancer.
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Affiliation(s)
- Yang Zhang
- Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China
| | - Jiannan Chen
- Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China
| | - Yu Wang
- Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China
| | - Dehua Wang
- Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China
| | - Weihui Cong
- Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China
| | - Bo Shiun Lai
- Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Yi Zhao
- Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China
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466
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Jung M, Ellinger J, Gevensleben H, Syring I, Lüders C, de Vos L, Pützer S, Bootz F, Landsberg J, Kristiansen G, Dietrich D. Cell-Free SHOX2 DNA Methylation in Blood as a Molecular Staging Parameter for Risk Stratification in Renal Cell Carcinoma Patients: A Prospective Observational Cohort Study. Clin Chem 2019; 65:559-568. [DOI: 10.1373/clinchem.2018.297549] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/19/2018] [Indexed: 01/27/2023]
Abstract
Abstract
BACKGROUND
Novel targeted treatments and immunotherapies have substantially changed therapeutic options for advanced and metastatic renal cell carcinomas (RCCs). However, accurate diagnostic tests for the identification of high-risk patients are urgently needed. Here, we analyzed SHOX2 mRNA expression in RCC tissues and SHOX2 gene body methylation quantitatively in circulating cell-free DNA (ccfDNA) and RCC tissues with regard to risk stratification.
METHODS
The clinical performance of SHOX2 methylation was tested retrospectively and prospectively in a training and testing cohort of RCC tissue samples (n = 760 in total). SHOX2 mRNA expression analysis was included in the training cohort. In matched blood plasma samples from the testing cohort (n = 100), we prospectively examined the capability of pretherapeutic quantitative SHOX2 ccfDNA methylation to assess disease stage and identify patients at high risk of death.
RESULTS
SHOX2 gene body methylation was positively correlated with mRNA expression in RCC tissues (training cohort: Spearman ρ = 0.23, P < 0.001). SHOX2 methylation in tissue and plasma strongly correlated with an advanced disease stage (training cohort: ρ = 0.28, P < 0.001; testing cohort/tissue: ρ = 0.40, P < 0.001; testing cohort/plasma: ρ = 0.34, P = 0.001) and risk of death after initial partial or radical nephrectomy [training cohort: hazard ratio (HR) = 1.40 (95% CI, 1.24–1.57), P < 0.001; testing cohort/tissue: HR = 1.16 (95% CI, 1.07–1.27), P = 0.001; testing cohort/plasma: HR = 1.50 (95% CI, 1.29–1.74), P < 0.001].
CONCLUSIONS
Pretherapeutic SHOX2 ccfDNA methylation testing allows for the identification of RCC patients at high risk of death after nephrectomy. These patients might benefit from an adjuvant treatment or early initiation of a palliative treatment.
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Affiliation(s)
- Maria Jung
- Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Jörg Ellinger
- Department of Urology, University Hospital Bonn, Bonn, Germany
| | | | - Isabella Syring
- Department of Urology, University Hospital Bonn, Bonn, Germany
| | | | - Luka de Vos
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Svenja Pützer
- Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Friedrich Bootz
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | | | | | - Dimo Dietrich
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
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467
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Tedesco L, Elguero B, Pacin DG, Senin S, Pollak C, Garcia Marchiñena PA, Jurado AM, Isola M, Labanca MJ, Palazzo M, Yankilevich P, Fuertes M, Arzt E. von Hippel-Lindau mutants in renal cell carcinoma are regulated by increased expression of RSUME. Cell Death Dis 2019; 10:266. [PMID: 30890701 PMCID: PMC6424967 DOI: 10.1038/s41419-019-1507-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/01/2019] [Accepted: 03/04/2019] [Indexed: 12/17/2022]
Abstract
Renal cell carcinoma (RCC) is the major cause of death among patients with von Hippel-Lindau (VHL) disease. Resistance to therapies targeting tumor angiogenesis opens the question about the underlying mechanisms. Previously we have described that RWDD3 or RSUME (RWD domain-containing protein SUMO Enhancer) sumoylates and binds VHL protein and negatively regulates HIF degradation, leading to xenograft RCC tumor growth in mice. In this study, we performed a bioinformatics analysis in a ccRCC dataset showing an association of RSUME levels with VHL mutations and tumor progression, and we demonstrate the molecular mechanism by which RSUME regulates the pathologic angiogenic phenotype of VHL missense mutations. We report that VHL mutants fail to downregulate RSUME protein levels accounting for the increased RSUME expression found in RCC tumors. Furthermore, we prove that targeting RSUME in RCC cell line clones carrying missense VHL mutants results in decreased early tumor angiogenesis. The mechanism we describe is that RSUME sumoylates VHL mutants and beyond its sumoylation capacity, interacts with Type 2 VHL mutants, reduces HIF-2α-VHL mutants binding, and negatively regulates the assembly of the Type 2 VHL, Elongins and Cullins (ECV) complex. Altogether these results show RSUME involvement in VHL mutants deregulation that leads to the angiogenic phenotype of RCC tumors.
