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Gourisankar S, Krokhotin A, Wenderski W, Crabtree GR. Context-specific functions of chromatin remodellers in development and disease. Nat Rev Genet 2024; 25:340-361. [PMID: 38001317 DOI: 10.1038/s41576-023-00666-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2023] [Indexed: 11/26/2023]
Abstract
Chromatin remodellers were once thought to be highly redundant and nonspecific in their actions. However, recent human genetic studies demonstrate remarkable biological specificity and dosage sensitivity of the thirty-two adenosine triphosphate (ATP)-dependent chromatin remodellers encoded in the human genome. Mutations in remodellers produce many human developmental disorders and cancers, motivating efforts to investigate their distinct functions in biologically relevant settings. Exquisitely specific biological functions seem to be an emergent property in mammals, and in many cases are based on the combinatorial assembly of subunits and the generation of stable, composite surfaces. Critical interactions between remodelling complex subunits, the nucleosome and other transcriptional regulators are now being defined from structural and biochemical studies. In addition, in vivo analyses of remodellers at relevant genetic loci have provided minute-by-minute insights into their dynamics. These studies are proposing new models for the determinants of remodeller localization and function on chromatin.
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Affiliation(s)
- Sai Gourisankar
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Andrey Krokhotin
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Wendy Wenderski
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Gerald R Crabtree
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University, Stanford, CA, USA.
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2
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Walhart TA, Vacca B, Hepperla AJ, Hamad SH, Petrongelli J, Wang Y, McKean EL, Moksa M, Cao Q, Yip S, Hirst M, Weissman BE. SMARCB1 Loss in Poorly Differentiated Chordomas Drives Tumor Progression. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:456-473. [PMID: 36657718 PMCID: PMC10123523 DOI: 10.1016/j.ajpath.2022.12.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/08/2022] [Accepted: 12/20/2022] [Indexed: 01/18/2023]
Abstract
Poorly differentiated (PD) chordoma, a rare, aggressive tumor originating from notochordal tissue, shows loss of SMARCB1 expression, a core component of the Switch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complexes. To determine the impact of SMARCB1 re-expression on cell growth and gene expression, two SMARCB1-negative PD chordoma cell lines with an inducible SMARCB1 expression system were generated. After 72 hours of induction of SMARCB1, both SMARCB1-negative PD chordoma cell lines continued to proliferate. This result contrasted with those observed with SMARCB1-negative rhabdoid cell lines in which SMARCB1 re-expression caused the rapid inhibition of growth. We found that the lack of growth inhibition may arise from the loss of CDKN2A (p16INK4A) expression in PD chordoma cell lines. RNA-sequencing of cell lines after SMARCB1 re-expression showed a down-regulation for rRNA and RNA processing as well as metabolic processing and increased expression of genes involved in cell adhesion, cell migration, and development. Taken together, these data establish that SMARCB1 re-expression in PD chordomas alters the repertoire of SWI/SNF complexes, perhaps restoring those associated with cellular differentiation. These novel findings support a model in which SMARCB1 inactivation blocks the conversion of growth-promoting SWI/SNF complexes to differentiation-inducing ones, and they implicate SMARCB1 loss as a late event in tumorigenic progression. Importantly, the absence of growth inhibition after SMARCB1 restoration creates a unique opportunity to identify therapeutic vulnerabilities.
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Affiliation(s)
- Tara A Walhart
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Bryanna Vacca
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina; Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Austin J Hepperla
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Samera H Hamad
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina; Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - James Petrongelli
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Yemin Wang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Erin L McKean
- Department of Otolaryngology and Neurosurgery, University of Michigan, Ann Arbor, Michigan
| | - Michelle Moksa
- Department of Microbiology & Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, British Columbia, Canada
| | - Qi Cao
- Department of Microbiology & Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, British Columbia, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Martin Hirst
- Department of Microbiology & Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, British Columbia, Canada
| | - Bernard E Weissman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina; Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina; Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina.
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Carcamo S, Nguyen CB, Grossi E, Filipescu D, Alpsoy A, Dhiman A, Sun D, Narang S, Imig J, Martin TC, Parsons R, Aifantis I, Tsirigos A, Aguirre-Ghiso JA, Dykhuizen EC, Hasson D, Bernstein E. Altered BAF occupancy and transcription factor dynamics in PBAF-deficient melanoma. Cell Rep 2022; 39:110637. [PMID: 35385731 PMCID: PMC9013128 DOI: 10.1016/j.celrep.2022.110637] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 01/04/2022] [Accepted: 03/16/2022] [Indexed: 12/25/2022] Open
Abstract
ARID2 is the most recurrently mutated SWI/SNF complex member in melanoma; however, its tumor-suppressive mechanisms in the context of the chromatin landscape remain to be elucidated. Here, we model ARID2 deficiency in melanoma cells, which results in defective PBAF complex assembly with a concomitant genomic redistribution of the BAF complex. Upon ARID2 depletion, a subset of PBAF and shared BAF-PBAF-occupied regions displays diminished chromatin accessibility and associated gene expression, while BAF-occupied enhancers gain chromatin accessibility and expression of genes linked to the process of invasion. As a function of altered accessibility, the genomic occupancy of melanoma-relevant transcription factors is affected and significantly correlates with the observed transcriptional changes. We further demonstrate that ARID2-deficient cells acquire the ability to colonize distal organs in multiple animal models. Taken together, our results reveal a role for ARID2 in mediating BAF and PBAF subcomplex chromatin dynamics with consequences for melanoma metastasis.
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Affiliation(s)
- Saul Carcamo
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute Bioinformatics for Next Generation Sequencing (BiNGS) Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christie B Nguyen
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elena Grossi
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dan Filipescu
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aktan Alpsoy
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Alisha Dhiman
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Dan Sun
- Division of Hematology and Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sonali Narang
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, New York, NY 10016, USA
| | - Jochen Imig
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, New York, NY 10016, USA
| | - Tiphaine C Martin
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ramon Parsons
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Iannis Aifantis
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, New York, NY 10016, USA
| | - Aristotelis Tsirigos
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, New York, NY 10016, USA; Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY 10016, USA
| | - Julio A Aguirre-Ghiso
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Hematology and Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Otolaryngology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute Bioinformatics for Next Generation Sequencing (BiNGS) Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emily Bernstein
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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4
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The impact of surgical resection and adjuvant therapy on survival in paediatric patients with Atypical Teratoid Rhabdoid Tumour: Systematic review and pooled survival analysis. World Neurosurg 2022; 164:216-227. [DOI: 10.1016/j.wneu.2022.04.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/17/2022] [Accepted: 04/18/2022] [Indexed: 11/17/2022]
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5
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Schaefer IM, Al-Ibraheemi A, Qian X. Cytomorphologic Spectrum of SMARCB1-Deficient Soft Tissue Neoplasms. Am J Clin Pathol 2021; 156:229-245. [PMID: 33608696 DOI: 10.1093/ajcp/aqaa223] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES The SWI/SNF complex core subunit SMARCB1 is inactivated in a variety of neoplasms that share characteristic "rhabdoid" cytomorphology. The aim of this study was to evaluate SMARCB1-deficient soft tissue neoplasms on cytology to identify diagnostic clues. METHODS Eleven SMARCB1-deficient tumors, including six epithelioid sarcomas, three malignant rhabdoid tumors, one epithelioid malignant peripheral nerve sheath tumor (MPNST), and one poorly differentiated chordoma with fine-needle aspiration (FNA), serous effusion, or touch prep (TP) from two institutions, were included. Targeted next-generation sequencing (NGS) was performed in two cases. RESULTS Evaluation of FNA (n = 4), effusion (n = 4), and TP (n = 3) in nine adult and two pediatric patients demonstrated cellular samples (n = 11), epithelioid cells with rhabdoid morphology (n = 9), eccentrically located nuclei with prominent nucleoli (n = 7), and cytoplasmic bodies (n = 4); two patients were diagnosed on FNA with cell block. Immunohistochemistry (IHC) demonstrated SMARCB1 loss in all cases and keratin and/or EMA expression in all but the epithelioid MPNST; NGS identified SMARCB1 inactivation in both cases. CONCLUSIONS SMARCB1-deficient soft tissue neoplasms comprise a variety of tumors with epithelioid morphology and frequent expression of keratin and/or EMA. Recognition of characteristic rhabdoid morphology on cytology can prompt IHC and/or NGS testing for SMARCB1 deficiency and help establish the diagnosis.
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Affiliation(s)
| | - Alyaa Al-Ibraheemi
- Department of Pathology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiaohua Qian
- Department of Pathology, Brigham and Women’s Hospital
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6
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Abstract
The SMARCB1/INI1 gene was first discovered in the mid-1990s, and since then it has been revealed that loss of function mutations in this gene result in aggressive rhabdoid tumors. Recently, the term "rhabdoid tumor" has become synonymous with decreased SMARCB1/INI1 expression. When genetic aberrations in the SMARCB1/INI1 gene occur, the result can cause complete loss of expression, decreased expression, and mosaic expression. Although SMARCB1/INI1-deficient tumors are predominantly sarcomas, this is a diverse group of tumors with mixed phenotypes, which can often make the diagnosis challenging. Prognosis for these aggressive tumors is often poor. Moreover, refractory and relapsing progressive disease is common. As a result, accurate and timely diagnosis is imperative. Despite the SMARCB1/INI1 gene itself and its implications in tumorigenesis being discovered over two decades ago, there is a paucity of rhabdoid tumor cases reported in the literature that detail SMARCB1/INI1 expression. Much work remains if we hope to provide additional therapeutic strategies for patients with aggressive SMARCB1/INI1-deficient tumors.
