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Chukwu W, Lee S, Crane A, Zhang S, Webster S, Mittra I, Imielinski M, Beroukhim R, Dubois F, Dalin S. Comparison of germline and somatic structural variants in cancers reveal systematic differences in variant generating and selection processes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.09.561462. [PMID: 38106141 PMCID: PMC10723258 DOI: 10.1101/2023.10.09.561462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Although several recent studies have characterized structural variants (SVs) in germline and cancer genomes, the features of SVs in these different contexts have not been directly compared. We examined similarities and differences between 2 million germline and 115 thousand tumor SVs from a cohort of 963 patients from The Cancer Genome Atlas (TCGA). We found significant differences in features related to their genomic sequences and localization that suggest differences between SV-generating processes and selective pressures. For example, we found that transposon-mediated processes shape germline much more than somatic SVs, while somatic SVs more frequently show features characteristic of chromoanagenesis. These differences were extensive enough to enable us to develop a classifier - "the great GaTSV" - that accurately distinguishes between germline and cancer SVs in tumor samples that lack a matched normal sample.
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Affiliation(s)
- Wolu Chukwu
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cancer Biology and Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Siyun Lee
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cancer Biology and Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alexander Crane
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cancer Biology and Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Shu Zhang
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cancer Biology and Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sophie Webster
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cancer Biology and Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ipsa Mittra
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Marcin Imielinski
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; New York Genome Center, New York, NY, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA; Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA; Department of Pathology and Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Rameen Beroukhim
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cancer Biology and Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Frank Dubois
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cancer Biology and Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin; Humboldt-Universität zu Berlin, Institute of Pathology
| | - Simona Dalin
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cancer Biology and Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
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2
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Belova T, Biondi N, Hsieh PH, Lutsik P, Chudasama P, Kuijjer M. Heterogeneity in the gene regulatory landscape of leiomyosarcoma. NAR Cancer 2023; 5:zcad037. [PMID: 37492373 PMCID: PMC10365024 DOI: 10.1093/narcan/zcad037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 07/06/2023] [Accepted: 07/18/2023] [Indexed: 07/27/2023] Open
Abstract
Characterizing inter-tumor heterogeneity is crucial for selecting suitable cancer therapy, as the presence of diverse molecular subgroups of patients can be associated with disease outcome or response to treatment. While cancer subtypes are often characterized by differences in gene expression, the mechanisms driving these differences are generally unknown. We set out to model the regulatory mechanisms driving sarcoma heterogeneity based on patient-specific, genome-wide gene regulatory networks. We developed a new computational framework, PORCUPINE, which combines knowledge on biological pathways with permutation-based network analysis to identify pathways that exhibit significant regulatory heterogeneity across a patient population. We applied PORCUPINE to patient-specific leiomyosarcoma networks modeled on data from The Cancer Genome Atlas and validated our results in an independent dataset from the German Cancer Research Center. PORCUPINE identified 37 heterogeneously regulated pathways, including pathways representing potential targets for treatment of subgroups of leiomyosarcoma patients, such as FGFR and CTLA4 inhibitory signaling. We validated the detected regulatory heterogeneity through analysis of networks and chromatin states in leiomyosarcoma cell lines. We showed that the heterogeneity identified with PORCUPINE is not associated with methylation profiles or clinical features, thereby suggesting an independent mechanism of patient heterogeneity driven by the complex landscape of gene regulatory interactions.
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Affiliation(s)
- Tatiana Belova
- Computational Biology and Systems Medicine Group, Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
| | - Nicola Biondi
- Precision Sarcoma Research Group, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases, Heidelberg, Germany
| | - Ping-Han Hsieh
- Computational Biology and Systems Medicine Group, Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Oncology, Catholic University (KU) Leuven, Leuven, Belgium
| | - Priya Chudasama
- Precision Sarcoma Research Group, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases, Heidelberg, Germany
| | - Marieke L Kuijjer
- Computational Biology and Systems Medicine Group, Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
- Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, the Netherlands
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3
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A New Signature of Sarcoma Based on the Tumor Microenvironment Benefits Prognostic Prediction. Int J Mol Sci 2023; 24:ijms24032961. [PMID: 36769292 PMCID: PMC9918054 DOI: 10.3390/ijms24032961] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/13/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Sarcomas are a group of malignant tumors derived from mesenchymal tissues that display complex and variable pathological types. The impact of the immune properties of the tumor microenvironment (TME) on the prognosis, treatment, and management of sarcomas has attracted attention, requiring the exploration of sensitive and accurate signatures. In this study, The Cancer Genome Atlas (TCGA) database was searched to screen for an RNA sequencing dataset, retrieving 263 sarcoma and 2 normal samples with survival data. Genes associated with immune regulation in sarcomas were retrieved from the Tumor Immune Estimation Resource database to estimate tumor purity and immune cell infiltration levels. The samples were then divided into the immune-high and immune-low groups. Then, we screened for differentially expressed genes (DEGs) between the two groups. The intersection between immune-related genes and DEGs was then determined. Univariate Cox and least absolute shrinkage and selection operator analyses were used to select ideal genes for prognostic prediction and subsequent construction of a risk signature. A survival analysis was performed to reveal the dissimilarity in survival between the high- and low-score groups. Finally, a nomogram was generated to verify the accuracy and reliability of the signature. Through Estimation of STromal and Immune cells in MAlignant Tumour tissues using Expression (ESTIMATE) analysis, high ESTIMATE, and low tumor purity were significantly associated with a favorable prognosis. Moreover, a total of 5259 DEGs were retrieved, the majority of which were downregulated. In total, 590 immune-associated genes overlapped with the DEGs, among which nine hub genes were identified. Finally, two candidate genes, ACVR2B and NFYA, were identified, based on which a risk signature was constructed. The risk signature constructed in this study is accurate and reliable for the prognostic prediction and phenotyping of sarcomas.
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Rincón-Riveros A, De la Peña J, Rubiano W, Olivella F, Martinez-Agüero M, Villegas VE. Primary Breast Angiosarcoma: Comparative Transcriptome Analysis. Int J Mol Sci 2022; 23:ijms232416032. [PMID: 36555675 PMCID: PMC9781631 DOI: 10.3390/ijms232416032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
Primary breast angiosarcoma, with de novo appearance and not associated with exposure to radiation or lymphedema, is a rare pathology representing less than 0.05% of the neoplasms related to this organ. The pathology is characterized by its aggressiveness, poor prognosis, and difficulties in its differential diagnosis. This article reports the case of a 55-year-old white woman with no family history of cancer, with a rapidly growing mass in the left mammary gland that ulcerates and bleeds. It is confirmed as primary breast angiosarcoma by immunostaining in the tumor tissue for CD31, CD34, and FLI-1. In addition, a sample of neoplastic and healthy tissues is collected from the patient for RNA sequencing; the results are contrasted with a tissue sample from a patient with Luminal A subtype of breast cancer, as well as data from other cases of angiosarcoma available in public databases. These findings revealed a genetic profile associated with the immune and inflammatory response in the patient's sample when compared to available angiosarcoma data; these molecular patterns are consistent with other recent studies. Due to the rarity of the disease, the studies carried out on each patient contribute to the expanding knowledge of the etiology and molecular pathways that are still partially known and continue to be the subject of research. Aside from a comparative transcriptome study, this article aims to provide an update on the state of knowledge about this disease.
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Affiliation(s)
- Andrés Rincón-Riveros
- Bioinformatics and Systems Biology Group, Universidad Nacional de Colombia, Bogotá 111221, Colombia
- Correspondence: (A.R.-R.); (V.E.V.); Tel.: +57-1-6012-418800 (ext. 281) (A.R.-R.); +57-1-6012-976200 (ext. 4029) (V.E.V.)
| | - Jairo De la Peña
- Servicio de Mastología, Hospital Universitario Mayor Méderi, Bogotá 111411, Colombia
| | - Wilson Rubiano
- Servicio de Mastología, Hospital Universitario Mayor Méderi, Bogotá 111411, Colombia
| | - Fabio Olivella
- Servicio de Mastología, Hospital Universitario Mayor Méderi, Bogotá 111411, Colombia
| | - María Martinez-Agüero
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia
| | - Victoria E. Villegas
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia
- Correspondence: (A.R.-R.); (V.E.V.); Tel.: +57-1-6012-418800 (ext. 281) (A.R.-R.); +57-1-6012-976200 (ext. 4029) (V.E.V.)
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5
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Li H, He J, Li M, Li K, Pu X, Guo Y. Immune landscape-based machine-learning-assisted subclassification, prognosis, and immunotherapy prediction for glioblastoma. Front Immunol 2022; 13:1027631. [PMID: 36532035 PMCID: PMC9751405 DOI: 10.3389/fimmu.2022.1027631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/15/2022] [Indexed: 12/04/2022] Open
Abstract
Introduction As a malignant brain tumor, glioblastoma (GBM) is characterized by intratumor heterogeneity, a worse prognosis, and highly invasive, lethal, and refractory natures. Immunotherapy has been becoming a promising strategy to treat diverse cancers. It has been known that there are highly heterogeneous immunosuppressive microenvironments among different GBM molecular subtypes that mainly include classical (CL), mesenchymal (MES), and proneural (PN), respectively. Therefore, an in-depth understanding of immune landscapes among them is essential for identifying novel immune markers of GBM. Methods and results In the present study, based on collecting the largest number of 109 immune signatures, we aim to achieve a precise diagnosis, prognosis, and immunotherapy prediction for GBM by performing a comprehensive immunogenomic analysis. Firstly, machine-learning (ML) methods were proposed to evaluate the diagnostic values of these immune signatures, and the optimal classifier was constructed for accurate recognition of three GBM subtypes with robust and promising performance. The prognostic values of these signatures were then confirmed, and a risk score was established to divide all GBM patients into high-, medium-, and low-risk groups with a high predictive accuracy for overall survival (OS). Therefore, complete differential analysis across GBM subtypes was performed in terms of the immune characteristics along with clinicopathological and molecular features, which indicates that MES shows much higher immune heterogeneity compared to CL and PN but has significantly better immunotherapy responses, although MES patients may have an immunosuppressive microenvironment and be more proinflammatory and invasive. Finally, the MES subtype is proved to be more sensitive to 17-AAG, docetaxel, and erlotinib using drug sensitivity analysis and three compounds of AS-703026, PD-0325901, and MEK1-2-inhibitor might be potential therapeutic agents. Conclusion Overall, the findings of this research could help enhance our understanding of the tumor immune microenvironment and provide new insights for improving the prognosis and immunotherapy of GBM patients.
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Brennan MF, Singer S. Five decades of sarcoma care at Memorial Sloan Kettering Cancer Center. J Surg Oncol 2022; 126:896-901. [PMID: 36087086 DOI: 10.1002/jso.27032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/02/2022] [Indexed: 11/07/2022]
Abstract
Early studies of the management of soft tissue sarcoma at Memorial Sloan Kettering Cancer Center were influenced by development of robust prospective long-term databases. Increasing capacity for molecular diagnostics has identified a myriad of subtypes with definable natural history. Accurate identification of tissue-specific risk of recurrence and disease-specific survival have increasingly allowed selective use of surgery, radiation therapy, and target-specific cytotoxic and immune therapies.
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Affiliation(s)
- Murray F Brennan
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Samuel Singer
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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Ko A, Coward VS, Gokgoz N, Dickson BC, Tsoi K, Wunder JS, Andrulis IL. Investigating the Potential of Isolating and Expanding Tumour-Infiltrating Lymphocytes from Adult Sarcoma. Cancers (Basel) 2022; 14:548. [PMID: 35158816 PMCID: PMC8833772 DOI: 10.3390/cancers14030548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/23/2021] [Accepted: 01/19/2022] [Indexed: 02/04/2023] Open
Abstract
Sarcomas are a heterogeneous group of mesenchymal neoplasms, many of which are associated with a high risk of metastasis and poor prognosis. Conventional chemotherapy and targeted therapies have varying effects across individuals and tumour subtypes. The current therapies frequently provide limited clinical benefit; hence, more effective treatments are urgently needed. Recent advances in immunotherapy, such as checkpoint inhibition or adoptive cell therapy (ACT), show potential in increasing efficacy by providing a more personalized treatment. Therapy with tumour-infiltrating lymphocytes (TILs) is an emerging field in immunotherapy. Here, we collected 190 sarcoma tumour specimens from patients without pre-operative adjuvant treatment in order to isolate TILs. We compared different methods of TIL expansion and optimized a protocol specifically for efficacy in culturing TILs from sarcoma. The expanded TIL populations were characterized by flow cytometry analysis using CD3, CD4, CD8, CD14, CD19 and CD56 markers. The TIL populations were non-specifically stimulated to establish TIL reactivity. Through an optimized expansion protocol, TILs were isolated and cultured from 54 of 92 primary sarcoma specimens. The isolated TILs varied in CD4+ and CD8+ T-cell compositions and retained their ability to release IFNγ upon stimulation. Our results suggest that certain sarcoma subtypes have the potential to yield a sufficient number of TILs for TIL therapy.
