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Montalvo-Javé EE, Nuño-Lámbarri N, López-Sánchez GN, Ayala-Moreno EA, Gutierrez-Reyes G, Beane J, Pawlik TM. Pancreatic Cancer: Genetic Conditions and Epigenetic Alterations. J Gastrointest Surg 2023; 27:1001-1010. [PMID: 36749558 DOI: 10.1007/s11605-022-05553-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 11/19/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND Pancreatic cancer is a lethal proliferative disease driven by multiple genetic and epigenetic alterations. Microarrays and omics-based sequencing techniques are potent tools that have facilitated a broader understanding of the complex biological processes that drive pancreatic ductal adenocarcinoma (PDAC). In turn, these tools have resulted in the identification of novel disease markers, prognostic factors, and therapeutic targets. Herein, we provide a review of the genetic and epigenetic drivers of PDAC relative to recent discoveries that impact patient management. METHODS A review of PubMed, Medline, Clinical Key, and Index Medicus was conducted to identify literature from January 1995 to July 2022 that is related to PDAC genetics and epigenetics. Articles in Spanish and English were considered during selection. RESULTS Molecular, genetic, and epigenetic diagnostic tools, novel biomarkers, and promising therapeutic targets have emerged in the treatment of pancreatic cancer. The implementation of microarray technology and application of large omics-based data repositories have facilitated recent discoveries in PDAC. Multiple molecular analyses based on RNA interference have been instrumental in the identification of novel therapeutic targets for patients with PDAC. Moreover, microarrays and next-generation omics-based discoveries have been instrumental in the characterization of subtypes of pancreatic cancer, thereby improving prognostication and refining patient selection for available targeted therapies. CONCLUSION Advances in molecular biology, genetics, and epigenetics have ushered in a new era of discovery in the pathobiology of PDAC. Current efforts are underway to translate these findings into clinical tools and therapies to improve outcomes in patients with PDAC.
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Affiliation(s)
- Eduardo E Montalvo-Javé
- Hepatopancreatobiliary Clinic, Department of Surgery, Hospital General de México "Dr. Eduardo Liceaga", Mexico City, Mexico. .,Department of Surgery, Faculty of Medicine, Universidad Nacional Autónoma de México, Mexico City, Mexico.
| | | | | | - Edwin A Ayala-Moreno
- Department of Surgery, Hospital General de México "Dr. Eduardo Liceaga", Mexico City, Mexico
| | - Gabriela Gutierrez-Reyes
- Liver, Pancreas and Motility Laboratory, Unit of Experimental Medicine, Hospital General de México "Dr. Eduardo Liceaga", Mexico City, Mexico
| | - Joal Beane
- Department of Surgery, The Ohio State University, Wexner Medical Center, Columbus, OH, USA
| | - Timothy M Pawlik
- Department of Surgery, The Ohio State University, Wexner Medical Center, Columbus, OH, USA
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2
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González-Barrios R, Alcaraz N, Montalvo-Casimiro M, Cervera A, Arriaga-Canon C, Munguia-Garza P, Hinojosa-Ugarte D, Sobrevilla-Moreno N, Torres-Arciga K, Mendoza-Perez J, Diaz-Chavez J, Cortes-González CC, Castro-Hernández C, Martínez-Cedillo J, Scavuzzo A, Pérez-Montiel D, Jiménez-Ríos MA, Herrera LA. Genomic Profile in a Non-Seminoma Testicular Germ-Cell Tumor Cohort Reveals a Potential Biomarker of Sensitivity to Platinum-Based Therapy. Cancers (Basel) 2022; 14:cancers14092065. [PMID: 35565196 PMCID: PMC9101377 DOI: 10.3390/cancers14092065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/07/2022] [Accepted: 04/17/2022] [Indexed: 11/16/2022] Open
Abstract
Despite having a favorable response to platinum-based chemotherapies, ~15% of Testicular Germ-Cell Tumor (TGCT) patients are platinum-resistant. Mortality rates among Latin American countries have remained constant over time, which makes the study of this population of particular interest. To gain insight into this phenomenon, we conducted whole-exome sequencing, microarray-based comparative genomic hybridization, and copy number analysis of 32 tumors from a Mexican cohort, of which 18 were platinum-sensitive and 14 were platinum-resistant. We incorporated analyses of mutational burden, driver mutations, and SNV and CNV signatures. DNA breakpoints in genes were also investigated and might represent an interesting research opportunity. We observed that sensitivity to chemotherapy does not seem to be explained by any of the mutations detected. Instead, we uncovered CNVs, particularly amplifications on segment 2q11.1 as a novel variant with chemosensitivity biomarker potential. Our data shed light into understanding platinum resistance in a Latin-origin population.
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Affiliation(s)
- Rodrigo González-Barrios
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico; (R.G.-B.); (M.M.-C.); (C.A.-C.); (P.M.-G.); (K.T.-A.); (J.D.-C.); (C.C.C.-G.); (C.C.-H.)
| | - Nicolás Alcaraz
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark;
- Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico;
| | - Michel Montalvo-Casimiro
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico; (R.G.-B.); (M.M.-C.); (C.A.-C.); (P.M.-G.); (K.T.-A.); (J.D.-C.); (C.C.C.-G.); (C.C.-H.)
| | | | - Cristian Arriaga-Canon
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico; (R.G.-B.); (M.M.-C.); (C.A.-C.); (P.M.-G.); (K.T.-A.); (J.D.-C.); (C.C.C.-G.); (C.C.-H.)
| | - Paulina Munguia-Garza
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico; (R.G.-B.); (M.M.-C.); (C.A.-C.); (P.M.-G.); (K.T.-A.); (J.D.-C.); (C.C.C.-G.); (C.C.-H.)
| | - Diego Hinojosa-Ugarte
- Departamento de Cirugía, Hospital Regional de Alta Especialidad del Bajío, Leon 37660, Mexico;
| | - Nora Sobrevilla-Moreno
- Departamento de Oncología Médica, Clínica de Tumores Genitourinarios, Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (N.S.-M.); (J.M.-C.)
| | - Karla Torres-Arciga
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico; (R.G.-B.); (M.M.-C.); (C.A.-C.); (P.M.-G.); (K.T.-A.); (J.D.-C.); (C.C.C.-G.); (C.C.-H.)
| | - Julia Mendoza-Perez
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - José Diaz-Chavez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico; (R.G.-B.); (M.M.-C.); (C.A.-C.); (P.M.-G.); (K.T.-A.); (J.D.-C.); (C.C.C.-G.); (C.C.-H.)
| | - Carlo Cesar Cortes-González
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico; (R.G.-B.); (M.M.-C.); (C.A.-C.); (P.M.-G.); (K.T.-A.); (J.D.-C.); (C.C.C.-G.); (C.C.-H.)
| | - Clementina Castro-Hernández
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico; (R.G.-B.); (M.M.-C.); (C.A.-C.); (P.M.-G.); (K.T.-A.); (J.D.-C.); (C.C.C.-G.); (C.C.-H.)
| | - Jorge Martínez-Cedillo
- Departamento de Oncología Médica, Clínica de Tumores Genitourinarios, Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (N.S.-M.); (J.M.-C.)
| | - Ana Scavuzzo
- Departamento de Urología, Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (A.S.); (M.A.J.-R.)
| | - Delia Pérez-Montiel
- Departamento de Patología, Instituto Nacional de Cancerología, Mexico City 14080, Mexico;
| | - Miguel A. Jiménez-Ríos
- Departamento de Urología, Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (A.S.); (M.A.J.-R.)
| | - Luis A. Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico; (R.G.-B.); (M.M.-C.); (C.A.-C.); (P.M.-G.); (K.T.-A.); (J.D.-C.); (C.C.C.-G.); (C.C.-H.)
- Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico;
- Correspondence: ; Tel.: +52-55-5350-1900
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Dehner C, Moon CI, Zhang X, Zhou Z, Miller C, Xu H, Wan X, Yang K, Mashl J, Gosline SJ, Wang Y, Zhang X, Godec A, Jones PA, Dahiya S, Bhatia H, Primeau T, Li S, Pollard K, Rodriguez FJ, Ding L, Pratilas CA, Shern JF, Hirbe AC. Chromosome 8 gain is associated with high-grade transformation in MPNST. JCI Insight 2021; 6:146351. [PMID: 33591953 PMCID: PMC8026192 DOI: 10.1172/jci.insight.146351] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/10/2021] [Indexed: 12/15/2022] Open
Abstract
One of the most common malignancies affecting adults with Neurofibromatosis type 1 (NF1) is the malignant peripheral nerve sheath tumor (MPNST), an aggressive and often fatal sarcoma that commonly arises from benign plexiform neurofibromas. Despite advances in our understanding of MPNST pathobiology, there are few effective therapeutic options, and no investigational agents have proven successful in clinical trials. To further understand the genomic heterogeneity of MPNST, and to generate a preclinical platform that encompasses this heterogeneity, we developed a collection of NF1-MPNST patient-derived xenografts (PDX). These PDX were compared with the primary tumors from which they were derived using copy number analysis, whole exome sequencing, and RNA sequencing. We identified chromosome 8 gain as a recurrent genomic event in MPNST and validated its occurrence by FISH in the PDX and parental tumors, in a validation cohort, and by single-cell sequencing in the PDX. Finally, we show that chromosome 8 gain is associated with inferior overall survival in soft-tissue sarcomas. These data suggest that chromosome 8 gain is a critical event in MPNST pathogenesis and may account for the aggressive nature and poor outcomes in this sarcoma subtype.
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Affiliation(s)
| | - Chang In Moon
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Xiyuan Zhang
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Zhaohe Zhou
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Chris Miller
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Hua Xu
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA.,The First Affiliated Hospital, Nanchang University, Nangchang, China
| | - Xiaodan Wan
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA.,The First Affiliated Hospital, Nanchang University, Nangchang, China
| | - Kuangying Yang
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jay Mashl
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Sara Jc Gosline
- Pacific Northwest National Laboratory, Seattle, Washington, USA
| | - Yuxi Wang
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Xiaochun Zhang
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Abigail Godec
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Paul A Jones
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Sonika Dahiya
- Department of Pathology and Immunology and.,Siteman Cancer Center Division of Pediatric Oncology, St. Louis, Missouri, USA
| | - Himanshi Bhatia
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Tina Primeau
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Shunqiang Li
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA.,Siteman Cancer Center Division of Pediatric Oncology, St. Louis, Missouri, USA
| | - Kai Pollard
- Division of Pediatric Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland, USA
| | - Fausto J Rodriguez
- Department of Pathology, John Hopkins University, Baltimore, Maryland, USA
| | - Li Ding
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA.,Siteman Cancer Center Division of Pediatric Oncology, St. Louis, Missouri, USA
| | - Christine A Pratilas
- Division of Pediatric Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland, USA
| | - Jack F Shern
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Angela C Hirbe
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA.,Siteman Cancer Center Division of Pediatric Oncology, St. Louis, Missouri, USA
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4
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Martin E, Acem I, Grünhagen DJ, Bovée JVMG, Verhoef C. Prognostic Significance of Immunohistochemical Markers and Genetic Alterations in Malignant Peripheral Nerve Sheath Tumors: A Systematic Review. Front Oncol 2020; 10:594069. [PMID: 33415076 PMCID: PMC7783392 DOI: 10.3389/fonc.2020.594069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/19/2020] [Indexed: 12/20/2022] Open
Abstract
Background Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive soft tissue sarcomas with dismal prognosis. Pathological and genetic markers may predict more aggressive behavior in MPNSTs but have uncommonly been investigated, and few are used in daily practice. This study reviews the prognostic value of immunohistochemical markers and genetic alterations in MPNST. Methods A systematic search was performed in PubMed and Embase databases according to the PRISMA guidelines. Search terms related to ‘MPNST’ and ‘prognostic’ were used. Studies investigating the association of immunohistochemical markers or genetic alterations with prognosis were included. Qualitative synthesis was performed on all studies. A distinction was made between univariable and multivariable associations. Results Forty-six studies were included after full-text screening. Sixty-seven different immunohistochemical markers were investigated. Absence of S100 and H3K27me3 and high Ki67 and p53 staining was most commonly independently associated with worse survival and disease-free survival. Several genetic alterations were investigated as well with varying association to survival. TP53, CDK4, RASSF1A alterations were independently associated with worse survival, as well as changes in chromosomal length in Xp, 10q, and 16p. Conclusions MPNSTs harbor complex and heterogeneous biology. Immunohistochemical markers and genetic alterations have variable prognostic value. Absence of S100 and H3K27me3 and increased Ki67 can be of prognostic value. Alterations in TP53 or increase in p53 staining may distinguish MPNSTs with worse outcomes. Genetic alterations and staining of other cell cycle regulatory and Ras pathway proteins may also help stratifying patients with worse outcomes. A combination of markers can increase the prognostic value.
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Affiliation(s)
- Enrico Martin
- Department of Surgical Oncology, Erasmus Medical Center, Rotterdam, Netherlands.,Department of Plastic and Reconstructive Surgery, University Medical Center Utrecht, Utrecht, Netherlands
| | - Ibtissam Acem
- Department of Surgical Oncology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Dirk J Grünhagen
- Department of Surgical Oncology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Judith V M G Bovée
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
| | - Cornelis Verhoef
- Department of Surgical Oncology, Erasmus Medical Center, Rotterdam, Netherlands
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5
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Pemov A, Li H, Presley W, Wallace MR, Miller DT. Genetics of human malignant peripheral nerve sheath tumors. Neurooncol Adv 2019; 2:i50-i61. [PMID: 32642732 PMCID: PMC7317054 DOI: 10.1093/noajnl/vdz049] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Malignant peripheral nerve sheath tumors (MPNSTs) are heterogeneous, highly aggressive tumors with no widely effective treatment other than surgery. Genomic architecture of MPNST is similar to other soft tissue sarcomas, with a relatively modest burden of single nucleotide variants and an elevated frequency of copy-number alterations. Recent advances in genomic studies identified previously unrecognized critical involvement of polycomb repressor complex 2 (PRC2) core components SUZ12 and EED in transition to malignancy. Notably, somatic changes in NF1, CDKN2A/B, and PRC2 are found in most MPNST regardless of their etiology (e.g. neurofibromatosis type 1-associated vs. sporadic vs. radiation-induced), indicating that similar molecular mechanisms impact pathogenesis in these neoplasms. The timing and specific order of genetic or epigenetic changes may, however, explain the typically poorer prognosis of NF1-associated MPNSTs. Studies that reveal genes and regulatory pathways uniquely altered in malignancies are essential to development of targeted tumor therapies. Characterization of MPNST molecular profiles may also contribute to tools for earlier detection, and prediction of prognosis or drug response. Here we review the genetic discoveries and their implications in understanding MPNST biology.