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Affiliation(s)
- Nathaniel A Parker
- University of Kansas School of Medicine, 1010 N Kansas St, Wichita, KS, 67214, USA
| | - Ammar Al-Obaidi
- University of Kansas School of Medicine, 1010 N Kansas St, Wichita, KS, 67214, USA
| | - Jeremy M Deutsch
- Cancer Center of Kansas, 818 N. Emporia #403, Wichita, KS, 67214, USA
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Innis SM, Cabot B. GBAF, a small BAF sub-complex with big implications: a systematic review. Epigenetics Chromatin 2020; 13:48. [PMID: 33143733 PMCID: PMC7607862 DOI: 10.1186/s13072-020-00370-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/23/2020] [Indexed: 12/01/2022] Open
Abstract
ATP-dependent chromatin remodeling by histone-modifying enzymes and chromatin remodeling complexes is crucial for maintaining chromatin organization and facilitating gene transcription. In the SWI/SNF family of ATP-dependent chromatin remodelers, distinct complexes such as BAF, PBAF, GBAF, esBAF and npBAF/nBAF are of particular interest regarding their implications in cellular differentiation and development, as well as in various diseases. The recently identified BAF subcomplex GBAF is no exception to this, and information is emerging linking this complex and its components to crucial events in mammalian development. Furthermore, given the essential nature of many of its subunits in maintaining effective chromatin remodeling function, it comes as no surprise that aberrant expression of GBAF complex components is associated with disease development, including neurodevelopmental disorders and numerous malignancies. It becomes clear that building upon our knowledge of GBAF and BAF complex function will be essential for advancements in both mammalian reproductive applications and the development of more effective therapeutic interventions and strategies. Here, we review the roles of the SWI/SNF chromatin remodeling subcomplex GBAF and its subunits in mammalian development and disease.
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Affiliation(s)
- Sarah M Innis
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Birgit Cabot
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA.
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8
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Schaefer IM, Hornick JL. SWI/SNF complex-deficient soft tissue neoplasms: An update. Semin Diagn Pathol 2020; 38:222-231. [PMID: 32646614 DOI: 10.1053/j.semdp.2020.05.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/12/2020] [Accepted: 05/18/2020] [Indexed: 01/04/2023]
Abstract
The SWItch Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex is a large multi-subunit protein assembly that orchestrates chromatin compaction and accessibility for gene transcription in an ATP-dependent manner. As a key epigenetic regulator, the SWI/SNF complex coordinates gene expression, cell proliferation and differentiation, and its biologic functions, in part, antagonize the polycomb repressive complex 2. The mammalian SWI/SNF complex consists of 15 subunits encoded by 29 genes, some of which are recurrently mutated in human cancers, in the germline or sporadic setting. Most SWI/SNF-deficient tumors share common "rhabdoid" cytomorphology. SMARCB1 (INI1) is the subunit most frequently inactivated in soft tissue neoplasms. Specifically, SMARCB1 deficiency is observed as the genetic hallmark in virtually all malignant rhabdoid tumors, and most cases of epithelioid sarcoma and poorly differentiated chordoma. In addition, subsets of myoepithelial carcinoma (10-40%), extraskeletal myxoid chondrosarcoma (20%), epithelioid schwannoma (40%), and epithelioid malignant peripheral nerve sheath tumor (70%) demonstrate SMARCB1 loss. The gene encoding the SS18 subunit is involved in the SS18-SSX rearrangement, which is pathognomonic of synovial sarcoma and indirectly inactivates SMARCB1. Finally, undifferentiated SMARCA4-deficient thoracic sarcomas are defined by SMARCA4 subunit inactivation, leading to SMARCA4 and SMARCA2 loss. Rarely, inactivation of alternate but biologically equivalent key regulators can substitute for canonical subunit deficiency, such as SMARCA4 inactivation in cases of SMARCB1-retained epithelioid sarcoma. This review briefly highlights SWI/SNF complex biologic functions and its roles in human cancer and provides a detailed update on recent advances in soft tissue neoplasms with canonical SWI/SNF complex deficiency, correlating morphologic, genomic, and immunohistochemical findings.
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Affiliation(s)
- Inga-Marie Schaefer
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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9
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Recurrent SMARCB1 Inactivation in Epithelioid Malignant Peripheral Nerve Sheath Tumors. Am J Surg Pathol 2020; 43:835-843. [PMID: 30864974 DOI: 10.1097/pas.0000000000001242] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Epithelioid malignant peripheral nerve sheath tumors (EMPNST) are characterized by diffuse S-100 and SOX10 positivity, frequent immunohistochemical loss of SMARCB1 expression (70%), and rare association with neurofibromatosis type 1. Some cases arise in a preexisting epithelioid schwannoma (ESCW), which also show SMARCB1 loss in 40% of cases. To date, little is known about the genomic landscape of this distinctive variant of malignant peripheral nerve sheath tumor. The aim of this study was to use targeted next-generation sequencing to identify recurrent genomic aberrations in EMPNST and a subset of ESCW, including the basis of SMARCB1 loss. Sixteen EMPNSTs (13 SMARCB1-lost, 3 SMARCB1-retained) and 5 ESCWs with SMARCB1 loss were selected for the cohort. Sequencing identified SMARCB1 gene inactivation in 12/16 (75%) EMPNST and all 5 (100%) ESCW through homozygous deletion (N=8), nonsense (N=7), frameshift (N=2), or splice site (N=2) mutations; 2 EMPNSTs harbored 2 concurrent mutations each. SMARCB1 immunohistochemistry status and SMARCB1 alterations were concordant in 20/21 of the sequenced tumors. Additional genetic alterations in a subset of EMPNST included inactivation of CDKN2A and gain of chromosome 2q. Among SMARCB1-wild-type EMPNSTs there were single cases each with NF1 and NF2 mutations. No cases had SUZ12 or EED mutations. In summary, we identified recurrent SMARCB1 alterations in EMPNST (and all 5 SMARCB1-negative ESCWs tested), supporting loss of SMARCB1 tumor suppressor function as a key oncogenic event. SMARCB1-retained EMPNSTs lack SMARCB1 mutations and harbor different driver events.
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10
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Germline Genetics and Childhood Cancer: Emerging Cancer Predisposition Syndromes and Psychosocial Impacts. Curr Oncol Rep 2019; 21:85. [PMID: 31414239 DOI: 10.1007/s11912-019-0836-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
PURPOSE OF REVIEW Germline genetic variants contribute to a substantial proportion of cases of cancer in childhood. The purpose of this review is to describe two emerging pediatric cancer predisposition syndromes, including published surveillance protocols, as well as the psychological impacts related to childhood cancer predisposition. RECENT FINDINGS DICER1 syndrome is pleotropic, predisposing to a variety of tumors and likely phenotypically broader than currently realized. Rhabdoid tumor predisposition syndrome carries a risk for development of aggressive malignancies occurring in nearly any tissue. New pediatric hereditary cancer syndromes are likely to be identified as genetic evaluation evolves. Advantages and disadvantages of genetic testing and surveillance protocols need to be discussed with patients and families in a team-based approach, with the input of a genetic counselor holding expertise in pediatric cancer predisposition. Finally, literature on psychosocial impacts of hereditary cancer syndromes in pediatric patients is sparse, necessitating further research.
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11
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Bhatt MD, Al-Karmi S, Druker H, Gupta A, Lu M, Malkin D, Somers G, Huang A, Bouffet E. Second rhabdoid tumor 8 years after treatment of atypical teratoid/rhabdoid tumor in a child with germline SMARCB1 mutation. Pediatr Blood Cancer 2019; 66:e27546. [PMID: 30393974 DOI: 10.1002/pbc.27546] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 10/19/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Mihir D Bhatt
- Division of Hematology/Oncology, Department of Pediatrics, McMaster Children's Hospital, McMaster University, Hamilton, Ontario, Canada
| | - Salma Al-Karmi
- Pediatric Brain Tumour Program, The Hospital for Sick Children, University of Toronto, Ontario, Canada
| | - Harriet Druker
- Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Ontario, Canada
| | - Abha Gupta
- Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Ontario, Canada
| | - Mei Lu
- Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - David Malkin
- Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Ontario, Canada
| | - Gino Somers
- Department of Laboratory Medicine and Pathology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Annie Huang
- Pediatric Brain Tumour Program, The Hospital for Sick Children, University of Toronto, Ontario, Canada.,Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Eric Bouffet
- Pediatric Brain Tumour Program, The Hospital for Sick Children, University of Toronto, Ontario, Canada
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12
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Agaimy A. SWI/SNF Complex-Deficient Soft Tissue Neoplasms: A Pattern-Based Approach to Diagnosis and Differential Diagnosis. Surg Pathol Clin 2019; 12:149-163. [PMID: 30709441 DOI: 10.1016/j.path.2018.10.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Loss of different components of the Switch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex has been increasingly recognized as a central molecular event driving the initiation and/or dedifferentiation of mostly lethal but histogenetically diverse neoplasms in different body organs. This review summarizes and discusses the morphologic and phenotypic diversity of primary soft tissue neoplasms characterized by SWI/SNF complex deficiency with an emphasis on convergent and divergent cytoarchitectural patterns.