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Affiliation(s)
- Alice Ko
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; (B.C.D.); (I.L.A.)
| | - Victoria S. Coward
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | - Nalan Gokgoz
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; (N.G.); (J.S.W.)
| | - Brendan C. Dickson
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; (B.C.D.); (I.L.A.)
- University of Toronto Musculoskeletal Oncology Unit, Sinai Health System, Toronto, ON M5G 1X5, Canada;
- Department of Pathology and Laboratory Medicine, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Kim Tsoi
- University of Toronto Musculoskeletal Oncology Unit, Sinai Health System, Toronto, ON M5G 1X5, Canada;
- Department of Surgery, University of Toronto, Toronto, ON M5T 1P5, Canada
| | - Jay S. Wunder
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; (N.G.); (J.S.W.)
- University of Toronto Musculoskeletal Oncology Unit, Sinai Health System, Toronto, ON M5G 1X5, Canada;
- Department of Surgery, University of Toronto, Toronto, ON M5T 1P5, Canada
| | - Irene L. Andrulis
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; (B.C.D.); (I.L.A.)
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada;
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; (N.G.); (J.S.W.)
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8
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Zhu S, Wang Q, Zheng D, Zhu L, Zhou Z, Xu S, Shi B, Jin C, Zheng G, Cai Y. A Novel and Effective Model to Predict Skip Metastasis in Papillary Thyroid Carcinoma Based on a Support Vector Machine. Front Endocrinol (Lausanne) 2022; 13:916121. [PMID: 35865315 PMCID: PMC9295388 DOI: 10.3389/fendo.2022.916121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/01/2022] [Indexed: 12/04/2022] Open
Abstract
INTRODUCTION Skip metastasis, referred to as lymph node metastases to the lateral neck compartment without involvement of the central compartment, is generally unpredictable in papillary thyroid carcinoma (PTC). This study aims to establish an effective predictive model for skip metastasis in PTC. METERIALS AND METHODS Retrospective analysis was performed of clinical samples from 18192 patients diagnosed with thyroid cancer between 2016 to 2020. The First Affiliated Hospital of Wenzhou Medical University. The lateral lymph node metastasis was occureed in the training set (630 PTC patients) and validation set (189 PTC patients). The univariate and multivariate analyses were performed to detect the predictors of skip metastasis and the support vector machine (SVM) was used to establish a model to predict skip metastasis. RESULTS The rate of skip metastasis was 13.3% (84/631). Tumor size (≤10 mm), upper location, Hashimoto's thyroiditis, extrathyroidal extension, absence of BRAFV600E mutation, and less number of central lymph node dissection were considered as independent predictors of skip metastasis in PTC. For the training set, these predictors performed with 91.7% accuracy, 86.4% sensitivity, 92.2% specificity, 45.2% positive predictive value (PPV), and 98.9% negative predictive value (NPV) in the model. Meanwhile, these predictors showed 91.5% accuracy,71.4% sensitivity, 93.1% specificity, 45.5% PPV, and 97.6% NPV in validation set. CONCLUSION This study screened the predictors of the skip lateral lymph node metastasis and to establish an effective and economic predictive model for skip metastasis in PTC. The model can accurately distinguish the skip metastasis in PTC using a simple and affordable method, which may have potential for daily clinical application in the future.
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Affiliation(s)
- Shuting Zhu
- Department of Ultrasound, The First Medical Center of Chinese People’s Liberation Army (PLA) General Hospital, Beijing, China
| | - Qingxuan Wang
- Department of Thyroid Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Danni Zheng
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lei Zhu
- Thyroid Surgery Department, The Fifth Hospital Affiliated to Wenzhou Medical University, Lishui Central Hospital, Lishui, China
| | - Zheng Zhou
- Department of Head and Neck Surgery, Bengbu Medical College Graduate School, Anhui, China
| | - Shiying Xu
- Zhejiang Chinese Medical University, The Second Clinical Medical, Hangzhou, China
| | - Binbin Shi
- Department of Medical Ultrasound, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Cong Jin
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Guowan Zheng
- Department of Head and Neck Surgery, Otolaryngology & Head and Neck Center, Cancer Center, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, China
- Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Hangzhou, China
- *Correspondence: Guowan Zheng, ; Yefeng Cai,
| | - Yefeng Cai
- Department of Thyroid Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Department of Head and Neck Surgery, Otolaryngology & Head and Neck Center, Cancer Center, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, China
- Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Hangzhou, China
- *Correspondence: Guowan Zheng, ; Yefeng Cai,
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9
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Milighetti M, Krasny L, Lee ATJ, Morani G, Szecsei C, Chen Y, Guljar N, McCarthy F, Wilding CP, Arthur A, Fisher C, Judson I, Thway K, Cheang MCU, Jones RL, Huang PH. Proteomic profiling of soft tissue sarcomas with SWATH mass spectrometry. J Proteomics 2021; 241:104236. [PMID: 33895336 PMCID: PMC8135130 DOI: 10.1016/j.jprot.2021.104236] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/02/2021] [Accepted: 04/14/2021] [Indexed: 12/15/2022]
Abstract
Soft tissue sarcomas (STS) are a group of rare and heterogeneous cancers. While large-scale genomic and epigenomic profiling of STS have been undertaken, proteomic analysis has thus far been limited. Here we utilise sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS) for proteomic profiling of formalin fixed paraffin embedded (FFPE) specimens from a cohort of STS patients (n = 36) across four histological subtypes (leiomyosarcoma, synovial sarcoma, undifferentiated pleomorphic sarcoma and dedifferentiated liposarcoma). We quantified 2951 proteins across all cases and show that there is a significant enrichment of gene sets associated with smooth muscle contraction in leiomyosarcoma, RNA splicing regulation in synovial sarcoma and leukocyte activation in undifferentiated pleomorphic sarcoma. We further identified a subgroup of STS cases that have a distinct expression profile in a panel of proteins, with worse survival outcomes when compared to the rest of the cohort. Our study highlights the value of comprehensive proteomic characterisation as a means to identify histotype-specific STS profiles that describe key biological pathways of clinical and therapeutic relevance; as well as for discovering new prognostic biomarkers in this group of rare and difficult-to-treat diseases. Proteomic analysis of FFPE specimens from four soft tissue sarcoma histological subtypes was performed by SWATH MS. Subtype-specific biological pathways and protein-protein interaction networks were identified. A panel of proteins associated with sarcoma patient survival outcome was defined. A subset of proteins identified by SWATH MS was validated by orthogonal immunohistochemical analysis.
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Affiliation(s)
- Martina Milighetti
- Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, SW3 6JB London, UK
| | - Lukas Krasny
- Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, SW3 6JB London, UK
| | - Alex T J Lee
- Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, SW3 6JB London, UK; Sarcoma Unit, The Royal Marsden NHS Foundation Trust, 203 Fulham Road, SW3 6JJ London, UK; Division of Clinical Studies, The Institute of Cancer Research, 15 Cotswold Road, SM2 5NG Sutton, London, UK
| | - Gabriele Morani
- Division of Clinical Studies, The Institute of Cancer Research, 15 Cotswold Road, SM2 5NG Sutton, London, UK; Clinical Trials and Statistics Unit, The Institute of Cancer Research, 15 Cotswold Road, SM2 5NG Sutton, London, UK
| | - Cornelia Szecsei
- Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, SW3 6JB London, UK
| | - Yingtong Chen
- Division of Clinical Studies, The Institute of Cancer Research, 15 Cotswold Road, SM2 5NG Sutton, London, UK; Clinical Trials and Statistics Unit, The Institute of Cancer Research, 15 Cotswold Road, SM2 5NG Sutton, London, UK
| | - Nafia Guljar
- Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, SW3 6JB London, UK
| | - Frank McCarthy
- Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, SW3 6JB London, UK
| | - Christopher P Wilding
- Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, SW3 6JB London, UK
| | - Amani Arthur
- Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, SW3 6JB London, UK
| | - Cyril Fisher
- Sarcoma Unit, The Royal Marsden NHS Foundation Trust, 203 Fulham Road, SW3 6JJ London, UK
| | - Ian Judson
- Sarcoma Unit, The Royal Marsden NHS Foundation Trust, 203 Fulham Road, SW3 6JJ London, UK
| | - Khin Thway
- Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, SW3 6JB London, UK; Sarcoma Unit, The Royal Marsden NHS Foundation Trust, 203 Fulham Road, SW3 6JJ London, UK
| | - Maggie C U Cheang
- Division of Clinical Studies, The Institute of Cancer Research, 15 Cotswold Road, SM2 5NG Sutton, London, UK; Clinical Trials and Statistics Unit, The Institute of Cancer Research, 15 Cotswold Road, SM2 5NG Sutton, London, UK
| | - Robin L Jones
- Sarcoma Unit, The Royal Marsden NHS Foundation Trust, 203 Fulham Road, SW3 6JJ London, UK; Division of Clinical Studies, The Institute of Cancer Research, 15 Cotswold Road, SM2 5NG Sutton, London, UK
| | - Paul H Huang
- Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, SW3 6JB London, UK.
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10
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Taylor BA, Cini A, Wyatt CDR, Reuter M, Sumner S. The molecular basis of socially mediated phenotypic plasticity in a eusocial paper wasp. Nat Commun 2021; 12:775. [PMID: 33536437 PMCID: PMC7859208 DOI: 10.1038/s41467-021-21095-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/12/2021] [Indexed: 01/30/2023] Open
Abstract
Phenotypic plasticity, the ability to produce multiple phenotypes from a single genotype, represents an excellent model with which to examine the relationship between gene expression and phenotypes. Analyses of the molecular foundations of phenotypic plasticity are challenging, however, especially in the case of complex social phenotypes. Here we apply a machine learning approach to tackle this challenge by analyzing individual-level gene expression profiles of Polistes dominula paper wasps following the loss of a queen. We find that caste-associated gene expression profiles respond strongly to queen loss, and that this change is partly explained by attributes such as age but occurs even in individuals that appear phenotypically unaffected. These results demonstrate that large changes in gene expression may occur in the absence of outwardly detectable phenotypic changes, resulting here in a socially mediated de-differentiation of individuals at the transcriptomic level but not at the levels of ovarian development or behavior.
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Affiliation(s)
- Benjamin A Taylor
- Centre for Biodiversity & Environment Research, University College London, London, UK.
- Department of Genetics, Evolution & Environment, University College London, London, UK.
| | - Alessandro Cini
- Centre for Biodiversity & Environment Research, University College London, London, UK
- Department of Genetics, Evolution & Environment, University College London, London, UK
- Dipartimento di Biologia, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Christopher D R Wyatt
- Centre for Biodiversity & Environment Research, University College London, London, UK
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Max Reuter
- Department of Genetics, Evolution & Environment, University College London, London, UK
- Centre for Life's Origins and Evolution, University College London, London, UK
| | - Seirian Sumner
- Centre for Biodiversity & Environment Research, University College London, London, UK
- Department of Genetics, Evolution & Environment, University College London, London, UK
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11
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Kun EHS, Tsang YTM, Lin S, Pan S, Medapalli T, Malpica A, Richards JS, Gershenson DM, Wong KK. Differences in gynecologic tumor development in Amhr2-Cre mice with KRAS G12D or KRAS G12V mutations. Sci Rep 2020; 10:20678. [PMID: 33244099 PMCID: PMC7693266 DOI: 10.1038/s41598-020-77666-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 11/10/2020] [Indexed: 01/05/2023] Open
Abstract
How different KRAS variants impact tumor initiation and progression in vivo has not been thoroughly examined. We hypothesize that the ability of either KRASG12D or KRASG12V mutations to initiate tumor formation is context dependent. Amhr2-Cre mice express Cre recombinase in tissues that develop into the fallopian tubes, uterus, and ovaries. We used these mice to conditionally express either the KRASG12V/+or KRASG12D/+ mutation. Mice with the genotype Amhr2-Cre Pten(fl/fl) KrasG12D/+(G12D mice) had abnormal follicle structures and developed low-grade serous ovarian carcinomas with 100% penetrance within 18 weeks. In contrast, mice with the genotype Amhr2-Cre Pten(fl/fl) KrasG12V/+ (G12V mice) had normal follicle structures, and about 90% of them developed uterine tumors with diverse histological features resembling those of leiomyoma and leiomyosarcoma. Granulosa cell tumors also developed in G12V mice. Differences in cell-signaling pathways in the uterine tissues of G12D and G12V mice were identified using RNA sequencing and reverse-phase protein array analyses. We found that CTNNB1, IL1A, IL1B, TNF, TGFB1, APP, and IL6 had the higher activity in G12V mice than in G12D mice. These mouse models will be useful for studying the differences in signaling pathways driven by KrasG12V/+ or KrasG12D/+ mutations to aid development of targeted therapies for specific KRAS mutant variants. Our leiomyoma model driven by the KrasG12V/+ mutation will also be useful in deciphering the malignant progression from leiomyoma to leiomyosarcoma.
