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Johansen M, Haskell GT, Arreola A, Riordan C, Gadi IK, Penton A, Papenhausen PR, Schwartz S. Prenatal detection of mosaicism for a genome wide uniparental disomy cell line in a cohort of patients: Implications and outcomes. Prenat Diagn 2024; 44:586-594. [PMID: 38558419 DOI: 10.1002/pd.6554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/21/2024] [Accepted: 03/03/2024] [Indexed: 04/04/2024]
Abstract
OBJECTIVES To investigate the prenatal detection rate of mosaicism by SNP microarray analysis, in which an individual has not one, but two, complete genomes (sets of DNA) in their body, a normal biparental line with a Genome Wide Uniparental Disomy (GWUPD) cell line was used. METHODS This study retrospectively examines the prenatal detection of GWUPD in a cohort of ∼90,000 prenatal specimens and ∼20,000 products of conceptions (POCs) that were studied by SNP microarray. RESULTS In total, 25 cases of GWUPD were detected; 16 cases were detected prenatally with GWUPD (∼0.018%) and 9 POCs revealed GWUPD (0.045%). The nine POC specimens presented with placental abnormalities. The 12 amniotic fluid specimens were ascertained because of abnormal ultrasound findings. Nine of 12 pregnancies had findings consistent with Beckwith-Wiedemann syndrome or because of abnormal placentas. However, three pregnancies were detected with GWUPD of maternal origin, with less common findings and demonstrated maternal origin. Four other pregnancies showed GWUPD in a chorionic villus sample, but normal findings in amniotic fluid and apparently normal fetal development. CONCLUSIONS This cohort with GWUPD mosaicism expands our understanding of GWUPD and has implications for prenatal care and counseling. Additional studies are necessary to understand the rarer maternal GWUPD.
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Affiliation(s)
- Margriet Johansen
- Center for Molecular Biology and Pathology, Labcorp, Research Triangle Park, North Carolina, USA
| | - Gloria T Haskell
- Center for Molecular Biology and Pathology, Labcorp, Research Triangle Park, North Carolina, USA
| | - Alexandra Arreola
- Center for Molecular Biology and Pathology, Labcorp, Research Triangle Park, North Carolina, USA
| | - Christine Riordan
- Center for Molecular Biology and Pathology, Labcorp, Research Triangle Park, North Carolina, USA
| | - Inder K Gadi
- Center for Molecular Biology and Pathology, Labcorp, Research Triangle Park, North Carolina, USA
| | - Andrea Penton
- Center for Molecular Biology and Pathology, Labcorp, Research Triangle Park, North Carolina, USA
| | - Peter R Papenhausen
- Center for Molecular Biology and Pathology, Labcorp, Research Triangle Park, North Carolina, USA
- Department of Pathology, The Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Stuart Schwartz
- Center for Molecular Biology and Pathology, Labcorp, Research Triangle Park, North Carolina, USA
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Tepperberg JH, Gadi IK, Arreola A, Papenhausen PR. 49. Cryptic Triple Hit Lymphoma: What's hiding in those chromosomes? A chromosome, FISH and microarray story. Cancer Genet 2021. [DOI: 10.1016/j.cancergen.2021.01.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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3
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Arreola A, Papenhausen PR, Gadi IK, Tepperberg JH, Heym K, Schwartz S. 4. ETV6-ABL1 variant rearrangement described in a childhood ALL patient. Cancer Genet 2021. [DOI: 10.1016/j.cancergen.2021.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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4
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Marchuk DS, Crooks K, Strande N, Kaiser-Rogers K, Milko LV, Brandt A, Arreola A, Tilley CR, Bizon C, Vora NL, Wilhelmsen KC, Evans JP, Berg JS. Increasing the diagnostic yield of exome sequencing by copy number variant analysis. PLoS One 2018; 13:e0209185. [PMID: 30557390 PMCID: PMC6296659 DOI: 10.1371/journal.pone.0209185] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 12/01/2018] [Indexed: 01/17/2023] Open
Abstract
As whole exome sequencing (WES) becomes more widely used in the clinical realm, a wealth of unanalyzed information will be routinely generated. Using WES read depth data to predict copy number variation (CNV) could extend the diagnostic utility of this previously underutilized data by providing clinically important information such as previously unsuspected deletions or duplications. We evaluated ExomeDepth, a free R package, in addition to an aneuploidy prediction method, to detect CNVs in WES data. First, in a blinded pilot study, five out of five genomic alterations were correctly identified from clinical samples with previously defined chromosomal gains or losses, including submicroscopic deletions, duplications, and chromosomal trisomy. We then examined CNV calls among 53 patients participating in the NCGENES research study and undergoing WES, who had existing clinical chromosomal microarray (CMA) data that could be used for validation. For unique CNVs that overlap well with WES coverage regions, sensitivity was 89% for deletions and 65% for duplications. While specificity of the algorithm calls remains a concern, this is less of an issue at high threshold filtering levels. When applied to all 672 patients from the exome sequencing study, ExomeDepth identified eleven diagnostically relevant CNVs ranging in size from a two exon deletion to whole chromosome duplications, as well as numerous other CNVs with varying clinical significance. This opportunistic analysis of WES data yields an additional 1.6% of patients in this study with pathogenic or likely pathogenic CNVs that are clinically relevant to their phenotype as well as clinically relevant secondary findings. Finally, we demonstrate the potential value of copy number analysis in cases where a single heterozygous likely or known pathogenic single nucleotide alteration is identified in a gene associated with an autosomal recessive condition.
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Affiliation(s)
- Daniel S. Marchuk
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
| | - Kristy Crooks
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, United States of America
| | - Natasha Strande
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, United States of America
| | - Kathleen Kaiser-Rogers
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, United States of America
- Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC, United Sates of America
| | - Laura V. Milko
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
| | - Alicia Brandt
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
| | - Alexandra Arreola
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, United States of America
| | - Christian R. Tilley
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
| | - Chris Bizon
- Renaissance Computing Institute, University of North Carolina, Chapel Hill, NC, United States of America
| | - Neeta L. Vora
- Department of Obstetrics and Gynecology, University of North Carolina, Chapel Hill, NC, United States of America
| | - Kirk C. Wilhelmsen
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
- Renaissance Computing Institute, University of North Carolina, Chapel Hill, NC, United States of America
| | - James P. Evans
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
| | - Jonathan S. Berg
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
- * E-mail:
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Arreola A, Payne LB, Julian MH, de Cubas AA, Daniels AB, Taylor S, Zhao H, Darden J, Bautch VL, Rathmell WK, Chappell JC. Von Hippel-Lindau mutations disrupt vascular patterning and maturation via Notch. JCI Insight 2018; 3:92193. [PMID: 29467323 DOI: 10.1172/jci.insight.92193] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 01/18/2018] [Indexed: 12/27/2022] Open
Abstract
Von Hippel-Lindau (VHL) gene mutations induce neural tissue hemangioblastomas, as well as highly vascularized clear cell renal cell carcinomas (ccRCCs). Pathological vessel remodeling arises from misregulation of HIFs and VEGF, among other genes. Variation in disease penetrance has long been recognized in relation to genotype. We show Vhl mutations also disrupt Notch signaling, causing mutation-specific vascular abnormalities, e.g., type 1 (null) vs. type 2B (murine G518A representing human R167Q). In conditional mutation retina vasculature, Vhl-null mutation (i.e., UBCCreER/+Vhlfl/fl) had little effect on initial vessel branching, but it severely reduced arterial and venous branching at later stages. Interestingly, this mutation accelerated arterial maturation, as observed in retina vessel morphology and aberrant α-smooth muscle actin localization, particularly in vascular pericytes. RNA sequencing analysis identified gene expression changes within several key pathways, including Notch and smooth muscle cell contractility. Notch inhibition failed to reverse later-stage branching defects but rescued the accelerated arterialization. Retinal vessels harboring the type 2B Vhl mutation (i.e., UBCCreER/+Vhlfl/2B) displayed stage-specific changes in vessel branching and an advanced progression toward an arterial phenotype. Disrupting Notch signaling in type 2B mutants increased both artery and vein branching and restored arterial maturation toward nonmutant levels. By revealing differential effects of the null and type 2B Vhl mutations on vessel branching and maturation, these data may provide insight into the variability of VHL-associated vascular changes - particularly the heterogeneity and aggressiveness in ccRCC vessel growth - and also suggest Notch pathway targets for treating VHL syndrome.
