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Wei EY, Chen YB, Hsieh JJ. Genomic characterisation of two cancers of unknown primary cases supports a kidney cancer origin. BMJ Case Rep 2015; 2015:bcr-2015-212685. [PMID: 26494726 DOI: 10.1136/bcr-2015-212685] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Cancer of unknown primary (CUP) comprises of 3-5% of new cancer diagnoses in the USA. Diagnostic work up typically includes CT of the chest, abdomen and pelvis, and histopathological review of tissue specimens. These measures are neither sensitive nor specific in determining tissue of origin (ToO) of primary tumours and, therefore, are unable to guide therapy. We present two cases of CUP for which we utilised ultra-deep genomic sequencing to identify the candidate ToO and to propose treatment. Patient 1 presented with metastases involving the lung, lymph nodes and bone. Patient 2 presented with an acute pathological fracture of the T7 vertebral body and metastases involving the bone, lymph nodes and soft tissue. No primary renal mass was found. Sequencing revealed SETD2 and NF2 mutations, and heterozygous loss of the short arm of chromosome 3 (3p). Mutations in conjunction with clinicopathological features strongly support a diagnosis of renal cell carcinoma. Both patients initially responded to mTORC1 inhibition therapy.
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Affiliation(s)
- Elizabeth Y Wei
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ying-Bei Chen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - James J Hsieh
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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152
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Waclaw B, Bozic I, Pittman ME, Hruban RH, Vogelstein B, Nowak MA. A spatial model predicts that dispersal and cell turnover limit intratumour heterogeneity. Nature 2015; 525:261-4. [PMID: 26308893 PMCID: PMC4782800 DOI: 10.1038/nature14971] [Citation(s) in RCA: 327] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 07/23/2015] [Indexed: 01/01/2023]
Abstract
Most cancers in humans are large, measuring centimetres in diameter, and composed of many billions of cells. An equivalent mass of normal cells would be highly heterogeneous as a result of the mutations that occur during each cell division. What is remarkable about cancers is that virtually every neoplastic cell within a large tumour often contains the same core set of genetic alterations, with heterogeneity confined to mutations that emerge late during tumour growth. How such alterations expand within the spatially constrained three-dimensional architecture of a tumour, and come to dominate a large, pre-existing lesion, has been unclear. Here we describe a model for tumour evolution that shows how short-range dispersal and cell turnover can account for rapid cell mixing inside the tumour. We show that even a small selective advantage of a single cell within a large tumour allows the descendants of that cell to replace the precursor mass in a clinically relevant time frame. We also demonstrate that the same mechanisms can be responsible for the rapid onset of resistance to chemotherapy. Our model not only provides insights into spatial and temporal aspects of tumour growth, but also suggests that targeting short-range cellular migratory activity could have marked effects on tumour growth rates.
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Affiliation(s)
- Bartlomiej Waclaw
- School of Physics and Astronomy, University of Edinburgh, JCMB, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Ivana Bozic
- Program for Evolutionary Dynamics, Harvard University, One Brattle Square, Cambridge, Massachusetts 02138, USA
- Department of Mathematics, Harvard University, One Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Meredith E Pittman
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, 401 North Broadway, Weinberg 2242, Baltimore, Maryland 21231, USA
| | - Ralph H Hruban
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, 401 North Broadway, Weinberg 2242, Baltimore, Maryland 21231, USA
| | - Bert Vogelstein
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, 401 North Broadway, Weinberg 2242, Baltimore, Maryland 21231, USA
- Ludwig Center and Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, 1650 Orleans Street, Baltimore, Maryland 21287, USA
| | - Martin A Nowak
- Program for Evolutionary Dynamics, Harvard University, One Brattle Square, Cambridge, Massachusetts 02138, USA
- Department of Mathematics, Harvard University, One Oxford Street, Cambridge, Massachusetts 02138, USA
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, Massachusetts 02138, USA
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153
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Abstract
Tumor heterogeneity is the topic de jour, partly because molecular biologists and researchers are identifying it using sophisticated gene/DNA analysis techniques. Clinicians and pathologists are well acquainted with marked variability in clinical presentations, tumor histology, and, more importantly, clinical outcomes of their patients. In this review, we address these issues head-on and document that tumor heterogeneity is an old friend (or, more correctly, a foe). We described heterogeneity that exists at all levels—clinical, histologic, and molecular—and briefly outline the strategies that have been used by clinicians and pathologists to tackle this complicated issue.