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Affiliation(s)
- Abbas Agaimy
- Institute of Pathology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), University Hospital, Krankenhausstrasse 8-10, 91054 Erlangen, Germany.
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13
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Abstract
Although some soft tissue and bone tumors can be identified based on histologic features alone, immunohistochemistry plays a critical diagnostic role for most mesenchymal tumor types. The discovery of recurrent genomic alterations in many benign and malignant mesenchymal neoplasms has added important biologic insights and expanded the spectrum of some diagnostic subgroups. Some tumors are defined by unique genomic alterations, whereas others share abnormalities that are not tumor-specific and can be observed in a sometimes broad range of biologically unrelated neoplasms. We herein focus on novel immunohistochemical markers, based on molecular genetic alterations, which are particularly useful in the diagnostic workup of selected groups of soft tissue and bone tumors, including recently described entities, specifically round cell sarcomas (Ewing sarcoma, CIC-rearranged sarcoma, and BCOR-rearranged sarcoma), vascular tumors (epithelioid hemangioma, epithelioid hemangioendothelioma, and pseudomyogenic hemangioendothelioma), SMARCB1-deficient neoplasms, adipocytic tumors (spindle cell/pleomorphic lipoma, atypical spindle cell lipomatous tumor, and conventional atypical lipomatous tumor), giant cell-rich bone tumors (giant cell tumor of bone and chondroblastoma), and biphenotypic sinonasal sarcoma. Given the complex nature of sarcoma classification, and the rarity of many mesenchymal tumor types, careful integration of clinical presentation, imaging features, histology, immunophenotype, and cytogenetic/molecular alterations is crucial for accurate diagnosis of soft tissue and bone tumors.
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14
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Pinto EM, Hamideh D, Bahrami A, Orr BA, Lin T, Pounds S, Zambetti GP, Pappo AS, Gajjar A, Agnihotri S, Broniscer A. Malignant rhabdoid tumors originating within and outside the central nervous system are clinically and molecularly heterogeneous. Acta Neuropathol 2018; 136:315-326. [PMID: 29428974 DOI: 10.1007/s00401-018-1814-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/09/2018] [Accepted: 01/29/2018] [Indexed: 01/19/2023]
Abstract
Multifocal synchronous or metachronous atypical teratoid rhabdoid tumors (ATRTs) and non-central nervous system malignant rhabdoid tumors (extra-CNS MRTs) are rare cancers. We reviewed the clinical and radiologic characteristics of affected patients seen at our institution. Genotyping and analysis of copy number abnormalities (CNAs) in SMARCB1 were performed in germline and tumor samples. Tumor samples underwent genome-wide DNA methylation and CNA analysis. The median age at diagnosis of 21 patients was 0.6 years. Two-thirds of ATRTs and extra-CNS MRTs were diagnosed synchronously. Although kidney tumors predominated, including two patients with bilateral involvement, at least 30% of cases lacked renal involvement. Histopathologic review confirmed MRTs in all cases and INI1 expression loss in all tumors tested. Fourteen (78%) of 18 patients tested had heterozygous germline SMARCB1 abnormalities. At least one allelic SMARCB1 abnormality was confirmed in 81 and 88% of ATRTs and extra-CNS MRTs, respectively. Unsupervised hierarchical clustering analysis of DNA methylation in 27 tumors and comparison with a reference group of 150 ATRTs classified the CNS tumors (n = 14) as sonic hedgehog (64%), tyrosinase (21%), and MYC (14%). The MYC subgroup accounted for 85% of 13 extra-CNS MRTs. Of 16 paired ATRTs and extra-CNS MRTs, the tumors in seven of eight patients showed a different pattern of genome-wide DNA methylation and/or CNAs suggestive of non-clonal origin. CNS and extra-CNS tumors had an identical SMARCB1 amplification (n = 1) or very similar DNA methylation pattern (n = 1) suggestive of clonal origin. All patients died of tumor progression. The clinical and molecular characteristics of multifocal ATRTs and extra-CNS MRTs are heterogeneous with most patients harboring a cancer predisposition. Although independent tumor origin was confirmed in most cases, metastatic spread was also documented. The recognition of their distinct molecular characteristics is critical in selecting new biologic therapies against these deadly cancers.
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Abu Arja MH, Patel P, Shah SH, Auletta JJ, Meyer EK, Conley SE, Aldrink JH, Pindrik JA, AbdelBaki MS. Synchronous Central Nervous System Atypical Teratoid/Rhabdoid Tumor and Malignant Rhabdoid Tumor of the Kidney: Case Report of a Long-Term Survivor and Review of the Literature. World Neurosurg 2018; 111:6-15. [DOI: 10.1016/j.wneu.2017.11.158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/27/2017] [Indexed: 10/18/2022]
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16
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Schaefer IM, Cote GM, Hornick JL. Contemporary Sarcoma Diagnosis, Genetics, and Genomics. J Clin Oncol 2018; 36:101-110. [DOI: 10.1200/jco.2017.74.9374] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Sarcomas include diverse mesenchymal neoplasms with widely varied prognosis, clinical behavior, and treatment. Owing to their rarity and histologic overlap, accurate diagnosis of sarcomas can be challenging. Our approach has evolved dramatically in the past few decades, where novel insights into the molecular pathogenetic basis for sarcomas has dramatically (re)shaped contemporary diagnosis, building on a largely morphology- and clinical presentation–based strategy. Examples include the introduction of novel immunohistochemical markers that serve as surrogates for molecular genetic alterations and identification of characteristic molecular alterations. Accordingly, cytogenetic and molecular genetic analyses, such as conventional karyotyping, fluorescence in situ hybridization, reverse transcription–polymerase chain reaction, and targeted sequencing, have increasingly been incorporated into the routine diagnostic work-up of these neoplasms. For those sarcomas with complex cytogenetic changes that lack specific alterations, additional testing is often directed toward identifying lines of differentiation and excluding pathognomonic (cyto-)genetic alterations. Although some gene rearrangements are diagnostic of particular sarcoma types, certain fusion partners, most notably EWSR1, are not tumor specific (and may, in fact, also be found in benign tumors). Correlation with clinical, radiologic, morphologic, and immunohistochemical findings is particularly important in tumors with such rearrangements to establish the correct diagnosis, acknowledging the inherent limitations of diagnostic tests. The recognition of sarcomas occurring in cancer predisposition syndromes is critical, with implications not only for the index patient but also potentially for family members, including the need for genetic counseling and sometimes particular types of surveillance. Together, contemporary sarcoma evaluation involves combining the initial morphologic evaluation with diagnostically relevant cytogenetic, molecular, and immunohistochemical testing methods.
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Affiliation(s)
- Inga-Marie Schaefer
- Inga-Marie Schaefer and Jason L. Hornick, Brigham and Women’s Hospital-Harvard Medical School; and Gregory M. Cote, Massachusetts General Hospital Cancer Center-Harvard Medical School, Boston, MA
| | - Gregory M. Cote
- Inga-Marie Schaefer and Jason L. Hornick, Brigham and Women’s Hospital-Harvard Medical School; and Gregory M. Cote, Massachusetts General Hospital Cancer Center-Harvard Medical School, Boston, MA
| | - Jason L. Hornick
- Inga-Marie Schaefer and Jason L. Hornick, Brigham and Women’s Hospital-Harvard Medical School; and Gregory M. Cote, Massachusetts General Hospital Cancer Center-Harvard Medical School, Boston, MA
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Barresi V, Lionti S, Raso A, Esposito F, Cannavò S, Angileri FF. Pituitary atypical teratoid rhabdoid tumor in a patient with prolactinoma: A unique description. Neuropathology 2017; 38:260-267. [DOI: 10.1111/neup.12440] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/04/2017] [Accepted: 10/04/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Valeria Barresi
- Department of Human Pathology in Adulthood and Evolutive Age; University of Messina; Messina Italy
| | - Simona Lionti
- Department of Human Pathology in Adulthood and Evolutive Age; University of Messina; Messina Italy
| | - Alessandro Raso
- Unit of Neurosurgery; Giannina Gaslini Institute; Genoa Italy
| | - Felice Esposito
- Unit of Neurosurgery, Department of Biomedical and Dental Sciences and Morphofunctional Imaging; University of Messina; Messina Italy
| | - Salvatore Cannavò
- Department of Human Pathology in Adulthood and Evolutive Age; University of Messina; Messina Italy
| | - Filippo F. Angileri
- Unit of Neurosurgery, Department of Biomedical and Dental Sciences and Morphofunctional Imaging; University of Messina; Messina Italy
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Ud Din N, Barakzai A, Memon A, Hasan S, Ahmad Z. Atypical Teratoid/ Rhabdoid Tumor of Brain: a Clinicopathologic Study of Eleven Patients and Review of Literature. Asian Pac J Cancer Prev 2017; 18:949-954. [PMID: 28545192 PMCID: PMC5494244 DOI: 10.22034/apjcp.2017.18.4.949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Background: Atypical teratoid/ rhabdoid tumor (AT/RT) is a rare aggressive embryonal central nervous system (CNS) tumor of infancy and early childhood. Majority of the cases arise in the posterior fossa, and remaining in the cerebrum. Aims: To analyze the clinicopathologic features of AT/RT on a cohort of cases. Materials and methods: All reported cases of AT/RT at the Department of Pathology and Laboratory Medicine, Aga Khan University Hospital (AKUH) from 2007 to 2016 were reviewed for clinical and pathological features. Immunohistochemical stain for INI-1 was performed in all 11 cases. Follow up was obtained. Results: A total of 11 cases were identified. Seven patients were males and 4 were females. The ages ranged from 1 month to 48 months (mean 26.6 months). Six tumors were located in the cerebrum and 3 in the posterior fossa. Exact Location was not known in 2 cases. Histologically, rhabdoid cells were present in sheets in variable proportions in five cases, Medulloblastoma and PNET like areas were seen in 2 cases each. Immunohistochemical stains EMA (10/10), vimentin (7/7), CKAE1/AE3 (8/9), and CD99 (3/4), GFAP (6/10), ASMA (3/4) and synaptophysin (3/4) were positive in varying proportions while desmin was negative in all 6 cases in which it was performed. All 11 tumors lacked immunoreactivity for INI-1 protein. Four patients died of disease with a follow up ranging from 5 to 24 months. Conclusions: AT/RT is a rare highly aggressive embryonal tumor of CNS. A male predominance was noted in our series. We report the first and largest series from Pakistan.