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Affiliation(s)
- Alexandra Arreola
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, North Carolina, USA
| | | | - Morgan H Julian
- Center for Heart and Regenerative Medicine and.,Department of Basic Science Education, Virginia Tech Carilion School of Medicine and Research Institute, Roanoke, Virginia, USA
| | | | - Anthony B Daniels
- Department of Ophthalmology and Visual Sciences.,Department of Biochemistry.,Department of Radiation Oncology, and.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Huaning Zhao
- Center for Heart and Regenerative Medicine and.,Department of Biomedical Engineering and Mechanics
| | - Jordan Darden
- Center for Heart and Regenerative Medicine and.,Graduate Program in Translational Biology, Medicine, and Health, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Victoria L Bautch
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, North Carolina, USA.,Department of Biology and.,McAllister Heart Institute, UNC-CH, Chapel Hill, North Carolina, USA
| | - W Kimryn Rathmell
- Department of Medicine, Division of Hematology and Oncology.,Department of Biochemistry.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - John C Chappell
- Center for Heart and Regenerative Medicine and.,Department of Basic Science Education, Virginia Tech Carilion School of Medicine and Research Institute, Roanoke, Virginia, USA.,Department of Biomedical Engineering and Mechanics.,Graduate Program in Translational Biology, Medicine, and Health, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
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6
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Couser NL, Marchuk DS, Smith LD, Arreola A, Kaiser-Rogers KA, Muenzer J, Pandya A, Gucsavas-Calikoglu M, Powell CM. Co-occurring Down syndrome and SUCLA2-related mitochondrial depletion syndrome. Am J Med Genet A 2017; 173:2720-2724. [PMID: 28749033 DOI: 10.1002/ajmg.a.38351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 06/09/2017] [Accepted: 06/14/2017] [Indexed: 01/23/2023]
Abstract
Mitochondrial DNA depletion syndrome 5 (MIM 612073) is a rare autosomal recessive disorder caused by homozygous or compound heterozygous pathogenic variants in the beta subunit of the succinate-CoA ligase gene located within the 13q14 band. We describe two siblings of Hispanic descent with SUCLA2-related mitochondrial depletion syndrome (encephalomyopathic form with methylmalonic aciduria); the older sibling is additionally affected with trisomy 21. SUCLA2 sequencing identified homozygous p.Arg284Cys pathogenic variants in both patients. This mutation has previously been identified in four individuals of Italian and Caucasian descent. The older sibling with concomitant disease has a more severe phenotype than what is typically described in patients with either SUCLA2-related mitochondrial depletion syndrome or Down syndrome alone. The younger sibling, who has a normal female chromosome complement, is significantly less affected compared to her brother. While the clinical and molecular findings have been reported in about 50 patients affected with a deficiency of succinate-CoA ligase caused by pathogenic variants in SUCLA2, this report describes the first known individual affected with both a mitochondrial depletion syndrome and trisomy 21.
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Affiliation(s)
- Natario L Couser
- Department of Pediatrics, Division of Genetics and Metabolism, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Ophthalmology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Daniel S Marchuk
- University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Laurie D Smith
- Department of Pediatrics, Division of Genetics and Metabolism, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Alexandra Arreola
- Department of Pathology & Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kathleen A Kaiser-Rogers
- Department of Pediatrics, Division of Genetics and Metabolism, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Pathology & Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Joseph Muenzer
- Department of Pediatrics, Division of Genetics and Metabolism, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Arti Pandya
- Department of Pediatrics, Division of Genetics and Metabolism, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Muge Gucsavas-Calikoglu
- Department of Pediatrics, Division of Genetics and Metabolism, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Cynthia M Powell
- Department of Pediatrics, Division of Genetics and Metabolism, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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7
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Block KI, Gyllenhaal C, Lowe L, Amedei A, Amin ARMR, Amin A, Aquilano K, Arbiser J, Arreola A, Arzumanyan A, Ashraf SS, Azmi AS, Benencia F, Bhakta D, Bilsland A, Bishayee A, Blain SW, Block PB, Boosani CS, Carey TE, Carnero A, Carotenuto M, Casey SC, Chakrabarti M, Chaturvedi R, Chen GZ, Chen H, Chen S, Chen YC, Choi BK, Ciriolo MR, Coley HM, Collins AR, Connell M, Crawford S, Curran CS, Dabrosin C, Damia G, Dasgupta S, DeBerardinis RJ, Decker WK, Dhawan P, Diehl AME, Dong JT, Dou QP, Drew JE, Elkord E, El-Rayes B, Feitelson MA, Felsher DW, Ferguson LR, Fimognari C, Firestone GL, Frezza C, Fujii H, Fuster MM, Generali D, Georgakilas AG, Gieseler F, Gilbertson M, Green MF, Grue B, Guha G, Halicka D, Helferich WG, Heneberg P, Hentosh P, Hirschey MD, Hofseth LJ, Holcombe RF, Honoki K, Hsu HY, Huang GS, Jensen LD, Jiang WG, Jones LW, Karpowicz PA, Keith WN, Kerkar SP, Khan GN, Khatami M, Ko YH, Kucuk O, Kulathinal RJ, Kumar NB, Kwon BS, Le A, Lea MA, Lee HY, Lichtor T, Lin LT, Locasale JW, Lokeshwar BL, Longo VD, Lyssiotis CA, MacKenzie KL, Malhotra M, Marino M, Martinez-Chantar ML, Matheu A, Maxwell C, McDonnell E, Meeker AK, Mehrmohamadi M, Mehta K, Michelotti GA, Mohammad RM, Mohammed SI, Morre DJ, Muralidhar V, Muqbil I, Murphy MP, Nagaraju GP, Nahta R, Niccolai E, Nowsheen S, Panis C, Pantano F, Parslow VR, Pawelec G, Pedersen PL, Poore B, Poudyal D, Prakash S, Prince M, Raffaghello L, Rathmell JC, Rathmell WK, Ray SK, Reichrath J, Rezazadeh S, Ribatti D, Ricciardiello L, Robey RB, Rodier F, Rupasinghe HPV, Russo GL, Ryan EP, Samadi AK, Sanchez-Garcia I, Sanders AJ, Santini D, Sarkar M, Sasada T, Saxena NK, Shackelford RE, Shantha Kumara HMC, Sharma D, Shin DM, Sidransky D, Siegelin MD, Signori E, Singh N, Sivanand S, Sliva D, Smythe C, Spagnuolo C, Stafforini DM, Stagg J, Subbarayan PR, Sundin T, Talib WH, Thompson SK, Tran PT, Ungefroren H, Vander Heiden MG, Venkateswaran V, Vinay DS, Vlachostergios PJ, Wang Z, Wellen KE, Whelan RL, Yang ES, Yang H, Yang X, Yaswen P, Yedjou C, Yin X, Zhu J, Zollo M. Designing a broad-spectrum integrative approach for cancer prevention and treatment. Semin Cancer Biol 2016; 35 Suppl:S276-S304. [PMID: 26590477 DOI: 10.1016/j.semcancer.2015.09.007] [Citation(s) in RCA: 190] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 08/12/2015] [Accepted: 09/14/2015] [Indexed: 12/14/2022]
Abstract
