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Vaughn H, Major H, Kadera E, Keck K, Dunham T, Qian Q, Brown B, Scott A, Bellizzi AM, Braun T, Breheny P, Quelle DE, Howe JR, Darbro B. Functional Copy-Number Alterations as Diagnostic and Prognostic Biomarkers in Neuroendocrine Tumors. Int J Mol Sci 2024; 25:7532. [PMID: 39062773 PMCID: PMC11277019 DOI: 10.3390/ijms25147532] [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: 06/11/2024] [Revised: 06/29/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
Functional copy-number alterations (fCNAs) are DNA copy-number changes with concordant differential gene expression. These are less likely to be bystander genetic lesions and could serve as robust and reproducible tumor biomarkers. To identify candidate fCNAs in neuroendocrine tumors (NETs), we integrated chromosomal microarray (CMA) and RNA-seq differential gene-expression data from 31 pancreatic (pNETs) and 33 small-bowel neuroendocrine tumors (sbNETs). Tumors were resected from 47 early-disease-progression (<24 months) and 17 late-disease-progression (>24 months) patients. Candidate fCNAs that accurately differentiated these groups in this discovery cohort were then replicated using fluorescence in situ hybridization (FISH) on formalin-fixed, paraffin-embedded (FFPE) tissues in a larger validation cohort of 60 pNETs and 82 sbNETs (52 early- and 65 late-disease-progression samples). Logistic regression analysis revealed the predictive ability of these biomarkers, as well as the assay-performance metrics of sensitivity, specificity, and area under the curve. Our results indicate that copy-number changes at chromosomal loci 4p16.3, 7q31.2, 9p21.3, 17q12, 18q21.2, and 19q12 may be used as diagnostic and prognostic NET biomarkers. This involves a rapid, cost-effective approach to determine the primary tumor site for patients with metastatic liver NETs and to guide risk-stratified therapeutic decisions.
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Affiliation(s)
- Hayley Vaughn
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA; (H.V.); (T.B.)
- Stead Family Department of Pediatrics, University of Iowa Health Care, Iowa City, IA 52242, USA; (H.M.); (E.K.); (T.D.); (Q.Q.)
| | - Heather Major
- Stead Family Department of Pediatrics, University of Iowa Health Care, Iowa City, IA 52242, USA; (H.M.); (E.K.); (T.D.); (Q.Q.)
| | - Evangeline Kadera
- Stead Family Department of Pediatrics, University of Iowa Health Care, Iowa City, IA 52242, USA; (H.M.); (E.K.); (T.D.); (Q.Q.)
| | - Kendall Keck
- Department of Surgery, University of Iowa Health Care, Iowa City, IA 52242, USA; (K.K.); (A.S.); (J.R.H.)
| | - Timothy Dunham
- Stead Family Department of Pediatrics, University of Iowa Health Care, Iowa City, IA 52242, USA; (H.M.); (E.K.); (T.D.); (Q.Q.)
| | - Qining Qian
- Stead Family Department of Pediatrics, University of Iowa Health Care, Iowa City, IA 52242, USA; (H.M.); (E.K.); (T.D.); (Q.Q.)
| | - Bartley Brown
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA;
| | - Aaron Scott
- Department of Surgery, University of Iowa Health Care, Iowa City, IA 52242, USA; (K.K.); (A.S.); (J.R.H.)
| | | | - Terry Braun
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA; (H.V.); (T.B.)
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA;
| | - Patrick Breheny
- Department of Biostatistics, University of Iowa, Iowa City, IA 52242, USA;
| | - Dawn E. Quelle
- Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, IA 52242, USA;
| | - James R. Howe
- Department of Surgery, University of Iowa Health Care, Iowa City, IA 52242, USA; (K.K.); (A.S.); (J.R.H.)
| | - Benjamin Darbro
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA; (H.V.); (T.B.)
- Stead Family Department of Pediatrics, University of Iowa Health Care, Iowa City, IA 52242, USA; (H.M.); (E.K.); (T.D.); (Q.Q.)
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2
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Diaz JEL, Barcessat V, Bahamon C, Hecht C, Das TK, Cagan RL. Functional exploration of copy number alterations in a Drosophila model of triple-negative breast cancer. Dis Model Mech 2024; 17:dmm050191. [PMID: 38721669 PMCID: PMC11247506 DOI: 10.1242/dmm.050191] [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: 03/14/2023] [Accepted: 04/30/2024] [Indexed: 07/04/2024] Open
Abstract
Accounting for 10-20% of breast cancer cases, triple-negative breast cancer (TNBC) is associated with a disproportionate number of breast cancer deaths. One challenge in studying TNBC is its genomic profile: with the exception of TP53 loss, most breast cancer tumors are characterized by a high number of copy number alterations (CNAs), making modeling the disease in whole animals challenging. We computationally analyzed 186 CNA regions previously identified in breast cancer tumors to rank genes within each region by likelihood of acting as a tumor driver. We then used a Drosophila p53-Myc TNBC model to identify 48 genes as functional drivers. To demonstrate the utility of this functional database, we established six 3-hit models; altering candidate genes led to increased aspects of transformation as well as resistance to the chemotherapeutic drug fluorouracil. Our work provides a functional database of CNA-associated TNBC drivers, and a template for an integrated computational/whole-animal approach to identify functional drivers of transformation and drug resistance within CNAs in other tumor types.
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Affiliation(s)
- Jennifer E L Diaz
- Department of Cell, Development, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Internal Medicine, UCLA David Geffen School of Medicine, CA 90095, USA
| | - Vanessa Barcessat
- Department of Cell, Development, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christian Bahamon
- Department of Cell, Development, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chana Hecht
- Department of Cell, Development, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tirtha K Das
- Department of Cell, Development, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ross L Cagan
- Department of Cell, Development, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- School of Cancer Sciences and Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow G61 1BD, UK
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3
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M S A, K C, Bhargavan RV, Somanathan T, Subhadradevi L. An overview on liposarcoma subtypes: Genetic alterations and recent advances in therapeutic strategies. J Mol Histol 2024; 55:227-240. [PMID: 38696048 DOI: 10.1007/s10735-024-10195-4] [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: 07/24/2023] [Accepted: 04/18/2024] [Indexed: 05/21/2024]
Abstract
Liposarcoma (LPS) is a rare malignancy of adipocytic differentiation. According to World Health Organization classification, LPS comprises of four principle subtypes Atypical lipomatous tumor/Well-differentiated liposarcoma (ATL/WDLPS), Dedifferentiated liposarcoma (WDLPS), Myxoid liposarcoma (MLPS), and Pleomorphic liposarcoma (PLPS). Each subtype can develop at any location and shows distinct clinical behavior and treatment sensitivity. ATL/ WDLPS subtype has a higher incidence rate, low recurrence, and is insensitive to radiation and chemotherapy. DDLPS is the focal progression of WDLPS, which is aggressive and highly metastasizing. MLPS is sensitive to radiation and chemotherapy, with a higher recurrence rate and metastasis. PLPS subtype is highly metastasizing, has a poor prognosis, and exhibiting higher recurrence rate. Initial histological analysis provides information for the characterization of LPS subtypes', further molecular and genetic analysis provides certain subtype specifications, such as gene amplifications and gene fusions. Such molecular genetic alterations will be useful as therapeutic targets in various cancers, including the LPS subtypes. A wide range of novel therapeutic agents based on genetic alterations that aim to target LPS subtypes specifically are under investigation. This review summarizes the LPS subtype classification, their molecular genetic characteristics, and the implications of genetic alterations in therapeutics.
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Affiliation(s)
- Anju M S
- Division of Cancer Research, Regional Cancer Centre (Research Centre, University of Kerala), Thiruvananthapuram, Kerala, 695011, India
| | - Chandramohan K
- Division of Surgical Oncology, Regional Cancer Centre (Research Centre, University of Kerala), Thiruvananthapuram, Kerala, 695011, India
| | - Rexeena V Bhargavan
- Division of Surgical Oncology, Regional Cancer Centre (Research Centre, University of Kerala), Thiruvananthapuram, Kerala, 695011, India
| | - Thara Somanathan
- Division of Pathology, Regional Cancer Centre (Research Centre, University of Kerala), Thiruvananthapuram, Kerala, 695011, India
| | - Lakshmi Subhadradevi
- Division of Cancer Research, Regional Cancer Centre (Research Centre, University of Kerala), Thiruvananthapuram, Kerala, 695011, India.
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4
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Doré S, Ali M, Sorin M, McDowell SAC, Desharnais L, Breton V, Yu MW, Arabzadeh A, Ryan MI, Milette S, Quail DF, Walsh LA. Exploring the prognostic significance of arm-level copy number alterations in triple-negative breast cancer. Oncogene 2024; 43:2015-2024. [PMID: 38744952 PMCID: PMC11196216 DOI: 10.1038/s41388-024-03051-y] [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: 07/31/2023] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/16/2024]
Abstract
Somatic copy number alterations (SCNAs) are prevalent in cancer and play a significant role in both tumorigenesis and therapeutic resistance. While focal SCNAs have been extensively studied, the impact of larger arm-level SCNAs remains poorly understood. Here, we investigated the association between arm-level SCNAs and overall survival in triple-negative breast cancer (TNBC), an aggressive subtype of breast cancer lacking targeted therapies. We identified frequent arm-level SCNAs, including 21q gain and 7p gain, which correlated with poor overall survival in TNBC patients. Further, we identified the expression of specific genes within these SCNAs associated with survival. Notably, we found that the expression of RIPK4, a gene located on 21q, exhibited a strong correlation with poor overall survival. In functional assays, we demonstrated that targeting Ripk4 in a murine lung metastatic TNBC model significantly reduced tumor burden, improved survival, and increased CD4+ and CD8+ T cell infiltration. RIPK4 enhanced the survival of triple-negative breast cancer cells at secondary sites, thereby facilitating the formation of metastatic lesions. Our findings highlight the significance of arm-level SCNAs in breast cancer progression and identify RIPK4 as a putative driver of TNBC metastasis and immunosuppression.
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Affiliation(s)
- Samuel Doré
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Mariam Ali
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Mark Sorin
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Sheri A C McDowell
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
- Department of Physiology, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Lysanne Desharnais
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Valérie Breton
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Miranda W Yu
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
- Department of Physiology, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Azadeh Arabzadeh
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
| | - Malcolm I Ryan
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
- Department of Surgery, McGill University Health Center, Montreal, QC, Canada
| | - Simon Milette
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
- Department of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Daniela F Quail
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
- Department of Physiology, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Department of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Logan A Walsh
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada.
- Department of Human Genetics, McGill University, Montreal, QC, Canada.
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5
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Unat B. The Rat Sarcoma Virus (RAS) Family of Proteins in Sarcomas. Cureus 2024; 16:e57082. [PMID: 38681356 PMCID: PMC11052699 DOI: 10.7759/cureus.57082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2024] [Indexed: 05/01/2024] Open
Abstract
The rat sarcoma virus (RAS) protein family plays a crucial role in facilitating communication both within and between cells, thereby governing fundamental cellular processes such as growth, survival, and differentiation. The RAS family comprises four members of small GTPases, namely Harvey RAS (H-RAS), Kirsten RAS (K-RAS, two splice variants, 4A and 4B), and Neuroblastoma RAS (N-RAS), and these are encoded by three cellular RAS genes. Mutations in these genes play a significant role in cancer development and progression. Accordingly, here we review and discuss currently available literature about the fate and function of the RAS family of proteins in sarcomas.