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154
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Soultati A, Stares M, Swanton C, Larkin J, Turajlic S. How should clinicians address intratumour heterogeneity in clear cell renal cell carcinoma? Curr Opin Urol 2015; 25:358-66. [PMID: 26125509 DOI: 10.1097/mou.0000000000000204] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PURPOSE OF REVIEW Despite the availability of multiple targeted therapies, the 5-year survival rate of patients with metastatic clear cell renal cell carcinoma (ccRCC) rarely exceeds 10%. Recent insights into the mutational landscape and evolutionary dynamics of ccRCC have offered up a plausible explanation for these outcomes. The purpose of this review is to link the research findings to potential changes in clinical practice. RECENT FINDINGS Intratumour heterogeneity (ITH) dominates the evolutionary landscape in ccRCC at the genetic, transcriptomic and proteomic level. Spatial and temporal separation of tumour subclones within the primary tumour as well as between primary and metastatic sites has been demonstrated at single nucleotide resolution. In the cases analysed to date, approximately two-thirds of somatic mutations are not shared between multiple biopsies from the same primary tumour. Very few of the key disease-driving events are shared across all primary tumour regions (with the exception of VHL and loss of chromosome 3p), whereas the majority are restricted to one or more tumour regions (TP53, SETD2, BAP1, PTEN, mTOR, PIK3CA and KDM5C). SUMMARY ITH must be considered in the management of ccRCC with respect to diagnostic procedures, prognostic and predictive biomarkers and drug development.
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Affiliation(s)
- Aspasia Soultati
- aGuys and St Thomas NHS Foundation Trust bThe Francis Crick Institute, 44 Lincoln's Inn Fields, London cUCL Cancer Institute, CRUK Lung Cancer Centre of Excellence, Huntley Street dRenal Unit, The Royal Marsden Hospital, London, UK
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155
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Pal SK, Singh P, Vogelzang NJ. PD-1/PD-L1 in Renal Cell Carcinoma: Projecting the Way Forward. Clin Genitourin Cancer 2015; 13:257-260. [DOI: 10.1016/j.clgc.2014.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/08/2014] [Accepted: 07/08/2014] [Indexed: 12/01/2022]
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156
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Ali SM, Stephens PJ, Miller VA, Ross JS, Pal SK. Selective Response to Mammalian Target of Rapamycin Inhibition in a Patient with Metastatic Renal Cell Carcinoma Bearing TSC1 Mutation. Eur Urol 2015; 68:341-3. [DOI: 10.1016/j.eururo.2015.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 03/03/2015] [Indexed: 10/23/2022]
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157
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Bodnar L, Stec R, Cierniak S, Synowiec A, Wcisło G, Jesiotr M, Koktysz R, Kozłowski W, Szczylik C. Clinical usefulness of PI3K/Akt/mTOR genotyping in companion with other clinical variables in metastatic renal cell carcinoma patients treated with everolimus in the second and subsequent lines. Ann Oncol 2015; 26:1385-9. [DOI: 10.1093/annonc/mdv166] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/18/2015] [Indexed: 02/03/2023] Open
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158
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159
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Sankin A, Hakimi AA, Hsieh JJ, Molina AM. Metastatic non-clear cell renal cell carcinoma: an evidence based review of current treatment strategies. Front Oncol 2015; 5:67. [PMID: 25905038 PMCID: PMC4389537 DOI: 10.3389/fonc.2015.00067] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 03/05/2015] [Indexed: 12/17/2022] Open
Abstract
Much progress has been made in the treatment of metastatic renal cell carcinoma (RCC) over the last decade, with the development of agents that block the vascular endothelial growth factor (VEGF) pathway or the mammalian target of rapamycin (mTOR) pathway. The incorporation of these agents into treatment algorithms has been the result of carefully conducted clinical trials leading to Food and Drug Administration (FDA) approval and subsequent adoption as the current standard of care. These trials, however, were dominated by patients with clear cell renal cell carcinoma (ccRCC), and little data are currently available on the treatment of non-clear cell renal cell carcinoma (nccRCC). nccRCC encompasses a biologically heterogeneous group of kidney tumors that portend very diverse prognoses and responses to therapy. This review is a pathway based approach that highlights the current systemic treatment strategies for metastatic nccRCC.
