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Kim W, Giannikou K, Dreier JR, Lee S, Tyburczy ME, Silverman EK, Radzikowska E, Wu S, Wu CL, Henske EP, Hunninghake G, Carel H, Roman A, Pujana MA, Moss J, Won S, Kwiatkowski DJ. A genome-wide association study implicates NR2F2 in lymphangioleiomyomatosis pathogenesis. Eur Respir J 2019; 53:13993003.00329-2019. [PMID: 31000673 DOI: 10.1183/13993003.00329-2019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/19/2019] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Lymphangioleiomyomatosis (LAM) occurs either associated with tuberous sclerosis complex (TSC) or as sporadic disease (S-LAM). Risk factors for development of S-LAM are unknown. We hypothesised that DNA sequence variants outside of TSC2/TSC1 might be associated with susceptibility for S-LAM and performed a genome-wide association study (GWAS). METHODS Genotyped and imputed data on 5 426 936 single nucleotide polymorphisms (SNPs) in 426 S-LAM subjects were compared, using conditional logistic regression, with similar data from 852 females from COPDGene in a matched case-control design. For replication studies, genotypes for 196 non-Hispanic White female S-LAM subjects were compared with three different sets of controls. RNA sequencing and immunohistochemistry analyses were also performed. RESULTS Two noncoding genotyped SNPs met genome-wide significance: rs4544201 and rs2006950 (p=4.2×10-8 and 6.1×10-9, respectively), which are in the same 35 kb linkage disequilibrium block on chromosome 15q26.2. This association was replicated in an independent cohort. NR2F2 (nuclear receptor subfamily 2 group F member 2), a nuclear receptor and transcription factor, was the only nearby protein-coding gene. NR2F2 expression was higher by RNA sequencing in one abdominal LAM tumour and four kidney angiomyolipomas, a LAM-related tumour, compared with all cancers from The Cancer Genome Atlas. Immunohistochemistry showed strong nuclear expression in both LAM and angiomyolipoma tumours. CONCLUSIONS SNPs on chromosome 15q26.2 are associated with S-LAM, and chromatin and expression data suggest that this association may occur through effects on NR2F2 expression, which potentially plays an important role in S-LAM development.
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Affiliation(s)
- Wonji Kim
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, Korea.,Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,These two authors contributed equally to this work
| | - Krinio Giannikou
- Division of Pulmonary and Critical Care Medicine and of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,These two authors contributed equally to this work
| | - John R Dreier
- Division of Pulmonary and Critical Care Medicine and of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sanghun Lee
- Dept of Medical Consilience, Graduate School, Dankook University, Yongin-si, Korea
| | - Magdalena E Tyburczy
- Division of Pulmonary and Critical Care Medicine and of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine and of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Shulin Wu
- Urology Research Laboratory, Massachusetts General Hospital, Boston, MA, USA
| | - Chin-Lee Wu
- Urology Research Laboratory, Massachusetts General Hospital, Boston, MA, USA
| | - Elizabeth P Henske
- Division of Pulmonary and Critical Care Medicine and of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Gary Hunninghake
- Division of Pulmonary and Critical Care Medicine and of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Havi Carel
- Dept of Philosophy, University of Bristol, Bristol, UK
| | - Antonio Roman
- Vall d'Hebron University Hospital, CIBERES, Barcelona, Spain
| | - Miquel Angel Pujana
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain
| | - Joel Moss
- Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sungho Won
- Dept of Public Health Sciences, Seoul National University, Seoul, Korea.,Institute of Health and Environment, Seoul National University, Seoul, Korea.,Joint senior authors
| | - David J Kwiatkowski
- Division of Pulmonary and Critical Care Medicine and of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA .,Joint senior authors
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2
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Treichel AM, Hamieh L, Nathan NR, Tyburczy ME, Wang JA, Oyerinde O, Raiciulescu S, Julien-Williams P, Jones AM, Gopalakrishnan V, Moss J, Kwiatkowski DJ, Darling TN. Phenotypic distinctions between mosaic forms of tuberous sclerosis complex. Genet Med 2019; 21:2594-2604. [PMID: 31114024 PMCID: PMC7875483 DOI: 10.1038/s41436-019-0520-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 11/16/2018] [Accepted: 04/12/2019] [Indexed: 11/09/2022] Open