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Affiliation(s)
- Eucharist H S Kun
- Department of Gynecologic Oncology and Reproductive Medicine, Unit 1362, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Yvonne T M Tsang
- Department of Gynecologic Oncology and Reproductive Medicine, Unit 1362, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Sophia Lin
- Department of Gynecologic Oncology and Reproductive Medicine, Unit 1362, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Sophia Pan
- Department of Gynecologic Oncology and Reproductive Medicine, Unit 1362, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Tejas Medapalli
- Department of Gynecologic Oncology and Reproductive Medicine, Unit 1362, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Anais Malpica
- Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - JoAnne S Richards
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - David M Gershenson
- Department of Gynecologic Oncology and Reproductive Medicine, Unit 1362, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Kwong-Kwok Wong
- Department of Gynecologic Oncology and Reproductive Medicine, Unit 1362, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.
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12
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Chua K, Virshup DM, Odono EG, Chang KTE, Tan NJH, Hue SSS, Sim AYL, Lee VKM. YJ5 as an immunohistochemical marker of osteogenic lineage. Pathology 2020; 53:229-238. [PMID: 33187685 DOI: 10.1016/j.pathol.2020.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 07/21/2020] [Accepted: 07/29/2020] [Indexed: 10/23/2022]
Abstract
Overexpression of WLS, an upstream protein in the Wnt pathway, has been implicated in several non-osteogenic tumours. This study represents the first attempt at evaluating WLS expression in various bone and soft tissue tumours using YJ5, a monoclonal antibody specific to WLS, with the aim of elucidating its utility in discerning tumours with aberrant Wnt signalling and as a marker of osteogenic lineage in challenging cases. Tumour tissue sections of 144 bone mass lesions and 63 soft tissue mass lesions were immunostained with the YJ5 antibody following standardised protocols. Subsequent assessment of immunoreactivity segregated cases into one of three groups: absent/weak, moderate, or strong YJ5 immunoreactivity. For the bone tumours, strong YJ5 immunoreactivity was seen in almost all osteosarcomas and chondroblastomas, all osteoblastomas and osteoid osteomas. In contrast, all other cartilaginous tumours, chordomas, aneurysmal bone cysts, chondromyxoid fibromas, most fibrous dysplasias and most giant cell tumours exhibited absent/weak YJ5 immunostaining. For the soft tissue tumours, a more heterogeneous pattern of YJ5 immunoreactivity was observed. Because diffuse and strong YJ5 expression is identified in almost all benign and malignant bone tumours with osteoblastic activity, it can be potentially utilised as an immunohistochemical marker to support osteogenic lineage. If interpreted in the appropriate context, this marker is useful in determining whether a malignant bone tumour is an osteosarcoma, particularly in those subtypes with no or minimal osteoid or unusual morphological features. This marker can also complement SATB2 to denote osteogenic lineage.
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Affiliation(s)
- Kenon Chua
- Department of Orthopaedic Surgery, Singapore General Hospital, Singapore; Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - David M Virshup
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Eugene G Odono
- Department of Pathology, College of Medicine, University of the Philippines, Manila, Philippines
| | - Kenneth Tou En Chang
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore
| | - Nicholas Jin Hong Tan
- Department of Pathology, National University Hospital, National University Health System, Singapore
| | - Susan Swee-Shan Hue
- Department of Pathology, NUH Advance Molecular Pathology Laboratory, Institute of Molecular and Cellular Biology, Singapore
| | - Arthur Yi Loong Sim
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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Synovial Sarcoma: A Complex Disease with Multifaceted Signaling and Epigenetic Landscapes. Curr Oncol Rep 2020; 22:124. [PMID: 33025259 DOI: 10.1007/s11912-020-00985-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2020] [Indexed: 12/29/2022]
Abstract
PURPOSE OF REVIEW Aside from a characteristic SS18-SSX translocation identified in almost all cases, no genetic anomalies have been reliably isolated yet to drive the pathogenesis of synovial sarcoma. In the following review, we explore the structural units of wild-type SS18 and SSX, particularly as they relate to the transcriptional alterations and cellular pathway changes imposed by SS18-SSX. RECENT FINDINGS Native SS18 and SSX contribute recognizable domains to the SS18-SSX chimeric proteins, which inflict transcriptional and epigenetic changes through selective protein interactions involving the SWI/SNF and Polycomb chromatin remodeling complexes. Multiple oncogenic and developmental pathways become altered, collectively reprogramming the cellular origin of synovial sarcoma and promoting its malignant transformation. Synovial sarcoma is characterized by complex epigenetic and signaling landscapes. Identifying the operational pathways and concomitant genetic changes induced by SS18-SSX fusions could help develop tailored therapeutic strategies to ultimately improve disease control and patient survivorship.
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Isidro U, O'Brien LM, Sebro R. Linear mixed-effects models for estimation of pulmonary metastasis growth rate: implications for CT surveillance in patients with sarcoma. Br J Radiol 2020; 93:20190856. [PMID: 32559116 DOI: 10.1259/bjr.20190856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES Sarcoma patients often undergo surveillance chest CT for detection of pulmonary metastases. No data exist on the optimal surveillance interval for chest CT. The aim of this study was to estimate pulmonary metastasis growth rate in sarcoma patients. METHODS This was a retrospective review of 95 patients with pulmonary metastases (43 patients with histologically confirmed metastases and 52 with clinically diagnosed metastases) from sarcoma treated at an academic tertiary-care center between 01 January 2000 and 01 June 2019. Age, sex, primary tumor size, grade, subtype, size and volume of the pulmonary metastasis over successive chest CT scans were recorded. Two metastases per patient were chosen if possible. Multivariate linear mixed-effects models with random effects for each pulmonary metastasis and each patient were used to estimate pulmonary metastasis growth rate, evaluating the impact of patient age, tumor size, tumor grade, chemotherapy and tumor subtype. We estimated the pulmonary metastasis volume doubling time using these analyses. RESULTS Maximal primary tumor size at diagnosis (LRT statistic = 2.58, df = 2, p = 0.275), tumor grade (LRT statistic = 1.13, df = 2, p = 0.567), tumor type (LRT statistic = 7.59, df = 6, p = 0.269), and patient age at diagnosis (LRT statistic = 0.735, df = 2, p = 0.736) were not statistically significant predictors of pulmonary nodule growth from baseline values. Chemotherapy decreased the rate of pulmonary nodule growth from baseline (LRT statistic = 7.96, df = 2, p = 0.0187). 95% of untreated pulmonary metastases are expected to grow less than 6 mm in 6.4 months. There was significant intrapatient and interpatient variation in pulmonary metastasis growth rate. Pulmonary metastasis volume growth rate was best fit with an exponential model in time. The volume doubling time for pulmonary metastases assuming an exponential model in time was 143 days (95% CI (104, 231) days). CONCLUSIONS Assuming a 2 mm nodule is the smallest reliably detectable nodule by CT, the data suggest that an untreated pulmonary metastasis is expected to grow to 8 mm in 8.4 months (95% CI (4.9, 10.2) months). Tumor size, grade and sarcoma subtype did not significantly alter pulmonary metastasis growth rate. However, chemotherapy slowed the pulmonary metastasis growth rate. ADVANCES IN KNOWLEDGE CT surveillance intervals for pulmonary metastases can be estimated based on metastasis growth rate. There was significant variation in the pulmonary metastasis growth rate between metastases within patient and between patients. Pulmonary nodule volume growth followed an exponential model, linear in time.
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Affiliation(s)
- Ulysses Isidro
- Department of Radiology, University of Pennsylvania, 3400 Civic Center, Philadelphia, PA 19104, USA
| | - Liam M O'Brien
- Department of Mathematics and Statistics, Colby College, Waterville, ME 04901, USA
| | - Ronnie Sebro
- Department of Radiology, University of Pennsylvania, 3400 Civic Center, Philadelphia, PA 19104, USA.,Department of Orthopaedic Surgery, University of Pennsylvania, 3737 Market Street, Philadelphia, PA 19104, USA.,Department of Genetics, University of Pennsylvania, 415 Curie Blvd, Philadelphia, PA 19104, USA.,Department of Biostatistics, Epidemiology and Informatics University of Pennsylvania, 423 Guardian Drive, Philadelphia, PA 19104, USA
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15
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Almeida PP, Cardoso CP, de Freitas LM. PDAC-ANN: an artificial neural network to predict pancreatic ductal adenocarcinoma based on gene expression. BMC Cancer 2020; 20:82. [PMID: 32005189 PMCID: PMC6995241 DOI: 10.1186/s12885-020-6533-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 01/13/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Although the pancreatic ductal adenocarcinoma (PDAC) presents high mortality and metastatic potential, there is a lack of effective therapies and a low survival rate for this disease. This PDAC scenario urges new strategies for diagnosis, drug targets, and treatment. METHODS We performed a gene expression microarray meta-analysis of the tumor against normal tissues in order to identify differentially expressed genes (DEG) shared among all datasets, named core-genes (CG). We confirmed the CG protein expression in pancreatic tissue through The Human Protein Atlas. It was selected five genes with the highest area under the curve (AUC) among these proteins with expression confirmed in the tumor group to train an artificial neural network (ANN) to classify samples. RESULTS This microarray included 461 tumor and 187 normal samples. We identified a CG composed of 40 genes, 39 upregulated, and one downregulated. The upregulated CG included proteins and extracellular matrix receptors linked to actin cytoskeleton reorganization. With the Human Protein Atlas, we verified that fourteen genes of the CG are translated, with high or medium expression in most of the pancreatic tumor samples. To train our ANN, we selected the best genes (AHNAK2, KRT19, LAMB3, LAMC2, and S100P) to classify the samples based on AUC using mRNA expression. The network classified tumor samples with an f1-score of 0.83 for the normal samples and 0.88 for the PDAC samples, with an average of 0.86. The PDAC-ANN could classify the test samples with a sensitivity of 87.6 and specificity of 83.1. CONCLUSION The gene expression meta-analysis and confirmation of the protein expression allow us to select five genes highly expressed PDAC samples. We could build a python script to classify the samples based on RNA expression. This software can be useful in the PDAC diagnosis.
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Affiliation(s)
- Palloma Porto Almeida
- Núcleo de Biointegração, Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista, Brazil
| | - Cristina Padre Cardoso
- Núcleo de Biointegração, Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista, Brazil
- Faculdade Santo Agostinho, Vitória da Conquista, Brazil
| | - Leandro Martins de Freitas
- Núcleo de Biointegração, Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista, Brazil.
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16
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El Beaino M, Jupiter DC, Assi T, Rassy E, Lazar AJ, Araujo DM, Lin PP. Diagnostic Value of TLE1 in Synovial Sarcoma: A Systematic Review and Meta-Analysis. Sarcoma 2020; 2020:7192347. [PMID: 32322158 PMCID: PMC7166261 DOI: 10.1155/2020/7192347] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/06/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Synovial sarcoma can present morphologically in multiple forms, including biphasic and monophasic subtypes. As a result, the histological diagnosis can sometimes be challenging. Transducin-Like Enhancer 1 (TLE1) is a transcriptional corepressor that normally is involved in embryogenesis and hematopoiesis but is also expressed in certain tumors. This systematic review examines the potential role of TLE1 as a diagnostic biomarker for the synovial sarcoma. Materials and Methods. A literature review and meta-analysis were conducted using the electronic databases Pubmed, the Cochrane Library, and Google Scholar. Thirteen studies met our eligibility criteria and were selected for in-depth analysis. RESULTS The mean sensitivity and specificity of TLE1 in detecting synovial sarcoma were 94% (95% CI 91%-97%) and 81% (95% CI 72%-91%), respectively, when all studies were aggregated together. The mean positive predictive value (PPV) of TLE1 was 75% (95% CI 62%-87%), whereas the negative predictive value (NPV) was 96% (95% CI 93%-98%). CONCLUSION TLE1 is a sensitive and specific marker for synovial sarcoma that can aid in its diagnosis. Due to its involvement in several relevant signaling pathways, TLE1 might have direct relevance to the pathophysiology of the disease.