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Affiliation(s)
- Lucas Tedesco
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Godoy Cruz 2390, C1425FQD, Buenos Aires, Argentina
| | - Belén Elguero
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Godoy Cruz 2390, C1425FQD, Buenos Aires, Argentina
| | - David Gonilski Pacin
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Godoy Cruz 2390, C1425FQD, Buenos Aires, Argentina
| | - Sergio Senin
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Godoy Cruz 2390, C1425FQD, Buenos Aires, Argentina
| | - Cora Pollak
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Godoy Cruz 2390, C1425FQD, Buenos Aires, Argentina
| | | | - Alberto M Jurado
- Departamento de Urología, Hospital Italiano de Buenos Aires, VHL Clinical Care Center, Buenos Aires, Argentina
| | - Mariana Isola
- Departamento de Patología, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - María J Labanca
- Departamento de Patología, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Martin Palazzo
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Godoy Cruz 2390, C1425FQD, Buenos Aires, Argentina
| | - Patricio Yankilevich
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Godoy Cruz 2390, C1425FQD, Buenos Aires, Argentina
| | - Mariana Fuertes
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Godoy Cruz 2390, C1425FQD, Buenos Aires, Argentina
| | - Eduardo Arzt
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Godoy Cruz 2390, C1425FQD, Buenos Aires, Argentina. .,Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Guiraldes 2160, Ciudad Universitaria, Pabellon II, 2do Piso, C1428EGA, Buenos Aires, Argentina.
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468
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Swami U, Nussenzveig RH, Haaland B, Agarwal N. Revisiting AJCC TNM staging for renal cell carcinoma: quest for improvement. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:S18. [PMID: 31032299 DOI: 10.21037/atm.2019.01.50] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Umang Swami
- Department of Hematology, Oncology and Blood and Marrow Transplantation, The Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Roberto H Nussenzveig
- Division of Oncology, Department of Internal Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Benjamin Haaland
- Department of Population Health Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Neeraj Agarwal
- Division of Oncology, Department of Internal Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
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469
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Linking Binary Gene Relationships to Drivers of Renal Cell Carcinoma Reveals Convergent Function in Alternate Tumor Progression Paths. Sci Rep 2019; 9:2899. [PMID: 30814637 PMCID: PMC6393532 DOI: 10.1038/s41598-019-39875-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/28/2019] [Indexed: 12/30/2022] Open
Abstract
Renal cell carcinoma (RCC) subtypes are characterized by distinct molecular profiles. Using RNA expression profiles from 1,009 RCC samples, we constructed a condition-annotated gene coexpression network (GCN). The RCC GCN contains binary gene coexpression relationships (edges) specific to conditions including RCC subtype and tumor stage. As an application of this resource, we discovered RCC GCN edges and modules that were associated with genetic lesions in known RCC driver genes, including VHL, a common initiating clear cell RCC (ccRCC) genetic lesion, and PBRM1 and BAP1 which are early genetic lesions in the Braided Cancer River Model (BCRM). Since ccRCC tumors with PBRM1 mutations respond to targeted therapy differently than tumors with BAP1 mutations, we focused on ccRCC-specific edges associated with tumors that exhibit alternate mutation profiles: VHL-PBRM1 or VHL-BAP1. We found specific blends molecular functions associated with these two mutation paths. Despite these mutation-associated edges having unique genes, they were enriched for the same immunological functions suggesting a convergent functional role for alternate gene sets consistent with the BCRM. The condition annotated RCC GCN described herein is a novel data mining resource for the assignment of polygenic biomarkers and their relationships to RCC tumors with specific molecular and mutational profiles.