Abstract
Purpose: To determine if mosaic tuberous sclerosis complex (TSC) can be stratified into subtypes that correspond with prognosis and extent of disease. Methods: Next-generation sequencing of skin tumor and other samples was used to identify patients with mosaic pathogenic variants in TSC1 or TSC2. Extent of disease, onset age, and family history of TSC were determined through retrospective analysis of patient records. Results: The median number of disease findings and age at penetrance differed between mosaic patients with asymmetrically distributed facial angiofibromas (4 findings, 24y, n=7), mosaic patients with bilaterally symmetric facial angiofibromas (8 findings, 10y, n=12), and germline TSC patients (10 findings, 4y, n=29). Cutaneous and internal organ involvement positively correlated in mosaic (R=0.62, p=0.005), but not germline (R=−0.24, p=0.24) TSC. Variant allele fraction (VAF) in the blood (range: 0-19%) positively correlated with the number of major features (R=0.55, p=0.028). Five had a TSC2 variant identified in the skin that was below detection in the blood. One of 12 children from a mosaic parent had TSC. Conclusion: The phenotype of mosaic TSC ranged from mild to indistinguishable from germline disease. Patients with mosaicism and asymmetric facial angiofibromas exhibited fewer findings, later onset, and lower VAF in the blood.
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Affiliation(s)
- Alison M Treichel
- Department of Dermatology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lana Hamieh
- Division of Pulmonary Medicine and of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Neera R Nathan
- Department of Dermatology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Magdalena E Tyburczy
- Division of Pulmonary Medicine and of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ji-An Wang
- Department of Dermatology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Oyetewa Oyerinde
- Department of Dermatology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sorana Raiciulescu
- Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Patricia Julien-Williams
- Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amanda M Jones
- Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vissaagan Gopalakrishnan
- Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Joel Moss
- Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - David J Kwiatkowski
- Division of Pulmonary Medicine and of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Thomas N Darling
- Department of Dermatology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
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Cao J, Tyburczy ME, Moss J, Darling TN, Widlund HR, Kwiatkowski DJ. Tuberous sclerosis complex inactivation disrupts melanogenesis via mTORC1 activation. J Clin Invest 2016; 127:349-364. [PMID: 27918305 DOI: 10.1172/jci84262] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 10/20/2016] [Indexed: 12/20/2022] Open
Abstract
Tuberous sclerosis complex (TSC) is an autosomal dominant tumor-suppressor gene syndrome caused by inactivating mutations in either TSC1 or TSC2, and the TSC protein complex is an essential regulator of mTOR complex 1 (mTORC1). Patients with TSC develop hypomelanotic macules (white spots), but the molecular mechanisms underlying their formation are not fully characterized. Using human primary melanocytes and a highly pigmented melanoma cell line, we demonstrate that reduced expression of either TSC1 or TSC2 causes reduced pigmentation through mTORC1 activation, which results in hyperactivation of glycogen synthase kinase 3β (GSK3β), followed by phosphorylation of and loss of β-catenin from the nucleus, thereby reducing expression of microphthalmia-associated transcription factor (MITF), and subsequent reductions in tyrosinase and other genes required for melanogenesis. Genetic suppression or pharmacological inhibition of this signaling cascade at multiple levels restored pigmentation. Importantly, primary melanocytes isolated from hypomelanotic macules from 6 patients with TSC all exhibited reduced TSC2 protein expression, and 1 culture showed biallelic mutation in TSC2, one of which was germline and the second acquired in the melanocytes of the hypomelanotic macule. These findings indicate that the TSC/mTORC1/AKT/GSK3β/β-catenin/MITF axis plays a central role in regulating melanogenesis. Interventions that enhance or diminish mTORC1 activity or other nodes in this pathway in melanocytes could potentially modulate pigment production.