Targeted therapies and the consequent adoption of "personalized" oncology have achieved notable successes in some cancers; however, significant problems remain with this approach. Many targeted therapies are highly toxic, costs are extremely high, and most patients experience relapse after a few disease-free months. Relapses arise from genetic heterogeneity in tumors, which harbor therapy-resistant immortalized cells that have adopted alternate and compensatory pathways (i.e., pathways that are not reliant upon the same mechanisms as those which have been targeted). To address these limitations, an international task force of 180 scientists was assembled to explore the concept of a low-toxicity "broad-spectrum" therapeutic approach that could simultaneously target many key pathways and mechanisms. Using cancer hallmark phenotypes and the tumor microenvironment to account for the various aspects of relevant cancer biology, interdisciplinary teams reviewed each hallmark area and nominated a wide range of high-priority targets (74 in total) that could be modified to improve patient outcomes. For these targets, corresponding low-toxicity therapeutic approaches were then suggested, many of which were phytochemicals. Proposed actions on each target and all of the approaches were further reviewed for known effects on other hallmark areas and the tumor microenvironment. Potential contrary or procarcinogenic effects were found for 3.9% of the relationships between targets and hallmarks, and mixed evidence of complementary and contrary relationships was found for 7.1%. Approximately 67% of the relationships revealed potentially complementary effects, and the remainder had no known relationship. Among the approaches, 1.1% had contrary, 2.8% had mixed and 62.1% had complementary relationships. These results suggest that a broad-spectrum approach should be feasible from a safety standpoint. This novel approach has potential to be relatively inexpensive, it should help us address stages and types of cancer that lack conventional treatment, and it may reduce relapse risks. A proposed agenda for future research is offered.
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Affiliation(s)
- Keith I Block
- Block Center for Integrative Cancer Treatment, Skokie, IL, United States.
| | | | - Leroy Lowe
- Getting to Know Cancer, Truro, Nova Scotia, Canada; Lancaster Environment Centre, Lancaster University, Bailrigg, Lancaster, United Kingdom.
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - A R M Ruhul Amin
- Winship Cancer Institute of Emory University, Atlanta, GA, United States
| | - Amr Amin
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Katia Aquilano
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Jack Arbiser
- Winship Cancer Institute of Emory University, Atlanta, GA, United States; Atlanta Veterans Administration Medical Center, Atlanta, GA, United States; Department of Dermatology, Emory University School of Medicine, Emory University, Atlanta, GA, United States
| | - Alexandra Arreola
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States
| | - Alla Arzumanyan
- Department of Biology, Temple University, Philadelphia, PA, United States
| | - S Salman Ashraf
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Asfar S Azmi
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, United States
| | - Fabian Benencia
- Department of Biomedical Sciences, Ohio University, Athens, OH, United States
| | - Dipita Bhakta
- School of Chemical and Bio Technology, SASTRA University, Thanjavur, Tamil Nadu, India
| | | | - Anupam Bishayee
- Department of Pharmaceutical Sciences, College of Pharmacy, Larkin Health Sciences Institute, Miami, FL, United States
| | - Stacy W Blain
- Department of Pediatrics, State University of New York, Downstate Medical Center, Brooklyn, NY, United States
| | - Penny B Block
- Block Center for Integrative Cancer Treatment, Skokie, IL, United States
| | - Chandra S Boosani
- Department of BioMedical Sciences, School of Medicine, Creighton University, Omaha, NE, United States
| | - Thomas E Carey
- Head and Neck Cancer Biology Laboratory, University of Michigan, Ann Arbor, MI, United States
| | - Amancio Carnero
- Instituto de Biomedicina de Sevilla, Consejo Superior de Investigaciones Cientificas, Seville, Spain
| | - Marianeve Carotenuto
- Centro di Ingegneria Genetica e Biotecnologia Avanzate, Naples, Italy; Department of Molecular Medicine and Medical Biotechnology, Federico II, Via Pansini 5, 80131 Naples, Italy
| | - Stephanie C Casey
- Stanford University, Division of Oncology, Department of Medicine and Pathology, Stanford, CA, United States
| | - Mrinmay Chakrabarti
- Department of Pathology, Microbiology, and Immunology, University of South Carolina, School of Medicine, Columbia, SC, United States
| | - Rupesh Chaturvedi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Georgia Zhuo Chen
- Winship Cancer Institute of Emory University, Atlanta, GA, United States
| | - Helen Chen
- Department of Pediatrics, University of British Columbia, Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Vancouver, British Columbia, Canada
| | - Sophie Chen
- Ovarian and Prostate Cancer Research Laboratory, Guildford, Surrey, United Kingdom
| | - Yi Charlie Chen
- Department of Biology, Alderson Broaddus University, Philippi, WV, United States
| | - Beom K Choi
- Cancer Immunology Branch, Division of Cancer Biology, National Cancer Center, Goyang, Gyeonggi, Republic of Korea
| | | | - Helen M Coley
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Andrew R Collins
- Department of Nutrition, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marisa Connell
- Department of Pediatrics, University of British Columbia, Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Vancouver, British Columbia, Canada
| | - Sarah Crawford
- Cancer Biology Research Laboratory, Southern Connecticut State University, New Haven, CT, United States
| | - Colleen S Curran
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Charlotta Dabrosin
- Department of Oncology and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Giovanna Damia
- Department of Oncology, Istituto Di Ricovero e Cura a Carattere Scientifico - Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Santanu Dasgupta
- Department of Cellular and Molecular Biology, the University of Texas Health Science Center at Tyler, Tyler, TX, United States
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas - Southwestern Medical Center, Dallas, TX, United States
| | - William K Decker
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Punita Dhawan
- Department of Surgery and Cancer Biology, Division of Surgical Oncology, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Anna Mae E Diehl
- Department of Medicine, Duke University Medical Center, Durham, NC, United States
| | - Jin-Tang Dong
- Winship Cancer Institute of Emory University, Atlanta, GA, United States
| | - Q Ping Dou
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, United States
| | - Janice E Drew
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Eyad Elkord
- College of Medicine & Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Bassel El-Rayes
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, United States
| | - Mark A Feitelson
- Department of Biology, Temple University, Philadelphia, PA, United States
| | - Dean W Felsher
- Stanford University, Division of Oncology, Department of Medicine and Pathology, Stanford, CA, United States
| | - Lynnette R Ferguson
- Discipline of Nutrition and Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Carmela Fimognari
- Dipartimento di Scienze per la Qualità della Vita Alma Mater Studiorum-Università di Bologna, Rimini, Italy
| | - Gary L Firestone
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, CA, United States
| | - Christian Frezza
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Hiromasa Fujii
- Department of Orthopedic Surgery, Nara Medical University, Kashihara, Nara, Japan
| | - Mark M Fuster
- Medicine and Research Services, Veterans Affairs San Diego Healthcare System & University of California, San Diego, CA, United States