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470
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Prendeville S, Richard PO, Jewett MAS, Kachura JR, Sweet JM, van der Kwast TH, Cheung CC, Finelli A, Evans AJ. Accuracy of renal tumour biopsy for the diagnosis and subtyping of papillary renal cell carcinoma: analysis of paired biopsy and nephrectomy specimens with focus on discordant cases. J Clin Pathol 2019; 72:363-367. [DOI: 10.1136/jclinpath-2018-205655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/14/2019] [Accepted: 01/14/2019] [Indexed: 01/20/2023]
Abstract
AimsRenal tumour biopsy (RTB) is increasingly recognised as a useful diagnostic tool in the management of small renal masses, particularly those that are incidentally found. Intratumoural heterogeneity with respect to morphology, grade and molecular features represents a frequently identified limitation to the use of RTB. While previous studies have evaluated pathological correlation between RTB and nephrectomy, no studies to date have focused specifically on the role of RTB for the diagnosis of papillary renal cell carcinoma (PRCC) and its further subclassification into clinically relevant subtypes.MethodsThis single-institution study evaluated 60 cases of PRCC for concordance between RTB and nephrectomy with respect to diagnosis, grading and subtyping (type 1/type 2).ResultsWe observed 93% concordance (55 of 59 evaluable cases) between RTB and nephrectomy for the diagnosis of PRCC, although seven tumours (12%) were undergraded on RTB. Subtyping of PRCC on RTB was concordant with nephrectomy in 89% of cases reported as type 1 PRCC on RTB (31/35), but only 40% of cases reported as type 2 PRCC on RTB (4/10). Morphological misclassification of PRCC on RTB was most likely to occur in tumours showing a solid growth pattern. Discordant PRCC subtyping most often occurred in tumours with eosinophilia/oncocytic change.ConclusionThere was good concordance between RTB and nephrectomy for the primary diagnosis of PRCC. Although further subtyping of PRCC can aid therapeutic stratification, this can be challenging on RTB and tumours with overlapping or ambiguous features are best reported as PRCC not otherwise specified pending development of more robust methods to facilitate definitive subclassification.