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Affiliation(s)
- Beytullah Unat
- Orthopedics and Traumatology, Gaziantep City Hospital, Gaziantep, TUR
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6
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Lesovaya EA, Fetisov TI, Bokhyan BY, Maksimova VP, Kulikov EP, Belitsky GA, Kirsanov KI, Yakubovskaya MG. Genetic, Epigenetic and Transcriptome Alterations in Liposarcoma for Target Therapy Selection. Cancers (Basel) 2024; 16:271. [PMID: 38254762 PMCID: PMC10813500 DOI: 10.3390/cancers16020271] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/25/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Liposarcoma (LPS) is one of the most common adult soft-tissue sarcomas (STS), characterized by a high diversity of histopathological features as well as to a lesser extent by a spectrum of molecular abnormalities. Current targeted therapies for STS do not include a wide range of drugs and surgical resection is the mainstay of treatment for localized disease in all subtypes, while many LPS patients initially present with or ultimately progress to advanced disease that is either unresectable, metastatic or both. The understanding of the molecular characteristics of liposarcoma subtypes is becoming an important option for the detection of new potential targets and development novel, biology-driven therapies for this disease. Innovative therapies have been introduced and they are currently part of preclinical and clinical studies. In this review, we provide an analysis of the molecular genetics of liposarcoma followed by a discussion of the specific epigenetic changes in these malignancies. Then, we summarize the peculiarities of the key signaling cascades involved in the pathogenesis of the disease and possible novel therapeutic approaches based on a better understanding of subtype-specific disease biology. Although heterogeneity in liposarcoma genetics and phenotype as well as the associated development of resistance to therapy make difficult the introduction of novel therapeutic targets into the clinic, recently a number of targeted therapy drugs were proposed for LPS treatment. The most promising results were shown for CDK4/6 and MDM2 inhibitors as well as for the multi-kinase inhibitors anlotinib and sunitinib.
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Affiliation(s)
- Ekaterina A. Lesovaya
- N.N. Blokhin Russian Cancer Research Center, Ministry of Health of Russia, 24 Kashirskoe Shosse, Moscow 115478, Russia; (E.A.L.); (T.I.F.); (B.Y.B.); (V.P.M.); (K.I.K.)
- Faculty of Oncology, I.P. Pavlov Ryazan State Medical University, Ministry of Health of Russia, 9 Vysokovol’tnaya St., Ryazan 390026, Russia;
- Laboratory of Single Cell Biology, Peoples’ Friendship University of Russia, 6 Miklukho-Maklaya St., Moscow 117198, Russia
| | - Timur I. Fetisov
- N.N. Blokhin Russian Cancer Research Center, Ministry of Health of Russia, 24 Kashirskoe Shosse, Moscow 115478, Russia; (E.A.L.); (T.I.F.); (B.Y.B.); (V.P.M.); (K.I.K.)
| | - Beniamin Yu. Bokhyan
- N.N. Blokhin Russian Cancer Research Center, Ministry of Health of Russia, 24 Kashirskoe Shosse, Moscow 115478, Russia; (E.A.L.); (T.I.F.); (B.Y.B.); (V.P.M.); (K.I.K.)
| | - Varvara P. Maksimova
- N.N. Blokhin Russian Cancer Research Center, Ministry of Health of Russia, 24 Kashirskoe Shosse, Moscow 115478, Russia; (E.A.L.); (T.I.F.); (B.Y.B.); (V.P.M.); (K.I.K.)
| | - Evgeny P. Kulikov
- Faculty of Oncology, I.P. Pavlov Ryazan State Medical University, Ministry of Health of Russia, 9 Vysokovol’tnaya St., Ryazan 390026, Russia;
| | - Gennady A. Belitsky
- N.N. Blokhin Russian Cancer Research Center, Ministry of Health of Russia, 24 Kashirskoe Shosse, Moscow 115478, Russia; (E.A.L.); (T.I.F.); (B.Y.B.); (V.P.M.); (K.I.K.)
| | - Kirill I. Kirsanov
- N.N. Blokhin Russian Cancer Research Center, Ministry of Health of Russia, 24 Kashirskoe Shosse, Moscow 115478, Russia; (E.A.L.); (T.I.F.); (B.Y.B.); (V.P.M.); (K.I.K.)
- Laboratory of Single Cell Biology, Peoples’ Friendship University of Russia, 6 Miklukho-Maklaya St., Moscow 117198, Russia
| | - Marianna G. Yakubovskaya
- N.N. Blokhin Russian Cancer Research Center, Ministry of Health of Russia, 24 Kashirskoe Shosse, Moscow 115478, Russia; (E.A.L.); (T.I.F.); (B.Y.B.); (V.P.M.); (K.I.K.)
- Laboratory of Single Cell Biology, Peoples’ Friendship University of Russia, 6 Miklukho-Maklaya St., Moscow 117198, Russia
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7
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Hadjimichael AC, Bekos A, Tsukamoto S, Nitta Y, Righi A, Errani C, Mavrogenis AF. Pleomorphic Liposarcoma Revisited. Orthopedics 2023; 46:e72-e80. [PMID: 35876778 DOI: 10.3928/01477447-20220719-05] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Pleomorphic liposarcoma (PLPS) is the rarest and more aggressive subtype of liposarcomas, accounting for 10% of all liposarcomas. The diagnosis should be considered after the detection of multivacuolated pleomorphic lipoblasts in biopsy specimens. Wide-margin resection is the treatment of choice. Complementary treatment options, such as radiation therapy and chemotherapy, are debatable in terms of their contribution to curing patients with PLPS. This article reviews the clinical, histopathological, and molecular characteristics of PLPS and discusses the latest trends in the management, therapeutic strategies, and novel investigations of the subject. [Orthopedics. 2023;46(2):e72-e80.].
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8
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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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9
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Computing microRNA-gene interaction networks in pan-cancer using miRDriver. Sci Rep 2022; 12:3717. [PMID: 35260634 PMCID: PMC8904490 DOI: 10.1038/s41598-022-07628-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/18/2022] [Indexed: 11/13/2022] Open
Abstract
DNA copy number aberrated regions in cancer are known to harbor cancer driver genes and the short non-coding RNA molecules, i.e., microRNAs. In this study, we integrated the multi-omics datasets such as copy number aberration, DNA methylation, gene and microRNA expression to identify the signature microRNA-gene associations from frequently aberrated DNA regions across pan-cancer utilizing a LASSO-based regression approach. We studied 7294 patient samples associated with eighteen different cancer types from The Cancer Genome Atlas (TCGA) database and identified several cancer-specific and common microRNA-gene interactions enriched in experimentally validated microRNA-target interactions. We highlighted several oncogenic and tumor suppressor microRNAs that were cancer-specific and common in several cancer types. Our method substantially outperformed the five state-of-art methods in selecting significantly known microRNA-gene interactions in multiple cancer types. Several microRNAs and genes were found to be associated with tumor survival and progression. Selected target genes were found to be significantly enriched in cancer-related pathways, cancer hallmark and Gene Ontology (GO) terms. Furthermore, subtype-specific potential gene signatures were discovered in multiple cancer types.
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10
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Thway K. What’s new in adipocytic neoplasia? Histopathology 2021; 80:76-97. [DOI: 10.1111/his.14548] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 12/22/2022]
Affiliation(s)
- Khin Thway
- Sarcoma Unit Royal Marsden Hospital London UK
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11
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Bartlett EK, Curtin CE, Seier K, Qin LX, Hameed M, Yoon SS, Crago AM, Brennan MF, Singer S. Histologic Subtype Defines the Risk and Kinetics of Recurrence and Death for Primary Extremity/Truncal Liposarcoma. Ann Surg 2021; 273:1189-1196. [PMID: 31283560 PMCID: PMC7561049 DOI: 10.1097/sla.0000000000003453] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE We sought to define the prognostic significance of histologic subtype for extremity/truncal liposarcoma (LPS). BACKGROUND LPS, the most common sarcoma, is comprised of 5 histologic subtypes. Despite their distinct behaviors, LPS outcomes are frequently reported as a single entity. METHODS We analyzed data on all patients from a single-institution prospective database treated from July 1982 to September 2017 for primary, nonmetastatic, extremity or truncal LPS of known subtype. Clinicopathologic variables were tested using competing risk analyses for association with disease-specific death (DSD), distant recurrence (DR), and local recurrence (LR). RESULTS Among 1001 patients, median follow-up in survivors was 5.4 years. Tumor size and subtype were independently associated with DSD and DR. Size, subtype, and R1 resection were independently associated with LR. DR was most frequent among pleomorphic and round cell LPS; the former recurred early (43% by 3 years), and the latter over a longer period (23%, 3 years; 37%, 10 years). LR was most common in dedifferentiated LPS, in which it occurred early (24%, 3 years; 33%, 5 years), followed by pleomorphic LPS (18%, 3 years; 25%, 10 years). CONCLUSIONS Histologic subtype is the factor most strongly associated with DSD, DR, and LR in extremity/truncal LPS. Both risk and timing of adverse outcomes vary by subtype. These data may guide selective use of systemic therapy for patients with round cell and pleomorphic LPS, which carry a high risk of DR, and radiotherapy for LPS subtypes at high risk of LR when treated with surgery alone.
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Affiliation(s)
- Edmund K. Bartlett
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Kenneth Seier
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Li-Xuan Qin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sam S. Yoon
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Aimee M. Crago
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Murray F. Brennan
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Samuel Singer
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
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12
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Establishment and characterization of NCC-PLPS1-C1, a novel patient-derived cell line of pleomorphic liposarcoma. Hum Cell 2020; 34:688-697. [PMID: 33205363 DOI: 10.1007/s13577-020-00457-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/05/2020] [Indexed: 12/20/2022]
Abstract
Pleomorphic liposarcoma (PLPS) is a rare subtype of liposarcoma, characterized by the presence of pleomorphic lipoblasts without definitive molecular aberrations; it accounts for less than 5% of all liposarcomas. PLPS is an aggressive cancer that exhibits frequent local recurrence and metastasis, with an overall 5-year survival rate of ~ 60%. Owing to the lack of effective treatment options in inoperable conditions and resistance to chemotherapeutics, novel therapies are required to treat PLPS. Although patient-derived cell lines are a critical tool for basic and pre-clinical research, only one PLPS cell line is reportedly available for analysis. A paucity of adequate cell line hinders the progress of research and treatments of PLPS. Thus, we aimed to establish and characterize a novel patient-derived cell line for PLPS. Using surgically resected tumor tissue from a 71-year-old male patient, we established the NCC-PLPS1-C1 cell line. The cells were maintained for more than 8 months and passaged ~ 40 times in the tissue culture condition. NCC-PLPS1-C1 cells were characterized by multiple genetic deletions and showed rapid growth, spheroid formation, and invasive potential. The NCC-PLPS1-C1 cells and the original tumor tissue shared similar kinase activity profiles for FES and PDGFR-β. NCC-PLPS1-C1 constantly proliferated, being suitable for the screening of anti-cancer drugs. A screen for the anti-proliferative effects of anti-cancer drugs on NCC-PLPS1-C1 cells showed a significant response for bortezomib, gemcitabine, romidepsin, topotecan, and vinblastine. In conclusion, NCC-PLPS1-C1 cells represent a useful tool for basic and pre-clinical studies related to PLPS, especially high-throughput drug screening.