| | - Daniele Generali
- Department of Medical, Surgery and Health Sciences, University of Trieste, Trieste, Italy; Molecular Therapy and Pharmacogenomics Unit, Azienda Ospedaliera Istituti Ospitalieri di Cremona, Cremona, Italy
| | - Alexandros G Georgakilas
- Physics Department, School of Applied Mathematics and Physical Sciences, National Technical University of Athens, Athens, Greece
| | - Frank Gieseler
- First Department of Medicine, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | | | - Michelle F Green
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States
| | - Brendan Grue
- Departments of Environmental Science, Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Gunjan Guha
- School of Chemical and Bio Technology, SASTRA University, Thanjavur, Tamil Nadu, India
| | - Dorota Halicka
- Department of Pathology, New York Medical College, Valhalla, NY, United States
| | | | - Petr Heneberg
- Charles University in Prague, Third Faculty of Medicine, Prague, Czech Republic
| | - Patricia Hentosh
- School of Medical Laboratory and Radiation Sciences, Old Dominion University, Norfolk, VA, United States
| | - Matthew D Hirschey
- Department of Medicine, Duke University Medical Center, Durham, NC, United States; Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States
| | - Lorne J Hofseth
- College of Pharmacy, University of South Carolina, Columbia, SC, United States
| | - Randall F Holcombe
- Tisch Cancer Institute, Mount Sinai School of Medicine, New York, NY, United States
| | - Kanya Honoki
- Department of Orthopedic Surgery, Nara Medical University, Kashihara, Nara, Japan
| | - Hsue-Yin Hsu
- Department of Life Sciences, Tzu-Chi University, Hualien, Taiwan
| | - Gloria S Huang
- Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, United States
| | - Lasse D Jensen
- Department of Medical and Health Sciences, Linköping University, Linköping, Sweden; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Wen G Jiang
- Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Lee W Jones
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, United States
| | | | | | - Sid P Kerkar
- Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | | | - Mahin Khatami
- Inflammation and Cancer Research, National Cancer Institute (Retired), National Institutes of Health, Bethesda, MD, United States
| | - Young H Ko
- University of Maryland BioPark, Innovation Center, KoDiscovery, Baltimore, MD, United States
| | - Omer Kucuk
- Winship Cancer Institute of Emory University, Atlanta, GA, United States
| | - Rob J Kulathinal
- Department of Biology, Temple University, Philadelphia, PA, United States
| | - Nagi B Kumar
- Moffitt Cancer Center, University of South Florida College of Medicine, Tampa, FL, United States
| | - Byoung S Kwon
- Cancer Immunology Branch, Division of Cancer Biology, National Cancer Center, Goyang, Gyeonggi, Republic of Korea; Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA, United States
| | - Anne Le
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Michael A Lea
- New Jersey Medical School, Rutgers University, Newark, NJ, United States
| | - Ho-Young Lee
- College of Pharmacy, Seoul National University, South Korea
| | - Terry Lichtor
- Department of Neurosurgery, Rush University Medical Center, Chicago, IL, United States
| | - Liang-Tzung Lin
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Jason W Locasale
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, United States
| | - Bal L Lokeshwar
- Department of Medicine, Georgia Regents University Cancer Center, Augusta, GA, United States
| | - Valter D Longo
- Andrus Gerontology Center, Division of Biogerontology, University of Southern California, Los Angeles, CA, United States
| | - Costas A Lyssiotis
- Department of Molecular and Integrative Physiology and Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, United States
| | - Karen L MacKenzie
- Children's Cancer Institute Australia, Kensington, New South Wales, Australia
| | - Meenakshi Malhotra
- Department of Biomedical Engineering, McGill University, Montréal, Canada
| | - Maria Marino
- Department of Science, University Roma Tre, Rome, Italy
| | - Maria L Martinez-Chantar
- Metabolomic Unit, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Technology Park of Bizkaia, Bizkaia, Spain
| | | | - Christopher Maxwell
- Department of Pediatrics, University of British Columbia, Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Vancouver, British Columbia, Canada
| | - Eoin McDonnell
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States
| | - Alan K Meeker
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Mahya Mehrmohamadi
- Field of Genetics, Genomics, and Development, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
| | - Kapil Mehta
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Gregory A Michelotti
- Department of Medicine, Duke University Medical Center, Durham, NC, United States
| | - Ramzi M Mohammad
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, United States
| | - Sulma I Mohammed
- Department of Comparative Pathobiology, Purdue University Center for Cancer Research, West Lafayette, IN, United States
| | - D James Morre
- Mor-NuCo, Inc, Purdue Research Park, West Lafayette, IN, United States
| | - Vinayak Muralidhar
- Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, United States; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Irfana Muqbil
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, United States
| | - Michael P Murphy
- MRC Mitochondrial Biology Unit, Wellcome Trust-MRC Building, Hills Road, Cambridge, United Kingdom
| | | | - Rita Nahta
- Winship Cancer Institute of Emory University, Atlanta, GA, United States
| | | | - Somaira Nowsheen
- Medical Scientist Training Program, Mayo Graduate School, Mayo Medical School, Mayo Clinic, Rochester, MN, United States
| | - Carolina Panis
- Laboratory of Inflammatory Mediators, State University of West Paraná, UNIOESTE, Paraná, Brazil
| | - Francesco Pantano
- Medical Oncology Department, University Campus Bio-Medico, Rome, Italy
| | - Virginia R Parslow
- Discipline of Nutrition and Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Graham Pawelec
- Center for Medical Research, University of Tübingen, Tübingen, Germany
| | - Peter L Pedersen
- Departments of Biological Chemistry and Oncology, Member at Large, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
| | - Brad Poore
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Deepak Poudyal
- College of Pharmacy, University of South Carolina, Columbia, SC, United States
| | - Satya Prakash
- Department of Biomedical Engineering, McGill University, Montréal, Canada
| | - Mark Prince
- Department of Otolaryngology-Head and Neck, Medical School, University of Michigan, Ann Arbor, MI, United States
| | | | - Jeffrey C Rathmell
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States
| | - W Kimryn Rathmell
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States
| | - Swapan K Ray
- Department of Pathology, Microbiology, and Immunology, University of South Carolina, School of Medicine, Columbia, SC, United States
| | - Jörg Reichrath
- Center for Clinical and Experimental Photodermatology, Clinic for Dermatology, Venerology and Allergology, The Saarland University Hospital, Homburg, Germany
| | - Sarallah Rezazadeh
- Department of Biology, University of Rochester, Rochester, NY, United States
| | - Domenico Ribatti
- Department of Basic Medical Sciences, Neurosciences and Sensory Organs, University of Bari Medical School, Bari, Italy & National Cancer Institute Giovanni Paolo II, Bari, Italy
| | - Luigi Ricciardiello