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471
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Hahn AW, Nussenzveig RH, Maughan BL, Agarwal N. Cell-free Circulating Tumor DNA (ctDNA) in Metastatic Renal Cell Carcinoma (mRCC): Current Knowledge and Potential Uses. KIDNEY CANCER 2019. [DOI: 10.3233/kca-180048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Andrew W. Hahn
- Department of Internal Medicine, Division of Oncology, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Roberto H. Nussenzveig
- Department of Internal Medicine, Division of Oncology, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Benjamin L. Maughan
- Department of Internal Medicine, Division of Oncology, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Neeraj Agarwal
- Department of Internal Medicine, Division of Oncology, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
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472
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Stenehjem DD, Hahn AW, Gill DM, Albertson D, Gowrishankar B, Merriman J, Agarwal AM, Thodima V, Harrington EB, Au TH, Maughan BL, Houldsworth J, Pal SK, Agarwal N. Predictive genomic markers of response to VEGF targeted therapy in metastatic renal cell carcinoma. PLoS One 2019; 14:e0210415. [PMID: 30682039 PMCID: PMC6347137 DOI: 10.1371/journal.pone.0210415] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/21/2018] [Indexed: 11/18/2022] Open
Abstract
Background First-line treatment for metastatic renal cell carcinoma (mRCC) is rapidly changing. It currently includes VEGF targeted therapies (TT), multi-target tyrosine kinase inhibitors (TKIs), mTOR inhibitors, and immunotherapy. To optimize outcomes for individual patients, genomic markers of response to therapy are needed. Here, we aim to identify tumor-based genomic markers of response to VEGF TT to optimize treatment selection. Methods From an institutional database, primary tumor tissue was obtained from 79 patients with clear cell mRCC, and targeted sequencing was performed. Clinical outcomes were obtained retrospectively. Progression-free survival (PFS) on first-line VEGF TT was correlated to genomic alterations (GAs) using Kaplan-Meier methodology and Cox proportional hazard models. A composite model of significant GAs predicting PFS in the first-line setting was developed. Results Absence of VHL mutation was associated with inferior PFS on first-line VEGF TT. A trend for inferior PFS was observed with GAs in TP53 and FLT1 C/C variant. A composite model of these 3 GAs was associated with inferior PFS in a dose-dependent manner. Conclusion In mRCC, a composite model of TP53 mutation, wild type VHL, and FLT1 C/C variant strongly predicted PFS on first-line VEGF TT in a dose-dependent manner. These findings require external validation.
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Affiliation(s)
- David D. Stenehjem
- College of Pharmacy, University of Minnesota, Duluth, MN, United States of America
| | - Andrew W. Hahn
- Department of Internal Medicine, Division of Medical Oncology, University of Utah Huntsman Cancer Institute, Salt Lake City, UT, United States of America
| | - David M. Gill
- Department of Internal Medicine, Division of Medical Oncology, University of Utah Huntsman Cancer Institute, Salt Lake City, UT, United States of America
| | - Daniel Albertson
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, UT, United States of America
| | | | - Joseph Merriman
- Department of Internal Medicine, Division of Medical Oncology, University of Utah Huntsman Cancer Institute, Salt Lake City, UT, United States of America
| | - Archana M. Agarwal
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, UT, United States of America
| | - Venkata Thodima
- Cancer Genetics Inc., Rutherford, NJ, United States of America
| | - Erik B. Harrington
- Pharmacotherapy Outcomes Research Center (PORC), College of Pharmacy, University of Utah, Salt Lake City, UT, United States of America
| | - Trang H. Au
- Pharmacotherapy Outcomes Research Center (PORC), College of Pharmacy, University of Utah, Salt Lake City, UT, United States of America
| | - Benjamin L. Maughan
- Department of Internal Medicine, Division of Medical Oncology, University of Utah Huntsman Cancer Institute, Salt Lake City, UT, United States of America
| | - Jane Houldsworth
- Cancer Genetics Inc., Rutherford, NJ, United States of America
- Department of Pathology, Mount Sinai School of Medicine, New York City, NY, United States of America
| | - Sumanta K. Pal
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, United States of America
| | - Neeraj Agarwal
- Department of Internal Medicine, Division of Medical Oncology, University of Utah Huntsman Cancer Institute, Salt Lake City, UT, United States of America
- * E-mail:
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473
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Elias R, Sharma A, Singla N, Brugarolas J. Next Generation Sequencing in Renal Cell Carcinoma: Towards Precision Medicine. KIDNEY CANCER JOURNAL : OFFICIAL JOURNAL OF THE KIDNEY CANCER ASSOCIATION 2019; 17:94-104. [PMID: 32206160 PMCID: PMC7089604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Roy Elias
- Department of Internal Medicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas TX, 75390
- Department of Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas TX, 75390
| | - Akanksha Sharma
- Department of Internal Medicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas TX, 75390