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Giannikou K, Malinowska IA, Pugh TJ, Yan R, Tseng YY, Oh C, Kim J, Tyburczy ME, Chekaluk Y, Liu Y, Alesi N, Finlay GA, Wu CL, Signoretti S, Meyerson M, Getz G, Boehm JS, Henske EP, Kwiatkowski DJ. Whole Exome Sequencing Identifies TSC1/TSC2 Biallelic Loss as the Primary and Sufficient Driver Event for Renal Angiomyolipoma Development. PLoS Genet 2016; 12:e1006242. [PMID: 27494029 PMCID: PMC4975391 DOI: 10.1371/journal.pgen.1006242] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [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: 05/30/2016] [Accepted: 07/14/2016] [Indexed: 11/19/2022] Open
Abstract
Renal angiomyolipoma is a kidney tumor in the perivascular epithelioid (PEComa) family that is common in patients with Tuberous Sclerosis Complex (TSC) and Lymphangioleiomyomatosis (LAM) but occurs rarely sporadically. Though histologically benign, renal angiomyolipoma can cause life-threatening hemorrhage and kidney failure. Both angiomyolipoma and LAM have mutations in TSC2 or TSC1. However, the frequency and contribution of other somatic events in tumor development is unknown. We performed whole exome sequencing in 32 resected tumor samples (n = 30 angiomyolipoma, n = 2 LAM) from 15 subjects, including three with TSC. Two germline and 22 somatic inactivating mutations in TSC2 were identified, and one germline TSC1 mutation. Twenty of 32 (62%) samples showed copy neutral LOH (CN-LOH) in TSC2 or TSC1 with at least 8 different LOH regions, and 30 of 32 (94%) had biallelic loss of either TSC2 or TSC1. Whole exome sequencing identified a median of 4 somatic non-synonymous coding region mutations (other than in TSC2/TSC1), a mutation rate lower than nearly all other cancer types. Three genes with mutations were known cancer associated genes (BAP1, ARHGAP35 and SPEN), but they were mutated in a single sample each, and were missense variants with uncertain functional effects. Analysis of sixteen angiomyolipomas from a TSC subject showed both second hit point mutations and CN-LOH in TSC2, many of which were distinct, indicating that they were of independent clonal origin. However, three tumors had two shared mutations in addition to private somatic mutations, suggesting a branching evolutionary pattern of tumor development following initiating loss of TSC2. Our results indicate that TSC2 and less commonly TSC1 alterations are the primary essential driver event in angiomyolipoma/LAM, whereas other somatic mutations are rare and likely do not contribute to tumor development. We performed comprehensive genome analysis of a kidney tumor called angiomyolipoma. These tumors are known to develop in most individuals who have Tuberous Sclerosis Complex (TSC) and those who have sporadic lymphangioleiomyomatosis (LAM), and are seen rarely in the general population. In these angiomyolipomas, we found consistent involvement of the TSC2 and TSC1 genes that are known to cause TSC, but very few (<5 on average) mutations elsewhere in the protein-coding regions. This is in stark contrast to other adult solid tumours that typically harbor hundreds to thousands of such mutations. Our results indicate that genetic alterations in TSC2/TSC1 are the primary and essential driver genetic events for development and progression of renal angiomyolipoma. Analysis of multiple angiomyolipomas from a single patient showed distinct genetic aberrations in the majority of samples, indicating that most of the tumors had developed independently. Branched clonal evolution was evident from the observation of three tumors that shared 2 mutations in addition to mutations private to each. Our results indicate that therapeutic approaches for treatment of patients with angiomyolipoma should focus on the consequences of TSC2/TSC1 loss, including but not limited to mTOR activation.