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13
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Esteves L, Caramelo F, Ribeiro IP, Carreira IM, de Melo JB. Probability distribution of copy number alterations along the genome: an algorithm to distinguish different tumour profiles. Sci Rep 2020; 10:14868. [PMID: 32913269 PMCID: PMC7483770 DOI: 10.1038/s41598-020-71859-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 08/13/2020] [Indexed: 11/11/2022] Open
Abstract
Copy number alterations (CNAs) comprise deletions or amplifications of fragments of genomic material that are particularly common in cancer and play a major contribution in its development and progression. High resolution microarray-based genome-wide technologies have been widely used to detect CNAs, generating complex datasets that require further steps to allow for the determination of meaningful results. In this work, we propose a methodology to determine common regions of CNAs from these datasets, that in turn are used to infer the probability distribution of disease profiles in the population. This methodology was validated using simulated data and assessed using real data from Head and Neck Squamous Cell Carcinoma and Lung Adenocarcinoma, from the TCGA platform. Probability distribution profiles were produced allowing for the distinction between different phenotypic groups established within that cohort. This method may be used to distinguish between groups in the diseased population, within well-established degrees of confidence. The application of such methods may be of greater value in the clinical context both as a diagnostic or prognostic tool and, even as a useful way for helping to establish the most adequate treatment and care plans.
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Affiliation(s)
- Luísa Esteves
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, 3000-354, Coimbra, Portugal
| | - Francisco Caramelo
- Laboratory of Biostatistics and Medical Informatics, IBILI-Faculty of Medicine, University of Coimbra, 3000-354, Coimbra, Portugal
| | - Ilda Patrícia Ribeiro
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, 3000-354, Coimbra, Portugal.,iCBR-CIMAGO-Center of Investigation on Environment, Genetics and Oncobiology-Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Isabel M Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, 3000-354, Coimbra, Portugal.,iCBR-CIMAGO-Center of Investigation on Environment, Genetics and Oncobiology-Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Joana Barbosa de Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, 3000-354, Coimbra, Portugal. .,iCBR-CIMAGO-Center of Investigation on Environment, Genetics and Oncobiology-Faculty of Medicine, University of Coimbra, Coimbra, Portugal.
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14
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Berg SH, Massoud CM, Jackson-Cook C, Boikos SA, Smith SC, Mochel MC. A Reappraisal of Superficial Pleomorphic Liposarcoma. Am J Clin Pathol 2020; 154:353-361. [PMID: 32525520 DOI: 10.1093/ajcp/aqaa045] [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] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES Superficial pleomorphic liposarcoma (PL) has a favorable prognosis compared to deeply seated PL. Given developments in the classification of lipomatous neoplasms, we reappraised a series of cases. METHODS Retrospective clinicopathologic evaluation and genome-wide single-nucleotide polymorphism (SNP) microarray studies were performed for cases previously designated superficial PL. RESULTS Four cases were identified (age, 48-70 years). Two were dermally confined, whereas two were superficial subcutaneous; no recurrences or metastases were reported. Tumors demonstrated pleomorphic spindled morphology with variable cellularity. Multivacuolated atypical lipoblasts were focal in 3 and abundant in 1. Dermal tumors demonstrated atypical cells within sclerotic collagen. Genome-wide SNP microarray studies revealed consistent gains and losses, including losses at the 13q14.2 locus encompassing RB1 and DLEU2 and deletion/disruption of the TP53 locus. Although subcutaneous examples showed genomic changes similar to deep PL, the dermal examples showed fewer genetic alterations, including changes reported in the spectrum of atypical spindle cell/pleomorphic lipomatous tumors (ASPLT). All lacked MDM2 amplification. CONCLUSIONS Careful integration of histologic and genetic features may improve classification of lipomatous neoplasms with atypia, allowing reclassification of some superficial PL as ASPLT.
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Affiliation(s)
| | | | - Colleen Jackson-Cook
- Department of Pathology, Virginia Commonwealth University Health System, Richmond
- Department of Human and Molecular Genetics, Virginia Commonwealth University Health System, Richmond
| | - Sosipatros Alexander Boikos
- Department of Hematology, Oncology, and Palliative Care, Virginia Commonwealth University Health System, Richmond
| | | | - Mark Cameron Mochel
- Department of Pathology, Virginia Commonwealth University Health System, Richmond
- Department of Dermatology, Virginia Commonwealth University Health System, Richmond
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15
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Cutigi JF, Evangelista AF, Simao A. Approaches for the identification of driver mutations in cancer: A tutorial from a computational perspective. J Bioinform Comput Biol 2020; 18:2050016. [PMID: 32698724 DOI: 10.1142/s021972002050016x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cancer is a complex disease caused by the accumulation of genetic alterations during the individual's life. Such alterations are called genetic mutations and can be divided into two groups: (1) Passenger mutations, which are not responsible for cancer and (2) Driver mutations, which are significant for cancer and responsible for its initiation and progression. Cancer cells undergo a large number of mutations, of which most are passengers, and few are drivers. The identification of driver mutations is a key point and one of the biggest challenges in Cancer Genomics. Many computational methods for such a purpose have been developed in Cancer Bioinformatics. Such computational methods are complex and are usually described in a high level of abstraction. This tutorial details some classical computational methods, from a computational perspective, with the transcription in an algorithmic format towards an easy access by researchers.
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Affiliation(s)
- Jorge Francisco Cutigi
- Federal Institute of São Paulo (IFSP), São Carlos, SP, Brazil.,University of São Paulo (USP), São Carlos, SP, Brazil
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16
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Zhang Z, Zhou C, Li X, Barnes SD, Deng S, Hoover E, Chen CC, Lee YS, Zhang Y, Wang C, Metang LA, Wu C, Tirado CR, Johnson NA, Wongvipat J, Navrazhina K, Cao Z, Choi D, Huang CH, Linton E, Chen X, Liang Y, Mason CE, de Stanchina E, Abida W, Lujambio A, Li S, Lowe SW, Mendell JT, Malladi VS, Sawyers CL, Mu P. Loss of CHD1 Promotes Heterogeneous Mechanisms of Resistance to AR-Targeted Therapy via Chromatin Dysregulation. Cancer Cell 2020; 37:584-598.e11. [PMID: 32220301 PMCID: PMC7292228 DOI: 10.1016/j.ccell.2020.03.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 11/04/2019] [Accepted: 02/28/2020] [Indexed: 12/25/2022]
Abstract
Metastatic prostate cancer is characterized by recurrent genomic copy number alterations that are presumed to contribute to resistance to hormone therapy. We identified CHD1 loss as a cause of antiandrogen resistance in an in vivo small hairpin RNA (shRNA) screen of 730 genes deleted in prostate cancer. ATAC-seq and RNA-seq analyses showed that CHD1 loss resulted in global changes in open and closed chromatin with associated transcriptomic changes. Integrative analysis of this data, together with CRISPR-based functional screening, identified four transcription factors (NR3C1, POU3F2, NR2F1, and TBX2) that contribute to antiandrogen resistance, with associated activation of non-luminal lineage programs. Thus, CHD1 loss results in chromatin dysregulation, thereby establishing a state of transcriptional plasticity that enables the emergence of antiandrogen resistance through heterogeneous mechanisms.
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MESH Headings
- Androgen Antagonists/pharmacology
- Animals
- Apoptosis
- Biomarkers, Tumor/genetics
- Cell Proliferation
- Chromatin/genetics
- Chromatin/metabolism
- DNA Helicases/antagonists & inhibitors
- DNA Helicases/genetics
- DNA-Binding Proteins/antagonists & inhibitors
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Drug Resistance, Neoplasm/genetics
- Gene Expression Regulation, Neoplastic
- High-Throughput Screening Assays
- Humans
- Male
- Mice
- Prostatic Neoplasms, Castration-Resistant/drug therapy
- Prostatic Neoplasms, Castration-Resistant/genetics
- Prostatic Neoplasms, Castration-Resistant/pathology
- RNA, Small Interfering/genetics
- Receptors, Androgen/chemistry
- Receptors, Androgen/genetics
- Transcription Factors/metabolism
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Zeda Zhang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chuanli Zhou
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaoling Li
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Spencer D Barnes
- Bioinformatics Core Facility of the Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Su Deng
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Elizabeth Hoover
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chi-Chao Chen
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA
| | - Young Sun Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Choushi Wang
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lauren A Metang
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chao Wu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Nickolas A Johnson
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - John Wongvipat
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Zhen Cao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA
| | - Danielle Choi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chun-Hao Huang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA
| | - Eliot Linton
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xiaoping Chen
- Department of Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yupu Liang
- Center for Clinical and Translational Science, Rockefeller University, New York, NY 10065, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Elisa de Stanchina
- Department of Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Amaia Lujambio
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sheng Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Joshua T Mendell
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Venkat S Malladi
- Bioinformatics Core Facility of the Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Charles L Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Ping Mu
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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17
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Xi J, Li A, Wang M. HetRCNA: A Novel Method to Identify Recurrent Copy Number Alternations from Heterogeneous Tumor Samples Based on Matrix Decomposition Framework. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:422-434. [PMID: 29994262 DOI: 10.1109/tcbb.2018.2846599] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A common strategy to discovering cancer associated copy number aberrations (CNAs) from a cohort of cancer samples is to detect recurrent CNAs (RCNAs). Although the previous methods can successfully identify communal RCNAs shared by nearly all tumor samples, detecting subgroup-specific RCNAs and their related subgroup samples from cancer samples with heterogeneity is still invalid for these existing approaches. In this paper, we introduce a novel integrated method called HetRCNA, which can identify statistically significant subgroup-specific RCNAs and their related subgroup samples. Based on matrix decomposition framework with weight constraint, HetRCNA can successfully measure the subgroup samples by coefficients of left vectors with weight constraint and subgroup-specific RCNAs by coefficients of the right vectors and significance test. When we evaluate HetRCNA on simulated dataset, the results show that HetRCNA gives the best performances among the competing methods and is robust to the noise factors of the simulated data. When HetRCNA is applied on a real breast cancer dataset, our approach successfully identifies a bunch of RCNA regions and the result is highly correlated with the results of the other two investigated approaches. Notably, the genomic regions identified by HetRCNA harbor many breast cancer related genes reported by previous researches.
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18
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Burns J, Wilding CP, L Jones R, H Huang P. Proteomic research in sarcomas - current status and future opportunities. Semin Cancer Biol 2019; 61:56-70. [PMID: 31722230 PMCID: PMC7083238 DOI: 10.1016/j.semcancer.2019.11.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 11/04/2019] [Indexed: 02/07/2023]
Abstract
Sarcomas are a rare group of mesenchymal cancers comprising over 70 different histological subtypes. For the majority of these diseases, the molecular understanding of the basis of their initiation and progression remains unclear. As such, limited clinical progress in prognosis or therapeutic regimens have been made over the past few decades. Proteomics techniques are being increasingly utilised in the field of sarcoma research. Proteomic research efforts have thus far focused on histological subtype characterisation for the improvement of biological understanding, as well as for the identification of candidate diagnostic, predictive, and prognostic biomarkers for use in clinic. However, the field itself is in its infancy, and none of these proteomic research findings have been translated into the clinic. In this review, we provide a brief overview of the proteomic strategies that have been employed in sarcoma research. We evaluate key proteomic studies concerning several rare and ultra-rare sarcoma subtypes including, gastrointestinal stromal tumours, osteosarcoma, liposarcoma, leiomyosarcoma, malignant rhabdoid tumours, Ewing sarcoma, myxofibrosarcoma, and alveolar soft part sarcoma. Consequently, we illustrate how routine implementation of proteomics within sarcoma research, integration of proteomics with other molecular profiling data, and incorporation of proteomics into clinical trial studies has the potential to propel the biological and clinical understanding of this group of complex rare cancers moving forward.