| | - Nirmish Singla
- Department of Urology, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas TX, 75390
| | - James Brugarolas
- Department of Internal Medicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas TX, 75390
- Department of Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas TX, 75390
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474
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Shapiro DD, Abel EJ. Predicting aggressive behavior in small renal tumors prior to treatment. ANNALS OF TRANSLATIONAL MEDICINE 2018; 6:S132. [PMID: 30740453 DOI: 10.21037/atm.2018.12.46] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Daniel D Shapiro
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - E Jason Abel
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
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475
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Chen Q, Cheng L, Li Q. The molecular characterization and therapeutic strategies of papillary renal cell carcinoma. Expert Rev Anticancer Ther 2018; 19:169-175. [PMID: 30474436 DOI: 10.1080/14737140.2019.1548939] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Introduction: Papillary renal cell carcinoma (pRCC) is an important subtype of kidney cancer with a problematic pathological classification and highly variable clinical behavior. In this review, we summarize the current progression on pRCC in molecular level. Our findings highlight the need for molecular markers to accurately subtype pRCC and may lead to the development of more targeted agents and better patient stratification in clinical trials for pRCC. Areas covered: This review highlights the need for molecular markers to accurately subtype PRCC and may lead to the development of more targeted agents and better patient stratification in clinical trials for pRCC. Expert commentary: There are mainly two subtypes of pRCC based on histology. However, little is known about the genetic characterization of the sporadic forms of pRCC and there are currently no standard forms of therapy for patients with advanced disease. Both MET inhibitors and immunotherapy may be effective in advanced pRCC treatment. Therefore, understanding the molecular basis of pRCC and identifying the main goal of treatment is crucial for the selection of the best strategy.
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Affiliation(s)
- Qiwei Chen
- a Department of Urology , First Affiliated Hospital of Dalian Medical University , Dalian , China
| | - Liang Cheng
- b Department of Pathology and Laboratory Medicine , Indiana University School of Medicine , Indianapolis , IN , USA
| | - Quanlin Li
- a Department of Urology , First Affiliated Hospital of Dalian Medical University , Dalian , China
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476
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Hsieh JJ, Le VH, Oyama T, Ricketts CJ, Ho TH, Cheng EH. Chromosome 3p Loss-Orchestrated VHL, HIF, and Epigenetic Deregulation in Clear Cell Renal Cell Carcinoma. J Clin Oncol 2018; 36:JCO2018792549. [PMID: 30372397 PMCID: PMC6299341 DOI: 10.1200/jco.2018.79.2549] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common renal cell carcinoma subtype, and metastatic ccRCC is associated with 5-year survival rates of 10% to 20%. Genetically, ccRCC originates from sequential losses of multiple tumor suppressor genes. Remarkably, chromosome 3p loss occurs in more than 90% of sporadic ccRCCs. This results in concurrent one-copy loss of four tumor suppressor genes that are also mutated individually at high frequency in ccRCC (ie, VHL, 80%; PBRM1, 29% to 46%; BAP1, 6% to 19%; and SETD2, 8% to 30%). Pathogenically, 3p loss probably represents the first genetic event that occurs in sporadic ccRCC and the second genetic event in VHL-mutated hereditary ccRCC. VHL constitutes the substrate recognition module of the VCB-Cul2 E3 ligase that degrades HIF1/2α, whereas PBRM1, BAP1, and SETD2 are epigenetic modulators that regulate gene transcription. Because 3p loss and VHL inactivation are nearly universal truncal events in ccRCC, the resulting HIF1/2 signaling overdrive and accompanied tumor hypervascularization probably underlie the therapeutic benefits observed with vascular endothelial growth factor receptor inhibitors, including sorafenib, sunitinib, pazopanib, axitinib, bevacizumab, cabozantinib, and lenvatinib. Furthermore, recent marked advances in ccRCC genomics, transcriptomics, proteomics, metabolomics, molecular mechanisms, mouse models, prognostic and predictive biomarkers, and clinical trials have rendered invaluable translational insights concerning precision kidney cancer therapeutics. With an armamentarium encompassing 13 drugs that exploit seven unique therapeutic mechanisms (ie, cytokines, vascular endothelial growth factor receptor, mTORC1, cMET/AXL, fibroblast growth factor receptor, programmed cell death-1 and programmed death-ligand 1, and cytotoxic T-cell lymphocyte associated-4) to treat metastatic renal cell carcinoma, one of the imminent clinical questions concerning care of patients with metastatic ccRCC is how a personalized treatment strategy, through rationally combining and sequencing different therapeutic modalities, can be formulated to offer the best clinical outcome for individual patients. Here, we attempt to integrate recent discoveries of immediate translational impacts and discuss future translational challenges and opportunities.