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Affiliation(s)
- Marc El Beaino
- Department of Orthopaedic Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Orthopaedic Surgery and Rehabilitation Medicine, State University of New York, Downstate Medical Center, Brooklyn, NY, USA
| | - Daniel C. Jupiter
- Department of Preventive Medicine and Community Health, University of Texas Medical Branch, Galveston, TX, USA
- Department of Orthopaedic Surgery and Rehabilitation, University of Texas Medical Branch, Galveston, TX, USA
| | - Tarek Assi
- Department of Cancer Medicine, Gustave Roussy Institute, F-94805 Villejuif, France
| | - Elie Rassy
- Department of Cancer Medicine, Gustave Roussy Institute, F-94805 Villejuif, France
| | - Alexander J. Lazar
- Departments of Pathology & Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dejka M. Araujo
- Department of Sarcoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Patrick P. Lin
- Department of Orthopaedic Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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17
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Shew M, New J, Wichova H, Koestler DC, Staecker H. Using Machine Learning to Predict Sensorineural Hearing Loss Based on Perilymph Micro RNA Expression Profile. Sci Rep 2019; 9:3393. [PMID: 30833669 PMCID: PMC6399453 DOI: 10.1038/s41598-019-40192-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/07/2019] [Indexed: 02/06/2023] Open
Abstract
Hearing loss (HL) is the most common neurodegenerative disease worldwide. Despite its prevalence, clinical testing does not yield a cell or molecular based identification of the underlying etiology of hearing loss making development of pharmacological or molecular treatments challenging. A key to improving the diagnosis of inner ear disorders is the development of reliable biomarkers for different inner ear diseases. Analysis of microRNAs (miRNA) in tissue and body fluid samples has gained significant momentum as a diagnostic tool for a wide variety of diseases. In previous work, we have shown that miRNA profiling in inner ear perilymph is feasible and may demonstrate distinctive miRNA expression profiles unique to different diseases. A first step in developing miRNAs as biomarkers for inner ear disease is linking patterns of miRNA expression in perilymph to clinically available metrics. Using machine learning (ML), we demonstrate we can build disease specific algorithms that predict the presence of sensorineural hearing loss using only miRNA expression profiles. This methodology not only affords the opportunity to understand what is occurring on a molecular level, but may offer an approach to diagnosing patients with active inner ear disease.
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Affiliation(s)
- Matthew Shew
- University of Kansas School of Medicine, Department of Otolaryngology-Head and Neck Surgery, Kansas City, KS, USA.
| | - Jacob New
- University of Kansas School of Medicine, Kansas City, KS, USA
| | - Helena Wichova
- University of Kansas School of Medicine, Department of Otolaryngology-Head and Neck Surgery, Kansas City, KS, USA
| | - Devin C Koestler
- University of Kansas School of Medicine, Department of Biostatistics, Kansas City, KS, USA
| | - Hinrich Staecker
- University of Kansas School of Medicine, Department of Otolaryngology-Head and Neck Surgery, Kansas City, KS, USA
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18
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Grizzi F, Borroni EM, Qehajaj D, Stifter S, Chiriva-Internati M, Cananzi FCM. The Complex Nature of Soft Tissue Sarcomas, Including Retroperitoneal Sarcomas. CURRENT TREATMENT OF RETROPERITONEAL SARCOMAS 2019:21-32. [DOI: 10.1007/978-88-470-3980-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
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19
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Pazopanib-induced changes in protein expression signatures of extracellular vesicles in synovial sarcoma. Biochem Biophys Res Commun 2018; 506:723-730. [DOI: 10.1016/j.bbrc.2018.10.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 10/02/2018] [Indexed: 01/14/2023]
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20
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van IJzendoorn DGP, Bovée JVMG. Vascular Tumors of Bone: The Evolvement of a Classification Based on Molecular Developments. Surg Pathol Clin 2018; 10:621-635. [PMID: 28797505 DOI: 10.1016/j.path.2017.04.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The classification of vascular tumors of bone has been under debate over time. Vascular tumors in bone are rare, display highly overlapping morphology, and, therefore, are considered difficult by pathologists. Compared with their soft tissue counterparts, they are more often multifocal and sometimes behave more aggressively. Over the past decade, with the advent of next-generation sequencing, recurrent molecular alterations have been found in some of the entities. The integration of morphology and molecular changes has led to a better characterization of these separate entities.
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Affiliation(s)
- David G P van IJzendoorn
- Department of Pathology, Leiden University Medical Center, Postzone L1-Q, Postbus 9600, Leiden 2300 RC, The Netherlands
| | - Judith V M G Bovée
- Department of Pathology, Leiden University Medical Center, Postzone L1-Q, Postbus 9600, Leiden 2300 RC, The Netherlands.
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21
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Impact of Insurance Coverage on Outcomes in Primary Breast Sarcoma. Sarcoma 2018; 2018:4626174. [PMID: 29736143 PMCID: PMC5875066 DOI: 10.1155/2018/4626174] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 12/06/2017] [Accepted: 12/17/2017] [Indexed: 11/17/2022] Open
Abstract
Private insurance is associated with better outcomes in multiple common cancers. We hypothesized that insurance status would significantly impact outcomes in primary breast sarcoma (PBS) due to the additional challenges of diagnosing and coordinating specialized care for a rare cancer. Using the National Cancer Database, we identified adult females diagnosed with PBS between 2004 and 2013. The influence of insurance status on overall survival (OS) was evaluated using the Kaplan-Meier estimator with log-rank tests and Cox proportional hazard models. Among a cohort of 607 patients, 67 (11.0%) had Medicaid, 217 (35.7%) had Medicare, and 323 (53.2%) had private insurance. Compared to privately insured patients, Medicaid patients were more likely to present with larger tumors and have their first surgical procedure further after diagnosis. Treatment was similar between patients with comparable disease stage. In multivariate analysis, Medicaid (hazard ratio (HR), 2.47; 95% confidence interval (CI), 1.62-3.77; p < 0.001) and Medicare (HR, 1.68; 95% CI, 1.10-2.57; p=0.017) were independently associated with worse OS. Medicaid insurance coverage negatively impacted survival compared to private insurance more in breast sarcoma than in breast carcinoma (interaction p < 0.001). In conclusion, patients with Medicaid insurance present with later stage disease and have worse overall survival than privately insured patients with PBS. Worse outcomes for Medicaid patients are exacerbated in this rare cancer.
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22
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Bai C, Liu X, Xu J, Qiu C, Wang R, Zheng J. Expression profiles of stemness genes in gastrointestinal stromal tumor. Hum Pathol 2018; 76:76-84. [PMID: 29486292 DOI: 10.1016/j.humpath.2018.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/13/2018] [Accepted: 02/16/2018] [Indexed: 12/12/2022]
Abstract
Gastrointestinal stromal tumor (GIST) is believed to originate from intestinal cells of Cajal or their stem cell precursors, and expresses stemness-related markers, such as CD117, CD34, DOG1 and nestin. To further characterize phenotypic features of GISTs, we examined expression profiles of a panel of stemness genes in GISTs, by analyzing existing gene expression profiling datasets. Our results showed that mRNA levels of B-lymphoma moloney murine leukaemia virus insertion region-1 (BMI1), kruppel-like factor 4 (KLF4), sal-like protein 4 (SALL4) and telomerase reverse transcriptase (TERT) were significantly unregulated in GISTs. Subsequently, protein expression of BMI1 and TERT was identified in GIST specimens by immunohistochemistry. Especially, we found that high expression of nuclear BMI1 was associated with large tumor size (P = .0239), high mitotic count (P < .01), high Ki-67 index (P = .0357), advanced National Institute of Health (NIH) criteria (P = .0025) and advanced World Health Organization (WHO) classification (P < .01) in GISTs. Functional and pathway enrichment analysis showed that most of BMI1's coexpressed genes were involved in tumor growth-related process, such as regulation of cell cycle and proliferation. Furthermore, we confirmed RAS oncogene family (RAB18) and limb development membrane protein 1 (LMBR1) genes as novel targets for BMI1 in GIST cells. These results provide valuable information for the expression profiles of stemness genes in GISTs, and identified nuclear BMI1 as an important marker of GIST cell proliferation and progression.
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Affiliation(s)
- Chenguang Bai
- Department of Pathology, Changhai Hospital, Second Milltary Medical University, Shanghai, 200433, China
| | - Xiaohong Liu
- Department of Pathology, Changhai Hospital, Second Milltary Medical University, Shanghai, 200433, China
| | - Jingjing Xu
- Department of Pathology, Changhai Hospital, Second Milltary Medical University, Shanghai, 200433, China
| | - Cen Qiu
- Department of Pathology, Changhai Hospital, Second Milltary Medical University, Shanghai, 200433, China
| | - Runqiu Wang
- Department of Pathology, Changhai Hospital, Second Milltary Medical University, Shanghai, 200433, China
| | - Jianming Zheng
- Department of Pathology, Changhai Hospital, Second Milltary Medical University, Shanghai, 200433, China.
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Ferreira MSV, Crysandt M, Braunschweig T, Jost E, Voss B, Bouillon AS, Knuechel R, Brümmendorf TH, Beier F. Presence of TERT Promoter Mutations is a Secondary Event and Associates with Elongated Telomere Length in Myxoid Liposarcomas. Int J Mol Sci 2018; 19:ijms19020608. [PMID: 29463038 PMCID: PMC5855830 DOI: 10.3390/ijms19020608] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 02/09/2018] [Accepted: 02/10/2018] [Indexed: 12/30/2022] Open
Abstract
The occurrence of TERT promoter mutations has been well described in soft tissue sarcomas (STS). However, the biological role of these mutations as well as their impact on telomere length in STS is still unclear. We analyzed 116 patient samples diagnosed with 22 distinct histological subtypes of bone and STS for the occurrence of TERT promoter mutations by Sanger sequencing. We observed TERT promoter mutations at an overall frequency of 9.5% distributed over 7 different sarcoma subtypes. Except for one chondrosarcoma case harboring a C250T mutation, all other mutations were detected at location C228T. By far the far highest frequency of TERT promoter mutations was found in myxoid liposarcoma (MLS) (4 out of 9 cases studied, i.e., 44%). Assessment of telomere length from tumor biopsies revealed that TERT promoter-mutated MLSs had significantly fewer shortened telomeres in comparison to TERT wildtype MLSs. Based on the frequency of TERT promoter mutations and the elongated telomere length in mutated compared to wildtype MLS, we hypothesize that occurrence of TERT promoter mutations has a pivotal role in the disease progression as a secondary genetic event at a time when tumor cells face the need for telomere elongation to allow further proliferation.
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Affiliation(s)
- Monica S Ventura Ferreira
- Department of Hematology, Oncology, Haemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical Faculty, 52074 Aachen, Germany.
| | - Martina Crysandt
- Department of Hematology, Oncology, Haemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical Faculty, 52074 Aachen, Germany.
| | - Till Braunschweig
- Institute of Pathology, RWTH Aachen University Medical Faculty, 52074 Aachen, Germany.
| | - Edgar Jost
- Department of Hematology, Oncology, Haemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical Faculty, 52074 Aachen, Germany.
| | - Barbara Voss
- Department of Hematology, Oncology, Haemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical Faculty, 52074 Aachen, Germany.
| | - Anne-Sophie Bouillon
- Department of Hematology, Oncology, Haemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical Faculty, 52074 Aachen, Germany.
| | - Ruth Knuechel
- Institute of Pathology, RWTH Aachen University Medical Faculty, 52074 Aachen, Germany.
| | - Tim H Brümmendorf
- Department of Hematology, Oncology, Haemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical Faculty, 52074 Aachen, Germany.
| | - Fabian Beier
- Department of Hematology, Oncology, Haemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical Faculty, 52074 Aachen, Germany.
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24
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Murakami T, Singh AS, Kiyuna T, Dry SM, Li Y, James AW, Igarashi K, Kawaguchi K, DeLong JC, Zhang Y, Hiroshima Y, Russell T, Eckardt MA, Yanagawa J, Federman N, Matsuyama R, Chishima T, Tanaka K, Bouvet M, Endo I, Eilber FC, Hoffman RM. Effective molecular targeting of CDK4/6 and IGF-1R in a rare FUS-ERG fusion CDKN2A-deletion doxorubicin-resistant Ewing's sarcoma patient-derived orthotopic xenograft (PDOX) nude-mouse model. Oncotarget 2018; 7:47556-47564. [PMID: 27286459 PMCID: PMC5216960 DOI: 10.18632/oncotarget.9879] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/22/2016] [Indexed: 11/25/2022] Open
Abstract
Ewing's sarcoma is a rare and aggressive malignancy. In the present study, tumor from a patient with a Ewing's sarcoma with cyclin-dependent kinase inhibitor 2A/B (CDKN2A/B) loss and FUS-ERG fusion was implanted in the right chest wall of nude mice to establish a patient-derived orthotopic xenograft (PDOX) model. The aim of the present study was to determine efficacy of cyclin-dependent kinase 4/6 (CDK4/6) and insulin-like growth factor-1 receptor (IGF-1R) inhibitors on the Ewing's sarcoma PDOX. The PDOX models were randomized into the following groups when tumor volume reached 50 mm3: G1, untreated control; G2, doxorubicin (DOX) (intraperitoneal (i.p.) injection, weekly, for 2 weeks); G3, CDK4/6 inhibitor (palbociclib, PD0332991, per oral (p.o.), daily, for 14 days); G4, IGF-1R inhibitor (linsitinib, OSI-906, p.o., daily, for 14 days). Tumor growth was significantly suppressed both in G3 (palbociclib) and in G4 (linsitinib) compared to G1 (untreated control) at all measured time points. In contrast, DOX did not inhibit tumor growth at any time point, which is consistent with the failure of DOX to control tumor growth in the patient. The results of the present study demonstrate the power of the PDOX model to identify effective targeted molecular therapy of a recalcitrant DOX-resistant Ewing's sarcoma with specific genetic alterations. The results of this study suggest the potential of PDOX models for individually-tailored, effective targeted therapy for recalcitrant cancer.