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Affiliation(s)
- Nasir Ud Din
- Department of Pathology and Laboratory Medicine, Aga Khan University Hospital, Karachi, Pakistan.
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Mondì V, Piersigilli F, Salvatori G, Auriti C. The Skin as an Early Expression of Malignancies in the Neonatal Age: A Review of the Literature and a Case Series. BIOMED RESEARCH INTERNATIONAL 2015; 2015:809406. [PMID: 26798643 PMCID: PMC4698537 DOI: 10.1155/2015/809406] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/15/2015] [Accepted: 11/29/2015] [Indexed: 12/13/2022]
Abstract
Skin lesions are a frequent finding in childhood, from infancy throughout adolescence. They can arise from many conditions, including infections and inflammation. Most neonatal rashes are benign and self-limiting and require no treatment. Other conditions may be an expression of malignancy or may be a marker for other abnormalities, such as neural tube defects. Therefore, skin lesions require an extensive evaluation and close follow-up to ensure the best possible outcome. This paper briefly reviews the main tumor types presenting with cutaneous involvement in neonates, followed by the description of some patients admitted to our Neonatal Intensive Care Unit with an early skin expression of malignancies.
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Affiliation(s)
- Vito Mondì
- Department of Medical and Surgical Neonatology, Bambino Gesù Children's Hospital, Piazza S. Onofrio 4, 00165 Rome, Italy
| | - Fiammetta Piersigilli
- Department of Medical and Surgical Neonatology, Bambino Gesù Children's Hospital, Piazza S. Onofrio 4, 00165 Rome, Italy
| | - Guglielmo Salvatori
- Department of Medical and Surgical Neonatology, Bambino Gesù Children's Hospital, Piazza S. Onofrio 4, 00165 Rome, Italy
| | - Cinzia Auriti
- Department of Medical and Surgical Neonatology, Bambino Gesù Children's Hospital, Piazza S. Onofrio 4, 00165 Rome, Italy
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Barresi V, Branca G, Raso A, Mascelli S, Caffo M, Tuccari G. Atypical teratoid rhabdoid tumor involving the nasal cavities and anterior skull base. Neuropathology 2015; 36:283-289. [PMID: 26567940 DOI: 10.1111/neup.12271] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 10/12/2015] [Accepted: 10/13/2015] [Indexed: 12/19/2022]
Abstract
Rhabdoid tumors are a spectrum of neoplasias composed of cells which show rhabdoid morphology but are devoid of skeletal muscle differentiation. These tumors are characterized by inactivation of the INI1/SMARCB1 gene and they have been described in virtually every anatomical site, including the central nervous system (CNS) and sinonasal tract. Rhabdoid tumor of the CNS was named atypical teratoid rhabdoid tumor (ATRT) and it mainly affects children under the age of 3 years with supra- or infra-tentorial location.Herein we report the first case of ATRT infiltrating the nasal cavities and skull base in an adolescent. Due to its unusual location, differential diagnosis was challenging and included several other entities such as sinonasal carcinoma or meningioma. Awareness that ATRT may infiltrate the nasal tract and knowledge of its clinico-pathological, immunohistochemical and biomolecular features are essential for its distinction from other rhabdoid tumors which more frequently involve this anatomical site and for appropriate therapeutic management.
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Affiliation(s)
- Valeria Barresi
- Department of Human Pathology, University of Messina, Messina, Italy
| | - Giovanni Branca
- Department of Human Pathology, University of Messina, Messina, Italy
| | - Alessandro Raso
- Departement of Neurosciences, University of Messina, Messina, Italy
| | | | | | - Giovanni Tuccari
- Department of Human Pathology, University of Messina, Messina, Italy
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Whole Exome- and mRNA-Sequencing of an AT/RT Case Reveals Few Somatic Mutations and Several Deregulated Signalling Pathways in the Context of SMARCB1 Deficiency. BIOMED RESEARCH INTERNATIONAL 2015; 2015:862039. [PMID: 26998479 PMCID: PMC4780067 DOI: 10.1155/2015/862039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 06/30/2015] [Accepted: 07/13/2015] [Indexed: 01/08/2023]
Abstract
Background. AT/RTs are rare aggressive brain tumours, mainly affecting young children. Most cases present with genetic inactivation of SMARCB1, a core member of the SWI/SNF chromatin-remodeling complex. We have performed whole exome- and mRNA-sequencing on an early onset AT/RT case for detection of genetic events potentially contributing to the disease. Results. A de novo germline variant in SMARCB1, c.601C>T p.Arg201∗, in combination with somatic deletion of the healthy allele is likely the major tumour causing event. Only seven somatic small scale mutations were discovered (hitting SEPT03, H2BFM, ZIC4, HIST2H2AB, ZIK1, KRTAP6-3, and IFNA8). All were found with subclonal allele frequencies (range 5.7–17%) and none were expressed. However, besides SMARCB1, candidate genes affected by predicted damaging germline variants that were expressed were detected (KDM5C, NUMA1, and PCM1). Analysis of differently expressed genes revealed many dysregulated pathways in the tumour, such as cell cycle, CXCR4 pathway, GPCR-signalling, and neuronal system. FGFR1, CXCR4, and MDK were upregulated and may represent possible drug targets. Conclusion. The loss of SMARCB1 function leads to AT/RT development and deregulated genes and pathways. Additional predisposing events may however contribute. Studies utilizing NGS technologies in larger cohorts will probably identify recurrent genetic and epigenetic alterations and molecular subgroups with implications for clinical practice and development of targeted therapies.
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22
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Mayes K, Qiu Z, Alhazmi A, Landry JW. ATP-dependent chromatin remodeling complexes as novel targets for cancer therapy. Adv Cancer Res 2015; 121:183-233. [PMID: 24889532 DOI: 10.1016/b978-0-12-800249-0.00005-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The progression to advanced stage cancer requires changes in many characteristics of a cell. These changes are usually initiated through spontaneous mutation. As a result of these mutations, gene expression is almost invariably altered allowing the cell to acquire tumor-promoting characteristics. These abnormal gene expression patterns are in part enabled by the posttranslational modification and remodeling of nucleosomes in chromatin. These chromatin modifications are established by a functionally diverse family of enzymes including histone and DNA-modifying complexes, histone deposition pathways, and chromatin remodeling complexes. Because the modifications these enzymes deposit are essential for maintaining tumor-promoting gene expression, they have recently attracted much interest as novel therapeutic targets. One class of enzyme that has not generated much interest is the chromatin remodeling complexes. In this review, we will present evidence from the literature that these enzymes have both causal and enabling roles in the transition to advanced stage cancers; as such, they should be seriously considered as high-value therapeutic targets. Previously published strategies for discovering small molecule regulators to these complexes are described. We close with thoughts on future research, the field should perform to further develop this potentially novel class of therapeutic target.
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Affiliation(s)
- Kimberly Mayes
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Zhijun Qiu
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Aiman Alhazmi
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Joseph W Landry
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA.