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Affiliation(s)
- Jessica Burns
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Christopher P Wilding
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Robin L Jones
- Division of Clinical Studies, The Institute of Cancer Research, London SW3 6JB, UK; Sarcoma Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Paul H Huang
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW3 6JB, UK.
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19
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Liao Y, Ma Z, Zhang Y, Li D, Lv D, Chen Z, Li P, Ai-Dherasi A, Zheng F, Tian J, Zou K, Wang Y, Wang D, Cordova M, Zhou H, Li X, Liu D, Yu R, Zhang Q, Zhang X, Zhang J, Zhang X, Zhang X, Li Y, Shao Y, Song L, Liu R, Wang Y, Sufiyan S, Liu Q, Owen GI, Li Z, Chen J. Targeted deep sequencing from multiple sources demonstrates increased NOTCH1 alterations in lung cancer patient plasma. Cancer Med 2019; 8:5673-5686. [PMID: 31369215 PMCID: PMC6745866 DOI: 10.1002/cam4.2458] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/13/2019] [Accepted: 07/18/2019] [Indexed: 12/19/2022] Open
Abstract
Introduction Targeted therapies are based on specific gene alterations. Various specimen types have been used to determine gene alterations, however, no systemic comparisons have yet been made. Herein, we assessed alterations in selected cancer‐associated genes across varying sample sites in lung cancer patients. Materials and Methods Targeted deep sequencing for 48 tumor‐related genes was applied to 153 samples from 55 lung cancer patients obtained from six sources: Formalin‐fixed paraffin‐embedded (FFPE) tumor tissues, pleural effusion supernatant (PES) and pleural effusion cell sediments (PEC), white blood cells (WBCs), oral epithelial cells (OECs), and plasma. Results Mutations were detected in 96% (53/55) of the patients and in 83% (40/48) of the selected genes. Each sample type exhibited a characteristic mutational pattern. As anticipated, TP53 was the most affected sequence (54.5% patients), however this was followed by NOTCH1 (36%, across all sample types). EGFR was altered in patient samples at a frequency of 32.7% and KRAS 10.9%. This high EGFR/ low KRAS frequency is in accordance with other TCGA cohorts of Asian origin but differs from the Caucasian population where KRAS is the more dominant mutation. Additionally, 66% (31/47) of PEC samples had copy number variants (CNVs) in at least one gene. Unlike the concurrent loss and gain in most genes, herein NOTCH1 loss was identified in 21% patients, with no gain observed. Based on the relative prevalence of mutations and CNVs, we divided lung cancer patients into SNV‐dominated, CNV‐dominated, and codominated groups. Conclusions Our results confirm previous reports that EGFR mutations are more prevalent than KRAS in Chinese lung cancer patients. NOTCH1 gene alterations are more common than previously reported and reveals a role of NOTCH1 modifications in tumor metastasis. Furthermore, genetic material from malignant pleural effusion cell sediments may be a noninvasive manner to identify CNV and participate in treatment decisions.
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Affiliation(s)
- Yuwei Liao
- The Second Hospital of Dalian Medical University, Dalian, China.,Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Zhaokui Ma
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Yu Zhang
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Dan Li
- The Second Hospital of Dalian Medical University, Dalian, China
| | - Dekang Lv
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Zhisheng Chen
- The Second Hospital of Dalian Medical University, Dalian, China
| | - Peiying Li
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Aisha Ai-Dherasi
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Feng Zheng
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, China
| | - Jichao Tian
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Kun Zou
- The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yue Wang
- The Second Hospital of Dalian Medical University, Dalian, China
| | - Dongxia Wang
- The Second Hospital of Dalian Medical University, Dalian, China
| | - Miguel Cordova
- Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Huan Zhou
- The Second Hospital of Dalian Medical University, Dalian, China
| | - Xiuhua Li
- The Second Hospital of Dalian Medical University, Dalian, China
| | - Dan Liu
- The Second Hospital of Dalian Medical University, Dalian, China
| | - Ruofei Yu
- The Second Hospital of Dalian Medical University, Dalian, China
| | - Qingzheng Zhang
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Xiaolong Zhang
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Jian Zhang
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Xuehong Zhang
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Xia Zhang
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Yulong Li
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Yanyan Shao
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Luyao Song
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Ruimei Liu
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Yichen Wang
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Sufiyan Sufiyan
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Quentin Liu
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Gareth I Owen
- Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Zhiguang Li
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China.,The Second Affiliated Hospital, School of Medicine, Zhengzhou University, Zhengzhou, China
| | - Jun Chen
- The Second Hospital of Dalian Medical University, Dalian, China
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20
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Suarez-Kelly LP, Baldi GG, Gronchi A. Pharmacotherapy for liposarcoma: current state of the art and emerging systemic treatments. Expert Opin Pharmacother 2019; 20:1503-1515. [PMID: 31136210 DOI: 10.1080/14656566.2019.1618271] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Introduction: Liposarcomas are a heterogeneous group of soft tissue tumors that arise from adipose tissue and are one of the most common soft tissue sarcomas found in adults. Liposarcomas are subclassified into four subtypes with distinct histologic and biologic features that influence their treatment and management. Areas covered: This manuscript reviews the key clinicopathologic and cytogenic characteristics of the liposarcoma histologic subtypes and summarizes the results of recent clinical trials, treatment options, and future directions in the pharmacotherapy for the management of liposarcoma. Expert opinion: Despite significant advancements in the management of this disease, the treatment of liposarcoma continues to be a challenge. Surgical resection remains the mainstay of treatment for localized disease; however, use of systemic therapies in conjunction with surgery may be considered in patients where tumor shrinkage could reduce surgical morbidity and in patients with high-risk of micrometastatic disease. Anthracycline-based chemotherapy regimens remain the standard first-line treatment for unresectable/metastatic liposarcoma. Trabectedin and eribulin are currently the two most promising and evidenced-based second-line treatment options for liposarcomas. However, multiple clinical trials dedicated to patients with liposarcoma evaluating novel targeted agents are ongoing. Every effort should be made to enroll patients with liposarcoma into histotype-specific clinical trials.
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Affiliation(s)
- Lorena P Suarez-Kelly
- Complex General Surgical Oncology Fellow, The Ohio State University , Columbus , OH , USA
| | - Giacomo G Baldi
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato , Prato , Italy.,Adult mesenchymal and Rare Tumor Unit, Department of Cancer Medicine, Fondazione IRCCS-Istituto Nazionale dei Tumori , Milan , Italy
| | - Alessandro Gronchi
- Sarcoma Service of the Department of Surgery, Fondazione IRCCS-Istituto Nazionale dei Tumori , Milan , Italy
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21
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Abstract
Adipocytic neoplasms include a diversity of both benign tumors (lipomas) and malignancies (liposarcomas), and each tumor type is characterized by its own unique molecular alterations driving tumorigenesis. Work over the past 30 years has established the diagnostic utility of several of these characteristic molecular alterations (e.g. MDM2 amplification in well- and dedifferentiated liposarcoma, FUS/EWSR1-DDIT3 gene fusions in myxoid liposarcoma, RB1 loss in spindle cell/pleomorphic lipoma). More recent studies have focused on additional molecular alterations which may have therapeutic or prognostic impact. This review will summarize several of the important molecular findings in adipocytic tumors that have been described over the past 10 years.
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Affiliation(s)
- Elizabeth G Demicco
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, and Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
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22
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Abstract
Myxoid adipocytic tumors encompass a broad heterogeneous group of benign and malignant adipocytic tumors, which are typically myxoid (e.g. myxoid liposarcoma, lipoblastoma and lipoblastoma-like tumor of the vulva) or may occasionally appear predominantly myxoid (e.g. pleomorphic liposarcoma, atypical lipomatous tumor, dedifferentiated liposarcoma, chondroid lipoma, spindle cell/pleomorphic lipoma, atypical spindle cell lipomatous tumor and atypical pleomorphic lipomatous tumor). There have been significant advances in recent years in classification and understanding the pathogenesis of adipocytic tumors, based on the correlation of histologic, immunohistochemical, and cytogenetic/molecular findings. Despite these advances, the morphologic diagnosis and accurate classification of a myxoid adipocytic tumor can be challenging due to major morphologic overlap between myxoid adipocytic and non-adipocytic tumors. This article will provide a review on the currently known morphological, immunohistochemical and molecular features of myxoid adipocytic tumors and their differential diagnosis.
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Affiliation(s)
- David Creytens
- Department of Pathology, Ghent University and Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium; CRIG, Cancer Research Institute Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.
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23
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Burkes JN, Campos L, Williams FC, Kim RY. Laryngeal Spindle Cell/Pleomorphic Lipoma: A Case Report. An In-Depth Review of the Adipocytic Tumors. J Oral Maxillofac Surg 2019; 77:1401-1410. [PMID: 30826392 DOI: 10.1016/j.joms.2019.01.050] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/28/2019] [Accepted: 01/28/2019] [Indexed: 02/06/2023]
Abstract
Spindle cell and pleomorphic lipomas (SC/PLs) are a rare form of lipomatous tumors. They typically occur as a slow-growing localized mass in the subcutaneous fatty tissue of the posterior neck, back, and shoulders. This benign variant represents less than 1.5% of all lipomas and is relatively uncommon in the head and neck area. A manifestation in the larynx is even rarer. Unlike other anatomic locations, laryngeal lipomas can pose life-threatening symptoms secondary to acute obstruction of the upper aerodigestive tract. This report presents a case of a large SC/PL of the larynx associated with hoarseness, dysphagia, globus sensation, and neck fullness. The tumor was successfully removed through an anterior transcervical approach with infrahyoid myotomy. The authors review the literature concerning head and neck adipocytic tumors with spindle cells and discuss the difficulties in distinguishing SC/PLs from liposarcomas. To the best of the authors' knowledge, this is the first case to be reported in the oral and maxillofacial surgery literature.
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Affiliation(s)
- Jason N Burkes
- Former Fellow, Head and Neck Oncologic and Microvascular Reconstructive Surgery, John Peter Smith Hospital, Fort Worth, TX; Associate Program Director, National Capital Consortium Oral Maxillofacial Surgery Residency Program, Walter Reed National Military Medical Center, Bethesda, MD
| | - Luisa Campos
- Resident, Department of Oral and Maxillofacial Surgery, Texas A&M College of Dentistry, Baylor University Medical Center, Dallas, TX
| | - Fayette C Williams
- Director of Maxillofacial Oncology and Reconstructive Surgery, John Peter Smith Hospital, Fort Worth, TX
| | - Roderick Y Kim
- Assistant Fellowship Director, Head and Neck Oncologic and Microvascular Reconstructive Surgery, John Peter Smith Hospital, Fort Worth, TX.