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Affiliation(s)
- Alexander Pemov
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Hua Li
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, Florida
| | - William Presley
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, Florida
| | - Margaret R Wallace
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, Florida.,University of Florida Health Cancer Center, University of Florida, Gainesville, Florida
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts
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6
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Kelleher FC, O'Sullivan H. FOXM1 in sarcoma: role in cell cycle, pluripotency genes and stem cell pathways. Oncotarget 2018; 7:42792-42804. [PMID: 27074562 PMCID: PMC5173172 DOI: 10.18632/oncotarget.8669] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 03/29/2016] [Indexed: 01/25/2023] Open
Abstract
FOXM1 is a pro-proliferative transcription factor that promotes cell cycle progression at the G1-S, and G2-M transitions. It is activated by phosphorylation usually mediated by successive cyclin – cyclin dependent kinase complexes, and is highly expressed in sarcoma. p53 down regulates FOXM1 and FOXM1 inhibition is also partly dependent on Rb and p21. Abnormalities of p53 or Rb are frequent in sporadic sarcomas with bone or soft tissue sarcoma, accounting for 36% of index cancers in the high penetrance TP53 germline disorder, Li-Fraumeni syndrome. FOXM1 stimulates transcription of pluripotency related genes including SOX2, KLF4, OCT4, and NANOG many of which are important in sarcoma, a disorder of mesenchymal stem cell/ partially committed progenitor cells. In a selected specific, SOX2 is uniformly expressed in synovial sarcoma. Embryonic pathways preferentially used in stem cell such as Hippo, Hedgehog, and Wnt dominate in FOXM1 stoichiometry to alter rates of FOXM1 production or degradation. In undifferentiated pleomorphic sarcoma, liposarcoma, and fibrosarcoma, dysregulation of the Hippo pathway increases expression of the effector co-transcriptional activator Yes-Associated Protein (YAP). A complex involving YAP and the transcription factor TEAD elevates FOXM1 in these sarcoma subtypes. In another scenario 80% of desmoid tumors have nuclear localization of β-catenin, the Wnt pathway effector molecule. Thiazole antibiotics inhibit FOXM1 and because they have an auto-regulator loop FOXM1 expression is also inhibited. Current systemic treatment of sarcoma is of limited efficacy and inhibiting FOXM1 represents a potential new strategy.
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Affiliation(s)
- Fergal C Kelleher
- St. James Hospital, Dublin, Ireland.,Trinity College Dublin, Dublin, Ireland
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7
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Castellsagué J, Gel B, Fernández-Rodríguez J, Llatjós R, Blanco I, Benavente Y, Pérez-Sidelnikova D, García-Del Muro J, Viñals JM, Vidal A, Valdés-Mas R, Terribas E, López-Doriga A, Pujana MA, Capellá G, Puente XS, Serra E, Villanueva A, Lázaro C. Comprehensive establishment and characterization of orthoxenograft mouse models of malignant peripheral nerve sheath tumors for personalized medicine. EMBO Mol Med 2016; 7:608-27. [PMID: 25810463 PMCID: PMC4492820 DOI: 10.15252/emmm.201404430] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Malignant peripheral nerve sheath tumors (MPNSTs) are soft-tissue sarcomas that can arise either sporadically or in association with neurofibromatosis type 1 (NF1). These aggressive malignancies confer poor survival, with no effective therapy available. We present the generation and characterization of five distinct MPNST orthoxenograft models for preclinical testing and personalized medicine. Four of the models are patient-derived tumor xenografts (PDTX), two independent MPNSTs from the same NF1 patient and two from different sporadic patients. The fifth model is an orthoxenograft derived from an NF1-related MPNST cell line. All MPNST orthoxenografts were generated by tumor implantation, or cell line injection, next to the sciatic nerve of nude mice, and were perpetuated by 7–10 mouse-to-mouse passages. The models reliably recapitulate the histopathological properties of their parental primary tumors. They also mimic distal dissemination properties in mice. Human stroma was rapidly lost after MPNST engraftment and replaced by murine stroma, which facilitated genomic tumor characterization. Compatible with an origin in a catastrophic event and subsequent genome stabilization, MPNST contained highly altered genomes that remained remarkably stable in orthoxenograft establishment and along passages. Mutational frequency and type of somatic point mutations were highly variable among the different MPNSTs modeled, but very consistent when comparing primary tumors with matched orthoxenografts generated. Unsupervised cluster analysis and principal component analysis (PCA) using an MPNST expression signature of ~1,000 genes grouped together all primary tumor–orthoxenograft pairs. Our work points to differences in the engraftment process of primary tumors compared with the engraftment of established cell lines. Following standardization and extensive characterization and validation, the orthoxenograft models were used for initial preclinical drug testing. Sorafenib (a BRAF inhibitor), in combination with doxorubicin or rapamycin, was found to be the most effective treatment for reducing MPNST growth. The development of genomically well-characterized preclinical models for MPNST allowed the evaluation of novel therapeutic strategies for personalized medicine.
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Affiliation(s)
- Joan Castellsagué
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain Translational Research Laboratory ICO-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Bernat Gel
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC), Badalona, Barcelona, Spain
| | - Juana Fernández-Rodríguez
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain Translational Research Laboratory ICO-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Roger Llatjós
- Pathology Service, HUB-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ignacio Blanco
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Yolanda Benavente
- Unit of Infections and Cancer (UNIC), Cancer Epidemiology Research Program ICO-IDIBELL and CIBER Epidemiología y Salud Pública (CIBERESP), L'Hospitalet de Llobregat, Barcelona, Spain
| | | | | | - Joan Maria Viñals
- Plastic Surgery Service HUB-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - August Vidal
- Pathology Service, HUB-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Rafael Valdés-Mas
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Ernest Terribas
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC), Badalona, Barcelona, Spain
| | - Adriana López-Doriga
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain Translational Research Laboratory ICO-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Miguel Angel Pujana
- Translational Research Laboratory ICO-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain Translational Research Laboratory ICO-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Xose S Puente
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Eduard Serra
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC), Badalona, Barcelona, Spain
| | - Alberto Villanueva
- Translational Research Laboratory ICO-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain Translational Research Laboratory ICO-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
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8
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The Challenge of Cancer Genomics in Rare Nervous System Neoplasms: Malignant Peripheral Nerve Sheath Tumors as a Paradigm for Cross-Species Comparative Oncogenomics. THE AMERICAN JOURNAL OF PATHOLOGY 2015; 186:464-77. [PMID: 26740486 DOI: 10.1016/j.ajpath.2015.10.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/20/2015] [Indexed: 12/12/2022]
Abstract
Comprehensive genomic analyses of common nervous system cancers provide new insights into their pathogenesis, diagnosis, and treatment. Although analogous studies of rare nervous system tumors are needed, there are major barriers to performing such studies. Cross-species comparative oncogenomics, identifying driver mutations in mouse cancer models and validating them in human tumors, is a promising alternative. Although still in its infancy, this approach is being applied to malignant peripheral nerve sheath tumors (MPNSTs), rare Schwann cell-derived malignancies that occur sporadically, after radiotherapy, and in neurofibromatosis type 1. Studies of human neurofibromatosis type 1-associated tumors suggest that NF1 tumor suppressor loss in Schwann cells triggers cell-autonomous and intercellular changes, resulting in development of benign neurofibromas; subsequent neurofibroma-MPNST progression is caused by aberrant growth factor signaling and mutations affecting the p16(INK4A)-cyclin D1-CDK4-Rb and p19(ARF)-Mdm2-p53 cell cycle pathways. Mice with Nf1, Trp53, and/or Cdkn2a mutations that overexpress the Schwann cell mitogen neuregulin-1 or overexpress the epidermal growth factor receptor validate observations in human tumors and, to various degrees, model human tumorigenesis. Genomic analyses of MPNSTs arising in neuregulin-1 and epidermal growth factor receptor-overexpressing mice and forward genetic screens with Sleeping Beauty transposons implicate additional signaling cascades in MPNST pathogenesis. These studies confirm the utility of mouse models for MPNST driver gene discovery and provide new insights into the complexity of MPNST pathogenesis.