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Affiliation(s)
- Krinio Giannikou
- Division of Pulmonary and Critical Care Medicine and of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Izabela A. Malinowska
- Division of Pulmonary and Critical Care Medicine and of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Trevor J. Pugh
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Rachel Yan
- Division of Pulmonary and Critical Care Medicine and of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yuen-Yi Tseng
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Coyin Oh
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Jaegil Kim
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Magdalena E. Tyburczy
- Division of Pulmonary and Critical Care Medicine and of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yvonne Chekaluk
- Division of Pulmonary and Critical Care Medicine and of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yang Liu
- Division of Pulmonary and Critical Care Medicine and of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Nicola Alesi
- Division of Pulmonary and Critical Care Medicine and of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Geraldine A. Finlay
- Tufts New England Medical Center, Boston, Massachusetts, United States of America
| | - Chin-Lee Wu
- Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Sabina Signoretti
- Division of Pulmonary and Critical Care Medicine and of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Matthew Meyerson
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Gad Getz
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Jesse S. Boehm
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Elizabeth P. Henske
- Division of Pulmonary and Critical Care Medicine and of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- * E-mail: (EPH); (DJK)
| | - David J. Kwiatkowski
- Division of Pulmonary and Critical Care Medicine and of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- * E-mail: (EPH); (DJK)
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5
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Kwiatkowski DJ, Choueiri TK, Fay AP, Rini BI, Thorner AR, de Velasco G, Tyburczy ME, Hamieh L, Albiges L, Agarwal N, Ho TH, Song J, Pignon JC, Barrios PM, Michaelson MD, Van Allen E, Krajewski KM, Porta C, Pal S, Bellmunt J, McDermott DF, Heng DYC, Gray KP, Signoretti S. Mutations in TSC1, TSC2, and MTOR Are Associated with Response to Rapalogs in Patients with Metastatic Renal Cell Carcinoma. Clin Cancer Res 2016; 22:2445-2452. [PMID: 26831717 DOI: 10.1158/1078-0432.ccr-15-2631] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 01/05/2016] [Indexed: 12/23/2022]
Abstract
PURPOSE We examined the hypothesis that mutations in mTOR pathway genes are associated with response to rapalogs in metastatic renal cell carcinoma (mRCC). EXPERIMENTAL DESIGN We studied a cohort of mRCC patients who were treated with mTOR inhibitors with distinct clinical outcomes. Tumor DNA from 79 subjects was successfully analyzed for mutations using targeted next-generation sequencing of 560 cancer genes. Responders were defined as those with partial response (PR) by RECIST v1.0 or stable disease with any tumor shrinkage for 6 months or longer. Nonresponders were defined as those with disease progression during the first 3 months of therapy. Fisher exact test assessed the association between mutation status in mTOR pathway genes and treatment response. RESULTS Mutations in MTOR, TSC1, or TSC2 were more common in responders, 12 (28%) of 43, than nonresponders, 4 (11%) of 36 (P = 0.06). Mutations in TSC1 or TSC2 alone were also more common in responders, 9 (21%), than nonresponders, 2(6%), (P = 0.05). Furthermore, 5 (42%) of 12 subjects with PR had mutations in MTOR, TSC1, or TSC2 compared with 4 (11%) of 36 nonresponders (P = 0.03). Eight additional non-mTOR pathway genes were found to be mutated in at least 4 of 79 tumors (5%); none were associated positively with response. CONCLUSIONS In this cohort of mRCC patients, mutations in MTOR, TSC1, or TSC2 were more common in patients who experienced clinical benefit from rapalogs than in those who progressed. However, a substantial fraction of responders (24 of 43, 56%) had no mTOR pathway mutation identified. Clin Cancer Res; 22(10); 2445-52. ©2016 AACRSee related commentary by Voss and Hsieh, p. 2320.