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Cho SJ, Yoon C, Lee JH, Chang KK, Lin JX, Kim YH, Kook MC, Aksoy BA, Park DJ, Ashktorab H, Smoot DT, Schultz N, Yoon SS. KMT2C Mutations in Diffuse-Type Gastric Adenocarcinoma Promote Epithelial-to-Mesenchymal Transition. Clin Cancer Res 2018; 24:6556-6569. [PMID: 30108106 PMCID: PMC6295255 DOI: 10.1158/1078-0432.ccr-17-1679] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 07/13/2017] [Accepted: 08/09/2018] [Indexed: 12/15/2022]
Abstract
PURPOSE Lauren diffuse-type gastric adenocarcinomas (DGAs) are generally genomically stable. We identified lysine (K)-specific methyltransferase 2C (KMT2C) as a frequently mutated gene and examined its role in DGA progression. EXPERIMENTAL DESIGN We performed whole exome sequencing on tumor samples of 27 patients with DGA who underwent gastrectomy. Lysine (K)-specific methyltransferase 2C (KMT2C) was analyzed in DGA cell lines and in patient tumors. RESULTS KMT2C was the most frequently mutated gene (11 of 27 tumors [41%]). KMT2C expression by immunohistochemistry in tumors from 135 patients with DGA undergoing gastrectomy inversely correlated with more advanced tumor stage (P = 0.023) and worse overall survival (P = 0.017). KMT2C shRNA knockdown in non-transformed HFE-145 gastric epithelial cells promoted epithelial-to-mesenchymal transition (EMT) as demonstrated by increased expression of EMT-related proteins N-cadherin and Slug. Migration and invasion in gastric epithelial cells following KMT2C knockdown increased by 47- to 88-fold. In the DGA cell lines MKN-45 and SNU-668, which have lost KMT2C expression, KMT2C re-expression decreased expression of EMT-related proteins, reduced cell migration by 52% to 60%, and reduced cell invasion by 50% to 74%. Flank xenografts derived from KMT2C-expressing DGA organoids, compared with wild-type organoids, grew more slowly and lost their infiltrative leading edge. EMT can lead to the acquisition of cancer stem cell (CSC) phenotypes. KMT2C re-expression in DGA cell lines reduced spheroid formation by 77% to 78% and reversed CSC resistance to chemotherapy via promotion of DNA damage and apoptosis. CONCLUSIONS KMT2C is frequently mutated in certain populations with DGA. KMT2C loss in DGA promotes EMT and is associated with worse overall survival.
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Affiliation(s)
- Soo-Jeong Cho
- Gastric and Mixed Tumor Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York
- Center for Gastric Cancer, National Cancer Center, Goyang, South Korea
| | - Changhwan Yoon
- Gastric and Mixed Tumor Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Jun Ho Lee
- Gastric and Mixed Tumor Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Kevin K Chang
- Gastric and Mixed Tumor Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Jian-Xian Lin
- Gastric and Mixed Tumor Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Young-Ho Kim
- Division of Clinical Research, Rare Cancer Branch, National Cancer Center, Goyang, South Korea
| | - Myeong-Cherl Kook
- Center for Gastric Cancer, National Cancer Center, Goyang, South Korea
| | - Bülent Arman Aksoy
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Do Joong Park
- Gastric and Mixed Tumor Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea
| | | | - Duane T Smoot
- Department of Internal Medicine, Meharry Medical College, Nashville, Tennessee
| | - Nikolaus Schultz
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Sam S Yoon
- Gastric and Mixed Tumor Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York.
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25
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Saha SK, Jeong Y, Cho S, Cho SG. Systematic expression alteration analysis of master reprogramming factor OCT4 and its three pseudogenes in human cancer and their prognostic outcomes. Sci Rep 2018; 8:14806. [PMID: 30287838 PMCID: PMC6172215 DOI: 10.1038/s41598-018-33094-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 09/21/2018] [Indexed: 12/13/2022] Open
Abstract
OCT4 is a master transcription factor that regulates the pluripotency of pluripotent stem cells and cancer stem cells along with other factors, including SOX2, KLF4, and C-MYC. Three different transcripts, OCT4A, OCT4B, and OCT4B1, are known to be generated by alternative splicing and eight OCT4 pseudogenes have been found in the human genome. Among them, we examined OCT4 and three pseudogenes (POU5F1P1, POU5F1P3, and POU5F1P4) because of their high expression possibility in cancer. In addition, previous studies indicated that OCT4 expression is augmented in cervical cancer and associated with poor prognosis, whereas OCT4 is down-regulated and correlated with good clinical outcomes in breast cancer. Because of these conflicting reports, we systematically evaluated whether expression of OCT4 and its pseudogenes can serve as oncogenic markers in various human cancers using the Oncomine database. Moreover, copy number alterations and mutations in OCT4 gene and its pseudogenes were analyzed using cBioPortal and the relationship between expression of OCT4 and pseudogenes and survival probability of cancer patients were explored using Kaplan-Meier plotter, OncoLnc, PROGgeneV2, and PrognoScan databases. Multivariate survival analysis was further conducted to determine the risk of the expression of the occurrence of OCT4 and its pseudogenes on certain cancer types using data from the Kaplan-Meier plotter. Overall, an association between expression of OCT4 and pseudogenes and cancer prognosis were established, which may serve as a therapeutic target for various human cancers.
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Affiliation(s)
- Subbroto Kumar Saha
- Department of Stem Cell and Regenerative Biotechnology, Incurable Disease Animal Model & Stem Cell Institute (IDASI), Konkuk University, Seoul, 05029, Republic of Korea
| | - Yeojin Jeong
- Department of Stem Cell and Regenerative Biotechnology, Incurable Disease Animal Model & Stem Cell Institute (IDASI), Konkuk University, Seoul, 05029, Republic of Korea
| | - Sungha Cho
- Department of Stem Cell and Regenerative Biotechnology, Incurable Disease Animal Model & Stem Cell Institute (IDASI), Konkuk University, Seoul, 05029, Republic of Korea
| | - Ssang-Goo Cho
- Department of Stem Cell and Regenerative Biotechnology, Incurable Disease Animal Model & Stem Cell Institute (IDASI), Konkuk University, Seoul, 05029, Republic of Korea.
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26
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Nagorski J, Allen GI. Genomic region detection via Spatial Convex Clustering. PLoS One 2018; 13:e0203007. [PMID: 30204756 PMCID: PMC6133280 DOI: 10.1371/journal.pone.0203007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 08/13/2018] [Indexed: 12/31/2022] Open
Abstract
Several modern genomic technologies, such as DNA-Methylation arrays, measure spatially registered probes that number in the hundreds of thousands across multiple chromosomes. The measured probes are by themselves less interesting scientifically; instead scientists seek to discover biologically interpretable genomic regions comprised of contiguous groups of probes which may act as biomarkers of disease or serve as a dimension-reducing pre-processing step for downstream analyses. In this paper, we introduce an unsupervised feature learning technique which maps technological units (probes) to biological units (genomic regions) that are common across all subjects. We use ideas from fusion penalties and convex clustering to introduce a method for Spatial Convex Clustering, or SpaCC. Our method is specifically tailored to detecting multi-subject regions of methylation, but we also test our approach on the well-studied problem of detecting segments of copy number variation. We formulate our method as a convex optimization problem, develop a massively parallelizable algorithm to find its solution, and introduce automated approaches for handling missing values and determining tuning parameters. Through simulation studies based on real methylation and copy number variation data, we show that SpaCC exhibits significant performance gains relative to existing methods. Finally, we illustrate SpaCC's advantages as a pre-processing technique that reduces large-scale genomics data into a smaller number of genomic regions through several cancer epigenetics case studies on subtype discovery, network estimation, and epigenetic-wide association.
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Affiliation(s)
- John Nagorski
- Department of Statistics, Rice University, Houston, TX, United States of America
| | - Genevera I. Allen
- Department of Statistics, Rice University, Houston, TX, United States of America
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, United States of America
- Jan and Dan Duncan Neurological Research Institute and Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, United States of America
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27
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Xie S, Shen C, Tan M, Li M, Song X, Wang C. Systematic analysis of gene expression alterations and clinical outcomes of adenylate cyclase-associated protein in cancer. Oncotarget 2018; 8:27216-27239. [PMID: 28423713 PMCID: PMC5432330 DOI: 10.18632/oncotarget.16111] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 02/20/2017] [Indexed: 12/21/2022] Open
Abstract
Adenylate Cyclase-associated protein (CAP) is an evolutionarily conserved protein that regulates actin dynamics. Our previous study indicates that CAP1 is overexpressed in NSCLC tissues and correlated with poor clinical outcomes, but CAP1 in HeLa cells actually inhibited migration and invasion, the role of CAP was discrepancy in different cancer types. The present study aims to determine whether CAP can serve as a prognostic marker in human cancers. The CAP expression was assessed using Oncomine database to determine the gene alteration during carcinogenesis, the copy number alteration, or mutations of CAP using cBioPortal, International Cancer Genome Consortium, and Tumorscape database investigated, and the association between CAP expression and the survival of cancer patient using Kaplan-Meier plotter and PrognoScan database evaluated. Therefore, the functional correlation between CAP expression and cancer phenotypes can be established; wherein CAP might serve as a diagnostic marker or therapeutic target for certain types of cancers.
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Affiliation(s)
- Shuanshuan Xie
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Changxing Shen
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Min Tan
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Ming Li
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Xiaolian Song
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Changhui Wang
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
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28
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Horn H, Lawrence MS, Chouinard CR, Shrestha Y, Hu JX, Worstell E, Shea E, Ilic N, Kim E, Kamburov A, Kashani A, Hahn WC, Campbell JD, Boehm JS, Getz G, Lage K. NetSig: network-based discovery from cancer genomes. Nat Methods 2018; 15:61-66. [PMID: 29200198 PMCID: PMC5985961 DOI: 10.1038/nmeth.4514] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 10/19/2017] [Indexed: 12/21/2022]
Abstract
Methods that integrate molecular network information and tumor genome data could complement gene-based statistical tests to identify likely new cancer genes; but such approaches are challenging to validate at scale, and their predictive value remains unclear. We developed a robust statistic (NetSig) that integrates protein interaction networks with data from 4,742 tumor exomes. NetSig can accurately classify known driver genes in 60% of tested tumor types and predicts 62 new driver candidates. Using a quantitative experimental framework to determine in vivo tumorigenic potential in mice, we found that NetSig candidates induce tumors at rates that are comparable to those of known oncogenes and are ten-fold higher than those of random genes. By reanalyzing nine tumor-inducing NetSig candidates in 242 patients with oncogene-negative lung adenocarcinomas, we find that two (AKT2 and TFDP2) are significantly amplified. Our study presents a scalable integrated computational and experimental workflow to expand discovery from cancer genomes.
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Affiliation(s)
- Heiko Horn
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
| | - Michael S. Lawrence
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
- Department of Pathology and MGH Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Candace R. Chouinard
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
| | - Yashaswi Shrestha
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
| | - Jessica Xin Hu
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
| | - Elizabeth Worstell
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
| | - Emily Shea
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
| | - Nina Ilic
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Eejung Kim
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Atanas Kamburov
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
- Department of Pathology and MGH Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alireza Kashani
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
| | - William C. Hahn
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Joshua D. Campbell
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Jesse S. Boehm
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
- Department of Pathology and MGH Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kasper Lage
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
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29
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Champion M, Brennan K, Croonenborghs T, Gentles AJ, Pochet N, Gevaert O. Module Analysis Captures Pancancer Genetically and Epigenetically Deregulated Cancer Driver Genes for Smoking and Antiviral Response. EBioMedicine 2018; 27:156-166. [PMID: 29331675 PMCID: PMC5828545 DOI: 10.1016/j.ebiom.2017.11.028] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/23/2017] [Accepted: 11/29/2017] [Indexed: 12/12/2022] Open
Abstract
The availability of increasing volumes of multi-omics profiles across many cancers promises to improve our understanding of the regulatory mechanisms underlying cancer. The main challenge is to integrate these multiple levels of omics profiles and especially to analyze them across many cancers. Here we present AMARETTO, an algorithm that addresses both challenges in three steps. First, AMARETTO identifies potential cancer driver genes through integration of copy number, DNA methylation and gene expression data. Then AMARETTO connects these driver genes with co-expressed target genes that they control, defined as regulatory modules. Thirdly, we connect AMARETTO modules identified from different cancer sites into a pancancer network to identify cancer driver genes. Here we applied AMARETTO in a pancancer study comprising eleven cancer sites and confirmed that AMARETTO captures hallmarks of cancer. We also demonstrated that AMARETTO enables the identification of novel pancancer driver genes. In particular, our analysis led to the identification of pancancer driver genes of smoking-induced cancers and 'antiviral' interferon-modulated innate immune response. SOFTWARE AVAILABILITY AMARETTO is available as an R package at https://bitbucket.org/gevaertlab/pancanceramaretto.