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Chen S, Yang K, Tuguntaev RG, Mozhi A, Zhang J, Wang PC, Liang XJ. Targeting tumor microenvironment with PEG-based amphiphilic nanoparticles to overcome chemoresistance. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2015; 12:269-86. [PMID: 26707818 DOI: 10.1016/j.nano.2015.10.020] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 10/24/2015] [Accepted: 10/30/2015] [Indexed: 12/15/2022]
Abstract
UNLABELLED Multidrug resistance is one of the biggest obstacles in the treatment of cancer. Recent research studies highlight that tumor microenvironment plays a predominant role in tumor cell proliferation, metastasis, and drug resistance. Hence, targeting the tumor microenvironment provides a novel strategy for the evolution of cancer nanomedicine. The blooming knowledge about the tumor microenvironment merging with the design of PEG-based amphiphilic nanoparticles can provide an effective and promising platform to address the multidrug resistant tumor cells. This review describes the characteristic features of tumor microenvironment and their targeting mechanisms with the aid of PEG-based amphiphilic nanoparticles for the development of newer drug delivery systems to overcome multidrug resistance in cancer cells. FROM THE CLINICAL EDITOR Cancer is a leading cause of death worldwide. Many cancers develop multidrug resistance towards chemotherapeutic agents with time and strategies are urgently needed to combat against this. In this review article, the authors discuss the current capabilities of using nanomedicine to target the tumor microenvironments, which would provide new insight to the development of novel delivery systems for the future.
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Affiliation(s)
- Shizhu Chen
- Key Laboratory of Chemical Biology of Hebei Province, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, College of Chemistry & Environmental Science, Hebei University, Baoding, PR China
| | - Keni Yang
- CAS Key Lab of Nanomaterials Bioeffects and Nanosafety, National Center for Nanoscience and Technology of China, Beijing, PR China
| | - Ruslan G Tuguntaev
- CAS Key Lab of Nanomaterials Bioeffects and Nanosafety, National Center for Nanoscience and Technology of China, Beijing, PR China
| | - Anbu Mozhi
- CAS Key Lab of Nanomaterials Bioeffects and Nanosafety, National Center for Nanoscience and Technology of China, Beijing, PR China
| | - Jinchao Zhang
- Key Laboratory of Chemical Biology of Hebei Province, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, College of Chemistry & Environmental Science, Hebei University, Baoding, PR China.
| | - Paul C Wang
- Fu Jen Catholic University, Taipei, Taiwan; Laboratory of Molecular Imaging, Department of Radiology, Howard University, WA, DC, USA
| | - Xing-Jie Liang
- CAS Key Lab of Nanomaterials Bioeffects and Nanosafety, National Center for Nanoscience and Technology of China, Beijing, PR China.
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Sherborne AL, Davidson PR, Yu K, Nakamura AO, Rashid M, Nakamura JL. Mutational Analysis of Ionizing Radiation Induced Neoplasms. Cell Rep 2015; 12:1915-26. [PMID: 26344771 DOI: 10.1016/j.celrep.2015.08.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 07/08/2015] [Accepted: 08/05/2015] [Indexed: 10/25/2022] Open
Abstract
Ionizing radiation (IR) is a mutagen that promotes tumorigenesis in multiple exposure contexts. One severe consequence of IR is the development of second malignant neoplasms (SMNs), a radiotherapy-associated complication in survivors of cancers, particularly pediatric cancers. SMN genomes are poorly characterized, and the influence of genetic background on genotoxin-induced mutations has not been examined. Using our mouse models of SMNs, we performed whole exome sequencing of neoplasms induced by fractionated IR in wild-type and Nf1 mutant mice. Using non-negative matrix factorization, we identified mutational signatures that did not segregate by genetic background or histology. Copy-number analysis revealed recurrent chromosomal alterations and differences in copy number that were background dependent. Pathway analysis identified enrichment of non-synonymous variants in genes responsible for cell assembly and organization, cell morphology, and cell function and maintenance. In this model system, ionizing radiation and Nf1 heterozygosity each exerted distinct influences on the mutational landscape.
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Affiliation(s)
- Amy L Sherborne
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Philip R Davidson
- Department of Finance and Statistical Analysis, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Katharine Yu
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alice O Nakamura
- Department of Finance and Statistical Analysis, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Mamunur Rashid
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Jean L Nakamura
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94158, USA.
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Kolberg M, Høland M, Lind GE, Ågesen TH, Skotheim RI, Hall KS, Mandahl N, Smeland S, Mertens F, Davidson B, Lothe RA. Protein expression of BIRC5, TK1, and TOP2A in malignant peripheral nerve sheath tumours--A prognostic test after surgical resection. Mol Oncol 2015; 9:1129-39. [PMID: 25769404 PMCID: PMC5528761 DOI: 10.1016/j.molonc.2015.02.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 01/22/2015] [Accepted: 02/10/2015] [Indexed: 11/26/2022] Open
Abstract
No consensus treatment regime exists beyond surgery for malignant peripheral nerve sheath tumours (MPNST), and the purpose of the present study was to find new approaches to stratify patients with good and poor prognosis and to better guide therapeutic intervention for this aggressive soft tissue cancer. From a total of 67 MPNSTs from Scandinavian patients with and without neurofibromatosis type 1, 30 MPNSTs were investigated by genome‐wide RNA expression profiling and 63 MPNSTs by immunohistochemical (IHC) analysis, and selected genes were submitted to analyses of disease‐specific survival. The potential drug target genes survivin (BIRC5), thymidine kinase 1 (TK1), and topoisomerase 2‐alpha (TOP2A), all encoded on chromosome arm 17q, were up‐regulated in MPNST as compared to benign neurofibromas. Each of them was found to be independent prognostic markers on the gene expression level, as well as on the protein level. A prognostic profile was identified by combining the nuclear expression scores of the three proteins. For patients with completely resected tumours only 15% in the high risk group were alive after two years, as compared to 78% in the low risk group. In conclusion, we found a novel protein expression profile which identifies MPNST patients with inferior prognosis even after assumed curative surgery. The tested proteins are drug targets; therefore the expression profile may provide predictive information guiding the design of future clinical trials. Importantly, as the effect is seen on the protein level using IHC, the biomarker panel can be readily implemented in routine clinical testing.
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Affiliation(s)
- Matthias Kolberg
- Department of Molecular Oncology, Institute for Cancer Research, Division of Cancer Medicine Surgery and Transplantation, Oslo University Hospital, Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Maren Høland
- Department of Molecular Oncology, Institute for Cancer Research, Division of Cancer Medicine Surgery and Transplantation, Oslo University Hospital, Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Guro E Lind
- Department of Molecular Oncology, Institute for Cancer Research, Division of Cancer Medicine Surgery and Transplantation, Oslo University Hospital, Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Trude H Ågesen
- Department of Molecular Oncology, Institute for Cancer Research, Division of Cancer Medicine Surgery and Transplantation, Oslo University Hospital, Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Rolf I Skotheim
- Department of Molecular Oncology, Institute for Cancer Research, Division of Cancer Medicine Surgery and Transplantation, Oslo University Hospital, Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Kirsten Sundby Hall
- Department of Oncology, Division of Cancer Medicine Surgery and Transplantation, Oslo University Hospital, Oslo, Norway
| | - Nils Mandahl
- Department of Clinical Genetics, Skåne University Hospital, Lund, Sweden
| | - Sigbjørn Smeland
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Oncology, Division of Cancer Medicine Surgery and Transplantation, Oslo University Hospital, Oslo, Norway
| | - Fredrik Mertens
- Department of Clinical Genetics, Skåne University Hospital, Lund, Sweden
| | - Ben Davidson
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Pathology, Division of Diagnostics and Intervention, Oslo University Hospital, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Division of Cancer Medicine Surgery and Transplantation, Oslo University Hospital, Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.