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Stockman DL, Curry JL, Torres-Cabala CA, Watson IR, Siroy AE, Bassett RL, Zou L, Patel KP, Luthra R, Davies MA, Wargo JA, Routbort MA, Broaddus RR, Prieto VG, Lazar AJ, Tetzlaff MT. Use of clinical next-generation sequencing to identify melanomas harboringSMARCB1mutations. J Cutan Pathol 2015; 42:308-17. [DOI: 10.1111/cup.12481] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 02/01/2015] [Indexed: 12/26/2022]
Affiliation(s)
- David L. Stockman
- Department of Pathology and Laboratory Medicine, Section of Dermatopathology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Jonathan L. Curry
- Department of Pathology and Laboratory Medicine, Section of Dermatopathology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Carlos A. Torres-Cabala
- Department of Pathology and Laboratory Medicine, Section of Dermatopathology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Ian R. Watson
- Department of Genomic Medicine; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Alan E. Siroy
- Department of Pathology and Laboratory Medicine, Section of Dermatopathology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Roland L. Bassett
- Department of Biostatistics; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Lihua Zou
- The Eli and Edythe L. Broad Institute of Massachusetts; Institute of Technology and Harvard University; Cambridge Massachusetts USA
| | - Keyur P. Patel
- Department of Pathology and Laboratory Medicine, Section of Dermatopathology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Rajyalakshmi Luthra
- Department of Pathology and Laboratory Medicine, Section of Dermatopathology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Michael A. Davies
- Department of Melanoma Medical Oncology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Jennifer A. Wargo
- Department of Surgery; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Mark A. Routbort
- Department of Pathology and Laboratory Medicine, Section of Dermatopathology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Russell R. Broaddus
- Department of Pathology and Laboratory Medicine, Section of Dermatopathology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Victor G. Prieto
- Department of Pathology and Laboratory Medicine, Section of Dermatopathology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Alexander J. Lazar
- Department of Pathology and Laboratory Medicine, Section of Dermatopathology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Michael T. Tetzlaff
- Department of Pathology and Laboratory Medicine, Section of Dermatopathology; The University of Texas MD Anderson Cancer Center; Houston TX USA
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Brat DJ, Cagle PT, Dillon DA, Hattab EM, McLendon RE, Miller MA, Buckner JC. Template for Reporting Results of Biomarker Testing of Specimens From Patients With Tumors of the Central Nervous System. Arch Pathol Lab Med 2015; 139:1087-93. [DOI: 10.5858/arpa.2014-0588-cp] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Daniel J. Brat
- From the Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia (Dr Brat); the Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas (Dr Cagle); the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Dr Dillon); the Department of Pathology, Indiana University Medical Center, Indianapolis
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25
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Abstract
Rhabdoid tumors (RT), or malignant rhabdoid tumors, are among the most aggressive and lethal forms of human cancer. They can arise in any location in the body but are most commonly observed in the brain, where they are called atypical teratoid/rhabdoid tumors (AT/RT), and in the kidneys, where they are called rhabdoid tumors of the kidney. The vast majority of rhabdoid tumors present with a loss of function in the SMARCB1 gene, also known as INI1, BAF47, and hSNF5, a core member of the SWI/SNF chromatin-remodeling complex. Recently, mutations in a 2nd locus of the SWI/SNF complex, the SMARCA4 gene, also known as BRG1, were found in rhabdoid tumors with retention of SMARCB1 expression. Familial cases may occur in a condition known as rhabdoid tumor predisposition syndrome (RTPS). In RTPS, germline inactivation of 1 allele of a gene occurs. When the mutation occurs in the SMARCB1 gene, the syndrome is called RTPS1, and when the mutation occurs in the SMARCA4 gene it is called RTPS2. Children presenting with RTPS tend to develop tumors at a younger age, but the impact that germline mutation has on survival remains unclear. Adults who carry the mutation tend to develop multiple schwannomas. The diagnosis of RTPS should be considered in patients with RT, especially if they have multiple primary tumors, and/or in individuals with a family history of RT. Because germline mutations result in an increased risk of carriers developing RT, genetic counseling for families with this condition is recommended.
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Affiliation(s)
- Simone T Sredni
- 1 Ann and Robert H. Lurie Children's Hospital of Chicago-Division of Pediatric Neurosurgery, 225 E. Chicago Avenue Box #28, Chicago, IL 60611, USA
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26
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The expanding family of SMARCB1(INI1)-deficient neoplasia: implications of phenotypic, biological, and molecular heterogeneity. Adv Anat Pathol 2014; 21:394-410. [PMID: 25299309 DOI: 10.1097/pap.0000000000000038] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Since the description of atypical teratoid/rhabdoid tumors of the central nervous system and renal/extrarenal malignant rhabdoid tumors in children, the clinicopathologic spectrum of neoplasms having in common a highly variable rhabdoid cell component (0% to 100%) and consistent loss of nuclear SMARCB1 (INI1) expression has been steadily expanding to include cribriform neuroepithelial tumor of the ventricle, renal medullary carcinoma and a subset of collecting duct carcinoma, epithelioid sarcoma, subsets of miscellaneous benign and malignant soft tissue tumors, and rare rhabdoid carcinoma variants of gastroenteropancreatic, sinonasal, and genitourinary tract origin. Although a majority of SMARCB1-deficient neoplasms arise de novo, the origin of SMARCB1-deficient neoplasia in the background of a phenotypically or genetically definable differentiated SMARCB1-intact "parent neoplasm" has been convincingly demonstrated, highlighting the rare occurrence of rhabdoid tumors as "double-hit neoplasia." As a group, SMARCB1-deficient neoplasms occur over a wide age range (0 to 80 y), may be devoid of rhabdoid cells or display uniform rhabdoid morphology, and follow a clinical course that varies from benign to highly aggressive causing death within a few months irrespective of aggressive multimodality therapy. Generally applicable criteria that would permit easy recognition of these uncommon neoplasms do not exist. Diagnosis is based on site-specific and entity-specific sets of clinicopathologic, immunophenotypic, and/or molecular criteria. SMARCB1 immunohistochemistry has emerged as a valuable tool in confirming or screening for SMARCB1-deficient neoplasms. This review summarizes the different phenotypic and topographic subgroups of SMARCB1-deficient neoplasms including sporadic and familial, benign and malignant, and rhabdoid and nonrhabdoid variants, highlighting their phenotypic heterogeneity and molecular complexity.
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27
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No small surprise - small cell carcinoma of the ovary, hypercalcaemic type, is a malignant rhabdoid tumour. J Pathol 2014; 233:209-14. [DOI: 10.1002/path.4362] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 04/11/2014] [Accepted: 04/13/2014] [Indexed: 01/20/2023]
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28
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Jeong JY, Suh YL, Hong S. Atypical teratoid/rhabdoid tumor arising in pleomorphic xanthoastrocytoma: A case report. Neuropathology 2014. [DOI: 10.1111/neup.12106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Ji Yun Jeong
- Department of Pathology; Kyungpook National University Hospital; Kyungpook National University School of Medicine; Daegu Korea
| | - Yeon-Lim Suh
- Department of Pathology; Samsung Medical Center; Sungkyunkwan University School of Medicine; Seoul Korea
| | - SoonWon Hong
- Department of Pathology; Gangnam Severance Hospital; Yonsei University, College of Medicine; Seoul Korea
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29
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Takita J, Chen Y, Kato M, Ohki K, Sato Y, Ohta S, Sugita K, Nishimura R, Hoshino N, Seki M, Sanada M, Oka A, Hayashi Y, Ogawa S. Genome-wide approach to identify second gene targets for malignant rhabdoid tumors using high-density oligonucleotide microarrays. Cancer Sci 2014; 105:258-64. [PMID: 24418192 PMCID: PMC4317948 DOI: 10.1111/cas.12352] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 12/24/2013] [Accepted: 01/04/2014] [Indexed: 12/20/2022] Open
Abstract
Malignant rhabdoid tumor (MRT) is a rare and highly lethal cancer that mainly affects infants and young children. The majority of MRT are characterized by loss of function of SMARCB1 on chromosome 22q11.2. However, little is known about genetic changes other than SMARCB1 alterations that are responsible for the development and/or progression of MRT. To explore additional gene targets in MRT, we analyzed 21 MRT specimens (12 fresh tumors and 9 MRT-derived cell lines) using high-density single nucleotide polymorphism genotyping microarrays. Although MRT genomes are characterized by common 22q11.2 deletions, affecting the SMARCB1 locus with a frequency of 95.2% (20/21 specimens), other genetic changes have been less frequent. Of the 20 specimens with deletions of 22q11.2, eight specimens showed uniparental disomy of the SMARCB1 locus with homozygous deletions or gene mutations. High-resolution analysis also disclosed the recurrent hemizygous/homozygous deletions of 7q35–q36.1, involving the CNTNAP2 locus in three specimens. Mutations analysis of CNTNAP2 showed a novel R157C missense mutation in a primary case, and methylation analysis showed recurrent hypermethylation of CNTNAP2 in three of nine cell lines. These results demonstrated that CNTNAP2 is one of the additional gene targets, other than SMARCB1, in MRT.