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Affiliation(s)
| | - A. Ari Hakimi
- Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - James J. Hsieh
- Memorial Sloan-Kettering Cancer Center, New York, NY, USA
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160
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Turajlic S, McGranahan N, Swanton C. Inferring mutational timing and reconstructing tumour evolutionary histories. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1855:264-75. [PMID: 25827356 DOI: 10.1016/j.bbcan.2015.03.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 03/17/2015] [Accepted: 03/19/2015] [Indexed: 12/28/2022]
Abstract
Cancer evolution can be considered within a Darwinian framework. Both micro and macro-evolutionary theories can be applied to understand tumour progression and treatment failure. Owing to cancers' complexity and heterogeneity the rules of tumour evolution, such as the role of selection, remain incompletely understood. The timing of mutational events during tumour evolution presents diagnostic, prognostic and therapeutic opportunities. Here we review the current sampling and computational approaches for inferring mutational timing and the evidence from next generation sequencing-informed data on mutational timing across all tumour types. We discuss how this knowledge can be used to illuminate the genes and pathways that drive cancer initiation and relapse; and to support drug development and clinical trial design.
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Affiliation(s)
- Samra Turajlic
- The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | | | - Charles Swanton
- The Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK; UCL Cancer Institute, CRUK Lung Cancer Centre of Excellence, Huntley Street, WC1E 6DD, UK.
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161
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Huynh H, Hao HX, Chan SL, Chen D, Ong R, Soo KC, Pochanard P, Yang D, Ruddy D, Liu M, Derti A, Balak MN, Palmer MR, Wang Y, Lee BH, Sellami D, Zhu AX, Schlegel R, Huang A. Loss of Tuberous Sclerosis Complex 2 (TSC2) Is Frequent in Hepatocellular Carcinoma and Predicts Response to mTORC1 Inhibitor Everolimus. Mol Cancer Ther 2015; 14:1224-35. [PMID: 25724664 DOI: 10.1158/1535-7163.mct-14-0768] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/17/2015] [Indexed: 11/16/2022]
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer deaths worldwide and hyperactivation of mTOR signaling plays a pivotal role in HCC tumorigenesis. Tuberous sclerosis complex (TSC), a heterodimer of TSC1 and TSC2, functions as a negative regulator of mTOR signaling. In the current study, we discovered that TSC2 loss-of-function is common in HCC. TSC2 loss was found in 4 of 8 HCC cell lines and 8 of 28 (28.6%) patient-derived HCC xenografts. TSC2 mutations and deletions are likely to be the underlying cause of TSC2 loss in HCC cell lines, xenografts, and primary tumors for most cases. We further demonstrated that TSC2-null HCC cell lines and xenografts had elevated mTOR signaling and, more importantly, were significantly more sensitive to RAD001/everolimus, an mTORC1 inhibitor. These preclinical findings led to the analysis of TSC2 status in HCC samples collected in the EVOLVE-1 clinical trial of everolimus using an optimized immunohistochemistry assay and identified 15 of 139 (10.8%) samples with low to undetectable levels of TSC2. Although the sample size is too small for formal statistical analysis, TSC2-null/low tumor patients who received everolimus tended to have longer overall survival than those who received placebo. Finally, we performed an epidemiology survey of more than 239 Asian HCC tumors and found the frequency of TSC2 loss to be approximately 20% in Asian HBV(+) HCC. Taken together, our data strongly argue that TSC2 loss is a predictive biomarker for the response to everolimus in HCC patients.