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Affiliation(s)
- Magali Champion
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine & Biomedical Data Science, Stanford University, United States
| | - Kevin Brennan
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine & Biomedical Data Science, Stanford University, United States
| | - Tom Croonenborghs
- Program in Translational Neuropsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Broad Institute of Harvard and Massachusetts Institute of Technology, United States; Advanced Integrated Sensing Lab, Campus Geel, Department of Computer Science, University of Leuven, Belgium
| | - Andrew J Gentles
- Department of Medicine, Center for Cancer Systems Biology, Stanford University, United States
| | - Nathalie Pochet
- Program in Translational Neuropsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Broad Institute of Harvard and Massachusetts Institute of Technology, United States
| | - Olivier Gevaert
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine & Biomedical Data Science, Stanford University, United States.
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Momtaz R, Ghanem NM, El-Makky NM, Ismail MA. Integrated analysis of SNP, CNV and gene expression data in genetic association studies. Clin Genet 2017; 93:557-566. [PMID: 28685831 DOI: 10.1111/cge.13092] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 06/20/2017] [Accepted: 07/01/2017] [Indexed: 02/02/2023]
Abstract
Integrative approaches that combine multiple forms of data can more accurately capture pathway associations and so provide a comprehensive understanding of the molecular mechanisms that cause complex diseases. Association analyses based on single nucleotide polymorphism (SNP) genotypes, copy number variant (CNV) genotypes, and gene expression profiles are the 3 most common paradigms used for gene set/pathway enrichment analyses. Many work has been done to leverage information from 2 types of data from these 3 paradigms. However, to the best of our knowledge, there is no work done before to integrate the 3 paradigms all together. In this article, we present an integrated analysis that combine SNP, CNV, and gene expression data to generate a single gene list. We present different methods to compare this gene list with the other 3 possible lists that result from the combinations of the following pairs of data: SNP genotype with gene expression, CNV genotype with gene expression, and SNP genotype with CNV genotype. The comparison is done using 3 different cancer datasets and 2 different methods of comparison. Our results show that integrating SNP, CNV, and gene expression data give better association results than integrating any pair of 3 data.
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Affiliation(s)
- R Momtaz
- Computer and Systems Engineering Department, Alexandria University, Alexandria, Egypt
| | - N M Ghanem
- Computer and Systems Engineering Department, Alexandria University, Alexandria, Egypt
| | - N M El-Makky
- Computer and Systems Engineering Department, Alexandria University, Alexandria, Egypt
| | - M A Ismail
- Computer and Systems Engineering Department, Alexandria University, Alexandria, Egypt
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Abstract
Liposarcomas are rare malignant tumors of adipocytic differentiation. The classification of liposarcomas into four principal subtypes reflects the distinct clinical behavior, treatment sensitivity, and underlying biology encompassed by these diseases. Increasingly, clinical management decisions and the development of investigational therapeutics are informed by an improved understanding of subtype-specific molecular pathology. Well-differentiated liposarcoma is the most common subtype and is associated with indolent behavior, local recurrence, and insensitivity to radiotherapy and chemotherapy. Dedifferentiated liposarcoma represents focal progression of well-differentiated disease into a more aggressive, metastasizing, and fatal malignancy. Both of these subtypes are characterized by recurrent amplifications within chromosome 12, resulting in the overexpression of disease-driving genes that have been the focus of therapeutic targeting. Myxoid liposarcoma is characterized by a pathognomonic chromosomal translocation that results in an oncogenic fusion protein, whereas pleomorphic liposarcoma is a karyotypically complex and especially poor-prognosis subtype that accounts for less than 10% of liposarcoma diagnoses. A range of novel pharmaceutical agents that aim to target liposarcoma-specific biology are under active investigation and offer hope of adding to the limited available treatment options for recurrent or inoperable disease.
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Affiliation(s)
- Alex Thomas John Lee
- Alex Thomas John Lee, Khin Thway, and Robin Lewis Jones, The Royal Marsden NHS Foundation Trust; Alex Thomas John Lee, Paul H. Huang, and Robin Lewis Jones, The Institute of Cancer Research, London, UK
| | - Khin Thway
- Alex Thomas John Lee, Khin Thway, and Robin Lewis Jones, The Royal Marsden NHS Foundation Trust; Alex Thomas John Lee, Paul H. Huang, and Robin Lewis Jones, The Institute of Cancer Research, London, UK
| | - Paul H Huang
- Alex Thomas John Lee, Khin Thway, and Robin Lewis Jones, The Royal Marsden NHS Foundation Trust; Alex Thomas John Lee, Paul H. Huang, and Robin Lewis Jones, The Institute of Cancer Research, London, UK
| | - Robin Lewis Jones
- Alex Thomas John Lee, Khin Thway, and Robin Lewis Jones, The Royal Marsden NHS Foundation Trust; Alex Thomas John Lee, Paul H. Huang, and Robin Lewis Jones, The Institute of Cancer Research, London, UK
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32
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DNA methylation regulates TMEM16A/ANO1 expression through multiple CpG islands in head and neck squamous cell carcinoma. Sci Rep 2017; 7:15173. [PMID: 29123240 PMCID: PMC5680248 DOI: 10.1038/s41598-017-15634-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/31/2017] [Indexed: 01/22/2023] Open
Abstract
ANO1 is a calcium-activated chloride channel that is frequently overexpressed in head and neck squamous cell carcinoma (HNSCC) and other cancers. While ANO1 expression negatively correlates with survival in several cancers, its epigenetic regulation is poorly understood. We analyzed HNSCC samples from TCGA and a separate dataset of HPV+ oropharyngeal squamous cell carcinoma (OPSCC) samples to identify differentially methylated regions. E6 and E7 transfected normal oral keratinocytes (NOK) were used to induce hypermethylation of the ANO1 promoter. We found three CpG islands that correlated with ANO1 expression, including two positively correlated with expression. Using two HNSCC datasets with differential expression of ANO1, we showed hypermethylation of positively correlated CpG islands potentiates ANO1 expression. E7 but not E6 transfection of NOK cells led to hypermethylation of a positively correlated CpG island without a change in ANO1 expression. ANO1 promoter methylation was also correlated with patient survival. Our results are the first to show the contribution of positively correlated CpG’s for regulating gene expression in HNSCC. Hypermethylation of the ANO1 promoter was strongly correlated with but not sufficient to increase ANO1 expression, suggesting methylation of positively correlated CpG’s likely serves as an adjunct to other mechanisms of ANO1 activation.
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Steady-State Levels of Phosphorylated Mitogen-Activated Protein Kinase Kinase 1/2 Determined by Mortalin/HSPA9 and Protein Phosphatase 1 Alpha in KRAS and BRAF Tumor Cells. Mol Cell Biol 2017; 37:MCB.00061-17. [PMID: 28674184 DOI: 10.1128/mcb.00061-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 06/26/2017] [Indexed: 12/31/2022] Open
Abstract
Although deregulation of MEK/extracellular signal-regulated kinase (ERK) activity is a key feature in cancer, high-magnitude MEK/ERK activity can paradoxically induce growth inhibition. Therefore, additional mechanisms may exist to modulate MEK/ERK activity in favor of tumor cell proliferation. We previously reported that mortalin/HSPA9 can facilitate proliferation of certain KRAS and BRAF tumor cells by modulating MEK/ERK activity. In this study, we demonstrated that mortalin can regulate MEK/ERK activity via protein phosphatase 1α (PP1α). We found that PP1α inhibition increases steady-state levels of phosphorylated MEK1/2 in various tumor cells expressing B-RafV600E or K-RasG12C/D Intriguingly, coimmunoprecipitation and in vitro binding assays revealed that mortalin facilitates PP1α-mediated MEK1/2 dephosphorylation by promoting PP1α-MEK1/2 interaction in an ATP-sensitive manner. The region spanning Val482 to Glu491 in the substrate-binding cavity and the substrate lid of mortalin were necessary for these physical interactions, which is consistent with conventional heat shock protein 70 (HSP70)-client interaction mechanisms. Nevertheless, mortalin depletion did not affect cellular PP1α levels or its regulatory phosphorylation, suggesting a nonconventional role for mortalin in promoting PP1α-MEK1/2 interaction. Of note, PP1α was upregulated in human melanoma and pancreatic cancer biopsy specimens in correlation with mortalin upregulation. PP1α may therefore have a role in tumorigenesis in concert with mortalin, which affects MEK/ERK activity in tumor cells.
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Ganjibakhsh M, Aminishakib P, Farzaneh P, Karimi A, Fazeli SAS, Rajabi M, Nasimian A, Naini FB, Rahmati H, Gohari NS, Mohebali N, Asadi M, Gorji ZE, Izadpanah M, Moghanjoghi SM, Ashouri S. Establishment and Characterization of Primary Cultures from Iranian Oral Squamous Cell Carcinoma Patients by Enzymatic Method and Explant Culture. JOURNAL OF DENTISTRY (TEHRAN, IRAN) 2017; 14:191-202. [PMID: 29285029 PMCID: PMC5745223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVES Oral Squamous Cell Carcinoma (OSCC) is the most frequent oral cancer worldwide. It is known as the eighth most common cancer in men and as the fifth most common cancer in women. Cytogenetic and biochemical studies in recent decades have emphasized the necessity of providing an appropriate tool for such researches. Cancer cell culture is a useful tool for investigations on biochemical, genetic, molecular and immunological characteristics of different cancers, including oral cancer. Here, we explain the establishment process of five primary oral cancer cells derived from an Iranian population. MATERIALS AND METHODS The specimens were obtained from five oral cancer patients. Enzymatic, explant culture and magnetic-activated cell sorting (MACS) methods were used for cell isolation. After quality control tests, characterization and authentication of primary oral cancer cells were performed by short tandem repeats (STR) profiling, chromosome analysis, species identification, and monitoring the growth, morphology and the expression of CD326 and CD133 markers. RESULTS Five primary oral cancer cells were established from an Iranian population. The flow cytometry results showed that the isolated cells were positive for CD326 and CD133 markers. Furthermore, the cells were free from mycoplasma, bacterial and fungal contamination. No misidentified or cross-contaminated cells were detected by STR analysis. CONCLUSIONS Human primary oral cancer cells provide an extremely useful platform for studying carcinogenesis pathways of oral cancer in Iranian population. They may be helpful in explaining the ethnic differences in cancer biology and the individuality in anticancer drug response in future studies.