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Affiliation(s)
- Junko Takita
- Department of Pediatrics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
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30
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Coffin CM, Davis JL, Borinstein SC. Syndrome-associated soft tissue tumours. Histopathology 2013; 64:68-87. [DOI: 10.1111/his.12280] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Cheryl M Coffin
- Department of Pathology, Microbiology, and Immunology; Vanderbilt University School of Medicine; Nashville TN USA
| | - Jessica L Davis
- Department of Anatomic Pathology; Laboratory Medicine; University of California at San Francisco; San Francisco CA USA
| | - Scott C Borinstein
- Division of Pediatric Hematology/Oncology; Department of Pediatrics; Vanderbilt University School of Medicine; Nashville TN USA
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De Amorim Bernstein K, Sethi R, Trofimov A, Zeng C, Fullerton B, Yeap BY, Ebb D, Tarbell NJ, Yock TI, MacDonald SM. Early clinical outcomes using proton radiation for children with central nervous system atypical teratoid rhabdoid tumors. Int J Radiat Oncol Biol Phys 2013; 86:114-20. [PMID: 23498870 DOI: 10.1016/j.ijrobp.2012.12.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 11/20/2012] [Accepted: 12/06/2012] [Indexed: 02/05/2023]
Abstract
PURPOSE Atypical teratoid/rhabdoid tumor (AT/RT) is an uncommon and aggressive tumor that often affects infants. Irradiation improves survival but has traditionally been avoided in patients under the age of 3 due to the increasing risk of neurocognitive side effects. We report the first cohort of AT/RT patients treated with proton therapy. METHODS AND MATERIALS All patients with AT/RT treated at Massachusetts General Hospital (MGH) Frances H. Burr Proton Beam Therapy Benter between July 2004 and November 2011 were included in this study. All patients were treated with 3-dimensional conformal proton therapy (3D-CPT). RESULTS Ten consecutive patients of a median 2.3 years of age and with a median follow-up of 27.3 months (range, 11.3-99.4 months) were identified. Two patients suffered distant relapse; 1 patient was successfully treated with involved field irradiation and chemotherapy, while the second patient died of disease. At last follow-up, 9 patients were alive without evidence of disease. Proton radiation demonstrated increasing sparing of the cerebrum, temporal lobe, cochlea, and hypothalamus. CONCLUSIONS Initial clinical outcomes with proton therapy are favorable. The advantages of proton therapy are particularly suited to the treatment of AT/RT, a tumor that often requires irradiation treatment at an age when avoiding irradiation to healthy tissues is most desirable.
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Affiliation(s)
- Karen De Amorim Bernstein
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
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Nageswara Rao AA, Packer RJ. Impact of molecular biology studies on the understanding of brain tumors in childhood. Curr Oncol Rep 2012; 14:206-12. [PMID: 22237928 DOI: 10.1007/s11912-012-0214-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Pediatric brain tumors are the second most common form of childhood malignancy. Brain tumors are a very heterogenous group of tumors and the pathogenesis of many of these tumors is yet to be clearly elucidated. Current diagnostic tools include histopathology and immunohistochemistry, but classification based on these means has significant limitations. As our understanding of the molecular biology of individual tumors continues to increase it has led to the identification of reliable and increasingly available molecular biomarkers. Molecular techniques are likely to complement current standard means of investigation and help not only overcome diagnostic challenges but may also result in better disease classification and risk stratification, leading to more personalized therapeutic approaches.
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Affiliation(s)
- Amulya A Nageswara Rao
- Division of Pediatric Hematology/Oncology, Department of Pediatrics and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA.
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Park ES, Sung KW, Baek HJ, Park KD, Park HJ, Won SC, Lim DH, Kim HS. Tandem high-dose chemotherapy and autologous stem cell transplantation in young children with atypical teratoid/rhabdoid tumor of the central nervous system. J Korean Med Sci 2012; 27:135-40. [PMID: 22323859 PMCID: PMC3271285 DOI: 10.3346/jkms.2012.27.2.135] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 11/07/2011] [Indexed: 11/20/2022] Open
Abstract
The feasibility and effectiveness of tandem high-dose chemotherapy and autologous stem cell transplantation (HDCT/autoSCT) were evaluated in children younger than 3 yr of age with atypical teratoid/rhabdoid tumors (ATRT). Tandem HDCT/autoSCT was administered following six cycles of induction chemotherapy. Radiotherapy (RT) was administered if the tumor relapsed or progressed, otherwise, it was administered after 3 yr of age. Tumors relapsed or progressed during induction chemotherapy in 5 of 9 patients enrolled; 3 of these 5 received tandem HDCT/autoSCT as a salvage treatment. One patient died from sepsis during induction chemotherapy. The remaining 3 patients proceeded to tandem HDCT/autoSCT; however, 2 of these patients showed tumor relapse/progression after tandem HDCT/autoSCT. All 7 relapses/progressions occurred at primary sites even in patients with leptomeningeal seeding. Toxicities during tandem HDCT/autoSCT were manageable. A total of 5 patients were alive with a median follow-up of 20 (range 16-70) months from diagnosis. Four of 5 patients who received RT after relapse/progression are alive. The probability of overall survival at 3 yr from diagnosis was 53.3% ± 17.3%. Our tandem HDCT/autoSCT is feasible; however, early administration of RT prior to tandem HDCT/autoSCT should be considered to improve the outcome after tandem HDCT/autoSCT.
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Affiliation(s)
- Eun Sil Park
- Department of Pediatrics, Institute of Health Science, Gyeongsang National University School of Medicine, Jinju, Korea
| | - Ki Woong Sung
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Jo Baek
- Department of Pediatrics, Chonnam National University Hwasun Hospital, Chonnam National University Medical School, Gwangju, Korea
| | - Kyung Duk Park
- Department of Pediatrics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Hyeon Jin Park
- Center for Pediatric Oncology, National Cancer Center, Goyang, Korea
| | - Sung Chul Won
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Korea
| | - Do Hoon Lim
- Department of Radiation Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Heung Sik Kim
- Department of Pediatrics, Keimyung University School of Medicine, Daegu, Korea
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Abstract
Cancer genome analyses have revealed that the enzymes involved in epigenetic gene regulation are frequently deregulated in cancer. Here we describe the enzymes that control the epigenetic state of the cell, how they are affected in cancer and how this knowledge can be exploited to treat cancer with a new arsenal of selective therapies.
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Affiliation(s)
- E-J Geutjes
- Division of Molecular Carcinogenesis, Centre for Biomedical Genetics and Cancer Genomics Centre, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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35
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Coccé MC, Lubieniecki F, Kordes U, Alderete D, Gallego MS. A complex karyotype in an atypical teratoid/rhabdoid tumor: case report and review of the literature. J Neurooncol 2010; 104:375-80. [PMID: 21127945 DOI: 10.1007/s11060-010-0478-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 11/08/2010] [Indexed: 11/26/2022]
Abstract
Atypical teratoid/rhabdoid tumor (AT/RT) is a highly aggressive and uncommon neoplasm of the central nervous system that usually occurs in children less than 2 years of age. It is characterized by deletions and/or mutations of the INI1 tumor suppressor gene located in chromosome band 22q11.2. We performed cytogenetic and molecular studies of an AT/RT on a 15-month-old boy. The tumor showed a complex karyotype with one cell line showing monosomy 22 and another near-tetraploid one with additional chromosomal abnormalities, involving chromosomes 2, 3, 5, 6, and Y, which had not been previously described. Sequence analysis of the tumor did not identify mutations of the INI1 gene. The karyotypic evolution observed in this tumor suggests that INI1 has an epigenetic role in the maintenance of genome integrity by affecting genes, which produces mitotic defects and polyploidy. Finally, this case is the first to support the theory that loss of INI1 could induce the chromosomal instability that might be responsible for the genesis of this tumor.
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Affiliation(s)
- Mariela C Coccé
- Cytogenetics Laboratory, Genetics Department, Garrahan Pediatrics Hospital, Combate de los Pozos 1881, 1245 Buenos Aires, Argentina.
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36
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Lafay-Cousin L, Payne E, Strother D, Chernos J, Chan M, Bernier FP. Goldenhar phenotype in a child with distal 22q11.2 deletion and intracranial atypical teratoid rhabdoid tumor. Am J Med Genet A 2010; 149A:2855-9. [PMID: 19938088 DOI: 10.1002/ajmg.a.33119] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Chromosome-specific low copy repeats (LCRs) are implicated in several clinically significant microdeletion and microduplication syndromes. The well-recognized phenotype of DiGeorge/velocardiofacial syndrome (DG/VCF) results from deletions of the long arm of chromosome 22 (22q11.2) mediated by the proximal LCRs in this region. More recent evidence suggests that the distal LCRs within 22q11.2 are also implicated in microdeletions and microduplications with less characterized phenotypes. Here we report on an infant diagnosed with Goldenhar syndrome (GS) phenotype who developed an atypical teratoid rhabdoid tumor (AT/RT) of the brain due to a distal deletion of the chromosome 22q11.2 region encompassing the INI1/SMARCB1 tumor suppressor. We also discuss the phenotype of patients with germline deletions of this region and the possible implication of the 22q11.2 region in the GS.
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Affiliation(s)
- Lucie Lafay-Cousin
- Division of Pediatric Oncology and Bone Marrow Transplantation, Alberta Children's Hospital, 2888 Shaganappi Trail NW, Calgary, AB, Canada T3B 6A8.