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Affiliation(s)
- Hung Huynh
- Laboratory of Molecular Endocrinology, Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre, Singapore.
| | - Huai-Xiang Hao
- Oncology Translational Medicine, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Stephen L Chan
- State Key Laboratory in Oncology in South China, Department of Clinical Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, PR China
| | - David Chen
- Oncology Global Development, Novartis Pharmaceuticals Corporation, East Hanover, New Jersey
| | - Richard Ong
- Laboratory of Molecular Endocrinology, Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre, Singapore
| | - Khee Chee Soo
- Laboratory of Molecular Endocrinology, Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre, Singapore
| | - Panisa Pochanard
- Oncology Translational Medicine, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - David Yang
- Oncology Translational Medicine, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - David Ruddy
- Oncology Translational Medicine, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Manway Liu
- Oncology Translational Medicine, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Adnan Derti
- Oncology Translational Medicine, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Marissa N Balak
- Oncology Translational Medicine, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Michael R Palmer
- Oncology Translational Medicine, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Yan Wang
- Oncology Translational Medicine, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Benjamin H Lee
- Oncology Translational Medicine, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Dalila Sellami
- Oncology Global Development, Novartis Pharmaceuticals Corporation, East Hanover, New Jersey
| | - Andrew X Zhu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Robert Schlegel
- Oncology Translational Medicine, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Alan Huang
- Oncology Translational Medicine, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts.
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162
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163
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Biomarkers for Renal Cell Carcinoma. KIDNEY CANCER 2015. [DOI: 10.1007/978-3-319-17903-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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164
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Affiliation(s)
- David J Kwiatkowski
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, United States ; Dana Farber Cancer Institute, Boston, MA 02115, United States ; Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
| | - Nikhil Wagle
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, United States ; Dana Farber Cancer Institute, Boston, MA 02115, United States ; Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
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165
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Incorporation of biomarkers in phase II studies of recurrent glioblastoma. Tumour Biol 2014; 36:153-62. [PMID: 25534238 DOI: 10.1007/s13277-014-2960-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 12/05/2014] [Indexed: 01/15/2023] Open
Abstract
The survival trends for glioblastoma (GBM) patients have remained largely static, reflecting a lack of improvement in the therapeutic options for patients. Less than 5 % of newly diagnosed GBM survives more than 5 years. Tumor relapse is nearly universal and the majority of patients do not respond to further systemic therapy. The results from phase II studies conducted with recurrent GBM patients have not translated to successful confirmatory studies and thus we have reached a significant roadblock in the development of new treatments for patients with recurrent GBM. The development of new, active, and potentially targeted drugs for the treatment of recurrent GBM represents a major unmet need. The incorporation of diagnostic/companion biomarker combinations into the phase II studies and appropriate stratification of the patients is lagging significantly behind other larger cancer groups such as breast, non-small cell lung cancer, and melanoma. We herein carried out a systematic review of the phase II clinical studies conducted in patients with recurrent GBM (2010-2013 inclusive) to assess the degree of biomarker incorporation within the clinical trial design.