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Thomas LE, Winston J, Rad E, Mort M, Dodd KM, Tee AR, McDyer F, Moore S, Cooper DN, Upadhyaya M. Evaluation of copy number variation and gene expression in neurofibromatosis type-1-associated malignant peripheral nerve sheath tumours. Hum Genomics 2015; 9:3. [PMID: 25884485 PMCID: PMC4367978 DOI: 10.1186/s40246-015-0025-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/18/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Neurofibromatosis type-1 (NF1) is a complex neurogenetic disorder characterised by the development of benign and malignant tumours of the peripheral nerve sheath (MPNSTs). Whilst biallelic NF1 gene inactivation contributes to benign tumour formation, additional cellular changes in gene structure and/or expression are required to induce malignant transformation. Although few molecular profiling studies have been performed on the process of progression of pre-existing plexiform neurofibromas to MPNSTs, the integrated analysis of copy number alterations (CNAs) and gene expression is likely to be key to understanding the molecular mechanisms underlying NF1-MPNST tumorigenesis. In a pilot study, we employed this approach to identify genes differentially expressed between benign and malignant NF1 tumours. RESULTS SPP1 (osteopontin) was the most differentially expressed gene (85-fold increase in expression), compared to benign plexiform neurofibromas. Short hairpin RNA (shRNA) knockdown of SPP1 in NF1-MPNST cells reduced tumour spheroid size, wound healing and invasion in four different MPNST cell lines. Seventy-six genes were found to exhibit concordance between CNA and gene expression level. CONCLUSIONS Pathway analysis of these genes suggested that glutathione metabolism and Wnt signalling may be specifically involved in NF1-MPNST development. SPP1 is associated with malignant transformation in NF1-associated MPNSTs and could prove to be an important target for therapeutic intervention.
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Affiliation(s)
- Laura E Thomas
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK.
| | - Jincy Winston
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK.
| | - Ellie Rad
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK.
| | - Matthew Mort
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK.
| | - Kayleigh M Dodd
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK.
| | - Andrew R Tee
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK.
| | - Fionnuala McDyer
- Almac Diagnostics, 19 Seagoe Industrial Estate, Craigavon, Northern Ireland, BT63 5QD, UK.
| | - Stephen Moore
- Almac Diagnostics, 19 Seagoe Industrial Estate, Craigavon, Northern Ireland, BT63 5QD, UK.
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK.
| | - Meena Upadhyaya
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK.
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Du X, Yang J, Ylipää A, Zhu Z. Genomic amplification and high expression of EGFR are key targetable oncogenic events in malignant peripheral nerve sheath tumor. J Hematol Oncol 2013; 6:93. [PMID: 24341609 PMCID: PMC3878771 DOI: 10.1186/1756-8722-6-93] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 12/13/2013] [Indexed: 12/15/2022] Open
Abstract
Background The dismal outcome of malignant peripheral nerve sheath tumor (MPNST) highlights the necessity of finding new therapeutic methods to benefit patients with this aggressive sarcoma. Our purpose was to investigate epidermal growth factor receptor (EGFR) as a potential therapeutic target in MPNSTs. Patients and methods We performed a microarray based-comparative genomic hybridization (aCGH) profiling of two cohorts of primary MPNST tissue samples including 25 patients treated at The University of Texas MD Anderson Cancer Center (MD Anderson) and 26 patients from Tianjin Medical University Cancer Institute & Hospital (TMUCIH). Fluorescence in situ hybridization (FISH) method was used to validate the gene amplification detected by aCGH analysis. Another independent cohort of 56 formalin fixed paraffin embedded (FFPE) MPNST samples was obtained to explore EGFR protein expression by immunohistochemical analysis. Cell biology detection and validation were performed on human MPNST cell lines ST88-14 and STS26T. Results aCGH and pathway analysis of the 51 MPNSTs identified significant gene amplification events in EGFR pathway, including frequent amplifications of EGFR gene itself, which was subsequently validated by FISH assay. High expression of EGFR protein was associated with poor disease-free and overall survival of human MPNST patients. In human MPNST cell lines ST88-14 and STS26T, inhibition of EGFR by siRNA or Gefitinib led to decreased cell proliferation, migration, and invasion accompanied by attenuation of PI3K/AKT and MAPK pathways. Conclusion These results suggest that EGFR is a potential therapeutic target for MPNST.
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Affiliation(s)
| | - Jilong Yang
- Department of Bone and Soft Tissue Tumor, National Clinical Cancer Research Center, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China.
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14
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Zhang G, Hoersch S, Amsterdam A, Whittaker CA, Beert E, Catchen JM, Farrington S, Postlethwait JH, Legius E, Hopkins N, Lees JA. Comparative oncogenomic analysis of copy number alterations in human and zebrafish tumors enables cancer driver discovery. PLoS Genet 2013; 9:e1003734. [PMID: 24009526 PMCID: PMC3757083 DOI: 10.1371/journal.pgen.1003734] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 07/05/2013] [Indexed: 01/11/2023] Open
Abstract
The identification of cancer drivers is a major goal of current cancer research. Finding driver genes within large chromosomal events is especially challenging because such alterations encompass many genes. Previously, we demonstrated that zebrafish malignant peripheral nerve sheath tumors (MPNSTs) are highly aneuploid, much like human tumors. In this study, we examined 147 zebrafish MPNSTs by massively parallel sequencing and identified both large and focal copy number alterations (CNAs). Given the low degree of conserved synteny between fish and mammals, we reasoned that comparative analyses of CNAs from fish versus human MPNSTs would enable elimination of a large proportion of passenger mutations, especially on large CNAs. We established a list of orthologous genes between human and zebrafish, which includes approximately two-thirds of human protein-coding genes. For the subset of these genes found in human MPNST CNAs, only one quarter of their orthologues were co-gained or co-lost in zebrafish, dramatically narrowing the list of candidate cancer drivers for both focal and large CNAs. We conclude that zebrafish-human comparative analysis represents a powerful, and broadly applicable, tool to enrich for evolutionarily conserved cancer drivers.
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Affiliation(s)
- GuangJun Zhang
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts, United States of America
| | - Sebastian Hoersch
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts, United States of America
- Bioinformatics Group, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Adam Amsterdam
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts, United States of America
| | - Charles A. Whittaker
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts, United States of America
| | - Eline Beert
- Department of Human Genetics, Catholic University Leuven, Leuven, Belgium
| | - Julian M. Catchen
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America
| | - Sarah Farrington
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts, United States of America
| | - John H. Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America
| | - Eric Legius
- Department of Human Genetics, Catholic University Leuven, Leuven, Belgium
| | - Nancy Hopkins
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts, United States of America
| | - Jacqueline A. Lees
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts, United States of America
- * E-mail:
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Yang J, Du X. Genomic and molecular aberrations in malignant peripheral nerve sheath tumor and their roles in personalized target therapy. Surg Oncol 2013; 22:e53-7. [PMID: 23830351 DOI: 10.1016/j.suronc.2013.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 06/11/2013] [Indexed: 11/28/2022]
Abstract
Malignant peripheral nerve sheath tumors (MPNSTs) are malignant tumors with a high rate of local recurrence and a significant tendency to metastasize. Its dismal outcome points to the urgent need to establish better therapeutic strategies for patients harboring MPNSTs. The investigations of genomic and molecular aberrations in MPNSTs which detect many chromosomal aberrations, pathway abnormalities, and specific molecular aberrant events would supply multiple potential therapy targets and contribute to achievement of personalized medicine. The involved genes in the significant gains aberrations include BIRC5, CCNE2, DAB2, DDX15, EGFR, DAB2, MSH2, CDK6, HGF, ITGB4, KCNK12, LAMA3, LOXL2, MET, and PDGFRA. The involved genes in the significant deletion aberrations include CDH1, GLTSCR2, EGR1, CTSB, GATA3, SULT2A1, GLTSCR2, HMMR/RHAMM, LICAM2, MMP13, p16/INK4a, RASSF2, NM-23H1, and TP53. These genetic aberrations involve in several important signaling pathways such as TFF, EGFR, ARF, IGF1R signaling pathways. The genomic and molecular aberrations of EGFR, IGF1R, SOX9, EYA4, TOP2A, ETV4, and BIRC5 exhibit great promise as personalized therapeutic targets for MPNST patients.
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Affiliation(s)
- Jilong Yang
- Departments of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Hospital and Institute, Tianjin 30060, China.