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Affiliation(s)
- James J. Hsieh
- James J. Hsieh, Valerie H. Le, and Toshinao Oyama, Washington University, St Louis, MO; Christopher J. Ricketts, National Institutes of Health, Bethesda, MA; Thai Huu Ho, Mayo Clinic, Phoenix, AZ; and Emily H. Cheng, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Valerie H. Le
- James J. Hsieh, Valerie H. Le, and Toshinao Oyama, Washington University, St Louis, MO; Christopher J. Ricketts, National Institutes of Health, Bethesda, MA; Thai Huu Ho, Mayo Clinic, Phoenix, AZ; and Emily H. Cheng, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Toshinao Oyama
- James J. Hsieh, Valerie H. Le, and Toshinao Oyama, Washington University, St Louis, MO; Christopher J. Ricketts, National Institutes of Health, Bethesda, MA; Thai Huu Ho, Mayo Clinic, Phoenix, AZ; and Emily H. Cheng, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Christopher J. Ricketts
- James J. Hsieh, Valerie H. Le, and Toshinao Oyama, Washington University, St Louis, MO; Christopher J. Ricketts, National Institutes of Health, Bethesda, MA; Thai Huu Ho, Mayo Clinic, Phoenix, AZ; and Emily H. Cheng, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Thai Huu Ho
- James J. Hsieh, Valerie H. Le, and Toshinao Oyama, Washington University, St Louis, MO; Christopher J. Ricketts, National Institutes of Health, Bethesda, MA; Thai Huu Ho, Mayo Clinic, Phoenix, AZ; and Emily H. Cheng, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Emily H. Cheng
- James J. Hsieh, Valerie H. Le, and Toshinao Oyama, Washington University, St Louis, MO; Christopher J. Ricketts, National Institutes of Health, Bethesda, MA; Thai Huu Ho, Mayo Clinic, Phoenix, AZ; and Emily H. Cheng, Memorial Sloan Kettering Cancer Center, New York, NY
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477
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McDermott DF, Carducci M. Progress in Kidney Cancer Outcomes Through Collaboration, Innovation, and Discovery. J Clin Oncol 2018; 36:JCO1801198. [PMID: 30372393 PMCID: PMC6299339 DOI: 10.1200/jco.18.01198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023] Open
Affiliation(s)
- David F. McDermott
- David F. McDermott, Dana-Farber/Harvard Cancer Center, Boston, MA; and Michael Carducci, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD
| | - Michael Carducci
- David F. McDermott, Dana-Farber/Harvard Cancer Center, Boston, MA; and Michael Carducci, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD
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478
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Chitty JL, Filipe EC, Lucas MC, Herrmann D, Cox TR, Timpson P. Recent advances in understanding the complexities of metastasis. F1000Res 2018; 7. [PMID: 30135716 DOI: 10.12688/f1000research.15064.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/24/2018] [Indexed: 12/14/2022] Open
Abstract
Tumour metastasis is a dynamic and systemic process. It is no longer seen as a tumour cell-autonomous program but as a multifaceted and complex series of events, which is influenced by the intrinsic cellular mutational burden of cancer cells and the numerous bidirectional interactions between malignant and non-malignant cells and fine-tuned by the various extrinsic cues of the extracellular matrix. In cancer biology, metastasis as a process is one of the most technically challenging aspects of cancer biology to study. As a result, new platforms and technologies are continually being developed to better understand this process. In this review, we discuss some of the recent advances in metastasis and how the information gleaned is re-shaping our understanding of metastatic dissemination.