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166
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Grünwald V, Keilholz U, Boehm A, Guntinas-Lichius O, Hennemann B, Schmoll HJ, Ivanyi P, Abbas M, Lehmann U, Koch A, Karch A, Zörner A, Gauler TC. TEMHEAD: a single-arm multicentre phase II study of temsirolimus in platin- and cetuximab refractory recurrent and/or metastatic squamous cell carcinoma of the head and neck (SCCHN) of the German SCCHN Group (AIO). Ann Oncol 2014; 26:561-7. [PMID: 25527417 DOI: 10.1093/annonc/mdu571] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Squamous cell carcinoma of the head and neck (SCCHN) is a common disease, which has a poor prognosis after failure of therapy. Activation of the PI3K-AKT-mTOR axis is commonly detected in recurrent or metastatic SCCHN, and provided the rationale for the clinical phase II trial in pretreated SCCHN. PATIENTS AND METHODS The primary end point was the progression-free survival rate (PFR) at 12 weeks. Forty eligible patients have been recruited after failure of platinum chemotherapy and cetuximab. A preplanned futility analysis was successfully passed after ≥1 success was detected in 20 patients. Secondary objectives consisted of progression-free survival (PFS), disease control rate (DCR), overall survival (OS), safety and tolerability, and predictive biomarkers for KRAS, BRAF, PIK3CA mutations, and HPV status. Archived tumor tissue was analyzed for DNA sequence. RESULTS A total of 40 patients were eligible. The PFR at 12 weeks was 40% (95% CI 25.0-54.6). The median PFS and OS were 56 days (95% CI 36-113 days) and 152 days (76-256 days), respectively. In 33 assessable patients, disease stabilization occurred in 57.6%, with tumor shrinkage in 13 patients (39.4%). Overall, the treatment was well tolerated. Fatigue (47.5%), anemia (25.0%), nausea (20.0%), and pneumonia (20.0%) were the most common adverse events. Neither PIK3CA mutations, nor HPV status were predictive for success with temsirolimus treatment. No mutations were found for KRAS or BRAF. CONCLUSION Tumor shrinkage and efficacy parameter indicate that inhibition of the PI3K-AKT-mTOR axis was a putative novel treatment paradigm for SCCHN. We could not identify parameters predictive for treatment success of temsirolimus, which underscores the need for refinement of the molecular analysis in future studies. CLINICAL TRIALS NUMBER NCT01172769.
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Affiliation(s)
- V Grünwald
- Clinic for Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover
| | - U Keilholz
- Charité Comprehensive Cancer Center, Berlin
| | - A Boehm
- Clinic and Policlinic for Ear, Nose and Throat, University Hospital, Leipzig
| | | | - B Hennemann
- Department for Hematology and Oncology, Ev. Bethesda- Johanniter Hospital, Duisburg
| | - H J Schmoll
- Clinic for Internal Medicine IV, University Hospital, Halle
| | - P Ivanyi
- Clinic for Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover
| | | | | | | | | | - A Zörner
- Clinical Pharmacology, Hannover Medical School, Hannover
| | - T C Gauler
- West-German Cancer Center, University Hospital, Essen, Germany
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167
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Yalniz Z, Tigli H, Tigli H, Sanli O, Dalay N, Buyru N. Novel mutations and role of the LKB1 gene as a tumor suppressor in renal cell carcinoma. Tumour Biol 2014; 35:12361-8. [DOI: 10.1007/s13277-014-2550-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 08/25/2014] [Indexed: 01/10/2023] Open
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168
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Brannon AR, Vakiani E, Sylvester BE, Scott SN, McDermott G, Shah RH, Kania K, Viale A, Oschwald DM, Vacic V, Emde AK, Cercek A, Yaeger R, Kemeny NE, Saltz LB, Shia J, D'Angelica MI, Weiser MR, Solit DB, Berger MF. Comparative sequencing analysis reveals high genomic concordance between matched primary and metastatic colorectal cancer lesions. Genome Biol 2014; 15:454. [PMID: 25164765 PMCID: PMC4189196 DOI: 10.1186/s13059-014-0454-7] [Citation(s) in RCA: 270] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 08/22/2014] [Indexed: 12/14/2022] Open
Abstract
Background Colorectal cancer is the second leading cause of cancer death in the United States, with over 50,000 deaths estimated in 2014. Molecular profiling for somatic mutations that predict absence of response to anti-EGFR therapy has become standard practice in the treatment of metastatic colorectal cancer; however, the quantity and type of tissue available for testing is frequently limited. Further, the degree to which the primary tumor is a faithful representation of metastatic disease has been questioned. As next-generation sequencing technology becomes more widely available for clinical use and additional molecularly targeted agents are considered as treatment options in colorectal cancer, it is important to characterize the extent of tumor heterogeneity between primary and metastatic tumors. Results We performed deep coverage, targeted next-generation sequencing of 230 key cancer-associated genes for 69 matched primary and metastatic tumors and normal tissue. Mutation profiles were 100% concordant for KRAS, NRAS, and BRAF, and were highly concordant for recurrent alterations in colorectal cancer. Additionally, whole genome sequencing of four patient trios did not reveal any additional site-specific targetable alterations. Conclusions Colorectal cancer primary tumors and metastases exhibit high genomic concordance. As current clinical practices in colorectal cancer revolve around KRAS, NRAS, and BRAF mutation status, diagnostic sequencing of either primary or metastatic tissue as available is acceptable for most patients. Additionally, consistency between targeted sequencing and whole genome sequencing results suggests that targeted sequencing may be a suitable strategy for clinical diagnostic applications. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0454-7) contains supplementary material, which is available to authorized users.