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Affiliation(s)
- Meysam Ganjibakhsh
- PhD Student, Human and Animal Cell Bank, Iranian Biological Resource Center, ACECR, Tehran, Iran; Department of Anatomy, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Pouyan Aminishakib
- Assistant Professor, Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran; Department of Oral and Maxillofacial Pathology, School of Dentistry, Tehran University of Medical Sciences, Tehran, Iran
| | - Parvaneh Farzaneh
- Assistant Professor, Human and Animal Cell Bank, Iranian Biological Resource Center, ACECR, Tehran, Iran
| | - Abbas Karimi
- Assistant Professor, Craniomaxillofacial Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran; Department of Oral and Maxillofacial Surgery, School of Dentistry, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Abolhassan Shahzadeh Fazeli
- Associate Professor, Human and Animal Cell Bank, Iranian Biological Resource Center, ACECR, Tehran, Iran; Department of Molecular and Cellular Biology, School of Basic Science and Advanced Technologies in Biology, University of Sciences and Culture, Tehran, Iran
| | - Moones Rajabi
- Adjunct Assistant Professor, Department of Oral and Maxillofacial Pathology, School of Dentistry, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Nasimian
- PhD Student, Human and Animal Cell Bank, Iranian Biological Resource Center, ACECR, Tehran, Iran; Department of Clinical Biochemistry, School of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fereshteh Baghai Naini
- Associate Professor, Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran; Department of Oral and Maxillofacial Pathology, School of Dentistry, Tehran University of Medical Sciences, Tehran, Iran,Corresponding author: F. Baghaei Naini, Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran,
| | - Hedieh Rahmati
- Researcher, Human and Animal Cell Bank, Iranian Biological Resource Center, ACECR, Tehran, Iran
| | - Neda Sadat Gohari
- Researcher, Human and Animal Cell Bank, Iranian Biological Resource Center, ACECR, Tehran, Iran
| | - Nazanin Mohebali
- Researcher, Human and Animal Cell Bank, Iranian Biological Resource Center, ACECR, Tehran, Iran
| | - Masoumeh Asadi
- Researcher, Human and Animal Cell Bank, Iranian Biological Resource Center, ACECR, Tehran, Iran
| | - Zahra Elyasi Gorji
- Researcher, Human and Animal Cell Bank, Iranian Biological Resource Center, ACECR, Tehran, Iran
| | - Mehrnaz Izadpanah
- PhD Student, Department of Applied Cell Science and Tissue Engineering, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Sepideh Ashouri
- Researcher, Human and Animal Cell Bank, Iranian Biological Resource Center, ACECR, Tehran, Iran
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Sorenson EC, Khanin R, Bamboat ZM, Cavnar MJ, Kim TS, Sadot E, Zeng S, Greer JB, Seifert AM, Cohen NA, Crawley MH, Green BL, Klimstra DS, DeMatteo RP. Genome and transcriptome profiling of fibrolamellar hepatocellular carcinoma demonstrates p53 and IGF2BP1 dysregulation. PLoS One 2017; 12:e0176562. [PMID: 28486549 PMCID: PMC5423588 DOI: 10.1371/journal.pone.0176562] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 04/12/2017] [Indexed: 01/17/2023] Open
Abstract
Fibrolamellar hepatocellular carcinoma (FL-HCC) is a rare variant of HCC that most frequently affects young adults. Because of its rarity and an absence of preclinical models, our understanding of FL-HCC is limited. Our objective was to analyze chromosomal alterations and dysregulated gene expression in tumor specimens collected at a single center during two decades of experience with FL-HCC. We analyzed 38 specimens from 26 patients by array comparative genomic hybridiziation (aCGH) and 35 specimens from 15 patients by transcriptome sequencing (RNA-seq). All tumor specimens exhibited genomic instability, with a higher frequency of genomic amplifications or deletions in metastatic tumors. The regions encoding 71 microRNAs (miRs) were deleted in at least 25% of tumor specimens. Five of these recurrently deleted miRs targeted the insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) gene product, and a correlating 100-fold upregulation of IGF2BP1 mRNA was seen in tumor specimens. Transcriptome analysis demonstrated intrapatient tumor similarity, independent of recurrence site or time. The p53 tumor suppressor pathway was downregulated as demonstrated by both aCGH and RNA-seq analysis. Notch, EGFR, NRAS, and RB1 pathways were also significantly dysregulated in tumors compared with normal liver tissue. The findings illuminate the genomic and transcriptomic landscape of this rare disease and provide insight into dysregulated oncogenic pathways and potential therapeutic targets in FL-HCC.
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Affiliation(s)
- Eric C. Sorenson
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Raya Khanin
- Department of Computational Biology and Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Zubin M. Bamboat
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Michael J. Cavnar
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Teresa S. Kim
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Eran Sadot
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Shan Zeng
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Jonathan B. Greer
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Adrian M. Seifert
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Noah A. Cohen
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Megan H. Crawley
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Benjamin L. Green
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - David S. Klimstra
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Ronald P. DeMatteo
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- * E-mail:
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36
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McFadden DG, Politi K, Bhutkar A, Chen FK, Song X, Pirun M, Santiago PM, Kim-Kiselak C, Platt JT, Lee E, Hodges E, Rosebrock AP, Bronson RT, Socci ND, Hannon GJ, Jacks T, Varmus H. Mutational landscape of EGFR-, MYC-, and Kras-driven genetically engineered mouse models of lung adenocarcinoma. Proc Natl Acad Sci U S A 2016; 113:E6409-E6417. [PMID: 27702896 PMCID: PMC5081629 DOI: 10.1073/pnas.1613601113] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Genetically engineered mouse models (GEMMs) of cancer are increasingly being used to assess putative driver mutations identified by large-scale sequencing of human cancer genomes. To accurately interpret experiments that introduce additional mutations, an understanding of the somatic genetic profile and evolution of GEMM tumors is necessary. Here, we performed whole-exome sequencing of tumors from three GEMMs of lung adenocarcinoma driven by mutant epidermal growth factor receptor (EGFR), mutant Kirsten rat sarcoma viral oncogene homolog (Kras), or overexpression of MYC proto-oncogene. Tumors from EGFR- and Kras-driven models exhibited, respectively, 0.02 and 0.07 nonsynonymous mutations per megabase, a dramatically lower average mutational frequency than observed in human lung adenocarcinomas. Tumors from models driven by strong cancer drivers (mutant EGFR and Kras) harbored few mutations in known cancer genes, whereas tumors driven by MYC, a weaker initiating oncogene in the murine lung, acquired recurrent clonal oncogenic Kras mutations. In addition, although EGFR- and Kras-driven models both exhibited recurrent whole-chromosome DNA copy number alterations, the specific chromosomes altered by gain or loss were different in each model. These data demonstrate that GEMM tumors exhibit relatively simple somatic genotypes compared with human cancers of a similar type, making these autochthonous model systems useful for additive engineering approaches to assess the potential of novel mutations on tumorigenesis, cancer progression, and drug sensitivity.
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Affiliation(s)
- David G McFadden
- David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139;
| | - Katerina Politi
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510; Section of Medical Oncology, Department of Medicine, Yale University School of Medicine, New Haven, CT 06510; Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06510;
| | - Arjun Bhutkar
- David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Frances K Chen
- David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Xiaoling Song
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06510
| | - Mono Pirun
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Philip M Santiago
- David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Caroline Kim-Kiselak
- David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - James T Platt
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06510
| | - Emily Lee
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Emily Hodges
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Adam P Rosebrock
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Roderick T Bronson
- Department of Pathology, Tufts University School of Medicine and Veterinary Medicine, North Grafton, MA 01536
| | - Nicholas D Socci
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Gregory J Hannon
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142;
| | - Harold Varmus
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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37
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Xi J, Li A. Discovering Recurrent Copy Number Aberrations in Complex Patterns via Non-Negative Sparse Singular Value Decomposition. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016; 13:656-668. [PMID: 26372614 DOI: 10.1109/tcbb.2015.2474404] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Recurrent copy number aberrations (RCNAs) in multiple cancer samples are strongly associated with tumorigenesis, and RCNA discovery is helpful to cancer research and treatment. Despite the emergence of numerous RCNA discovering methods, most of them are unable to detect RCNAs in complex patterns that are influenced by complicating factors including aberration in partial samples, co-existing of gains and losses and normal-like tumor samples. Here, we propose a novel computational method, called non-negative sparse singular value decomposition (NN-SSVD), to address the RCNA discovering problem in complex patterns. In NN-SSVD, the measurement of RCNA is based on the aberration frequency in a part of samples rather than all samples, which can circumvent the complexity of different RCNA patterns. We evaluate NN-SSVD on synthetic dataset by comparison on detection scores and Receiver Operating Characteristics curves, and the results show that NN-SSVD outperforms existing methods in RCNA discovery and demonstrate more robustness to RCNA complicating factors. Applying our approach on a breast cancer dataset, we successfully identify a number of genomic regions that are strongly correlated with previous studies, which harbor a bunch of known breast cancer associated genes.
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38
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Pfarr N, Penzel R, Klauschen F, Heim D, Brandt R, Kazdal D, Jesinghaus M, Herpel E, Schirmacher P, Warth A, Weichert W, Endris V, Stenzinger A. Copy number changes of clinically actionable genes in melanoma, non-small cell lung cancer and colorectal cancer-A survey across 822 routine diagnostic cases. Genes Chromosomes Cancer 2016; 55:821-33. [PMID: 27218826 DOI: 10.1002/gcc.22378] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/19/2016] [Accepted: 05/19/2016] [Indexed: 12/29/2022] Open
Abstract
Targeted deep massive parallel sequencing has been implemented in routine molecular diagnostics for high-throughput genetic profiling of formalin-fixed paraffin-embedded (FFPE) cancer samples. This approach is widely used to interrogate simple somatic mutations but experience with the analysis of copy number variations (CNV) is limited. Here, we retrospectively analyzed CNV in 822 cancer cases (135 melanoma, 468 non-small cell lung cancers (NSCLC), 219 colorectal cancers (CRC)). We observed a decreasing frequency of CNV in clinically actionable genes from melanoma to NSCLC to CRC. The overall cohort displayed 168 (20%) amplifications in 17 druggable targets. The majority of BRAF mutant melanomas (54%) showed co-occurring CNV in other genes, mainly affecting CDKN2A. Subsets showed clustered deletions in ABL1, NOTCH1, RET or STK11, GNA11, and JAK3. Most NRAS mutant melanomas (49%) harbored CNVs in other genes with CDKN2A and FGFR3 being most frequently affected. Five BRAF/NRASwt tumors had co-amplifications of KDR, KIT, PDGFRA and another six mutated KIT. Among all NSCLC, we identified 14 EGFRamp (with ten EGFRmut) and eight KRASamp (with seven KRASmut). KRASmut tumors displayed frequent amplifications of MYC (n = 10) and MDM2 (n = 5). Fifteen KRAS/EGFR/BRAFwt tumors had MET mutations/amplifications. In CRC, amplified IGF2 was most prevalent (n = 13) followed by MYC (n = 9). Two cases showed amplified KRAS wildtype alleles. Two of the KRASmut cases harbored amplifications of NRAS and three KRASwt cases amplification of EGFR. In conclusion, we demonstrate that our approach i) facilitates detection of CNV, ii) enables detection of known CNV patterns, and iii) uncovers new CNV of clinically actionable genes in FFPE tissue samples across cancers. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Nicole Pfarr
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Institute of Pathology, Technical University Munich (TUM), Munich, Germany
| | - Roland Penzel
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Daniel Heim
- Institute of Pathology, Charité University Hospital, Berlin, Germany
| | - Regine Brandt
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Daniel Kazdal
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Moritz Jesinghaus
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Institute of Pathology, Technical University Munich (TUM), Munich, Germany
| | - Esther Herpel
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Arne Warth
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Lung Research (DZL), Heidelberg, Germany
| | - Wilko Weichert
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Institute of Pathology, Technical University Munich (TUM), Munich, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Volker Endris
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany. .,National Center for Tumor Diseases (NCT), Heidelberg, Germany.