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Affiliation(s)
- David J Kwiatkowski
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, US.,Department of Medicine, Brigham and Women's Hospital, Boston, MA, US.,Harvard Medical School, Boston, MA, US
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, US.,Department of Medicine, Brigham and Women's Hospital, Boston, MA, US.,Harvard Medical School, Boston, MA, US
| | - André P Fay
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, US.,PUCRS School of Medicine, Porto Alegre, Brazil
| | - Brian I Rini
- Department of Medical Oncology, Cleveland Clinic, Cleveland, US
| | - Aaron R Thorner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, US.,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA, US
| | | | | | - Lana Hamieh
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, US
| | - Laurence Albiges
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, US.,Institut Gustave Roussy, Villejuif, France
| | - Neeraj Agarwal
- Department of Medical Oncology, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Thai H Ho
- Department of Medical Oncology, Mayo Clinic, Arizona, Scottsdale, AZ, US
| | - Jiaxi Song
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, US
| | - Jean-Christophe Pignon
- Harvard Medical School, Boston, MA, US.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, US
| | | | - M Dror Michaelson
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, MA
| | - Eliezer Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, US.,Department of Medicine, Brigham and Women's Hospital, Boston, MA, US.,Harvard Medical School, Boston, MA, US
| | | | - Camillo Porta
- San Matteo University Hospital Foundation, Pavia, Italy
| | - Sumanta Pal
- Department of Medical Oncology & Therapeutics Research, City of Hope, US
| | - Joaquim Bellmunt
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, US.,Department of Medicine, Brigham and Women's Hospital, Boston, MA, US.,Harvard Medical School, Boston, MA, US
| | - David F McDermott
- Harvard Medical School, Boston, MA, US.,Deparment of Medical Oncology, Beth-Israel Deaconess Medical Center, Boston, MA, US
| | - Daniel Y C Heng
- Tom Baker Cancer Center and University of Calgary, Calgary, Canada
| | - Kathryn P Gray
- Biostatistics & Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, US
| | - Sabina Signoretti
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, US.,Harvard Medical School, Boston, MA, US.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, US
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Malik AR, Liszewska E, Skalecka A, Urbanska M, Iyer AM, Swiech LJ, Perycz M, Parobczak K, Pietruszka P, Zarebska MM, Macias M, Kotulska K, Borkowska J, Grajkowska W, Tyburczy ME, Jozwiak S, Kwiatkowski DJ, Aronica E, Jaworski J. Tuberous sclerosis complex neuropathology requires glutamate-cysteine ligase. Acta Neuropathol Commun 2015. [PMID: 26220190 PMCID: PMC4518593 DOI: 10.1186/s40478-015-0225-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION Tuberous sclerosis complex (TSC) is a genetic disease resulting from mutation in TSC1 or TSC2 and subsequent hyperactivation of mammalian Target of Rapamycin (mTOR). Common TSC features include brain lesions, such as cortical tubers and subependymal giant cell astrocytomas (SEGAs). However, the current treatment with mTOR inhibitors has critical limitations. We aimed to identify new targets for TSC pharmacotherapy. RESULTS The results of our shRNA screen point to glutamate-cysteine ligase catalytic subunit (GCLC), a key enzyme in glutathione synthesis, as a contributor to TSC-related phenotype. GCLC inhibition increased cellular stress and reduced mTOR hyperactivity in TSC2-depleted neurons and SEGA-derived cells. Moreover, patients' brain tubers showed elevated GCLC and stress markers expression. Finally, GCLC inhibition led to growth arrest and death of SEGA-derived cells. CONCLUSIONS We describe GCLC as a part of redox adaptation in TSC, needed for overgrowth and survival of mutant cells, and provide a potential novel target for SEGA treatment.
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Tyburczy ME, Jozwiak S, Malinowska IA, Chekaluk Y, Pugh TJ, Wu CL, Nussbaum RL, Seepo S, Dzik T, Kotulska K, Kwiatkowski DJ. A shower of second hit events as the cause of multifocal renal cell carcinoma in tuberous sclerosis complex. Hum Mol Genet 2014; 24:1836-42. [PMID: 25432535 DOI: 10.1093/hmg/ddu597] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Tuberous sclerosis complex (TSC) is a genetic disorder characterized by seizures and tumor formation in multiple organs, mainly in the brain, skin, kidney, lung and heart. Renal cell carcinoma (RCC) occurs in ∼3% of TSC patients, and typically develops at age <50. Here we describe genetic findings in two TSC patients with multiple renal tumors, each of whom had the germline mutation TSC2 p.R905Q. The first (female) TSC patient had a left followed by a right nephrectomy at ages 24 and 27. Both kidneys showed multifocal TSC-associated papillary RCC (PRCC). Targeted, next-generation sequencing (NGS) analysis of TSC2 in five tumors (four from the left kidney, one from the right) showed loss of heterozygosity in one tumor, and four different TSC2 point mutations (p.E1351*, p.R1032*, p.R1713H, c.4178_4179delCT) in the other four samples. Only one of the 11 other tumors available from this patient had one of the TSC2 second hit mutations identified. Whole-exome analysis of the five tumors identified a very small number of additional mutated genes, with an average of 3.4 nonsilent coding, somatic mutations per tumor, none of which were seen in >1 tumor. The second (male) TSC patient had bilateral partial nephrectomies (both at age 36), with similar findings of multifocal PRCC. NGS analysis of TSC2 in two of these tumors identified a second hit mutation c.2355+1G>T in one sample that was not seen in other tumors. In conclusion, we report the first detailed genetic analysis of RCCs in TSC patients. Molecular studies indicate that tumors developed independently due to various second hit events, suggesting that these patients experienced a 'shower' of second hit mutations in TSC2 during kidney development leading to this severe phenotype.