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Schiffman JD. Genome-wide analyses of sarcoma: implications for future treatment options. Future Oncol 2013; 9:307-10. [PMID: 23469965 DOI: 10.2217/fon.13.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Kazmi SJ, Byer SJ, Eckert JM, Turk AN, Huijbregts RP, Brossier NM, Grizzle WE, Mikhail FM, Roth KA, Carroll SL. Transgenic mice overexpressing neuregulin-1 model neurofibroma-malignant peripheral nerve sheath tumor progression and implicate specific chromosomal copy number variations in tumorigenesis. THE AMERICAN JOURNAL OF PATHOLOGY 2013; 182:646-67. [PMID: 23321323 PMCID: PMC3586689 DOI: 10.1016/j.ajpath.2012.11.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 10/19/2012] [Accepted: 11/13/2012] [Indexed: 12/12/2022]
Abstract
Patients with neurofibromatosis type 1 (NF1) develop benign plexiform neurofibromas that frequently progress to become malignant peripheral nerve sheath tumors (MPNSTs). A genetically engineered mouse model that accurately models plexiform neurofibroma-MPNST progression in humans would facilitate identification of somatic mutations driving this process. We previously reported that transgenic mice overexpressing the growth factor neuregulin-1 in Schwann cells (P(0)-GGFβ3 mice) develop MPNSTs. To determine whether P(0)-GGFβ3 mice accurately model human neurofibroma-MPNST progression, cohorts of these animals were monitored through death and were necropsied; 94% developed multiple neurofibromas, with 70% carrying smaller numbers of MPNSTs. Nascent MPNSTs were identified within neurofibromas, suggesting that these sarcomas arise from neurofibromas. Although neurofibromin expression was maintained, P(0)-GGFβ3 MPNSTs exhibited Ras hyperactivation, as in human NF1-associated MPNSTs. P(0)-GGFβ3 MPNSTs also exhibited abnormalities in the p16(INK4A)-cyclin D/CDK4-Rb and p19(ARF)-Mdm-p53 pathways, analogous to their human counterparts. Array comparative genomic hybridization (CGH) demonstrated reproducible chromosomal alterations in P(0)-GGFβ3 MPNST cells (including universal chromosome 11 gains) and focal gains and losses affecting 39 neoplasia-associated genes (including Pten, Tpd52, Myc, Gli1, Xiap, and Bbc3/PUMA). Array comparative genomic hybridization also identified recurrent focal copy number variations affecting genes not previously linked to neurofibroma or MPNST pathogenesis. We conclude that P(0)-GGFβ3 mice represent a robust model of neurofibroma-MPNST progression useful for identifying novel genes driving neurofibroma and MPNST pathogenesis.
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Affiliation(s)
- Syed J. Kazmi
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Stephanie J. Byer
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Jenell M. Eckert
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Amy N. Turk
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama
| | | | - Nicole M. Brossier
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama
- Department of Cell Biology, The University of Alabama at Birmingham, Birmingham, Alabama
- Medical Scientist Training Program, The University of Alabama at Birmingham, Birmingham, Alabama
| | - William E. Grizzle
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Fady M. Mikhail
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Kevin A. Roth
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Steven L. Carroll
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama
- Department of Cell Biology, The University of Alabama at Birmingham, Birmingham, Alabama
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Lo FY, Chang JW, Chang IS, Chen YJ, Hsu HS, Huang SFK, Tsai FY, Jiang SS, Kanteti R, Nandi S, Salgia R, Wang YC. The database of chromosome imbalance regions and genes resided in lung cancer from Asian and Caucasian identified by array-comparative genomic hybridization. BMC Cancer 2012; 12:235. [PMID: 22691236 PMCID: PMC3488578 DOI: 10.1186/1471-2407-12-235] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 05/12/2012] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Cancer-related genes show racial differences. Therefore, identification and characterization of DNA copy number alteration regions in different racial groups helps to dissect the mechanism of tumorigenesis. METHODS Array-comparative genomic hybridization (array-CGH) was analyzed for DNA copy number profile in 40 Asian and 20 Caucasian lung cancer patients. Three methods including MetaCore analysis for disease and pathway correlations, concordance analysis between array-CGH database and the expression array database, and literature search for copy number variation genes were performed to select novel lung cancer candidate genes. Four candidate oncogenes were validated for DNA copy number and mRNA and protein expression by quantitative polymerase chain reaction (qPCR), chromogenic in situ hybridization (CISH), reverse transcriptase-qPCR (RT-qPCR), and immunohistochemistry (IHC) in more patients. RESULTS We identified 20 chromosomal imbalance regions harboring 459 genes for Caucasian and 17 regions containing 476 genes for Asian lung cancer patients. Seven common chromosomal imbalance regions harboring 117 genes, included gain on 3p13-14, 6p22.1, 9q21.13, 13q14.1, and 17p13.3; and loss on 3p22.2-22.3 and 13q13.3 were found both in Asian and Caucasian patients. Gene validation for four genes including ARHGAP19 (10q24.1) functioning in Rho activity control, FRAT2 (10q24.1) involved in Wnt signaling, PAFAH1B1 (17p13.3) functioning in motility control, and ZNF322A (6p22.1) involved in MAPK signaling was performed using qPCR and RT-qPCR. Mean gene dosage and mRNA expression level of the four candidate genes in tumor tissues were significantly higher than the corresponding normal tissues (P<0.001~P=0.06). In addition, CISH analysis of patients indicated that copy number amplification indeed occurred for ARHGAP19 and ZNF322A genes in lung cancer patients. IHC analysis of paraffin blocks from Asian Caucasian patients demonstrated that the frequency of PAFAH1B1 protein overexpression was 68% in Asian and 70% in Caucasian. CONCLUSIONS Our study provides an invaluable database revealing common and differential imbalance regions at specific chromosomes among Asian and Caucasian lung cancer patients. Four validation methods confirmed our database, which would help in further studies on the mechanism of lung tumorigenesis.
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Affiliation(s)
- Fang-Yi Lo
- Department of Pharmacology and Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, No,1, University Road, Tainan 701, Taiwan
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Microarray-based copy number analysis of neurofibromatosis type-1 (NF1)-associated malignant peripheral nerve sheath tumors reveals a role for Rho-GTPase pathway genes in NF1 tumorigenesis. Hum Mutat 2012; 33:763-76. [DOI: 10.1002/humu.22044] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Accepted: 01/18/2012] [Indexed: 01/22/2023]
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Yang J, Ylipää A, Sun Y, Zheng H, Chen K, Nykter M, Trent J, Ratner N, Lev DC, Zhang W. Genomic and molecular characterization of malignant peripheral nerve sheath tumor identifies the IGF1R pathway as a primary target for treatment. Clin Cancer Res 2011; 17:7563-73. [PMID: 22042973 DOI: 10.1158/1078-0432.ccr-11-1707] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Malignant peripheral nerve sheath tumor (MPNST) is a rare sarcoma that lacks effective therapeutic strategies. We gain insight into the most recurrent genetically altered pathways with the purpose of scanning possible therapeutic targets. EXPERIMENTAL DESIGN We conducted a microarray-based comparative genomic hybridization profiling of two cohorts of primary MPNST tissue samples including 25 patients treated at The University of Texas MD Anderson Cancer Center and 26 patients from Tianjin Cancer Hospital. Immunohistochemistry (IHC) and cell biology detection and validation were carried out on human MPNST tissues and cell lines. RESULTS Genomic characterization of 51 MPNST tissue samples identified several frequently amplified regions harboring 2,599 genes and regions of deletion including 4,901 genes. At the pathway level, we identified a significant enrichment of copy number-altering events in the insulin-like growth factor 1 receptor (IGF1R) pathway, including frequent amplifications of the IGF1R gene itself. To validate the IGF1R pathway as a potential target in MPNSTs, we first confirmed that high IGF1R protein correlated with worse tumor-free survival in an independent set of samples using IHC. Two MPNST cell lines (ST88-14 and STS26T) were used to determine the effect of attenuating IGF1R. Inhibition of IGF1R in ST88-14 cells using siRNAs or an IGF1R inhibitor, MK-0646, led to significant decreases in cell proliferation, invasion, and migration accompanied by attenuation of the PI3K/AKT and mitogen-activated protein kinase pathways. CONCLUSION These integrated genomic and molecular studies provide evidence that the IGF1R pathway is a potential therapeutic target for patients with MPNST.