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - R Brooks Robey
- White River Junction Veterans Affairs Medical Center, White River Junction, VT, United States; Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Francis Rodier
- Centre de Rechercher du Centre Hospitalier de l'Université de Montréal and Institut du Cancer de Montréal, Montréal, Quebec, Canada; Université de Montréal, Département de Radiologie, Radio-Oncologie et Médicine Nucléaire, Montréal, Quebec, Canada
| | - H P Vasantha Rupasinghe
- Department of Environmental Sciences, Faculty of Agriculture and Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Gian Luigi Russo
- Institute of Food Sciences National Research Council, Avellino, Italy
| | - Elizabeth P Ryan
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States
| | | | - Isidro Sanchez-Garcia
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC-Universidad de Salamanca, Salamanca, Spain
| | - Andrew J Sanders
- Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Daniele Santini
- Medical Oncology Department, University Campus Bio-Medico, Rome, Italy
| | - Malancha Sarkar
- Department of Biology, University of Miami, Miami, FL, United States
| | - Tetsuro Sasada
- Department of Immunology, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Neeraj K Saxena
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Rodney E Shackelford
- Department of Pathology, Louisiana State University, Health Shreveport, Shreveport, LA, United States
| | - H M C Shantha Kumara
- Department of Surgery, St. Luke's Roosevelt Hospital, New York, NY, United States
| | - Dipali Sharma
- Department of Oncology, Johns Hopkins University School of Medicine and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, United States
| | - Dong M Shin
- Winship Cancer Institute of Emory University, Atlanta, GA, United States
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Markus David Siegelin
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States
| | - Emanuela Signori
- National Research Council, Institute of Translational Pharmacology, Rome, Italy
| | - Neetu Singh
- Advanced Molecular Science Research Centre (Centre for Advanced Research), King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Sharanya Sivanand
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Daniel Sliva
- DSTest Laboratories, Purdue Research Park, Indianapolis, IN, United States
| | - Carl Smythe
- Department of Biomedical Science, Sheffield Cancer Research Centre, University of Sheffield, Sheffield, United Kingdom
| | - Carmela Spagnuolo
- Institute of Food Sciences National Research Council, Avellino, Italy
| | - Diana M Stafforini
- Huntsman Cancer Institute and Department of Internal Medicine, University of Utah, Salt Lake City, UT, United States
| | - John Stagg
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Faculté de Pharmacie et Institut du Cancer de Montréal, Montréal, Quebec, Canada
| | - Pochi R Subbarayan
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Tabetha Sundin
- Department of Molecular Diagnostics, Sentara Healthcare, Norfolk, VA, United States
| | - Wamidh H Talib
- Department of Clinical Pharmacy and Therapeutics, Applied Science University, Amman, Jordan
| | - Sarah K Thompson
- Department of Surgery, Royal Adelaide Hospital, Adelaide, Australia
| | - Phuoc T Tran
- Departments of Radiation Oncology & Molecular Radiation Sciences, Oncology and Urology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Hendrik Ungefroren
- First Department of Medicine, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Vasundara Venkateswaran
- Department of Surgery, University of Toronto, Division of Urology, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Dass S Vinay
- Section of Clinical Immunology, Allergy, and Rheumatology, Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA, United States
| | - Panagiotis J Vlachostergios
- Department of Internal Medicine, New York University Lutheran Medical Center, Brooklyn, New York, NY, United States
| | - Zongwei Wang
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Kathryn E Wellen
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Richard L Whelan
- Department of Surgery, St. Luke's Roosevelt Hospital, New York, NY, United States
| | - Eddy S Yang
- Department of Radiation Oncology, University of Alabama at Birmingham School of Medicine, Birmingham, AL, United States
| | - Huanjie Yang
- The School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Xujuan Yang
- University of Illinois at Urbana Champaign, Champaign, IL, United States
| | - Paul Yaswen
- Life Sciences Division, Lawrence Berkeley National Lab, Berkeley, CA, United States
| | - Clement Yedjou
- Department of Biology, Jackson State University, Jackson, MS, United States
| | - Xin Yin
- Medicine and Research Services, Veterans Affairs San Diego Healthcare System & University of California, San Diego, CA, United States
| | - Jiyue Zhu
- Washington State University College of Pharmacy, Spokane, WA, United States
| | - Massimo Zollo
- Centro di Ingegneria Genetica e Biotecnologia Avanzate, Naples, Italy; Department of Molecular Medicine and Medical Biotechnology, Federico II, Via Pansini 5, 80131 Naples, Italy
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Brooks SA, Khandani AH, Fielding JR, Lin W, Sills T, Lee Y, Arreola A, Milowsky MI, Wallen EM, Woods ME, Smith AB, Nielsen ME, Parker JS, Lalush DS, Rathmell WK. Alternate Metabolic Programs Define Regional Variation of Relevant Biological Features in Renal Cell Carcinoma Progression. Clin Cancer Res 2016; 22:2950-9. [PMID: 26787754 DOI: 10.1158/1078-0432.ccr-15-2115] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 12/13/2015] [Indexed: 01/18/2023]
Abstract
PURPOSE Clear cell renal cell carcinoma (ccRCC) has recently been redefined as a highly heterogeneous disease. In addition to genetic heterogeneity, the tumor displays risk variability for developing metastatic disease, therefore underscoring the urgent need for tissue-based prognostic strategies applicable to the clinical setting. We have recently employed the novel PET/magnetic resonance (MR) image modality to enrich our understanding of how tumor heterogeneity can relate to gene expression and tumor biology to assist in defining individualized treatment plans. EXPERIMENTAL DESIGN ccRCC patients underwent PET/MR imaging, and these images subsequently used to identify areas of varied intensity for sampling. Samples from 8 patients were subjected to histologic, immunohistochemical, and microarray analysis. RESULTS Tumor subsamples displayed a range of heterogeneity for common features of hypoxia-inducible factor expression and microvessel density, as well as for features closely linked to metabolic processes, such as GLUT1 and FBP1. In addition, gene signatures linked with disease risk (ccA and ccB) also demonstrated variable heterogeneity, with most tumors displaying a dominant panel of features across the sampled regions. Intriguingly, the ccA- and ccB-classified samples corresponded with metabolic features and functional imaging levels. These correlations further linked a variety of metabolic pathways (i.e., the pentose phosphate and mTOR pathways) with the more aggressive, and glucose avid ccB subtype. CONCLUSIONS Higher tumor dependency on exogenous glucose accompanies the development of features associated with the poor risk ccB subgroup. Linking these panels of features may provide the opportunity to create functional maps to enable enhanced visualization of the heterogeneous biologic processes of an individual's disease. Clin Cancer Res; 22(12); 2950-9. ©2016 AACR.