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Affiliation(s)
- Magdalena E Tyburczy
- Division of Pulmonary Medicine and of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Izabela A Malinowska
- Division of Pulmonary Medicine and of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Yvonne Chekaluk
- Division of Pulmonary Medicine and of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Chin-Lee Wu
- Pathology Department, Massachusetts General Hospital, Boston, MA, USA
| | - Robert L Nussbaum
- Division of Genomic Medicine, Helen Diller Family Comprehensive Cancer Center and Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Sara Seepo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Tomasz Dzik
- Children's Memorial Health Institute of Warsaw, Warsaw, Poland
| | | | - David J Kwiatkowski
- Division of Pulmonary Medicine and of Genetics, Brigham and Women's Hospital, Boston, MA, USA,
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8
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Tyburczy ME, Wang JA, Li S, Thangapazham R, Chekaluk Y, Moss J, Kwiatkowski DJ, Darling TN. Sun exposure causes somatic second-hit mutations and angiofibroma development in tuberous sclerosis complex. Hum Mol Genet 2014; 23:2023-9. [PMID: 24271014 PMCID: PMC3959815 DOI: 10.1093/hmg/ddt597] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 11/19/2013] [Accepted: 11/21/2013] [Indexed: 01/09/2023] Open
Abstract
Tuberous sclerosis complex (TSC) is characterized by the formation of tumors in multiple organs and is caused by germline mutation in one of two tumor suppressor genes, TSC1 and TSC2. As for other tumor suppressor gene syndromes, the mechanism of somatic second-hit events in TSC tumors is unknown. We grew fibroblast-like cells from 29 TSC skin tumors from 22 TSC subjects and identified germline and second-hit mutations in TSC1/TSC2 using next-generation sequencing. Eighteen of 22 (82%) subjects had a mutation identified, and 8 of the 18 (44%) subjects were mosaic with mutant allele frequencies of 0 to 19% in normal tissue DNA. Multiple tumors were available from four patients, and in each case, second-hit mutations in TSC2 were distinct indicating they arose independently. Most remarkably, 7 (50%) of the 14 somatic point mutations were CC>TT ultraviolet 'signature' mutations, never seen as a TSC germline mutation. These occurred exclusively in facial angiofibroma tumors from sun-exposed sites. These results implicate UV-induced DNA damage as a cause of second-hit mutations and development of TSC facial angiofibromas and suggest that measures to limit UV exposure in TSC children and adults should reduce the frequency and severity of these lesions.