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Affiliation(s)
- Jilong Yang
- Departments of Bone and Soft Tissue Tumor, Pathology, and Epidemiology and Biostatistics, Tianjin Medical University Cancer Hospital and Institute, Tianjin, China.
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Gu Y, Zhao W, Xia J, Zhang Y, Wu R, Wang C, Guo Z. Analysis of pathway mutation profiles highlights collaboration between cancer-associated superpathways. Hum Mutat 2011; 32:1028-35. [PMID: 21618647 DOI: 10.1002/humu.21541] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 05/16/2011] [Indexed: 12/21/2022]
Abstract
The biological interpretation of the complexity of cancer somatic mutation profiles is a major challenge in current cancer research. It has been suggested that mutations in multiple genes that participate in different pathways are collaborative in conferring growth advantage to tumor cells. Here, we propose a powerful pathway-based approach to study the functional collaboration of gene mutations in carcinogenesis. We successfully identify many pairs of significantly comutated pathways for a large-scale somatic mutation profile of lung adenocarcinoma. We find that the coordinated pathway pairs detected by comutations are also likely to be coaltered by other molecular changes, such as alterations in multifunctional genes in cancer. Then, we cluster comutated pathways into comutated superpathways and show that the derived superpathways also tend to be significantly coaltered by DNA copy number alterations. Our results support the hypothesis that comprehensive cooperation among a few basic functions is required for inducing cancer. The results also suggest biologically plausible models for understanding the heterogeneous mechanisms of cancers. Finally, we suggest an approach to identify candidate cancer genes from the derived comutated pathways. Together, our results provide guidelines to distill the pathway collaboration in carcinogenesis from the complexity of cancer somatic mutation profiles.
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Affiliation(s)
- Yunyan Gu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People's Republic of China
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Abstract
Abstract
Context.—Soft tissue pathology encompasses a remarkably diverse assortment of benign and malignant soft tissue tumors. Rendering a definitive diagnosis is complicated not only by the large volume of existing histologic subtypes (>100) but also frequently by the presence of overlapping clinical, histologic, immunohistochemical, and/or radiographic features. During the past 3 decades, mesenchymal tumor–specific, cytogenetic and molecular genetic abnormalities have demonstrated an increasingly important, ancillary role in mesenchymal tumor diagnostics.
Objectives.—To review molecular diagnostic tools available to the pathologist to further classify specific soft tissue tumor types and recurrent aberrations frequently examined. Advantages and limitations of individual approaches will also be highlighted.
Data Sources.—Previously published review articles, peer-reviewed research publications, and the extensive cytogenetic and molecular diagnostic experience of the authors to include case files of The University of Nebraska Medical Center.
Conclusions.—Cytogenetic and molecular genetic assays are used routinely for diagnostic purposes in soft tissue pathology and represent a powerful adjunct to complement conventional microscopy and clinicoradiographic evaluation in the formulation of an accurate diagnosis. Care should be taken, however, to recognize the limitations of these approaches. Ideally, more than one technical approach should be available to a diagnostic laboratory to compensate for the shortcomings of each approach in the assessment of individual specimens.
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McCabe MG, Bäcklund LM, Leong HS, Ichimura K, Collins VP. Chromosome 17 alterations identify good-risk and poor-risk tumors independently of clinical factors in medulloblastoma. Neuro Oncol 2011; 13:376-83. [PMID: 21292688 PMCID: PMC3064691 DOI: 10.1093/neuonc/noq192] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Current risk stratification schemas for medulloblastoma, based on combinations of clinical variables and histotype, fail to accurately identify particularly good- and poor-risk tumors. Attempts have been made to improve discriminatory power by combining clinical variables with cytogenetic data. We report here a pooled analysis of all previous reports of chromosomal copy number related to survival data in medulloblastoma. We collated data from previous reports that explicitly quoted survival data and chromosomal copy number in medulloblastoma. We analyzed the relative prognostic significance of currently used clinical risk stratifiers and the chromosomal aberrations previously reported to correlate with survival. In the pooled dataset metastatic disease, incomplete tumor resection and severe anaplasia were associated with poor outcome, while young age at presentation was not prognostically significant. Of the chromosomal variables studied, isolated 17p loss and gain of 1q correlated with poor survival. Gain of 17q without associated loss of 17p showed a trend to improved outcome. The most commonly reported alteration, isodicentric chromosome 17, was not prognostically significant. Sequential multivariate models identified isolated 17p loss, isolated 17q gain, and 1q gain as independent prognostic factors. In a historical dataset, we have identified isolated 17p loss as a marker of poor outcome and 17q gain as a novel putative marker of good prognosis. Biological markers of poor-risk and good-risk tumors will be critical in stratifying treatment in future trials. Our findings should be prospectively validated independently in future clinical studies.
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Affiliation(s)
- Martin G McCabe
- Manchester Academic Health Science Centre, School of Cancer and Enabling Sciences, University of Manchester, The Christie NHS Foundation Trust, Withington, Manchester M20 4BX, UK.
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Abstract
The development of microarray technology has revolutionized RNA and deoxyribonucleic acid (DNA) research. In contrast with traditional biological assays, microarrays allow the simultaneous measurement of tens of thousands of messenger RNA (mRNA) transcripts for gene expression or of genomic DNA fragments for copy number variation analysis. Over the past decade, genome-wide RNA or DNA microarray analysis has become an essential component of biology and biomedical research. The successful use of microarrays requires attention to unique issues of experimental design and execution. This chapter provides an overview of the methodology and applications of RNA and DNA microarrays in various areas of biological research.
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Pasmant E, Vidaud D, Harrison M, Upadhyaya M. Different sized somatic NF1 locus rearrangements in neurofibromatosis 1-associated malignant peripheral nerve sheath tumors. J Neurooncol 2010; 102:341-6. [PMID: 20686819 DOI: 10.1007/s11060-010-0328-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Accepted: 07/21/2010] [Indexed: 11/30/2022]
Abstract
Neurofibromatosis type 1 (NF1) patients are at increased risk of developing both benign (neurofibromas) and malignant (malignant peripheral nerve sheath tumors, MPNST) tumors. Molecular data on tumor progression are scarce, and few studies have compared the NF1 locus copy number in these two tumor types. To further explore the role of such NF1 locus rearrangements in NF1 tumorigenesis, and the likely disruption to the associated genes, the NF1 gene region was analyzed in NF1-associated tumors. DNA from three MPNSTs and one neurofibroma, excised from three unrelated NF1 patients, were analyzed using an NF1 region customized array-based comparative genomic hybridization. The somatic NF1 inactivation mutational mechanisms associated with MPNSTs appear to be different from those in benign neurofibromas. Interestingly, the MPNST-associated deletion breakpoints did not involve the paralogous repetitive sequences that are involved in most germline NF1 deletions. The somatic smallest common region of deletion overlap, however, was restricted to approximately the same ~2.2-Mb interval that encompassed most of the genes deleted in NF1 recurrent constitutional deletions. A number of genes in addition to NF1 on 17q (centromere to 17q24.2) may be involved in MPNST development. A larger study is warranted to confirm these findings. As NF1 patients with such germline NF1 deletions do exhibit increased risk of developing MPNST, these present findings emphasize the likely role of at least some of these NF1 flanking genes in MPNST pathobiology.
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Affiliation(s)
- Eric Pasmant
- UMR745 INSERM, Université Paris Descartes, Faculté des Sciences Pharmaceutiques et Biologiques, 75006 Paris, France.