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Affiliation(s)
- Takashi Murakami
- AntiCancer, Inc., San Diego, CA, USA.,Department of Surgery, University of California, San Diego, CA, USA.,Department of Gastroenterological Surgery, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Arun S Singh
- Division of Hematology-Oncology, University of California, Los Angeles, CA, USA
| | | | - Sarah M Dry
- Department of Pathology, University of California, Los Angeles, CA, USA
| | - Yunfeng Li
- Department of Pathology, University of California, Los Angeles, CA, USA
| | - Aaron W James
- Department of Pathology, University of California, Los Angeles, CA, USA
| | | | | | | | | | - Yukihiko Hiroshima
- Department of Gastroenterological Surgery, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Tara Russell
- Division of Surgical Oncology, University of California, Los Angeles, CA, USA
| | - Mark A Eckardt
- Division of Surgical Oncology, University of California, Los Angeles, CA, USA.,Department of Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - Jane Yanagawa
- Division of Surgical Oncology, University of California, Los Angeles, CA, USA
| | - Noah Federman
- Department of Pediatrics and Department of Orthopaedics, University of California, Los Angeles, CA, USA
| | - Ryusei Matsuyama
- Department of Gastroenterological Surgery, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Takashi Chishima
- Department of Gastroenterological Surgery, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Kuniya Tanaka
- Department of Gastroenterological Surgery, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Michael Bouvet
- Department of Surgery, University of California, San Diego, CA, USA
| | - Itaru Endo
- Department of Gastroenterological Surgery, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Fritz C Eilber
- Division of Surgical Oncology, University of California, Los Angeles, CA, USA.,UCLA Sarcoma Program, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA
| | - Robert M Hoffman
- AntiCancer, Inc., San Diego, CA, USA.,Department of Surgery, University of California, San Diego, CA, USA.,UCLA Sarcoma Program, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA.,PDOX Inc., San Diego, CA, USA
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25
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Huang S, Cai N, Pacheco PP, Narrandes S, Wang Y, Xu W. Applications of Support Vector Machine (SVM) Learning in Cancer Genomics. Cancer Genomics Proteomics 2018; 15:41-51. [PMID: 29275361 PMCID: PMC5822181 DOI: 10.21873/cgp.20063] [Citation(s) in RCA: 335] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/03/2017] [Accepted: 10/23/2017] [Indexed: 12/23/2022] Open
Abstract
Machine learning with maximization (support) of separating margin (vector), called support vector machine (SVM) learning, is a powerful classification tool that has been used for cancer genomic classification or subtyping. Today, as advancements in high-throughput technologies lead to production of large amounts of genomic and epigenomic data, the classification feature of SVMs is expanding its use in cancer genomics, leading to the discovery of new biomarkers, new drug targets, and a better understanding of cancer driver genes. Herein we reviewed the recent progress of SVMs in cancer genomic studies. We intend to comprehend the strength of the SVM learning and its future perspective in cancer genomic applications.
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Affiliation(s)
- Shujun Huang
- College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
- Research Institute of Oncology and Hematology, CancerCare Manitoba, Winnipeg, Canada
| | - Nianguang Cai
- Research Institute of Oncology and Hematology, CancerCare Manitoba, Winnipeg, Canada
| | - Pedro Penzuti Pacheco
- Research Institute of Oncology and Hematology, CancerCare Manitoba, Winnipeg, Canada
| | - Shavira Narrandes
- Research Institute of Oncology and Hematology, CancerCare Manitoba, Winnipeg, Canada
- Departments of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Yang Wang
- Department of Computer Science, Faculty of Sciences, University of Manitoba, Winnipeg, Canada
| | - Wayne Xu
- Research Institute of Oncology and Hematology, CancerCare Manitoba, Winnipeg, Canada
- Departments of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
- College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
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26
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Wu SP, Cooper BT, Bu F, Bowman CJ, Killian JK, Serrano J, Wang S, Jackson TM, Gorovets D, Shukla N, Meyers PA, Pisapia DJ, Gorlick R, Ladanyi M, Thomas K, Snuderl M, Karajannis MA. DNA Methylation-Based Classifier for Accurate Molecular Diagnosis of Bone Sarcomas. JCO Precis Oncol 2017; 2017. [PMID: 29354796 DOI: 10.1200/po.17.00031] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Purpose Pediatric sarcomas provide a unique diagnostic challenge. There is considerable morphologic overlap between entities, increasing the importance of molecular studies in the diagnosis, treatment, and identification of therapeutic targets. We developed and validated a genome-wide DNA methylation based classifier to differentiate between osteosarcoma, Ewing's sarcoma, and synovial sarcoma. Materials and Methods DNA methylation status of 482,421 CpG sites in 10 Ewing's sarcoma, 11 synovial sarcoma, and 15 osteosarcoma samples were determined using the Illumina Infinium HumanMethylation450 array. We developed a random forest classifier trained from the 400 most differentially methylated CpG sites within the training set of 36 sarcoma samples. This classifier was validated on data drawn from The Cancer Genome Atlas (TCGA) synovial sarcoma, TARGET Osteosarcoma, and a recently published series of Ewing's sarcoma. Results Methylation profiling revealed three distinct patterns, each enriched with a single sarcoma subtype. Within the validation cohorts, all samples from TCGA were accurately classified as synovial sarcoma (10/10, sensitivity and specificity 100%), all but one sample from TARGET-OS were classified as osteosarcoma (85/86, sensitivity 98%, specificity 100%) and 14/15 Ewing's sarcoma samples classified correctly (sensitivity 93%, specificity 100%). The single misclassified osteosarcoma sample demonstrated high EWSR1 and ETV1 expression on RNA-seq although no fusion was found on manual curation of the transcript sequence. Two additional clinical samples, that were difficult to classify by morphology and molecular methods, were classified as osteosarcoma when previously suspected to be a synovial sarcoma and Ewing's sarcoma on initial diagnosis, respectively. Conclusion Osteosarcoma, synovial sarcoma, and Ewing's sarcoma have distinct epigenetic profiles. Our validated methylation-based classifier can be used to provide diagnostic assistance when histological and standard techniques are inconclusive.
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Affiliation(s)
- S Peter Wu
- Department of Radiation Oncology, NYU Langone Medical Center, New York, NY
| | - Benjamin T Cooper
- Department of Radiation Oncology, NYU Langone Medical Center, New York, NY
| | - Fang Bu
- Department of Pathology, NYU Langone Medical Center, New York, NY
| | | | - J Keith Killian
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jonathan Serrano
- Department of Pathology, NYU Langone Medical Center, New York, NY
| | - Shiyang Wang
- Department of Pediatrics, NYU Langone Medical Center, New York, NY
| | - Twana M Jackson
- Department of Pediatrics, NYU Langone Medical Center, New York, NY
| | - Daniel Gorovets
- Department of Radiation Oncology, NYU Langone Medical Center, New York, NY
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Paul A Meyers
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David J Pisapia
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Richard Gorlick
- Department of Pediatrics, Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, NY
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kristen Thomas
- Department of Pathology, NYU Langone Medical Center, New York, NY
| | - Matija Snuderl
- Department of Pathology, NYU Langone Medical Center, New York, NY
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27
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Wilson JM, Ginsberg J, Cutts K, Urban S. A Case of Non-Islet Cell Tumor Hypoglycemia (NICTH) Associated with Gastrointestinal Stromal Tumor (GIST). AMERICAN JOURNAL OF CASE REPORTS 2017; 18:984-988. [PMID: 28900071 PMCID: PMC5608149 DOI: 10.12659/ajcr.904753] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Patient: Male, 60 Final Diagnosis: Non-islet cell tumor hypoglycemia (NICTH) associated with gastrointestinal stromal tumor (GIST) Symptoms: Hypoglycemia Medication: — Clinical Procedure:— Specialty: Gastroenterology and Hepatology
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Affiliation(s)
- John M Wilson
- Texas Tech University Health Sciences Center School of Medicine, Amarillo, TX, USA
| | - Jessica Ginsberg
- Texas Tech University Health Sciences Center School of Medicine, Amarillo, TX, USA
| | - Karen Cutts
- Department of Internal Medicine, Texas Tech University Health Sciences Center School of Medicine, Amarillo, TX, USA
| | - Steve Urban
- Department of Internal Medicine, Texas Tech University Health Sciences Center School of Medicine, Amarillo, TX, USA
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28
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Al-Zaid T, Wang WL, Somaiah N, Lazar AJ. Molecular profiling of sarcomas: new vistas for precision medicine. Virchows Arch 2017; 471:243-255. [PMID: 28664413 DOI: 10.1007/s00428-017-2174-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 06/06/2017] [Accepted: 06/08/2017] [Indexed: 12/27/2022]
Abstract
Sarcoma is a large and heterogeneous group of malignant mesenchymal neoplasms with significant histological overlap. Accurate diagnosis can be challenging yet important for selecting the appropriate treatment approach and prognosis. The currently torrid pace of new genomic discoveries aids our classification and diagnosis of sarcomas, understanding of pathogenesis, development of new medications, and identification of alterations that predict prognosis and response to therapy. Unfortunately, demonstrating effective targets for precision oncology has been elusive in most sarcoma types. The list of potential targets greatly outnumbers the list of available inhibitors at the present time. This review will discuss the role of molecular profiling in sarcomas in general with emphasis on selected entities with particular clinical relevance.
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Affiliation(s)
- Tariq Al-Zaid
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Wei-Lien Wang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Boulevard-Unit 85, Houston, TX, 77030-4009, USA.,Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Sarcoma Research Center, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Neeta Somaiah
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexander J Lazar
- Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Boulevard-Unit 85, Houston, TX, 77030-4009, USA. .,Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Sarcoma Research Center, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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29
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MicroRNAs in the pathobiology of sarcomas. J Transl Med 2015; 95:987-94. [PMID: 26121318 DOI: 10.1038/labinvest.2015.81] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 04/17/2015] [Accepted: 05/02/2015] [Indexed: 12/19/2022] Open
Abstract
Sarcomas are a rare and heterogeneous group of tumors. The last decade has witnessed extensive efforts to understand the pathobiology of many aggressive sarcoma types. In parallel, we have also begun to unravel the complex gene regulation processes mediated by microRNAs (miRNAs) in sarcomas and other cancers, discovering that microRNAs have critical roles in the majority of both oncogenic and tumor suppressor signaling networks. Expression profiles and a greater understanding of the biologic roles of microRNAs and other noncoding RNAs have considerably expanded our current knowledge and provided key pathobiological insights into many sarcomas, and helped identify novel therapeutic targets. The limited number of sarcoma patients in each sarcoma type and their heterogeneity pose distinct challenges in translating this knowledge into the clinic. It will be critical to prioritize these novel targets and choose those that have a broad applicability. A small group of microRNAs have conserved roles across many types of sarcomas and other cancers. Therapies that target these key microRNA-gene signaling and regulatory networks, in combination with standard of care treatment, may be the pivotal component in significantly improving treatment outcomes in patients with sarcoma or other cancers.