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Affiliation(s)
- Jessica L Chitty
- Garvan Institute of Medical Research & the Kinghorn Cancer Centre, Cancer Division, Sydney, NSW, 2010, Australia
| | - Elysse C Filipe
- Garvan Institute of Medical Research & the Kinghorn Cancer Centre, Cancer Division, Sydney, NSW, 2010, Australia
| | - Morghan C Lucas
- Garvan Institute of Medical Research & the Kinghorn Cancer Centre, Cancer Division, Sydney, NSW, 2010, Australia
| | - David Herrmann
- Garvan Institute of Medical Research & the Kinghorn Cancer Centre, Cancer Division, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, NSW , 2010, Australia
| | - Thomas R Cox
- Garvan Institute of Medical Research & the Kinghorn Cancer Centre, Cancer Division, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, NSW , 2010, Australia
| | - Paul Timpson
- Garvan Institute of Medical Research & the Kinghorn Cancer Centre, Cancer Division, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, NSW , 2010, Australia
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479
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Abstract
Renal cell carcinoma (RCC) is the most common kidney cancer and includes several molecular and histological subtypes with different clinical characteristics. While survival rates are high if RCC is diagnosed when still confined to the kidney and treated definitively, there are no specific diagnostic screening tests available and symptoms are rare in early stages of the disease. Management of advanced RCC has changed significantly with the advent of targeted therapies, yet survival is usually increased by months due to acquired resistance to these therapies. DNA methylation, the covalent addition of a methyl group to a cytosine, is essential for normal development and transcriptional regulation, but becomes altered commonly in cancer. These alterations result in broad transcriptional changes, including in tumor suppressor genes. Because DNA methylation is one of the earliest molecular changes in cancer and is both widespread and stable, its role in cancer biology, including RCC, has been extensively studied. In this review, we examine the role of DNA methylation in RCC disease etiology and progression, the preclinical use of DNA methylation alterations as diagnostic, prognostic and predictive biomarkers, and the potential for DNA methylation-directed therapies.
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Affiliation(s)
- Brittany N Lasseigne
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806-2908, USA.
| | - James D Brooks
- Department of Urology, Stanford University Medical Center, 300 Pasteur Drive, Stanford, CA, 94305-5118, USA
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480
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Chitty JL, Filipe EC, Lucas MC, Herrmann D, Cox TR, Timpson P. Recent advances in understanding the complexities of metastasis. F1000Res 2018; 7. [PMID: 30135716 PMCID: PMC6073095 DOI: 10.12688/f1000research.15064.2] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/05/2018] [Indexed: 12/14/2022] Open
Abstract
Tumour metastasis is a dynamic and systemic process. It is no longer seen as a tumour cell-autonomous program but as a multifaceted and complex series of events, which is influenced by the intrinsic cellular mutational burden of cancer cells and the numerous bidirectional interactions between malignant and non-malignant cells and fine-tuned by the various extrinsic cues of the extracellular matrix. In cancer biology, metastasis as a process is one of the most technically challenging aspects of cancer biology to study. As a result, new platforms and technologies are continually being developed to better understand this process. In this review, we discuss some of the recent advances in metastasis and how the information gleaned is re-shaping our understanding of metastatic dissemination.