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169
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Fisher R, Horswell S, Rowan A, Salm MP, de Bruin EC, Gulati S, McGranahan N, Stares M, Gerlinger M, Varela I, Crockford A, Favero F, Quidville V, André F, Navas C, Grönroos E, Nicol D, Hazell S, Hrouda D, O’Brien T, Matthews N, Phillimore B, Begum S, Rabinowitz A, Biggs J, Bates PA, McDonald NQ, Stamp G, Spencer-Dene B, Hsieh JJ, Xu J, Pickering L, Gore M, Larkin J, Swanton C. Development of synchronous VHL syndrome tumors reveals contingencies and constraints to tumor evolution. Genome Biol 2014; 15:433. [PMID: 25159823 PMCID: PMC4166471 DOI: 10.1186/s13059-014-0433-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 08/08/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Genomic analysis of multi-focal renal cell carcinomas from an individual with a germline VHL mutation offers a unique opportunity to study tumor evolution. RESULTS We perform whole exome sequencing on four clear cell renal cell carcinomas removed from both kidneys of a patient with a germline VHL mutation. We report that tumors arising in this context are clonally independent and harbour distinct secondary events exemplified by loss of chromosome 3p, despite an identical genetic background and tissue microenvironment. We propose that divergent mutational and copy number anomalies are contingent upon the nature of 3p loss of heterozygosity occurring early in tumorigenesis. However, despite distinct 3p events, genomic, proteomic and immunohistochemical analyses reveal evidence for convergence upon the PI3K-AKT-mTOR signaling pathway. Four germline tumors in this young patient, and in a second, older patient with VHL syndrome demonstrate minimal intra-tumor heterogeneity and mutational burden, and evaluable tumors appear to follow a linear evolutionary route, compared to tumors from patients with sporadic clear cell renal cell carcinoma. CONCLUSIONS In tumors developing from a germline VHL mutation, the evolutionary principles of contingency and convergence in tumor development are complementary. In this small set of patients with early stage VHL-associated tumors, there is reduced mutation burden and limited evidence of intra-tumor heterogeneity.