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30
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Tran D, Verma K, Ward K, Diaz D, Kataria E, Torabi A, Almeida A, Malfoy B, Stratford EW, Mitchell DC, Bryan BA. Functional genomics analysis reveals a MYC signature associated with a poor clinical prognosis in liposarcomas. THE AMERICAN JOURNAL OF PATHOLOGY 2015; 185:717-28. [PMID: 25622542 DOI: 10.1016/j.ajpath.2014.11.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 11/17/2014] [Accepted: 11/20/2014] [Indexed: 11/19/2022]
Abstract
Liposarcomas, which are malignant fatty tumors, are the second most common soft-tissue sarcomas. Several histologically defined liposarcoma subtypes exist, yet little is known about the molecular pathology that drives the diversity in these tumors. We used functional genomics to classify a panel of diverse liposarcoma cell lines based on hierarchical clustering of their gene expression profiles, indicating that liposarcoma gene expression profiles and histologic classification are not directly correlated. Boolean probability approaches based on cancer-associated properties identified differential expression in multiple genes, including MYC, as potentially affecting liposarcoma signaling networks and cancer outcome. We confirmed our method with a large panel of lipomatous tumors, revealing that MYC protein expression is correlated with patient survival. These data encourage increased reliance on genomic features in conjunction with histologic features for liposarcoma clinical characterization and lay the groundwork for using Boolean-based probabilities to identify prognostic biomarkers for clinical outcome in tumor patients.
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Affiliation(s)
- Dat Tran
- Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas
| | - Kundan Verma
- Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas
| | - Kristin Ward
- Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas
| | - Dolores Diaz
- Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas
| | - Esha Kataria
- Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas
| | - Alireza Torabi
- Department of Pathology, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas
| | | | | | - Eva W Stratford
- Cancer Stem Cell Innovation Centre and the Department of Tumor Biology, Institute of Cancer Research, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway
| | - Dianne C Mitchell
- Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas
| | - Brad A Bryan
- Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas.
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31
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Demicco EG, Boland GM, Brewer Savannah KJ, Lusby K, Young ED, Ingram D, Watson KL, Bailey M, Guo X, Hornick JL, van de Rijn M, Wang WL, Torres KE, Lev D, Lazar AJ. Progressive loss of myogenic differentiation in leiomyosarcoma has prognostic value. Histopathology 2015; 66:627-38. [PMID: 24889065 DOI: 10.1111/his.12466] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Accepted: 05/24/2014] [Indexed: 01/15/2023]
Abstract
AIMS Well-differentiated leiomyosarcomas show morphologically recognizable smooth muscle differentiation, whereas poorly differentiated tumours may form a spectrum with a subset of undifferentiated pleomorphic sarcomas. The expression of certain muscle markers has been reported to have prognostic impact. We investigated the correlation between the morphological spectrum and the muscle marker expression profile of leiomyosarcoma, and the impact of these factors on patient outcomes. METHODS AND RESULTS Tissue microarrays including 202 non-uterine and 181 uterine leiomyosarcomas with a spectrum of tumour morphologies were evaluated for expression of immunohistochemical markers of muscle differentiation. Poorly differentiated tumours frequently lost one or more conventional smooth muscle markers [smooth muscle actin, desmin, h-caldesmon, and smooth muscle myosin (P < 0.0001)], as well as the more recently described markers SLMAP, MYLK, and ACTG2 (P < 0.0001). In primary tumours, both desmin and CFL2 expression predicted improved overall survival in multivariate analyses (P = 0.0111 and P = 0.043, respectively). Patients with muscle marker-enriched tumours (expressing all four conventional markers or any three of ACTG2, CFL2, CASQ2, MYLK, and SLMAP) had improved overall survival (P < 0.05) in univariate analyses. CONCLUSIONS Morphologically and immunohistochemically, poorly differentiated leiomyosarcomas can masquerade as undifferentiated pleomorphic sarcomas with progressive loss of muscle markers. The expression of muscle markers has prognostic significance in primary leiomyosarcomas independently of tumour morphology.
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Affiliation(s)
- Elizabeth G Demicco
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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32
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Becerikli M, Merwart B, Lam MC, Suppelna P, Rittig A, Mirmohammedsadegh A, Stricker I, Theiss C, Singer BB, Jacobsen F, Steinstraesser L. EPHB4 tyrosine-kinase receptor expression and biological significance in soft tissue sarcoma. Int J Cancer 2014; 136:1781-91. [PMID: 25274141 DOI: 10.1002/ijc.29244] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 08/09/2014] [Accepted: 08/22/2014] [Indexed: 12/22/2022]
Abstract
Soft tissue sarcomas (STS) are heterogeneous malignant tumors of mesenchymal origin. Due to low incidence and high number of different histological subtypes, their pathogenesis and thus potential targets for their therapy remain barely investigated. Several studies revealed significant higher EPHB4 expression in malignancies such as prostate and colorectal cancer showing survival advantages for these tumor cells. Therefore we studied the expression of EPHB4 in a total of 46 clinical human specimens of different STS and human fibroblasts. EPHB4 mRNA and protein expression were significantly increased in synovial sarcoma. After targeting EPHB4 in fibrosarcoma, synovial sarcoma, liposarcoma and MFH sarcoma cell lines by siRNA or by inhibition of autophosphorylation using the specific EPHB4 kinase inhibitor NVP-BHG712 a decreased proliferation rate/vitality of synovial- and fibrosarcoma cells was observed. Silencing of EPHB4 significantly reduced the transmigration of synovial sarcoma cells towards fibroblasts and endothelial cells. In addition, we assessed the anti-metastatic effect of EPHB4 inhibition in vivo by intraperitoneal administration of the EPHB4 inhibitor in an appropriate sarcoma lung metastasis xenograft model. As result 43% of NVP-BHG712 treated mice (n = 3/7) developed pulmonary metastases whereas all control mice (n = 5) revealed lung metastases. The residual 57% of mice (n = 4/7) showed only small local tumor cell spots. Size measurements of the Vimentin positive area explained significant decrease in lung metastasis formation (p < 0.05) after EPHB4 kinase inhibition. In summary, these data provide first evidence of the importance of EPHB4 in the tumorigenesis of synovial sarcoma and present EPHB4 as a potential target in the therapy of this malignancy.
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Affiliation(s)
- M Becerikli
- Department of Plastic and Reconstructive Surgery, BG University Hospital Bergmannsheil, Ruhr-University Bochum, Germany
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33
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Stebbing J, Paz K, Schwartz GK, Wexler LH, Maki R, Pollock RE, Morris R, Cohen R, Shankar A, Blackman G, Harding V, Vasquez D, Krell J, Ciznadija D, Katz A, Sidransky D. Patient-derived xenografts for individualized care in advanced sarcoma. Cancer 2014; 120:2006-15. [PMID: 24705963 PMCID: PMC4298787 DOI: 10.1002/cncr.28696] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 12/18/2013] [Accepted: 01/02/2014] [Indexed: 01/06/2023]
Abstract
BACKGROUND Patients with advanced, metastatic sarcoma have a poor prognosis, and the overall benefit from the few standard-of-care therapeutics available is small. The rarity of this tumor, combined with the wide range of subtypes, leads to difficulties in conducting clinical trials. The authors previously reported the outcome of patients with a variety of common solid tumors who received treatment with drug regimens that were first tested in patient-derived xenografts using a proprietary method ("TumorGrafts"). METHODS Tumors resected from 29 patients with sarcoma were implanted into immunodeficient mice to identify drug targets and drugs for clinical use. The results of drug sensitivity testing in the TumorGrafts were used to personalize cancer treatment. RESULTS Of 29 implanted tumors, 22 (76%) successfully engrafted, permitting the identification of treatment regimens for these patients. Although 6 patients died before the completion of TumorGraft testing, a correlation between TumorGraft results and clinical outcome was observed in 13 of 16 (81%) of the remaining individuals. No patients progressed during the TumorGraft-predicted therapy. CONCLUSIONS The current data support the use of the personalized TumorGraft model as an investigational platform for therapeutic decision-making that can guide treatment for rare tumors such as sarcomas. A randomized phase 3 trial versus physician's choice is warranted.
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Affiliation(s)
- Justin Stebbing
- Department of Oncology, Imperial College and Imperial Healthcare National Health Service Trust, Hammersmith HospitalLondon, United Kingdom
| | - Keren Paz
- Department of Oncology, Champions OncologyBaltimore, Maryland
| | - Gary K Schwartz
- Department of Oncology, Memorial Sloan-Kettering Cancer CenterNew York, New York
| | - Leonard H Wexler
- Department of Oncology, Memorial Sloan-Kettering Cancer CenterNew York, New York
| | - Robert Maki
- Department of Oncology, Mount Sinai School of MedicineNew York, New York
| | - Raphael E Pollock
- Department of Oncology, The University of Texas MD Anderson Cancer CenterHouston, Texas
| | - Ronnie Morris
- Department of Oncology, Champions OncologyBaltimore, Maryland
| | - Richard Cohen
- Department of Surgery, University College HospitalsLondon, United Kingdom
| | - Arjun Shankar
- Department of Surgery, University College HospitalsLondon, United Kingdom
| | - Glen Blackman
- Department of Radiotherapy, University College HospitalsLondon, United Kingdom
| | - Victoria Harding
- Department of Oncology, Imperial College and Imperial Healthcare National Health Service Trust, Hammersmith HospitalLondon, United Kingdom
| | - David Vasquez
- Department of Oncology, Champions OncologyBaltimore, Maryland
| | - Jonathan Krell
- Department of Oncology, Imperial College and Imperial Healthcare National Health Service Trust, Hammersmith HospitalLondon, United Kingdom
| | | | - Amanda Katz
- Department of Oncology, Champions OncologyBaltimore, Maryland
| | - David Sidransky
- Department of Oncology, Johns Hopkins University School of MedicineBaltimore, Maryland
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Skubitz KM, Skubitz APN, Xu WW, Luo X, Lagarde P, Coindre JM, Chibon F. Gene expression identifies heterogeneity of metastatic behavior among high-grade non-translocation associated soft tissue sarcomas. J Transl Med 2014; 12:176. [PMID: 24950699 PMCID: PMC4082412 DOI: 10.1186/1479-5876-12-176] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 06/06/2014] [Indexed: 01/16/2023] Open
Abstract
Background The biologic heterogeneity of soft tissue sarcomas (STS), even within histological subtypes, complicates treatment. In earlier studies, gene expression patterns that distinguish two subsets of clear cell renal carcinoma (RCC), serous ovarian carcinoma (OVCA), and aggressive fibromatosis (AF) were used to separate 73 STS into two or four groups with different probabilities of developing metastatic disease (PrMet). This study was designed to confirm our earlier observations in a larger independent data set. Methods We utilized these gene sets, hierarchical clustering (HC), and Kaplan-Meier analysis, to examine 309 STS, using Affymetrix chip expression profiling. Results HC using the combined AF-, RCC-, and OVCA-gene sets identified subsets of the STS samples. Analysis revealed differences in PrMet between the clusters defined by the first branch point of the clustering dendrogram (p = 0.048), and also among the four different clusters defined by the second branch points (p < 0.0001). Analysis also revealed differences in PrMet between the leiomyosarcomas (LMS), dedifferentiated liposarcomas (LipoD), and undifferentiated pleomorphic sarcomas (UPS) (p = 0.0004). HC of both the LipoD and UPS sample sets divided the samples into two groups with different PrMet (p = 0.0128, and 0.0002, respectively). HC of the UPS samples also showed four groups with different PrMet (p = 0.0007). HC found no subgroups of the LMS samples. Conclusions These data confirm our earlier studies, and suggest that this approach may allow the identification of more than two subsets of STS, each with distinct clinical behavior, and may be useful to stratify STS in clinical trials and in patient management.
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Affiliation(s)
- Keith M Skubitz
- Department of Medicine, University Hospital, Minneapolis, MN, USA.
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Tisdale EJ, Shisheva A, Artalejo CR. Overexpression of atypical protein kinase C in HeLa cells facilitates macropinocytosis via Src activation. Cell Signal 2014; 26:1235-42. [PMID: 24582589 PMCID: PMC4149413 DOI: 10.1016/j.cellsig.2014.02.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 02/18/2014] [Indexed: 01/08/2023]
Abstract
Atypical protein kinase C (aPKC) is the first recognized kinase oncogene. However, the specific contribution of aPKC to cancer progression is unclear. The pseudosubstrate domain of aPKC is different from the other PKC family members, and therefore a synthetic peptide corresponding to the aPKC pseudosubstrate (aPKC-PS) sequence, which specifically blocks aPKC kinase activity, is a valuable tool to assess the role of aPKC in various cellular processes. Here, we learned that HeLa cells incubated with membrane permeable aPKC-PS peptide displayed dilated heterogeneous vesicles labeled with peptide that were subsequently identified as macropinosomes. A quantitative membrane binding assay revealed that aPKC-PS peptide stimulated aPKC recruitment to membranes and activated Src. Similarly, aPKC overexpression in transfected HeLa cells activated Src and induced macropinosome formation. Src-aPKC interaction was essential; substitution of the proline residues in aPKC that associate with the Src-SH3 binding domain rendered the mutant kinase unable to induce macropinocytosis in transfected cells. We propose that aPKC overexpression is a contributing factor to cell transformation by interacting with and consequently promoting Src activation and constitutive macropinocytosis, which increases uptake of extracellular factors, required for altered cell growth and accelerated cell migration.