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Affiliation(s)
- Jessica L Chitty
- Garvan Institute of Medical Research & the Kinghorn Cancer Centre, Cancer Division, Sydney, NSW, 2010, Australia
| | - Elysse C Filipe
- Garvan Institute of Medical Research & the Kinghorn Cancer Centre, Cancer Division, Sydney, NSW, 2010, Australia
| | - Morghan C Lucas
- Garvan Institute of Medical Research & the Kinghorn Cancer Centre, Cancer Division, Sydney, NSW, 2010, Australia
| | - David Herrmann
- Garvan Institute of Medical Research & the Kinghorn Cancer Centre, Cancer Division, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, NSW , 2010, Australia
| | - Thomas R Cox
- Garvan Institute of Medical Research & the Kinghorn Cancer Centre, Cancer Division, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, NSW , 2010, Australia
| | - Paul Timpson
- Garvan Institute of Medical Research & the Kinghorn Cancer Centre, Cancer Division, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, NSW , 2010, Australia
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481
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Lindgren D, Sjölund J, Axelson H. Tracing Renal Cell Carcinomas back to the Nephron. Trends Cancer 2018; 4:472-484. [DOI: 10.1016/j.trecan.2018.05.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 11/25/2022]
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482
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Hoadley KA, Yau C, Hinoue T, Wolf DM, Lazar AJ, Drill E, Shen R, Taylor AM, Cherniack AD, Thorsson V, Akbani R, Bowlby R, Wong CK, Wiznerowicz M, Sanchez-Vega F, Robertson AG, Schneider BG, Lawrence MS, Noushmehr H, Malta TM, Stuart JM, Benz CC, Laird PW. Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. Cell 2018; 173:291-304.e6. [PMID: 29625048 PMCID: PMC5957518 DOI: 10.1016/j.cell.2018.03.022] [Citation(s) in RCA: 1399] [Impact Index Per Article: 233.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 02/12/2018] [Accepted: 03/08/2018] [Indexed: 02/07/2023]
Abstract
We conducted comprehensive integrative molecular analyses of the complete set of tumors in The Cancer Genome Atlas (TCGA), consisting of approximately 10,000 specimens and representing 33 types of cancer. We performed molecular clustering using data on chromosome-arm-level aneuploidy, DNA hypermethylation, mRNA, and miRNA expression levels and reverse-phase protein arrays, of which all, except for aneuploidy, revealed clustering primarily organized by histology, tissue type, or anatomic origin. The influence of cell type was evident in DNA-methylation-based clustering, even after excluding sites with known preexisting tissue-type-specific methylation. Integrative clustering further emphasized the dominant role of cell-of-origin patterns. Molecular similarities among histologically or anatomically related cancer types provide a basis for focused pan-cancer analyses, such as pan-gastrointestinal, pan-gynecological, pan-kidney, and pan-squamous cancers, and those related by stemness features, which in turn may inform strategies for future therapeutic development.
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Affiliation(s)
- Katherine A Hoadley
- Department of Genetics, Lineberger Comprehensive Cancer Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Christina Yau
- Buck Institute for Research on Aging, Novato, CA 94945, USA; Department of Surgery, University of California, San Francisco, San Francisco, CA 94115, USA
| | | | - Denise M Wolf
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Alexander J Lazar
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Esther Drill
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ronglai Shen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alison M Taylor
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Andrew D Cherniack
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Rehan Akbani
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Christopher K Wong
- Department of Biomolecular Engineering, Center for Biomolecular Sciences and Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Maciej Wiznerowicz
- Poznań University of Medical Sciences, 61-701 Poznań, Poland; Greater Poland Cancer Centre, 61-866 Poznań, Poland; International Institute for Molecular Oncology, 60-203 Poznań, Poland
| | - Francisco Sanchez-Vega
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - A Gordon Robertson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Barbara G Schneider
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Michael S Lawrence
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Massachusetts General Hospital Cancer Center and Department of Pathology, Harvard Medical School, Charlestown, MA 02129, USA
| | - Houtan Noushmehr
- Department of Neurosurgery, Henry Ford Health System, Detroit, MI 48202, USA; Department of Genetics, University of Sao Paulo, Ribeirao Preto, SP, 14049-900, Brazil
| | - Tathiane M Malta
- Department of Neurosurgery, Henry Ford Health System, Detroit, MI 48202, USA; Department of Genetics, University of Sao Paulo, Ribeirao Preto, SP, 14049-900, Brazil
| | - Joshua M Stuart
- Department of Biomolecular Engineering, Center for Biomolecular Sciences and Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Peter W Laird
- Van Andel Research Institute, Grand Rapids, MI 49503, USA.
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