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Affiliation(s)
- Rosalie Fisher
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
- />Royal Marsden NHS Foundation Trust, London, SW3 6JJ UK
| | - Stuart Horswell
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | - Andrew Rowan
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | | | - Elza C de Bruin
- />University College London Cancer Institute, London, WC1E 6DD UK
| | - Sakshi Gulati
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | - Nicholas McGranahan
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
- />Centre for Mathematics & Physics in the Life Science & Experimental Biology (CoMPLEX), University College London, London, WC1E 6BT UK
| | - Mark Stares
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
- />Royal Marsden NHS Foundation Trust, London, SW3 6JJ UK
| | - Marco Gerlinger
- />Centre for Evolution and Cancer, Institute of Cancer Research, London, SW7 3RP UK
| | - Ignacio Varela
- />Instituto de Biomedicina y Biotecnología de Cantabria (CSIC-UC-Sodercan), Departamento de Biología Molecular, Universidad de Cantabria, Santander, 39011 Spain
| | - Andrew Crockford
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | - Francesco Favero
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
- />Cancer System Biology, Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, DK-2800 Denmark
| | | | | | - Carolina Navas
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | - Eva Grönroos
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | - David Nicol
- />Royal Marsden NHS Foundation Trust, London, SW3 6JJ UK
| | - Steve Hazell
- />Royal Marsden NHS Foundation Trust, London, SW3 6JJ UK
| | - David Hrouda
- />Imperial College Healthcare NHS Trust, London, W6 8RF UK
| | - Tim O’Brien
- />Guy’s and St Thomas’ NHS Foundation Trust, London, SE1 9RT UK
| | - Nik Matthews
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | - Ben Phillimore
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | - Sharmin Begum
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | - Adam Rabinowitz
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | - Jennifer Biggs
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | - Paul A Bates
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | - Neil Q McDonald
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | - Gordon Stamp
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
| | | | - James J Hsieh
- />Department of Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, 10065 USA
| | - Jianing Xu
- />Department of Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, 10065 USA
| | - Lisa Pickering
- />Royal Marsden NHS Foundation Trust, London, SW3 6JJ UK
| | - Martin Gore
- />Royal Marsden NHS Foundation Trust, London, SW3 6JJ UK
| | - James Larkin
- />Royal Marsden NHS Foundation Trust, London, SW3 6JJ UK
| | - Charles Swanton
- />Cancer Research UK London Research Institute, London, WC2A 3LY UK
- />University College London Cancer Institute, London, WC1E 6DD UK
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170
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Intlekofer AM, Younes A. Precision therapy for lymphoma--current state and future directions. Nat Rev Clin Oncol 2014; 11:585-96. [PMID: 25135367 DOI: 10.1038/nrclinonc.2014.137] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Modern advances in genomics and cancer biology have produced an unprecedented body of knowledge regarding the molecular pathogenesis of lymphoma. The diverse histological subtypes of lymphoma are molecularly heterogeneous, and most likely arise from distinct oncogenic mechanisms. In parallel to these advances in lymphoma biology, several new classes of molecularly targeted agents have been developed with varying degrees of efficacy across the different types of lymphoma. In general, the development of new drugs for treating lymphoma has been mostly empiric, with a limited knowledge of the molecular target, its involvement in the disease, and the effect of the drug on the target. Thus, the variability observed in clinical responses likely results from underlying molecular heterogeneity. In the era of personalized medicine, the challenge for the treatment of patients with lymphoma will involve correctly matching a molecularly targeted therapy to the unique genetic and molecular composition of each individual lymphoma. In this Review, we discuss current and emerging biomarkers that can guide treatment decisions for patients with lymphoma, and explore the potential challenges and strategies for making biomarker-driven personalized medicine a reality in the cure and management of this disease.