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Affiliation(s)
- Samira A Brooks
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina. Curriculum in Toxicology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Amir H Khandani
- Department of Radiology, University of North Carolina, Chapel Hill, North Carolina. Department of Radiology, Nuclear Medicine, University of North Carolina at Chapel Hill, North Carolina.
| | - Julia R Fielding
- Department of Radiology, University of North Carolina, Chapel Hill, North Carolina
| | - Weili Lin
- Department of Radiology, University of North Carolina, Chapel Hill, North Carolina
| | - Tiffany Sills
- Department of Urology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Yueh Lee
- Department of Radiology, University of North Carolina, Chapel Hill, North Carolina
| | - Alexandra Arreola
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina
| | - Mathew I Milowsky
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina. Department of Urology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Eric M Wallen
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina. Department of Urology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Michael E Woods
- Department of Radiology, University of North Carolina, Chapel Hill, North Carolina
| | - Angie B Smith
- Department of Urology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Mathew E Nielsen
- Department of Urology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Joel S Parker
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina. Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - David S Lalush
- Department of Radiology, Nuclear Medicine, University of North Carolina at Chapel Hill, North Carolina. Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, Raleigh, North Carolina
| | - W Kimryn Rathmell
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina. Department of Urology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina. Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
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9
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Wang Z, Dabrosin C, Yin X, Fuster MM, Arreola A, Rathmell WK, Generali D, Nagaraju GP, El-Rayes B, Ribatti D, Chen YC, Honoki K, Fujii H, Georgakilas AG, Nowsheen S, Amedei A, Niccolai E, Amin A, Ashraf SS, Helferich B, Yang X, Guha G, Bhakta D, Ciriolo MR, Aquilano K, Chen S, Halicka D, Mohammed SI, Azmi AS, Bilsland A, Keith WN, Jensen LD. Broad targeting of angiogenesis for cancer prevention and therapy. Semin Cancer Biol 2015; 35 Suppl:S224-S243. [PMID: 25600295 PMCID: PMC4737670 DOI: 10.1016/j.semcancer.2015.01.001] [Citation(s) in RCA: 312] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 12/25/2014] [Accepted: 01/08/2015] [Indexed: 12/20/2022]
Abstract
Deregulation of angiogenesis – the growth of new blood vessels from an existing vasculature – is a main driving force in many severe human diseases including cancer. As such, tumor angiogenesis is important for delivering oxygen and nutrients to growing tumors, and therefore considered an essential pathologic feature of cancer, while also playing a key role in enabling other aspects of tumor pathology such as metabolic deregulation and tumor dissemination/metastasis. Recently, inhibition of tumor angiogenesis has become a clinical anti-cancer strategy in line with chemotherapy, radiotherapy and surgery, which underscore the critical importance of the angiogenic switch during early tumor development. Unfortunately the clinically approved anti-angiogenic drugs in use today are only effective in a subset of the patients, and many who initially respond develop resistance over time. Also, some of the anti-angiogenic drugs are toxic and it would be of great importance to identify alternative compounds, which could overcome these drawbacks and limitations of the currently available therapy. Finding “the most important target” may, however, prove a very challenging approach as the tumor environment is highly diverse, consisting of many different cell types, all of which may contribute to tumor angiogenesis. Furthermore, the tumor cells themselves are genetically unstable, leading to a progressive increase in the number of different angiogenic factors produced as the cancer progresses to advanced stages. As an alternative approach to targeted therapy, options to broadly interfere with angiogenic signals by a mixture of non-toxic natural compound with pleiotropic actions were viewed by this team as an opportunity to develop a complementary anti-angiogenesis treatment option. As a part of the “Halifax Project” within the “Getting to know cancer” framework, we have here, based on a thorough review of the literature, identified 10 important aspects of tumor angiogenesis and the pathological tumor vasculature which would be well suited as targets for anti-angiogenic therapy: (1) endothelial cell migration/tip cell formation, (2) structural abnormalities of tumor vessels, (3) hypoxia, (4) lymphangiogenesis, (5) elevated interstitial fluid pressure, (6) poor perfusion, (7) disrupted circadian rhythms, (8) tumor promoting inflammation, (9) tumor promoting fibroblasts and (10) tumor cell metabolism/acidosis. Following this analysis, we scrutinized the available literature on broadly acting anti-angiogenic natural products, with a focus on finding qualitative information on phytochemicals which could inhibit these targets and came up with 10 prototypical phytochemical compounds: (1) oleanolic acid, (2) tripterine, (3) silibinin, (4) curcumin, (5) epigallocatechin-gallate, (6) kaempferol, (7) melatonin, (8) enterolactone, (9) withaferin A and (10) resveratrol. We suggest that these plant-derived compounds could be combined to constitute a broader acting and more effective inhibitory cocktail at doses that would not be likely to cause excessive toxicity. All the targets and phytochemical approaches were further cross-validated against their effects on other essential tumorigenic pathways (based on the “hallmarks” of cancer) in order to discover possible synergies or potentially harmful interactions, and were found to generally also have positive involvement in/effects on these other aspects of tumor biology. The aim is that this discussion could lead to the selection of combinations of such anti-angiogenic compounds which could be used in potent anti-tumor cocktails, for enhanced therapeutic efficacy, reduced toxicity and circumvention of single-agent anti-angiogenic resistance, as well as for possible use in primary or secondary cancer prevention strategies.