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Affiliation(s)
- Ellen J Tisdale
- Department of Pharmacology, Wayne State University School of Medicine, 540 E. Canfield Ave., 6374 Scott Hall, Detroit, MI 48201, USA.
| | - Assia Shisheva
- Department of Physiology, Wayne State University School of Medicine, 540 E. Canfield Ave., 5374 Scott Hall, Detroit, MI 48201, USA
| | - Cristina R Artalejo
- Department of Pharmacology, Wayne State University School of Medicine, 540 E. Canfield Ave., 6374 Scott Hall, Detroit, MI 48201, USA
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Specht K, Sung YS, Zhang L, Richter GHS, Fletcher CD, Antonescu CR. Distinct transcriptional signature and immunoprofile of CIC-DUX4 fusion-positive round cell tumors compared to EWSR1-rearranged Ewing sarcomas: further evidence toward distinct pathologic entities. Genes Chromosomes Cancer 2014; 53:622-33. [PMID: 24723486 DOI: 10.1002/gcc.22172] [Citation(s) in RCA: 180] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 03/21/2014] [Indexed: 01/19/2023] Open
Abstract
Round cell sarcomas harboring CIC-DUX4 fusions have recently been described as highly aggressive soft tissue tumors of children and young adults. Due to partial morphologic and immunohistochemical overlap with Ewing sarcoma (ES), CIC-DUX4-positive tumors have generally been classified as ES-like and managed similarly; however, a systematic comparison at the molecular and immunohistochemical levels between these two groups has not yet been conducted. Based on an initial observation that CIC-DUX4-positive tumors show nuclear immunoreactivity for WT1 and ETS transcription factors, FLI1 and ERG, we performed a detailed immunohistochemical and molecular analysis including these markers, to further investigate the relationship between CIC-DUX4 tumors and ES. The study group included 21 CIC-DUX4-positive sarcomas and 20 EWSR1-rearranged ES. Immunohistochemically, CIC-DUX4 sarcomas showed membranous CD99 positivity in 18 (86%) cases, but only 5 (24%) with a diffuse pattern, while WT1 and FLI1 were strongly positive in all cases. ERG was positive in 18% of cases. All ES expressed CD99 and FLI1, while ERG positivity was only seen in EWSR1-ERG fusion positive ES. WT1 was negative in all ES. Expression profiling validated by q-PCR revealed a distinct gene signature associated with CIC-DUX4 fusion, with upregulation of ETS transcription factors (ETV4, ETV1, and ETV5) and WT1, among top overexpressed genes compared to ES, other sarcomas and normal tissue. In conclusion, the distinct gene signature and immunoprofile of CIC-DUX4 sarcomas suggest a distinct pathogenesis from ES. The consistent WT1 expression may provide a useful clue in the diagnosis in the context of round cell sarcomas negative for EWSR1 rearrangement. © 2014 Wiley Periodicals, Inc.
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Affiliation(s)
- Katja Specht
- Institute of Pathology, Technische Universität München, Munich, Germany
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Rutkowski P, Przybył J, Świtaj T. Genetics of rare mesenchymal tumors: implications for targeted treatment in DFSP, ASPS, CCS, GCTB and PEComa. Int J Biochem Cell Biol 2014; 53:466-74. [PMID: 24704529 DOI: 10.1016/j.biocel.2014.03.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 03/24/2014] [Indexed: 12/24/2022]
Abstract
Soft tissue and bone sarcomas comprise a heterogeneous group of mesenchymal tumors that include roughly 130 distinct diagnostic entities. Many of them are exceptionally rare, with only few cases diagnosed worldwide each year. Development of novel targeted treatment in this group of tumors is of special importance since many sarcoma subtypes are resistant to conventional chemotherapy and the effective therapeutic options are limited. In this review we aim to discuss the molecular implications for targeted therapy in selected rare soft tissue and bone sarcoma subtypes, including dermatofibrosarcoma protuberans (DFSP), alveolar soft part sarcoma (ASPS), clear cell sarcoma (CCS), giant cell tumor of bone (GCTB) and perivascular epithelioid cell neoplasms (PEComas). This article is part of a Directed Issue entitled: Rare cancers.
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Affiliation(s)
- Piotr Rutkowski
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 5 Roentgen Street, Warsaw, Poland.
| | - Joanna Przybył
- Department of Molecular and Translational Biology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 5 Roentgen Street, Warsaw, Poland
| | - Tomasz Świtaj
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 5 Roentgen Street, Warsaw, Poland
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Chen C, Borker R, Ewing J, Tseng WY, Hackshaw MD, Saravanan S, Dhanda R, Nadler E. Epidemiology, treatment patterns, and outcomes of metastatic soft tissue sarcoma in a community-based oncology network. Sarcoma 2014; 2014:145764. [PMID: 24683310 PMCID: PMC3942092 DOI: 10.1155/2014/145764] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 12/13/2013] [Accepted: 12/15/2013] [Indexed: 11/22/2022] Open
Abstract
Purpose. To assess epidemiology, treatment patterns, and outcomes of metastatic soft tissue sarcoma (mSTS) patients in USA community oncology practices. Methods. This retrospective, descriptive study used US Oncology's iKnowMed electronic health records database. Adults (≥18 years) with mSTS and at least two visits between July 2007 and June 2010 were included. Key outcomes were practice patterns, overall survival (OS), and progression-free survival (PFS). Results. 363 mSTS patients (174 treated and 189 untreated) met the prespecified exclusion/inclusion criteria. The most common subtypes were leiomyosarcoma (n = 104; 29%), liposarcoma (n = 40; 11%), and synovial sarcoma (n = 12; 3%); the remainder (n = 207; 57%) comprised 27 histologic subtypes. Treated patients were younger and had lower ECOG scores; 75% and 25% received first-line combination or monotherapy, respectively. Median OS of treated and untreated patients was 22 and 17 months, respectively, and 29 months in patients with the three most common subtypes. Before controlling for effects of covariates, younger age and lower ECOG scores were associated with better OS and PFS. Conclusion. This study provides insights into mSTS epidemiology, treatment patterns, and outcomes in a large community-based oncology network. These results warrant further studies with larger cohorts.
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Affiliation(s)
- Clara Chen
- Department of Information Technology, Health Economics and Outcomes Research, McKesson Specialty Health, The Woodlands, TX, USA
| | | | - James Ewing
- Department of Information Technology, Health Economics and Outcomes Research, McKesson Specialty Health, The Woodlands, TX, USA
- Texas Oncology, Dallas, TX, USA
- Baylor Charles A. Sammons Cancer Center, Dallas, TX, USA
- Baylor University Medical Center at Dallas, Dallas, TX, USA
| | - Wan-Yu Tseng
- Department of Information Technology, Health Economics and Outcomes Research, McKesson Specialty Health, The Woodlands, TX, USA
| | | | - Shanmugapriya Saravanan
- Department of Information Technology, Health Economics and Outcomes Research, McKesson Specialty Health, The Woodlands, TX, USA
| | - Rahul Dhanda
- Department of Information Technology, Health Economics and Outcomes Research, McKesson Specialty Health, The Woodlands, TX, USA
| | - Eric Nadler
- Department of Information Technology, Health Economics and Outcomes Research, McKesson Specialty Health, The Woodlands, TX, USA
- Texas Oncology, Dallas, TX, USA
- Baylor Charles A. Sammons Cancer Center, Dallas, TX, USA
- Baylor University Medical Center at Dallas, Dallas, TX, USA
- Texas Oncology, Baylor Sammons Cancer Center, 3410 Worth Street, Dallas, TX 75246, USA
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Rapidis AD. Sarcomas of the head and neck in adult patients: current concepts and future perspectives. Expert Rev Anticancer Ther 2014; 8:1271-97. [DOI: 10.1586/14737140.8.8.1271] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Trautmann M, Sievers E, Aretz S, Kindler D, Michels S, Friedrichs N, Renner M, Kirfel J, Steiner S, Huss S, Koch A, Penzel R, Larsson O, Kawai A, Tanaka S, Sonobe H, Waha A, Schirmacher P, Mechtersheimer G, Wardelmann E, Büttner R, Hartmann W. SS18-SSX fusion protein-induced Wnt/β-catenin signaling is a therapeutic target in synovial sarcoma. Oncogene 2013; 33:5006-16. [PMID: 24166495 DOI: 10.1038/onc.2013.443] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 09/11/2013] [Accepted: 09/16/2013] [Indexed: 12/11/2022]
Abstract
Synovial sarcoma is a high-grade soft tissue malignancy characterized by a specific reciprocal translocation t(X;18), which leads to the fusion of the SS18 (SYT) gene to one of three SSX genes (SSX1, SSX2 or SSX4). The resulting chimeric SS18-SSX protein is suggested to act as an oncogenic transcriptional regulator. Despite multimodal therapeutic approaches, metastatic disease is often lethal and the development of novel targeted therapeutic strategies is required. Several expression-profiling studies identified distinct gene expression signatures, implying a consistent role of Wnt/β-catenin signaling in synovial sarcoma tumorigenesis. Here we investigate the functional and therapeutic relevance of Wnt/β-catenin pathway activation in vitro and in vivo. Immunohistochemical analyses of nuclear β-catenin and Wnt downstream targets revealed activation of canonical Wnt signaling in a significant subset of 30 primary synovial sarcoma specimens. Functional aspects of Wnt signaling including dependence of Tcf/β-catenin complex activity on the SS18-SSX fusion proteins were analyzed. Efficient SS18-SSX-dependent activation of the Tcf/β-catenin transcriptional complex was confirmed by TOPflash reporter luciferase assays and immunoblotting. In five human synovial sarcoma cell lines, inhibition of the Tcf/β-catenin protein-protein interaction significantly blocked the canonical Wnt/β-catenin signaling cascade, accompanied by the effective downregulation of Wnt targets (AXIN2, CDC25A, c-MYC, DKK1, CyclinD1 and Survivin) and the specific suppression of cell viability associated with the induction of apoptosis. In SYO-1 synovial sarcoma xenografts, administration of small molecule Tcf/β-catenin complex inhibitors significantly reduced tumor growth, associated with diminished AXIN2 protein levels. In summary, SS18-SSX-induced Wnt/β-catenin signaling appears to be of crucial biological importance in synovial sarcoma tumorigenesis and progression, representing a potential molecular target for the development of novel therapeutic strategies.
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Affiliation(s)
- M Trautmann
- 1] Department of Pathology, University Hospital Cologne, Cologne, Germany [2] Department of Pathology, University Hospital Bonn, Bonn, Germany
| | - E Sievers
- Department of Pathology, University Hospital Cologne, Cologne, Germany
| | - S Aretz
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - D Kindler
- Department of Pathology, University Hospital Cologne, Cologne, Germany
| | - S Michels
- Department of Pathology, University Hospital Cologne, Cologne, Germany
| | - N Friedrichs
- Department of Pathology, University Hospital Cologne, Cologne, Germany
| | - M Renner
- Department of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - J Kirfel
- Department of Pathology, University Hospital Bonn, Bonn, Germany
| | - S Steiner
- Department of Pathology, University Hospital Bonn, Bonn, Germany
| | - S Huss
- Department of Pathology, University Hospital Cologne, Cologne, Germany
| | - A Koch
- Department of Neuropathology, Charité-Universitätsmedizin, Berlin, Germany
| | - R Penzel
- Department of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - O Larsson
- Departments of Oncology & Pathology, The Karolinska Institute, Stockholm, Sweden
| | - A Kawai
- Division of Orthopaedic Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - S Tanaka
- Laboratory of Molecular & Cellular Pathology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - H Sonobe
- Department of Laboratory Medicine, Chungoku Central Hospital, Fukuyama, Hiroshima, Japan
| | - A Waha
- Department of Neuropathology, University Hospital Bonn, Bonn, Germany
| | - P Schirmacher
- Department of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - G Mechtersheimer
- Department of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - E Wardelmann
- Department of Pathology, University Hospital Cologne, Cologne, Germany
| | - R Büttner
- Department of Pathology, University Hospital Cologne, Cologne, Germany
| | - W Hartmann
- Department of Pathology, University Hospital Cologne, Cologne, Germany
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Saito T. The SYT-SSX fusion protein and histological epithelial differentiation in synovial sarcoma: relationship with extracellular matrix remodeling. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2013; 6:2272-2279. [PMID: 24228088 PMCID: PMC3816795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 08/31/2013] [Indexed: 06/02/2023]
Abstract
Synovial sarcoma (SS) tumor cells, which have the chromosomal translocation t(X;18)(p11.2;q11.2), have an inherently greater propensity for epithelial differentiation than other mesenchymal tumors, especially spindle cell sarcomas. This is caused by de-repression of the transcription of E-cadherin by SYT-SSX1 and SYT-SSX2, which dissociate Snail or Slug, respectively, from the E-cadherin promoter. However, a subset of SS with SYT-SSX1 loses E-cadherin expression despite adequate de-repression because of mutations in E-cadherin, resulting in monophasic histology. The ratio of the expression levels of SYT-SSX1 and Snail is also associated with E-cadherin expression: the lower the SYT-SSX1/Snail ratio, the lower the level of E-cadherin expression, and vice versa, thus affecting tumor histology. In addition, Wnt signal activation caused by mutation of β-catenin, APC, or Axin 1 and 2 is associated with monophasic histology. Remodeling of the extracellular matrix is also important. Only cells that survive all of these steps can finally exhibit biphasic histology. On the other hand, the SYT-SSX2 fusion has a weaker de-repression effect on the E-cadherin promoter than does SYT-SSX1, so it is difficult for SYT-SSX2-expressing tumors to achieve sufficient capacity for epithelial differentiation to form glandular structures. This review provides an interesting model for this epithelial differentiation that shows a possible mechanism for the aberrant mesenchymal to epithelial transition of SS and suggests that it might better be considered an epithelial to mesenchymal transition.