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Affiliation(s)
- Andrew M Intlekofer
- Lymphoma Service, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 330, New York, NY 10065, USA
| | - Anas Younes
- Lymphoma Service, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 330, New York, NY 10065, USA
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171
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Sankin A, Hakimi AA, Mikkilineni N, Ostrovnaya I, Silk MT, Liang Y, Mano R, Chevinsky M, Motzer RJ, Solomon SB, Cheng EH, Durack JC, Coleman JA, Russo P, Hsieh JJ. The impact of genetic heterogeneity on biomarker development in kidney cancer assessed by multiregional sampling. Cancer Med 2014; 3:1485-92. [PMID: 25124064 PMCID: PMC4298374 DOI: 10.1002/cam4.293] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 05/22/2014] [Accepted: 06/06/2014] [Indexed: 12/12/2022] Open
Abstract
Primary clear cell renal cell carcinoma (ccRCC) genetic heterogeneity may lead to an underestimation of the mutational burden detected from a single site evaluation. We sought to characterize the extent of clonal branching involving key tumor suppressor mutations in primary ccRCC and determine if genetic heterogeneity could limit the mutation profiling from a single region assessment. Ex vivo core needle biopsies were obtained from three to five different regions of resected renal tumors at a single institution from 2012 to 2013. DNA was extracted and targeted sequencing was performed on five genes associated with ccRCC (von-Hippel Lindau [VHL], PBRM1, SETD2, BAP1, and KDM5C). We constructed phylogenetic trees by inferring clonal evolution based on the mutations present within each core and estimated the predictive power of detecting a mutation for each successive tumor region sampled. We obtained 47 ex vivo biopsy cores from 14 primary ccRCC's (median tumor size 4.5 cm, IQR 4.0–5.9 cm). Branching patterns of various complexities were observed in tumors with three or more mutations. A VHL mutation was detected in nine tumors (64%), each time being present ubiquitously throughout the tumor. Other genes had various degrees of regional mutational variation. Based on the mutations' prevalence we estimated that three different tumor regions should be sampled to detect mutations in PBRM1, SETD2, BAP1, and/or KDM5C with 90% certainty. The mutational burden of renal tumors varies by region sampled. Single site assessment of key tumor suppressor mutations in primary ccRCC may not adequately capture the genetic predictors of tumor behavior.
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Affiliation(s)
- Alexander Sankin
- Urology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York City, New York
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172
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Bielecka ZF, Czarnecka AM, Szczylik C. Genomic Analysis as the First Step toward Personalized Treatment in Renal Cell Carcinoma. Front Oncol 2014; 4:194. [PMID: 25120953 PMCID: PMC4110478 DOI: 10.3389/fonc.2014.00194] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 07/09/2014] [Indexed: 12/13/2022] Open
Abstract
Drug resistance mechanisms in renal cell carcinoma (RCC) still remain elusive. Although most patients initially respond to targeted therapy, acquired resistance can still develop eventually. Most of the patients suffer from intrinsic (genetic) resistance as well, suggesting that there is substantial need to broaden our knowledge in the field of RCC genetics. As molecular abnormalities occur for various reasons, ranging from single nucleotide polymorphisms to large chromosomal defects, conducting whole-genome association studies using high-throughput techniques seems inevitable. In principle, data obtained via genome-wide research should be continued and performed on a large scale for the purposes of drug development and identification of biological pathways underlying cancerogenesis. Genetic alterations are mostly unique for each histological RCC subtype. According to recently published data, RCC is a highly heterogeneous tumor. In this paper, the authors discuss the following: (1) current state-of-the-art knowledge on the potential biomarkers of RCC subtypes; (2) significant obstacles encountered in the translational research on RCC; and (3) recent molecular findings that may have a crucial impact on future therapeutic approaches.
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Affiliation(s)
- Zofia Felicja Bielecka
- Department of Oncology with the Laboratory of Molecular Oncology, Military Institute of Medicine , Warsaw , Poland ; Postgraduate School of Molecular Medicine, Medical University of Warsaw , Warsaw , Poland
| | - Anna Małgorzata Czarnecka
- Department of Oncology with the Laboratory of Molecular Oncology, Military Institute of Medicine , Warsaw , Poland
| | - Cezary Szczylik
- Department of Oncology with the Laboratory of Molecular Oncology, Military Institute of Medicine , Warsaw , Poland
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173
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Chism DD, Rathmell WK. Seeing the forest for the trees: kidney oncogenomes in relation to therapeutic outcomes. Clin Cancer Res 2014; 20:1721-3. [PMID: 24634386 DOI: 10.1158/1078-0432.ccr-14-0056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Renal cell carcinoma is a heterogeneous disease, and tissue investigations provide clues that may predict treatment response. Oncogenomic analysis of five outliers, who achieved a sustained response with rapalogs, implicates alterations of the TSC1 and mTOR genes and reveals insights into the conserved evolution of tumors.
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Affiliation(s)
- David D Chism
- Authors' Affiliation: Division of Hematology and Oncology, University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina
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