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Affiliation(s)
- Zongwei Wang
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Charlotta Dabrosin
- Department of Oncology, Linköping University, Linköping, Sweden; Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Xin Yin
- Medicine and Research Services, Veterans Affairs San Diego Healthcare System & University of California, San Diego, San Diego, CA, USA
| | - Mark M Fuster
- Medicine and Research Services, Veterans Affairs San Diego Healthcare System & University of California, San Diego, San Diego, CA, USA
| | - Alexandra Arreola
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - W Kimryn Rathmell
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Daniele Generali
- Molecular Therapy and Pharmacogenomics Unit, AO Isituti Ospitalieri di Cremona, Cremona, Italy
| | - Ganji P Nagaraju
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA
| | - Bassel El-Rayes
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA
| | - Domenico Ribatti
- Department of Basic Medical Sciences, Neurosciences and Sensory Organs, University of Bari Medical School, Bari, Italy; National Cancer Institute Giovanni Paolo II, Bari, Italy
| | - Yi Charlie Chen
- Department of Biology, Alderson Broaddus University, Philippi, WV, USA
| | - Kanya Honoki
- Department of Orthopedic Surgery, Arthroplasty and Regenerative Medicine, Nara Medical University, Nara, Japan
| | - Hiromasa Fujii
- Department of Orthopedic Surgery, Arthroplasty and Regenerative Medicine, Nara Medical University, Nara, Japan
| | - Alexandros G Georgakilas
- Physics Department, School of Applied Mathematics and Physical Sciences, National Technical University of Athens, Athens, Greece
| | - Somaira Nowsheen
- Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Elena Niccolai
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Amr Amin
- Department of Biology, College of Science, United Arab Emirate University, United Arab Emirates; Faculty of Science, Cairo University, Cairo, Egypt
| | - S Salman Ashraf
- Department of Chemistry, College of Science, United Arab Emirate University, United Arab Emirates
| | - Bill Helferich
- University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Xujuan Yang
- University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Gunjan Guha
- School of Chemical and Bio Technology, SASTRA University, Thanjavur, India
| | - Dipita Bhakta
- School of Chemical and Bio Technology, SASTRA University, Thanjavur, India
| | | | - Katia Aquilano
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Sophie Chen
- Ovarian and Prostate Cancer Research Trust Laboratory, Guilford, Surrey, UK
| | | | - Sulma I Mohammed
- Department of Comparative Pathobiology, Purdue University Center for Cancer Research, West Lafayette, IN, USA
| | - Asfar S Azmi
- School of Medicine, Wayne State University, Detroit, MI, USA
| | - Alan Bilsland
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - W Nicol Keith
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Lasse D Jensen
- Department of Medical, and Health Sciences, Linköping University, Linköping, Sweden; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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Arreola A, Cowey CL, Coloff JL, Rathmell JC, Rathmell WK. HIF1α and HIF2α exert distinct nutrient preferences in renal cells. PLoS One 2014; 9:e98705. [PMID: 24879016 PMCID: PMC4039535 DOI: 10.1371/journal.pone.0098705] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 05/06/2014] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Hypoxia Inducible Factors (HIF1α and HIF2α) are commonly stabilized and play key roles related to cell growth and metabolic programming in clear cell renal cell carcinoma. The relationship of these factors to discretely alter cell metabolic activities has largely been described in cancer cells, or in hypoxic conditions, where other confounding factors undoubtedly compete. These transcription factors and their specific roles in promoting cancer metabolic phenotypes from the earliest stages are poorly understood in pre-malignant cells. METHODS We undertook an analysis of SV40-transformed primary kidney epithelial cells derived from newborn mice genetically engineered to express a stabilized HIF1α or HIF2α transgene. We examined the metabolic profile in relation to each gene. RESULTS Although the cells proliferated similarly, the metabolic profile of each genotype of cell was markedly different and correlated with altered gene expression of factors influencing components of metabolic signaling. HIF1α promoted high levels of glycolysis as well as increased oxidative phosphorylation in complete media, but oxidative phosphorylation was suppressed when supplied with single carbon source media. HIF2α, in contrast, supported oxidative phosphorylation in complete media or single glucose carbon source, but these cells were not responsive to glutamine nutrient sources. This finding correlates to HIF2α-specific induction of Glul, effectively reducing glutamine utilization by limiting the glutamate pool, and knockdown of Glul allows these cells to perform oxidative phosphorylation in glutamine media. CONCLUSION HIF1α and HIF2α support highly divergent patterns of kidney epithelial cell metabolic phenotype. Expression of these factors ultimately alters the nutrient resource utilization and energy generation strategy in the setting of complete or limiting nutrients.
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Affiliation(s)
- Alexandra Arreola
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Genetics Department, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - C. Lance Cowey
- Department of Medicine, Division of Hematology and Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Now at Baylor Sammons Cancer Center, Dallas, Texas, United States of America
| | - Jonathan L. Coloff
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina, United States of America
- Now at Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jeffrey C. Rathmell
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - W. Kimryn Rathmell
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Genetics Department, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Medicine, Division of Hematology and Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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11
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Gameiro PA, Yang J, Metelo AM, Pérez-Carro R, Baker R, Wang Z, Arreola A, Rathmell WK, Olumi A, López-Larrubia P, Stephanopoulos G, Iliopoulos O. In vivo HIF-mediated reductive carboxylation is regulated by citrate levels and sensitizes VHL-deficient cells to glutamine deprivation. Cell Metab 2013; 17:372-85. [PMID: 23473032 PMCID: PMC4003458 DOI: 10.1016/j.cmet.2013.02.002] [Citation(s) in RCA: 243] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 09/24/2012] [Accepted: 02/05/2013] [Indexed: 02/06/2023]
Abstract
Hypoxic and VHL-deficient cells use glutamine to generate citrate and lipids through reductive carboxylation (RC) of α-ketoglutarate. To gain insights into the role of HIF and the molecular mechanisms underlying RC, we took advantage of a panel of disease-associated VHL mutants and showed that HIF expression is necessary and sufficient for the induction of RC in human renal cell carcinoma (RCC) cells. HIF expression drastically reduced intracellular citrate levels. Feeding VHL-deficient RCC cells with acetate or citrate or knocking down PDK-1 and ACLY restored citrate levels and suppressed RC. These data suggest that HIF-induced low intracellular citrate levels promote the reductive flux by mass action to maintain lipogenesis. Using [(1-13)C]glutamine, we demonstrated in vivo RC activity in VHL-deficient tumors growing as xenografts in mice. Lastly, HIF rendered VHL-deficient cells sensitive to glutamine deprivation in vitro, and systemic administration of glutaminase inhibitors suppressed the growth of RCC cells as mice xenografts.
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Affiliation(s)
- Paulo A Gameiro
- Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
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Kelley DR, Arreola A, Gallagher TL, Gasser CS. ETTIN (ARF3) physically interacts with KANADI proteins to form a functional complex essential for integument development and polarity determination in Arabidopsis. Development 2012; 139:1105-9. [PMID: 22296848 DOI: 10.1242/dev.067918] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
KANADI (KAN) transcription factors promote abaxial cell fate throughout plant development and are required for organ formation during embryo, leaf, carpel and ovule development. ABERRANT TESTA SHAPE (ATS, or KAN4) is necessary during ovule development to maintain the boundary between the two ovule integuments and to promote inner integument growth. Yeast two-hybrid assays identified ETTIN (ETT, or AUXIN RESPONSE FACTOR 3) as a transcription factor that could physically interact with ATS. ATS and ETT were shown to physically interact in vivo in transiently transformed tobacco epidermal cells using bimolecular fluorescence complementation. ATS and ETT were found to share an overlapping expression pattern during Arabidopsis ovule development and loss of either gene resulted in congenital fusion of the integuments and altered seed morphology. We hypothesize that in wild-type ovules a physical interaction between ATS and ETT allows these proteins to act in concert to define the boundary between integument primordia. We further show protein-protein interaction in yeast between ETT and KAN1, a paralog of ATS. Thus, a direct physical association between ETT and KAN proteins underpins their previously described common role in polarity establishment and organogenesis. We propose that ETT-KAN protein complex(es) constitute part of an auxin-dependent regulatory module that plays a conserved role in a variety of developmental contexts.