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37
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Dagar V, Chow CW, Ashley DM, Algar EM. Rapid detection of SMARCB1 sequence variation using high resolution melting. BMC Cancer 2009; 9:437. [PMID: 20003390 PMCID: PMC2801682 DOI: 10.1186/1471-2407-9-437] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Accepted: 12/13/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rhabdoid tumors are rare cancers of early childhood arising in the kidney, central nervous system and other organs. The majority are caused by somatic inactivating mutations or deletions affecting the tumor suppressor locus SMARCB1 [OMIM 601607]. Germ-line SMARCB1 inactivation has been reported in association with rhabdoid tumor, epitheloid sarcoma and familial schwannomatosis, underscoring the importance of accurate mutation screening to ascertain recurrence and transmission risks. We describe a rapid and sensitive diagnostic screening method, using high resolution melting (HRM), for detecting sequence variations in SMARCB1. METHODS Amplicons, encompassing the nine coding exons of SMARCB1, flanking splice site sequences and the 5' and 3' UTR, were screened by both HRM and direct DNA sequencing to establish the reliability of HRM as a primary mutation screening tool. Reaction conditions were optimized with commercially available HRM mixes. RESULTS The false negative rate for detecting sequence variants by HRM in our sample series was zero. Nine amplicons out of a total of 140 (6.4%) showed variant melt profiles that were subsequently shown to be false positive. Overall nine distinct pathogenic SMARCB1 mutations were identified in a total of 19 possible rhabdoid tumors. Two tumors had two distinct mutations and two harbored SMARCB1 deletion. Other mutations were nonsense or frame-shifts. The detection sensitivity of the HRM screening method was influenced by both sequence context and specific nucleotide change and varied from 1: 4 to 1:1000 (variant to wild-type DNA). A novel method involving digital HRM, followed by re-sequencing, was used to confirm mutations in tumor specimens containing associated normal tissue. CONCLUSIONS This is the first report describing SMARCB1 mutation screening using HRM. HRM is a rapid, sensitive and inexpensive screening technology that is likely to be widely adopted in diagnostic laboratories to facilitate whole gene mutation screening.
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Affiliation(s)
- Vinod Dagar
- Children's Cancer Centre, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Australia.
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38
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Weissman B, Knudsen KE. Hijacking the chromatin remodeling machinery: impact of SWI/SNF perturbations in cancer. Cancer Res 2009; 69:8223-30. [PMID: 19843852 DOI: 10.1158/0008-5472.can-09-2166] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
There is increasing evidence that alterations in chromatin remodeling play a significant role in human disease. The SWI/SNF chromatin remodeling complex family mobilizes nucleosomes and functions as a master regulator of gene expression and chromatin dynamics whose functional specificity is driven by combinatorial assembly of a central ATPase and association with 10 to 12 unique subunits. Although the biochemical consequence of SWI/SNF in model systems has been extensively reviewed, the present article focuses on the evidence linking SWI/SNF perturbations to cancer initiation and tumor progression in human disease.
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Affiliation(s)
- Bernard Weissman
- Department of Pathology and Laboratory and Lineberger Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
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39
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Loss of the epigenetic tumor suppressor SNF5 leads to cancer without genomic instability. Mol Cell Biol 2008; 28:6223-33. [PMID: 18710953 DOI: 10.1128/mcb.00658-08] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
There is a growing appreciation of the role that epigenetic alterations can play in oncogenesis. However, given the large number of genetic anomalies present in most cancers, it has been difficult to evaluate the extent to which epigenetic changes contribute to cancer. SNF5 (INI1/SMARCB1/BAF47) is a tumor suppressor that regulates the epigenome as a core member of the SWI/SNF chromatin remodeling complex. While the SWI/SNF complex displays potent tumor suppressor activity, it is unknown whether this activity is exerted genetically via maintenance of genome integrity or epigenetically via transcriptional regulation. Here we show that Snf5-deficient primary cells do not show altered sensitivity to DNA damaging agents, defects in gamma-H2AX induction, or an abrogated DNA damage checkpoint. Further, the aggressive malignancies that arise following SNF5 loss are diploid and genomically stable. Remarkably, we demonstrate that most human SNF5-deficient cancers lack genomic amplifications/deletions and, aside from SNF5 loss, are indistinguishable from normal cells on single-nucleotide polymorphism arrays. Finally, we show that epigenetically based changes in transcription that occur following SNF5 loss correlate with the tumor phenotype. Collectively, our results provide novel insight into the mechanisms of oncogenesis by demonstrating that disruption of a chromatin remodeling complex can largely, if not completely, substitute for genomic instability in the genesis of aggressive cancer.
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40
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Narendran A, Coppes L, Jayanthan A, Coppes M, Teja B, Bernoux D, George D, Strother D. Establishment of atypical-teratoid/rhabdoid tumor (AT/RT) cell cultures from disseminated CSF cells: a model to elucidate biology and potential targeted therapeutics. J Neurooncol 2008; 90:171-80. [PMID: 18651103 DOI: 10.1007/s11060-008-9653-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Accepted: 06/27/2008] [Indexed: 01/15/2023]
Abstract
Atypical teratoid/rhabdoid tumor (AT/RT) is a highly malignant central nervous system neoplasm that usually affects infants and young children. In this report, we describe culture conditions that enabled the sustained growth of tumor cells obtained from the cerebrospinal fluid (CSF) of an infant with AT/RT. These cells retained the morphological and biomarker characteristics of the original tumor. A screening of receptor tyrosine kinases identified the presence of phosphorylated ErbB4, Insulin-R, PDGFR and IGF-IR, which appear to depend on Hsp90 to maintain their active form. IGF-IR activity is consistent with data from other established AT/RT cell lines. Inhibition of IGF-IR by the small molecular weight inhibitor AEW541 led to growth suppression of cultured AT/RT cells. In addition, neutralizing antibodies to IGF-II also inhibited the growth of these cells suggesting a potential autocrine function for this cytokine. We also compared cultured AT/RT cells to established cell lines to identify consistent drug sensitivity patterns among these cells. In addition to previously described cell lines and xenograft models, continuous culture of CSF derived cells may also provide an effective way to study the biology of AT/RT and to identify potential targets for future therapeutics for this tumor.
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Affiliation(s)
- Aru Narendran
- Translational Research Laboratories, Southern Alberta Children's Cancer Program, The University of Calgary, Calgary, AB, Canada.
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41
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Boyd C, Smith MJ, Kluwe L, Balogh A, Maccollin M, Plotkin SR. Alterations in the SMARCB1 (INI1) tumor suppressor gene in familial schwannomatosis. Clin Genet 2008; 74:358-66. [PMID: 18647326 DOI: 10.1111/j.1399-0004.2008.01060.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Schwannomatosis is a third major form of neurofibromatosis that has recently been linked to mutations in the SMARCB1 (hSnf5/INI1) tumor suppressor gene. We analyzed the coding region of SMARCB1 by direct sequencing and multiplex ligation-dependent probe amplification (MLPA) in genomic DNA from 19 schwannomatosis kindreds. Microsatellite markers in the SMARCB1 region were developed to determine loss of heterozygosity (LOH) in associated tumors. We detected four alterations in conserved splice acceptor or donor sequences of exons 3, 4 and 6. Two alterations that likely affect splicing were seen in introns 4 and 5. An additional four alterations of unclear pathogenicity were found to segregate on the affected allele in eight families including two non-conservative missense alterations in three families. No constitutional deletions or duplications were detected by MLPA. Nine of 13 tumors examined showed partial LOH of the SMARCB1 region consistent with 'second hits.' Alterations were detected in tumors both with and without somatic NF2 gene changes. These findings support the hypothesis that SMARCB1 is a tumor suppressor for schwannomas in the context of familial disease. Further work is needed to determine its role in other multiple and single tumor syndromes.
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Affiliation(s)
- C Boyd
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
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42
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Sestini R, Bacci C, Provenzano A, Genuardi M, Papi L. Evidence of a four-hit mechanism involving SMARCB1 and NF2 in schwannomatosis-associated schwannomas. Hum Mutat 2008; 29:227-31. [PMID: 18072270 DOI: 10.1002/humu.20679] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Schwannomatosis is characterized by the onset of multiple intracranial, spinal, or peripheral schwannomas, without involvement of the vestibular nerve, which is instead pathognomonic of neurofibromatosis type 2 (NF2). Recently, a schwannomatosis family with a germline mutation of the SMARCB1 gene on chromosome 22 has been described. We report on the molecular analysis of the SMARCB1 and NF2 genes in a series of 21 patients with schwannomatosis and in eight schwannomatosis-associated tumors from four different patients. A novel germline SMARCB1 mutation was found in one patient; inactivating somatic mutations of NF2, associated with loss of heterozygosity (LOH) of 22q, were found in two schwannomas of this patient. This is the second report of a germline SMARCB1 mutation in patients affected by schwannomatosis and the first report of SMARCB1 mutations associated with somatic NF2 mutations in schwannomatosis-associated tumors. The latter observation suggests that a four-hit mechanism involving the SMARCB1 and NF2 genes may be implicated in schwannomatosis-related tumorigenesis.