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Abstract
Soft tissue sarcomas (STS) with complex genomic profiles (50% of all STS) are predominantly composed of spindle cell/pleomorphic sarcomas, including leiomyosarcoma, myxofibrosarcoma, pleomorphic liposarcoma, pleomorphic rhabdomyosarcoma, malignant peripheral nerve sheath tumor, angiosarcoma, extraskeletal osteosarcoma, and spindle cell/pleomorphic unclassified sarcoma (previously called spindle cell/pleomorphic malignant fibrous histiocytoma). These neoplasms show, characteristically, gains and losses of numerous chromosomes or chromosome regions, as well as amplifications. Many of them share recurrent aberrations (e.g., gain of 5p13-p15) that seem to play a significant role in tumor progression and/or metastatic dissemination. In this paper, we review the cytogenetic, molecular genetic, and clinicopathologic characteristics of the most common STS displaying complex genomic profiles. Features of diagnostic or prognostic relevance will be discussed when needed.
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Affiliation(s)
- Louis Guillou
- University Institute of Pathology, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Rue du Bugnon 25, Lausanne, Switzerland.
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Molecular evolution of a neurofibroma to malignant peripheral nerve sheath tumor (MPNST) in an NF1 patient: correlation between histopathological, clinical and molecular findings. J Cancer Res Clin Oncol 2010; 136:1869-80. [DOI: 10.1007/s00432-010-0846-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Accepted: 02/15/2010] [Indexed: 10/25/2022]
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Brekke HR, Ribeiro FR, Kolberg M, Agesen TH, Lind GE, Eknaes M, Hall KS, Bjerkehagen B, van den Berg E, Teixeira MR, Mandahl N, Smeland S, Mertens F, Skotheim RI, Lothe RA. Genomic changes in chromosomes 10, 16, and X in malignant peripheral nerve sheath tumors identify a high-risk patient group. J Clin Oncol 2010; 28:1573-82. [PMID: 20159821 DOI: 10.1200/jco.2009.24.8989] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE The purpose of this study was to identify genetic aberrations contributing to clinical aggressiveness of malignant peripheral nerve sheath tumors (MPNSTs). PATIENTS AND METHODS Samples from 48 MPNSTs and 10 neurofibromas were collected from 51 patients with (n = 31) or without (n = 20) neurofibromatosis type 1 (NF1). Genome-wide DNA copy number changes were assessed by chromosomal and array-based comparative genomic hybridization (CGH) and examined for prognostic significance. For a subset of 20 samples, RNA microarray data were integrated with the genome data to identify potential target genes. RESULTS Forty-four (92%) MPNSTs displayed DNA copy number changes (median, 18 changes per tumor; range, 2 to 35 changes). Known frequent chromosomal gains at chromosome arms 8q (69%), 17q (67%), and 7p (52%) and losses from 9p (50%), 11q (48%), and 17p (44%) were confirmed. Additionally, gains at 16p or losses from 10q or Xq identified a high-risk group with only 11% 10-year disease-specific survival (P = .00005). Multivariate analyses including NF1 status, tumor location, size, grade, sex, complete remission, and initial metastatic status showed that the genomic high-risk group was the most significant predictor of poor survival. Several genes whose expression was affected by the DNA copy number aberrations were identified. CONCLUSION The presence of specific genetic aberrations was strongly associated with poor survival independent of known clinical risk factors. Conversely, within the total patient cohort with 34% 10-year disease-specific survival, a low-risk group was identified: without changes at chromosomes 10q, 16p, or Xq in their MPNSTs, the patients had 74% 10-year survival.
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Affiliation(s)
- Helge R Brekke
- Department of Cancer Prevention, Institute for Cancer Research, The Norwegian Radium Hospital, Rikshospitalet, Oslo University Hospital, Oslo, Norway
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Mantripragada KK, Díaz de Ståhl T, Patridge C, Menzel U, Andersson R, Chuzhanova N, Kluwe L, Guha A, Mautner V, Dumanski JP, Upadhyaya M. Genome-wide high-resolution analysis of DNA copy number alterations in NF1-associated malignant peripheral nerve sheath tumors using 32K BAC array. Genes Chromosomes Cancer 2009; 48:897-907. [PMID: 19603524 DOI: 10.1002/gcc.20695] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Neurofibromatosis Type I (NF1) is an autosomal dominant disorder characterized by the development of both benign and malignant tumors. The lifetime risk for developing a malignant peripheral nerve sheath tumor (MPNST) in NF1 patients is approximately 10% with poor survival rates. To date, the molecular basis of MPNST development remains unclear. Here, we report the first genome-wide and high-resolution analysis of DNA copy number alterations in MPNST using the 32K bacterial artificial chromosome microarray on a series of 24 MPNSTs and three neurofibroma samples. In the benign neurofibromas, apart from loss of one copy of the NF1 gene and copy number polymorphisms, no other changes were found. The profiles of malignant samples, however, revealed specific loss of chromosomal regions including 1p35-33, 1p21, 9p21.3, 10q25, 11q22-23, 17q11, and 20p12.2 as well as gain of 1q25, 3p26, 3q13, 5p12, 5q11.2-q14, 5q21-23, 5q31-33, 6p23-p21, 6p12, 6q15, 6q23-q24, 7p22, 7p14-p13, 7q21, 7q36, 8q22-q24, 14q22, and 17q21-q25. Copy number gains were more frequent than deletions in the MPNST samples (62% vs. 38%). The genes resident within common regions of gain were NEDL1 (7p14), AP3B1 (5q14.1), and CUL1 (7q36.1) and these were identified in >63% MPNSTs. The most frequently deleted locus encompassed CDKN2A, CDKN2B, and MTAP genes on 9p21.3 (33% cases). These genes have previously been implicated in other cancer conditions and therefore, should be considered for their therapeutic, prognostic, and diagnostic relevance in NF1 tumorigenesis.
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Affiliation(s)
- Kiran K Mantripragada
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, UK.
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Hollosi P, Yakushiji JK, Fong KSK, Csiszar K, Fong SFT. Lysyl oxidase-like 2 promotes migration in noninvasive breast cancer cells but not in normal breast epithelial cells. Int J Cancer 2009; 125:318-27. [PMID: 19330836 DOI: 10.1002/ijc.24308] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A growing number of studies indicate the importance of the lysyl oxidase family in the promotion of epithelial neoplasms towards their more aggressive forms. However, the role of individual family members in carcinoma progression has yet to be ascertained. In this study, we analyzed LOXL2 expression in malignantly transformed MCF-7 and normal MCF-10A mammary epithelial cell line clones stably transduced with LOXL2 in vitro, and in normal and cancerous breast tissue samples in vivo. We found LOXL2 to be catalytically active in both MCF-7 and MCF-10 clones. LOXL2 overexpression promoted a more mesenchymal morphology in both cell types, but LOXL2-induced increase in migratory ability could only be established in MCF-7 clones. We demonstrated altered localization of the LOXL2 protein in breast cancer tissue compared to normal mammary tissue, and altered localization and processing of LOXL2 protein in breast cancer cell lines compared to normal cell lines, which may allow LOXL2 to interact with different intra and extracellular components during tumor progression. Results support the role of LOXL2 in selectively promoting a metastatic phenotype in breast tumor cells. Additional data suggest epigenetic molecular mechanisms in tumor specific regulation of LOXL2 expression that could be explored as a molecular target in the prevention of breast cancer progression.
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Affiliation(s)
- Peter Hollosi
- Cardiovascular Research Center, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
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Alvegård T, Hall KS, Bauer H, Rydholm A. The Scandinavian Sarcoma Group: 30 years' experience. ACTA ORTHOPAEDICA. SUPPLEMENTUM 2009; 80:1-104. [PMID: 19919379 DOI: 10.1080/17453690610046602] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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