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Affiliation(s)
- Dior R Kelley
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
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Arreola A, Rathmell WK. Abstract 4276: Characterization of an ex vivo primary multicellular renal cell culture as a potential model system for renal cell carcinoma tumorigenesis. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-4276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Sporadic and germline mutations or loss of the von Hippel-Lindau (VHL) tumor suppressor gene have been linked to varying levels of risk for Renal Cell Carcinoma (RCC). RCC is a highly prevalent malignancy that affects roughly 56,000 people annually in the United States. With no true murine model for RCC, patient derived renal carcinoma cell lines and mouse embryonic stem cell lines have been largely used for the study of this malignancy. The purpose of this study is to generate an ex vivo model for Renal Cell Carcinoma using primary neonatal epithelial kidney cells grown as multicellular cultures. To better understand the genetic changes associated with RCC tumor formation following VHL loss or inactivation, primary epithelial kidney cells from newborn conditional Vhl null and Vhl G518A mutant genetically engineered mouse lines are undergoing investigation. Analysis of primary neonatal epithelial kidney cells cultured under mild hypoxia show that these cells preferentially grow in an organized multicellular spherical culture. Additionally, these multicellular cultures, termed “renospheres”, display focal expression of progenitor cell marker CD133, and also globally express Oct4 while select cells in the renospheres express renal cell type markers as seen by immunohistochemistry. Current work is aimed at identifying the cellular makeup of these spheres and determining any role individual cellular components may have in tumorigenesis. Future plans will compare growth characteristics and cellular components of renospheres in the setting of VHL mutation or loss with those with an intact VHL network. This ex vivo system can provide insight into both the cellular characteristics and molecular events that contribute substantially to RCC tumor formation as growth conditions of the renospheres are meant to mimic as close to a physiological state as possible, a factor not currently being addressed by common practices in the field.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4276. doi:10.1158/1538-7445.AM2011-4276
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Liu H, Brannon AR, Reddy AR, Alexe G, Seiler MW, Arreola A, Oza JH, Yao M, Juan D, Liou LS, Ganesan S, Levine AJ, Rathmell WK, Bhanot GV. Identifying mRNA targets of microRNA dysregulated in cancer: with application to clear cell Renal Cell Carcinoma. BMC Syst Biol 2010; 4:51. [PMID: 20420713 PMCID: PMC2876063 DOI: 10.1186/1752-0509-4-51] [Citation(s) in RCA: 204] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Accepted: 04/27/2010] [Indexed: 12/19/2022]
Abstract
BACKGROUND MicroRNA regulate mRNA levels in a tissue specific way, either by inducing degradation of the transcript or by inhibiting translation or transcription. Putative mRNA targets of microRNA identified from seed sequence matches are available in many databases. However, such matches have a high false positive rate and cannot identify tissue specificity of regulation. RESULTS We describe a simple method to identify direct mRNA targets of microRNA dysregulated in cancers from expression level measurements in patient matched tumor/normal samples. The word "direct" is used here in a strict sense to: a) represent mRNA which have an exact seed sequence match to the microRNA in their 3'UTR, b) the seed sequence match is strictly conserved across mouse, human, rat and dog genomes, c) the mRNA and microRNA expression levels can distinguish tumor from normal with high significance and d) the microRNA/mRNA expression levels are strongly and significantly anti-correlated in tumor and/or normal samples. We apply and validate the method using clear cell Renal Cell Carcinoma (ccRCC) and matched normal kidney samples, limiting our analysis to mRNA targets which undergo degradation of the mRNA transcript because of a perfect seed sequence match. Dysregulated microRNA and mRNA are first identified by comparing their expression levels in tumor vs normal samples. Putative dysregulated microRNA/mRNA pairs are identified from these using seed sequence matches, requiring that the seed sequence be conserved in human/dog/rat/mouse genomes. These are further pruned by requiring a strong anti-correlation signature in tumor and/or normal samples. The method revealed many new regulations in ccRCC. For instance, loss of miR-149, miR-200c and mir-141 causes gain of function of oncogenes (KCNMA1, LOX), VEGFA and SEMA6A respectively and increased levels of miR-142-3p, miR-185, mir-34a, miR-224, miR-21 cause loss of function of tumor suppressors LRRC2, PTPN13, SFRP1, ERBB4, and (SLC12A1, TCF21) respectively. We also found strong anti-correlation between VEGFA and the miR-200 family of microRNA: miR-200a*, 200b, 200c and miR-141. Several identified microRNA/mRNA pairs were validated on an independent set of matched ccRCC/normal samples. The regulation of SEMA6A by miR-141 was verified by a transfection assay. CONCLUSIONS We describe a simple and reliable method to identify direct gene targets of microRNA in any cancer. The constraints we impose (strong dysregulation signature for microRNA and mRNA levels between tumor/normal samples, evolutionary conservation of seed sequence and strong anti-correlation of expression levels) remove spurious matches and identify a subset of robust, tissue specific, functional mRNA targets of dysregulated microRNA.
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Affiliation(s)
- Huiqing Liu
- BioMaPS Institute, Rutgers University, Piscataway, NJ 08854, USA
- Current address: Bioinformatics, Centocor R&D Inc, 145 King of Prussia Road, Radnor, PA 19087, USA
| | - Angela R Brannon
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Anupama R Reddy
- BioMaPS Institute, Rutgers University, Piscataway, NJ 08854, USA
| | - Gabriela Alexe
- Broad Institute of MIT and Harvard, 7 Cambridge Center, MA, 02142, USA
| | - Michael W Seiler
- BioMaPS Institute, Rutgers University, Piscataway, NJ 08854, USA
| | - Alexandra Arreola
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jay H Oza
- Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
| | - Ming Yao
- Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
| | - David Juan
- Department of Pathology, Boston University Medical School, Boston, MA 02118, USA
| | - Louis S Liou
- Department of Pathology, Boston University Medical School, Boston, MA 02118, USA
- Cambridge Health Alliance, Harvard Medical School, Cambridge MA 02139, USA
| | - Shridar Ganesan
- Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
| | - Arnold J Levine
- Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ 08540, USA
| | - WK Rathmell
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Departments of Medicine and Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Gyan V Bhanot
- BioMaPS Institute, Rutgers University, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
- Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ 08540, USA
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA
- Department of Physics, Rutgers University, Piscataway, NJ 08854, USA
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Brannon AR, Reddy A, Seiler M, Arreola A, Moore DT, Pruthi RS, Wallen EM, Nielsen ME, Liu H, Nathanson KL, Ljungberg B, Zhao H, Brooks JD, Ganesan S, Bhanot G, Rathmell WK. Molecular Stratification of Clear Cell Renal Cell Carcinoma by Consensus Clustering Reveals Distinct Subtypes and Survival Patterns. Genes Cancer 2010; 1:152-163. [PMID: 20871783 DOI: 10.1177/1947601909359929] [Citation(s) in RCA: 246] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the predominant RCC subtype, but even within this classification, the natural history is heterogeneous and difficult to predict. A sophisticated understanding of the molecular features most discriminatory for the underlying tumor heterogeneity should be predicated on identifiable and biologically meaningful patterns of gene expression. Gene expression microarray data were analyzed using software that implements iterative unsupervised consensus clustering algorithms to identify the optimal molecular subclasses, without clinical or other classifying information. ConsensusCluster analysis identified two distinct subtypes of ccRCC within the training set, designated clear cell type A (ccA) and B (ccB). Based on the core tumors, or most well-defined arrays, in each subtype, logical analysis of data (LAD) defined a small, highly predictive gene set that could then be used to classify additional tumors individually. The subclasses were corroborated in a validation data set of 177 tumors and analyzed for clinical outcome. Based on individual tumor assignment, tumors designated ccA have markedly improved disease-specific survival compared to ccB (median survival of 8.6 vs 2.0 years, P = 0.002). Analyzed by both univariate and multivariate analysis, the classification schema was independently associated with survival. Using patterns of gene expression based on a defined gene set, ccRCC was classified into two robust subclasses based on inherent molecular features that ultimately correspond to marked differences in clinical outcome. This classification schema thus provides a molecular stratification applicable to individual tumors that has implications to influence treatment decisions, define biological mechanisms involved in ccRCC tumor progression, and direct future drug discovery.
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Affiliation(s)
- A Rose Brannon
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
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