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Affiliation(s)
- Magdalena E. Tyburczy
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ji-an Wang
- Department of Dermatology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA and
| | - Shaowei Li
- Department of Dermatology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA and
| | - Rajesh Thangapazham
- Department of Dermatology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA and
| | - Yvonne Chekaluk
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Joel Moss
- Cardiovascular and Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David J. Kwiatkowski
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas N. Darling
- Department of Dermatology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA and
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Tyburczy ME, Kotulska K, Pokarowski P, Mieczkowski J, Grajkowska W, Jozwiak S, Kaminska B. Abstract 4353: Identification of proteins regulated by mTOR in brain tumors of patients with tuberous sclerosis complex. Cancer Res 2010. [DOI: 10.1158/1538-7445.am10-4353] [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
Tuberous sclerosis complex (TSC) is characterized by the formation of benign tumors in many organs (mainly brain, heart, kidneys, skin or lungs) and is often associated with epilepsy, mental retardation and autism. Brain lesions include subependymal giant cell astrocytomas (SEGAs), low-grade tumors of a mixed glioneuronal lineage, which are the major cause of morbidity in children and young adults with TSC. The disease is caused by mutations in tumor suppressor genes: TSC1 (Hamartin) or TSC2 (Tuberin) leading to enhancement of mammalian Target Of Rapamycin (mTOR) kinase activity, deregulation of cell growth and tumorigenesis. Signaling via mTOR participates in complex genomic responses but its effectors in the brain are largely unknown. Therefore, we performed first genome-wide expression profiling on SEGAs using Affymetrix Human Genome arrays. We identified differentially expressed specific genes involved in tumorigenesis (up-regulated) and the nervous system development (down-regulated) in SEGAs and SEGA-derived cell cultures when compared to the normal brain or cultured human astrocytes. Out of genes differentially expressed in TSC, 11 were validated by real time PCR on independent tumor samples and 3 SEGA-derived cultures. Immunohistochemistry on paraffin-embedded sections confirmed up-regulated levels of several identified proteins in SEGAs. ANXA1, GPNMB, LTF, RND3, S100A11, SFRP4 and NPTX1 were shown to be mTOR effector genes in SEGA, as their expression was modulated by an mTOR inhibitor - rapamycin in SEGA-derived cell cultures. We are currently investigating the role of ANXA1, GPNMB and S100A11 in regulation of cell viability, migration, adhesion, size and shape of cultured SEGA cells using RNA interference. Furthermore, we observed that combined pharmacological inhibition of mTOR and extracellular signal regulated kinase (ERK) signaling pathways in SEGA cells affected their viability (MTT metabolism test), proliferation (BrdU assay), migration (scratch assay), morphology and size (volume, area and height measured with confocal microscopy). For the first time, we identified genes related to the occurrence of SEGA and regulated by mTOR, and showed an effective modulation of SEGA growth by inhibition of both mTOR and ERK signaling pathways, which could represent a novel therapeutic approach. The study was supported by Ministry of Science and Higher Education grant N N301 263536.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4353.
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Affiliation(s)
| | | | | | | | | | | | - Bozena Kaminska
- 1The Nencki Institute of Experimental Biology, Warsaw, Poland
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Mieczkowski J, Tyburczy ME, Dabrowski M, Pokarowski P. Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measurements. BMC Bioinformatics 2010; 11:104. [PMID: 20181266 PMCID: PMC2841208 DOI: 10.1186/1471-2105-11-104] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Accepted: 02/24/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Affymetrix GeneChip microarrays are popular platforms for expression profiling in two types of studies: detection of differential expression computed by p-values of t-test and estimation of fold change between analyzed groups. There are many different preprocessing algorithms for summarizing Affymetrix data. The main goal of these methods is to remove effects of non-specific hybridization, and to optimally combine information from multiple probes annotated to the same transcript. The methods are benchmarked by comparison with reference methods, such as quantitative reverse-transcription PCR (qRT-PCR). RESULTS We present a comprehensive analysis of agreement between Affymetrix GeneChip and qRT-PCR results. We analyzed the influence of filtering by fraction Present calls introduced by J.N. McClintick and H.J. Edenberg (2006) and 2 mapping procedures: updated probe sets definitions proposed by Dai et al. (2005) and our "naive mapping" method. Because of evolution of genome sequence annotations since the time when microarrays were designed, we also studied the effect of the annotation release date. These comparisons were prepared for 6 popular preprocessing algorithms (MAS5, PLIER, RMA, GC-RMA, MBEI, and MBEImm) in the 2 above-mentioned types of studies. We used data sets from 6 independent biological experiments. As a measure of reproducibility of microarray and qRT-PCR values, we used linear and rank correlation coefficients. CONCLUSIONS We show that filtering by fraction Present calls increased correlations for all 6 preprocessing algorithms. We observed the difference in performance of PM-MM and PM-only methods: using MM probes increased correlations in fold change studies, but PM-only methods proved to perform better in detection of differential expression. We recommend using GC-RMA for detection of differential expression and PLIER for estimation of fold change. The use of the more recent annotation improves the results in both types of studies, encouraging re-analysis of old data.
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Affiliation(s)
- Jakub Mieczkowski
- Laboratory of Transcription Regulation, Department of Cell Biology, The Nencki Institute of Experimental Biology, Pasteur 3, 02-093 Warsaw, Poland.
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