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Affiliation(s)
- Roberta Sestini
- Medical Genetics Unit, Department of Clinical Physiopathology, University of Florence, Florence, Italy
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43
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Chacko G, Chacko AG, Dunham CP, Judkins AR, Biegel JA, Perry A. Atypical teratoid/rhabdoid tumor arising in the setting of a pleomorphic xanthoastrocytoma. J Neurooncol 2007; 84:217-22. [PMID: 17431546 DOI: 10.1007/s11060-007-9361-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Accepted: 02/20/2007] [Indexed: 10/23/2022]
Abstract
We present a case of a 23-year-old man with a tumor containing glial and rhabdoid elements where the former had features of a pleomorphic xanthoastrocytoma (PXA) and the latter had the immunophenotype and genetic profile of an atypical rhabdoid/teratoid tumor. The patient presented with a short history of raised intracranial pressure with rapid deterioration in sensorium. He had a poor outcome despite surgery and radiotherapy. We report this case because of its unusual presentation in adulthood and its occurrence in association with a PXA. We speculate that the PXA was a quiescent tumor and that the secondary genetic alterations, including inactivation of the INI1 gene led to clinical progression.
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Affiliation(s)
- Geeta Chacko
- Division of Neuropathology, Department of Neurological Sciences, Christian Medical College, Vellore, India
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44
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Janson K, Nedzi LA, David O, Schorin M, Walsh JW, Bhattacharjee M, Pridjian G, Tan L, Judkins AR, Biegel JA. Predisposition to atypical teratoid/rhabdoid tumor due to an inherited INI1 mutation. Pediatr Blood Cancer 2006; 47:279-84. [PMID: 16261613 DOI: 10.1002/pbc.20622] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND Germline mutations of the INI1 gene predispose children to the development of rhabdoid tumors. Reports of familial cases, however, are extremely rare. PROCEDURE We have identified a three-generation family in which two half-brothers were diagnosed with central nervous system atypical teratoid/rhabdoid tumors (AT/RT). The two boys, diagnosed at 2 months and 17 months of age, had a germline insertion mutation in exon 4 of the INI1 gene that was inherited from their healthy mother. A maternal uncle died in childhood from a brain tumor and a malignant rhabdoid tumor of the kidney, and presumably carried the same germline mutation. As the mother and uncle had different fathers, the grandmother is also an obligate carrier of the mutation. CONCLUSION The identification of two unaffected carriers in a family segregating a germline mutation and rhabdoid tumor supports the hypothesis that there may be variable risks of development of rhabdoid tumor in the context of a germline mutation. There may be a developmental window in which most rhabdoid tumors occur. This family highlights the importance of mutation analysis in all patients with a suspected rhabdoid tumor.
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Affiliation(s)
- Kristin Janson
- Department of Radiation Oncology, Tulane University, New Orleans, Los Angeles, USA
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45
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46
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Owen-Hughes T. The role of Snf2-related proteins in cancer. ERNST SCHERING RESEARCH FOUNDATION WORKSHOP 2006:47-59. [PMID: 16568948 DOI: 10.1007/3-540-37633-x_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Several HDAC inhibitors that exhibit impressive anti-tumour activity are now in clinical trials. Proteins that function in the same pathways might also serve as valuable therapeutic targets. A subset of histone deacetylase activities are found to be physically associated with ATP-dependent remodelling enzymes and may assist their function. This raises the possibility that ATP-dependent remodelling enzymes should be considered as therapeutic targets. Here some of the links between ATP-dependent chromatin remodelling enzymes and cancer are reviewed.
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Affiliation(s)
- T Owen-Hughes
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Scotland, UK.
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47
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Fuller CE, Perry A. Fluorescence in situ hybridization (FISH) in diagnostic and investigative neuropathology. Brain Pathol 2006; 12:67-86. [PMID: 11770903 PMCID: PMC8095867 DOI: 10.1111/j.1750-3639.2002.tb00424.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Over the last decade, fluorescence in situ hybridization (FISH) has emerged as a powerful clinical and research tool for the assessment of target DNA dosages within interphase nuclei. Detectable alterations include aneusomies, deletions, gene amplifications, and translocations, with primary advantages to the pathologist including its basis in morphology, its applicability to archival, formalin-fixed paraffin-embedded (FFPE) material, and its similarities to immunohistochemistry. Recent technical advances such as improved hybridization protocols, markedly expanded probe availability resulting from the human genome sequencing initiative, and the advent of high-throughput assays such as gene chip and tissue microarrays have greatly enhanced the applicability of FISH. In our lab, we currently utilize only a limited battery of DNA probes for routine diagnostic purposes, with determination of chromosome 1p and 19q dosage in oligodendroglial neoplasms representing the most common application. However, research applications are numerous and will likely translate into a growing list of clinically useful markers in the near future. In this review, we highlight the advantages and disadvantages of FISH and familiarize the reader with current applications in diagnostic and investigative neuropathology.
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Affiliation(s)
- Christine E. Fuller
- Division of Neuropathology, Washington University School of Medicine, St. Louis, Mo
| | - Arie Perry
- Division of Neuropathology, Washington University School of Medicine, St. Louis, Mo
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48
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Abstract
Atypical teratoid/rhabdoid tumor (AT/RT) is a highly malignant central nervous system neoplasm that usually affects very young children and is typically deadly despite very aggressive treatment. Considered rare, the tumor was not recognized as a distinct entity until the 80's, due to its similar features with other primitive tumors. Although AT/RT has become increasingly recognized, published data has been based on small series and are retrospective. Based on these data, there are occasional long-term survivors, most of whom received intensive multi-modal therapy. AT/RT is the first pediatric brain tumor for which a candidate tumor suppressor gene has been identified. A mutation or deletion in the INI1 gene occurs in the majority of AT/RT tumors. The function of the gene is not yet understood. Prospective clinical and biologic trials are greatly needed to understand the efficacy of therapeutic interventions, as well as the role of the gene.
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Affiliation(s)
- Alyssa T Reddy
- University of Alabama at Birmingham, Birmingham, AL 35233, USA.
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49
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Strother D. Atypical teratoid rhabdoid tumors of childhood: diagnosis, treatment and challenges. Expert Rev Anticancer Ther 2006; 5:907-15. [PMID: 16221059 DOI: 10.1586/14737140.5.5.907] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Atypical teratoid rhabdoid tumor of the brain was described as a unique entity in the late 1980s. It occurs primarily in early childhood but the true incidence of the disease is not yet known. At presentation, the differential diagnosis includes medulloblastoma, primitive neuroectodermal tumor, ependymoma and choroid plexus carcinoma. Atypical teratoid rhabdoid tumor behaves in a very aggressive manner and while cure is possible for a small minority of patients, no standard or effective therapy has been defined for most patients. Since its first description, considerable pathologic, cytogenetic and molecular characterizations, as described in this review, have been accomplished that provide insight into the possible molecular etiology of the disease and of malignant rhabdoid tumors that occur outside the CNS. Co-operative group clinical trials that focus solely on atypical teratoid rhabdoid tumor are needed that incorporate biologic studies along with evaluations of aggressive treatment approaches. The goal of these trials should be to increase the cure rate for children with atypical teratoid rhabdoid tumor and further increase our understanding not only of atypical teratoid rhabdoid tumor, but also of other pediatric brain tumors.
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Affiliation(s)
- Douglas Strother
- University of Calgary, Faculty of Medicine, Alberta Children's Hospital, Calgary, Alberta, T2T 5C7, Canada.
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50
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Chai J, Charboneau AL, Betz BL, Weissman BE. Loss of the hSNF5 gene concomitantly inactivates p21CIP/WAF1 and p16INK4a activity associated with replicative senescence in A204 rhabdoid tumor cells. Cancer Res 2006; 65:10192-8. [PMID: 16288006 DOI: 10.1158/0008-5472.can-05-1896] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
hSNF5, the smallest member of the SWI/SNF chromatin remodeling complex, is lost in most malignant rhabdoid tumors (MRT). In MRT cell lines, reexpression of hSNF5 induces G1 cell cycle arrest, elevated p16INK4a, and activated replicative senescence markers, such as beta-galactosidase (beta-Gal) and plasminogen activator inhibitor-1. To compare the replicative senescence caused by hSNF5 in A204 cells to normal cellular senescence, we examined the activation of both p16INK4a and p21CIP/WAF1. Analogous to normal cellular senescence, both p16INK4a and p21CIP/WAF1 were up-regulated following hSNF5 restoration. Furthermore, we found that hSNF5 bound the p16INK4a and p21CIP/WAF1 promoters, suggesting that it directly regulates transcription of these genes. Using p16INK4a RNA interference, we showed its requirement for the replicative senescence caused by hSNF5 but not the growth arrest. Instead, p21CIP/WAF1 remained activated by hSNF5 in the absence of high p16INK4a expression, apparently causing the growth arrest in A204. Interestingly, we also found that, in the absence of p16INK4a, reexpression of hSNF5 also increased protein levels of a second cyclin-dependent kinase (CDK) inhibitor, p18INK4c. However, our data show that lack of hSNF5 does not abrogate cellular responsiveness to DNA damage or growth-inhibitory factors. In summary, our studies suggest that hSNF5 loss may influence the regulation of multiple CDK inhibitors involved in replicative senescence.
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Affiliation(s)
- Jingjing Chai
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina 27599-7295, USA
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