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Affiliation(s)
- Tsuyoshi Saito
- Department of Human Pathology, Juntendo University, School of Medicine Hongo 2-1-1, Bunkyo-ku, Tokyo 113-8421, Japan
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42
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Mosquera JM, Sboner A, Zhang L, Chen CL, Sung YS, Chen HW, Agaram NP, Briskin D, Basha BM, Singer S, Rubin MA, Tuschl T, Antonescu CR. Novel MIR143-NOTCH fusions in benign and malignant glomus tumors. Genes Chromosomes Cancer 2013; 52:1075-87. [PMID: 23999936 DOI: 10.1002/gcc.22102] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 07/24/2013] [Accepted: 07/24/2013] [Indexed: 12/17/2022] Open
Abstract
Glomus tumors (GT) have been classified among tumors of perivascular smooth muscle differentiation, together with myopericytoma, myofibroma/tosis, and angioleiomyoma, based on their morphologic overlap. However, no molecular studies have been carried out to date to investigate their genetic phenotype and to confirm their shared pathogenesis. RNA sequencing was performed in three index cases (GT1, malignant GT; GT2, benign GT and M1, multifocal myopericytoma), followed by FusionSeq data analysis, a modular computational tool developed to discover gene fusions from paired-end RNA-seq data. A gene fusion involving MIR143 in band 5q32 was identified in both GTs with either NOTCH2 in 1p13 in GT1 or NOTCH1 in 9q34 in GT2, but none in M1. After being validated by FISH and RT-PCR, these abnormalities were screened on 33 GTs, 6 myopericytomas, 9 myofibroma/toses, 18 angioleiomyomas and in a control group of 5 sino-nasal hemangiopericytomas. Overall NOTCH2 gene rearrangements were identified in 52% of GT, including all malignant cases and one NF1-related GT. No additional cases showed NOTCH1 rearrangement. As NOTCH3 shares similar functions with NOTCH2 in regulating vascular smooth muscle development, the study group was also investigated for abnormalities in this gene by FISH. Indeed, NOTCH3 rearrangements were identified in 9% of GTs, all present in benign soft tissue GT, one case being fused to MIR143. Only 1/18 angioleiomyomas showed NOTCH2 gene rearrangement, while all the myopericytomas and myofibroma/toses were negative. In summary, we describe novel NOTCH1-3 rearrangements in benign and malignant, visceral, and soft tissue GTs.
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Affiliation(s)
- Juan-Miguel Mosquera
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, NY
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Samuels BL, Chawla S, Patel S, von Mehren M, Hamm J, Kaiser PE, Schuetze S, Li J, Aymes A, Demetri GD. Clinical outcomes and safety with trabectedin therapy in patients with advanced soft tissue sarcomas following failure of prior chemotherapy: results of a worldwide expanded access program study. Ann Oncol 2013; 24:1703-9. [PMID: 23385197 DOI: 10.1093/annonc/mds659] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND This expanded access program (EAP) was designed to provide trabectedin access for patients with incurable soft tissue sarcoma (STS) following progression of disease with standard therapy. The outcomes of trial participants accrued over approximately 5 years are reported. PATIENTS AND METHODS Adult patients with advanced STS of multiple histologies, including leiomyosarcoma and liposarcoma (L-sarcomas), following relapse or disease progression following standard-of-care chemotherapy, were enrolled. Trabectedin treatment cycles (1.5 mg/m(2), intravenously over 24 h) were repeated q21 days. Objective response, overall survival (OS), and safety were evaluated. RESULTS Of 1895 patients enrolled, 807 (43%) had evaluable objective response data, with stable disease reported in 343 (43%) as best response. L-sarcoma patients exhibited longer, OS compared with other histologies [16.2 months (95% confidence interval (CI) 14.1-19.5) versus 8.4 months (95% CI 7.1-10.7)], and a slightly higher objective response rate [6.9% (95% CI 4.8-9.6) versus 4.0% (95% CI 2.1-6.8)]. The median treatment duration was 70 days representing a median of three treatment cycles; 30% of patients received ≥ 6 cycles. Safety and tolerability in this EAP were consistent with prior clinical trial data. CONCLUSION Results of this EAP are consistent with previous reports of trabectedin, demonstrating disease control despite a low incidence of objective responses in advanced STS patients after failure of standard chemotherapy. CLINICALTRIALS.GOV: NCT00210665.
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Affiliation(s)
- B L Samuels
- Department of Medical Oncology, Kootenai Cancer Center, Post Falls, ID 83854, USA
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Italiano A, Lagarde P, Brulard C, Terrier P, Laë M, Marques B, Ranchere-Vince D, Michels JJ, Trassard M, Cioffi A, Piperno-Neumann S, Chevreau C, Blay JY, Delcambre C, Isambert N, Penel N, Bay JO, Bonvalot S, Le Cesne A, Coindre JM, Chibon F. Genetic Profiling Identifies Two Classes of Soft-Tissue Leiomyosarcomas with Distinct Clinical Characteristics. Clin Cancer Res 2013; 19:1190-6. [DOI: 10.1158/1078-0432.ccr-12-2970] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Tuna M, Ju Z, Amos CI, Mills GB. Soft tissue sarcoma subtypes exhibit distinct patterns of acquired uniparental disomy. BMC Med Genomics 2012; 5:60. [PMID: 23217126 PMCID: PMC3541987 DOI: 10.1186/1755-8794-5-60] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 11/24/2012] [Indexed: 01/09/2023] Open
Abstract
Background Soft tissue sarcomas (STS) are heterogeneous mesenchymal tumors with diverse subtypes. STS can be classified into two main categories according to the type of genomic alteration: recurrent translocation driven STS, and non-recurrent translocations. However, little has known about acquired uniparental disomy in STS. Methods In this study, we analyzed SNP microarray data to determine the frequency and distribution patterns of acquired uniparental disomy (aUPD) in major soft tissue sarcoma (STS) subtypes using CNAG and R softwares. Results We identified recurrent aUPD regions specific to alveolar rhabdomyosarcoma with the most frequent at 11p15.4, gastrointestinal stromal tumor at 1p36.11-p35.3, leiomyosarcoma at 17p13.3-p13.1, myxofibrosarcoma at 1p35.1-p34.2 and 16q23.3-q24.1, and pleomorphic liposarcoma at 13q13.2-q13.3 and 13q14.11-q14.2. In contrast, specific recurrent aUPD regions were not identified in dedifferentiated liposarcoma, Ewing sarcoma, myxoid/round cell liposarcoma, and synovial sarcoma. Strikingly total, centromeric and segmental aUPD regions are more frequent in STS that do not exhibit recurrent translocation events. Conclusions Our study yields a detailed map of aUPD across 9 diverse STS subtypes and suggests the potential location of several novel tumor suppressor genes and oncogenes.
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Affiliation(s)
- Musaffe Tuna
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA.
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Rota R, Ciarapica R, Miele L, Locatelli F. Notch signaling in pediatric soft tissue sarcomas. BMC Med 2012; 10:141. [PMID: 23158439 PMCID: PMC3520771 DOI: 10.1186/1741-7015-10-141] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 11/16/2012] [Indexed: 02/07/2023] Open
Abstract
Pediatric soft tissue sarcomas are rare tumors of childhood, frequently characterized by specific chromosome translocations. Despite improvements in treatment, their clinical management is often challenging due to the low responsiveness of metastatic forms and aggressive variants to conventional therapeutic approaches, which leads to poor overall survival. It is widely thought that soft tissue sarcomas derive from mesenchymal progenitor cells that, during embryonic life, have developed chromosomal aberrations with de-regulation of the main pathways governing tissue morphogenesis. The Notch signaling pathway is one of the most important molecular networks involved in differentiation processes. Emerging evidence highlights the role of Notch signaling de-regulation in the biology of these pediatric sarcomas. In this review, we present an outline of recently gathered evidence on the role of Notch signaling in soft tissue sarcomas, highlighting its importance in tumor cell biology. The potential challenges and opportunities of targeting Notch signaling in the treatment of pediatric soft tissue sarcomas are also discussed.
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Affiliation(s)
- Rossella Rota
- Department of Oncohematology, Ospedale Pediatrico Bambino Gesù, IRCCS, Piazza Sant'Onofrio 4, Roma, 00165, Italy.
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Secreted protein, acidic and rich in cysteine-like 1 (SPARCL1) is down regulated in aggressive prostate cancers and is prognostic for poor clinical outcome. Proc Natl Acad Sci U S A 2012; 109:14977-82. [PMID: 22927397 DOI: 10.1073/pnas.1203525109] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Prostate cancer is the second leading cause of cancer death among United States men. However, disease aggressiveness is varied, with low-grade disease often being indolent and high-grade cancer accounting for the greatest density of deaths. Outcomes are also disparate among men with high-grade prostate cancer, with upwards of 65% having disease recurrence even after primary treatment. Identification of men at risk for recurrence and elucidation of the molecular processes that drive their disease is paramount, as these men are the most likely to benefit from multimodal therapy. We previously showed that androgen-induced expression profiles in prostate development are reactivated in aggressive prostate cancers. Herein, we report the down-regulation of one such gene, Sparcl1, a secreted protein, acidic and rich in cysteine (SPARC) family matricellular protein, during invasive phases of prostate development and regeneration. We further demonstrate a parallel process in prostate cancer, with decreased expression of SPARCL1 in high-grade/metastatic prostate cancer. Mechanistically, we demonstrate that SPARCL1 loss increases the migratory and invasive properties of prostate cancer cells through Ras homolog gene family, member C (RHOC), a known mediator of metastatic progression. By using models incorporating clinicopathologic parameters to predict prostate cancer recurrence after treatment, we show that SPARCL1 loss is a significant, independent prognostic marker of disease progression. Thus, SPARCL1 is a potent regulator of cell migration/invasion and its loss is independently associated with prostate cancer recurrence.
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48
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Davicioni E, Wai DH, Anderson MJ. Diagnostic and Prognostic Sarcoma Signatures. Mol Diagn Ther 2012; 12:359-74. [DOI: 10.1007/bf03256302] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Coffin CM, Alaggio R, Dehner LP. Some general considerations about the clinicopathologic aspects of soft tissue tumors in children and adolescents. Pediatr Dev Pathol 2012; 15:11-25. [PMID: 22375909 DOI: 10.2350/11-08-1081-pb.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Soft tissue tumors in children and adolescents are an important group of neoplasms, pseudoneoplasms, and tumefactive malformations with some distinctive clinicopathologic, genetic, syndromic, and therapeutic implications. In addition to the basic pathologic examination, there is the availability of diagnostic adjuncts in various settings based upon the histopathologic features that facilitate and/or corroborate a diagnosis. Immunohistochemistry, cytogenetics, molecular genetics, and an ever-increasing array of new technologies are available to address specific diagnostic questions and even potential therapeutic strategies. This review focuses upon some of the unique aspects of soft tissue tumors in children, including the classification, approach to the diagnosis, grading, clinical and pathologic staging, therapy-related changes, pathogenesis, and risk factors.
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Affiliation(s)
- Cheryl M Coffin
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN, USA.
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Wagner AJ, Goldberg JM, DuBois SG, Choy E, Rosen L, Pappo A, Geller J, Judson I, Hogg D, Senzer N, Davis IJ, Chai F, Waghorne C, Schwartz B, Demetri GD. Tivantinib (ARQ 197), a selective inhibitor of MET, in patients with microphthalmia transcription factor-associated tumors. Cancer 2012; 118:5894-902. [DOI: 10.1002/cncr.27582] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 02/02/2012] [Accepted: 02/27/2012] [Indexed: 11/07/2022]
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