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Kovatcheva M, Liu DD, Dickson MA, Klein ME, O'Connor R, Wilder FO, Socci ND, Tap WD, Schwartz GK, Singer S, Crago AM, Koff A. MDM2 turnover and expression of ATRX determine the choice between quiescence and senescence in response to CDK4 inhibition. Oncotarget 2016; 6:8226-43. [PMID: 25803170 PMCID: PMC4480747 DOI: 10.18632/oncotarget.3364] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 01/15/2015] [Indexed: 12/19/2022] Open
Abstract
CDK4 inhibitors (CDK4i) earned Breakthrough Therapy Designation from the FDA last year and are entering phase III clinical trials in several cancers. However, not all tumors respond favorably to these drugs. CDK4 activity is critical for progression through G1 phase and into the mitotic cell cycle. Inhibiting this kinase induces Rb-positive cells to exit the cell cycle into either a quiescent or senescent state. In this report, using well-differentiated and dedifferentiated liposarcoma (WD/DDLS) cell lines, we show that the proteolytic turnover of MDM2 is required for CDK4i-induced senescence. Failure to reduce MDM2 does not prevent CDK4i-induced withdrawal from the cell cycle but the cells remain in a reversible quiescent state. Reducing MDM2 in these cells drives them into the more stable senescent state. CDK4i-induced senescence associated with loss of MDM2 is also observed in some breast cancer, lung cancer and glioma cell lines indicating that this is not limited to WD/DDLS cells in which MDM2 is overexpressed or in cells that contain wild type p53. MDM2 turnover depends on its E3 ligase activity and expression of ATRX. Interestingly, in seven patients the changes in MDM2 expression were correlated with outcome. These insights identify MDM2 and ATRX as new regulators controlling geroconversion, the process by which quiescent cells become senescent, and this insight may be exploited to improve the activity of CDK4i in cancer therapy.
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Affiliation(s)
- Marta Kovatcheva
- The Louis V. Gerstner Graduate School of Biomedical Sciences, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, USA.,Program in Molecular Biology, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - David D Liu
- The Graduate Program in Biochemistry, Cellular and Molecular Biology, Weill College of Medicine, Cornell University, New York, USA.,Program in Molecular Biology, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Mark A Dickson
- Department of Medicine, Weill College of Medicine, Cornell University, New York, USA.,Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Mary E Klein
- The Louis V. Gerstner Graduate School of Biomedical Sciences, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, USA.,Program in Molecular Biology, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Rachael O'Connor
- Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Fatima O Wilder
- Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Nicholas D Socci
- Program in Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - William D Tap
- Department of Medicine, Weill College of Medicine, Cornell University, New York, USA.,Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Gary K Schwartz
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, USA.,Current address: Columbia University, New York, USA
| | - Samuel Singer
- Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Aimee M Crago
- Program in Molecular Biology, Memorial Sloan-Kettering Cancer Center, New York, USA.,Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Andrew Koff
- The Louis V. Gerstner Graduate School of Biomedical Sciences, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, USA.,The Graduate Program in Biochemistry, Cellular and Molecular Biology, Weill College of Medicine, Cornell University, New York, USA.,Program in Molecular Biology, Memorial Sloan-Kettering Cancer Center, New York, USA
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40
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Shivakumar BM, Chakrabarty S, Rotti H, Seenappa V, Rao L, Geetha V, Tantry BV, Kini H, Dharamsi R, Pai CG, Satyamoorthy K. Comparative analysis of copy number variations in ulcerative colitis associated and sporadic colorectal neoplasia. BMC Cancer 2016; 16:271. [PMID: 27080994 PMCID: PMC4831153 DOI: 10.1186/s12885-016-2303-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 04/07/2016] [Indexed: 12/12/2022] Open
Abstract
Background The incidence of and mortality from colorectal cancers (CRC) can be reduced by early detection. Currently there is a lack of established markers to detect early neoplastic changes. We aimed to identify the copy number variations (CNVs) and the associated genes which could be potential markers for the detection of neoplasia in both ulcerative colitis-associated neoplasia (UC-CRN) and sporadic colorectal neoplasia (S-CRN). Methods We employed array comparative genome hybridization (aCGH) to identify CNVs in tissue samples of UC nonprogressor, progressor and sporadic CRC. Select genes within these CNV regions as a panel of markers were validated using quantitative real time PCR (qRT-PCR) method along with the microsatellite instability (MSI) in an independent cohort of samples. Immunohistochemistry (IHC) analysis was also performed. Results Integrated analysis showed 10 overlapping CNV regions between UC-Progressor and S-CRN, with the 8q and 12p regions showing greater overlap. The qRT-PCR based panel of MYC, MYCN, CCND1, CCND2, EGFR and FNDC3A was successful in detecting neoplasia with an overall accuracy of 54 % in S-CRN compared to that of 29 % in UC neoplastic samples. IHC study showed that p53 and CCND1 were significantly overexpressed with an increasing frequency from pre-neoplastic to neoplastic stages. EGFR and AMACR were expressed only in the neoplastic conditions. Conclusion CNVs that are common and unique to both UC-associated and sporadic colorectal neoplasm could be the key players driving carcinogenesis. Comparative analysis of CNVs provides testable driver aberrations but needs further evaluation in larger cohorts of samples. These markers may help in developing more effective neoplasia-detection strategies during screening and surveillance programs. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2303-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- B M Shivakumar
- Department of Gastroenterology and Hepatology, Kasturba Medical College, Manipal University, Manipal, India.,School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India
| | | | - Harish Rotti
- School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India
| | - Venu Seenappa
- School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India
| | - Lakshmi Rao
- Department of Pathology, Kasturba Medical College, Manipal University, Manipal, India
| | - Vasudevan Geetha
- Department of Pathology, Kasturba Medical College, Manipal University, Manipal, India
| | - B V Tantry
- Department of Gastroenterology and Hepatology, Kasturba Medical College, Manipal University, Mangalore, India
| | - Hema Kini
- Department of Pathology, Kasturba Medical College, Manipal University, Mangalore, India
| | - Rajesh Dharamsi
- Dharamsi Hospital, Chandni Chowk, Sangli, Maharashtra, India
| | - C Ganesh Pai
- Department of Gastroenterology and Hepatology, Kasturba Medical College, Manipal University, Manipal, India
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41
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Harryman WL, Pond E, Singh P, Little AS, Eschbacher JM, Nagle RB, Cress AE. Laminin-binding integrin gene copy number alterations in distinct epithelial-type cancers. Am J Transl Res 2016; 8:940-954. [PMID: 27158381 PMCID: PMC4846938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 01/29/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND The laminin-binding integrin (LBI) family are cell adhesion molecules that are essential for invasion and metastasis of human epithelial cancers and cell adhesion mediated drug resistance. We investigated whether copy number alteration (CNA) or mutations of a five-gene signature (ITGB4, ITGA3, LAMB3, PLEC, and SYNE3), representing essential genes for LBI adhesion, would correlate with patient outcomes within human epithelial-type tumor data sets currently available in an open access format. METHODS We investigated the relative alteration frequency of an LBI signature panel (integrin β4 (ITGB4), integrin α3 (ITGA3), laminin β3 chain (LAMB3), plectin (PLEC), and nesprin 3 (SYNE3)), independent of the epithelial cancer type, within publically available and published data using cBioPortal and Oncomine software. We rank ordered the results using a 20% alteration frequency cut-off and limited the analysis to studies containing at least 100 samples. Kaplan-Meier survival curves were analyzed to determine if alterations in the LBI signature correlated with patient survival. The Oncomine data mining tool was used to compare the heat map expression of the LBI signature without SYNE3 (as this was not included in the Oncomine database) to drug resistance patterns. RESULTS Twelve different cancer types, representing 5,647 samples, contained at least a 20% alteration frequency of the five-gene LBI signature. The frequency of alteration ranged from 38.3% to 19.8%. Within the LBI signature, PLEC was the most commonly altered followed by LAMB3, ITGB4, ITGA3, and SYNE3 across all twelve cancer types. Within cancer types, there was little overlap of the individual amplified genes from each sample, suggesting different specific amplicons may alter the LBI adhesion structures. Of the twelve cancer types, overall survival was altered by CNA presence in bladder urothelial carcinoma (p=0.0143*) and cervical squamous cell carcinoma and endocervical adenocarcinoma (p=0.0432*). Querying the in vitro drug resistance profiles with the LBI signature demonstrated a positive correlation with cells resistant to inhibitors of HDAC (Vorinostat, Panobinostat) and topoisomerase II (Irinotecan). No correlation was found with the following agents: Bleomycin, Doxorubicin, Methotrexate, Gemcitabine, Docetaxel, Bortezomib, and Shikonen. CONCLUSIONS Our work has identified epithelial-types of human cancer that have significant CNA in our selected five-gene signature, which was based on the essential and genetically-defined functions of the protein product networks (in this case, the LBI axis). CNA of the gene signature not only predicted overall survival in bladder, cervical, and endocervical adenocarcinoma but also response to chemotherapy. This work suggests that future studies designed to optimize the gene signature are warranted. GENERAL SIGNIFICANCE The copy number alteration of structural components of the LBI axis in epithelial-type tumors may be promising biomarkers and rational targets for personalized therapy in preventing or arresting metastatic spread.
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Affiliation(s)
- William L Harryman
- The University of Arizona Cancer Center1515 N. Campbell Ave., Tucson, Arizona, United States
| | - Erika Pond
- The University of Arizona Cancer Center1515 N. Campbell Ave., Tucson, Arizona, United States
| | - Parminder Singh
- The University of Arizona Cancer Center1515 N. Campbell Ave., Tucson, Arizona, United States
| | - Andrew S Little
- Barrow Neurological Institute, St. Joseph’s Hospital and Medical Center350 W. Thomas Rd., Phoenix, Arizona, United States
| | - Jennifer M Eschbacher
- Department of Pathology, Barrow Neurological Institute, St. Joseph’s Hospital and Medical Center350 W. Thomas Rd., Phoenix, Arizona, United States
| | - Raymond B Nagle
- The University of Arizona Cancer Center1515 N. Campbell Ave., Tucson, Arizona, United States
| | - Anne E Cress
- The University of Arizona Cancer Center1515 N. Campbell Ave., Tucson, Arizona, United States
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42
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Garcia-Rendueles MER, Ricarte-Filho JC, Untch BR, Landa I, Knauf JA, Voza F, Smith VE, Ganly I, Taylor BS, Persaud Y, Oler G, Fang Y, Jhanwar SC, Viale A, Heguy A, Huberman KH, Giancotti F, Ghossein R, Fagin JA. NF2 Loss Promotes Oncogenic RAS-Induced Thyroid Cancers via YAP-Dependent Transactivation of RAS Proteins and Sensitizes Them to MEK Inhibition. Cancer Discov 2015; 5:1178-93. [PMID: 26359368 PMCID: PMC4642441 DOI: 10.1158/2159-8290.cd-15-0330] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 09/08/2015] [Indexed: 11/16/2022]
Abstract
UNLABELLED Ch22q LOH is preferentially associated with RAS mutations in papillary and in poorly differentiated thyroid cancer (PDTC). The 22q tumor suppressor NF2, encoding merlin, is implicated in this interaction because of its frequent loss of function in human thyroid cancer cell lines. Nf2 deletion or Hras mutation is insufficient for transformation, whereas their combined disruption leads to murine PDTC with increased MAPK signaling. Merlin loss induces RAS signaling in part through inactivation of Hippo, which activates a YAP-TEAD transcriptional program. We find that the three RAS genes are themselves YAP-TEAD1 transcriptional targets, providing a novel mechanism of promotion of RAS-induced tumorigenesis. Moreover, pharmacologic disruption of YAP-TEAD with verteporfin blocks RAS transcription and signaling and inhibits cell growth. The increased MAPK output generated by NF2 loss in RAS-mutant cancers may inform therapeutic strategies, as it generates greater dependency on the MAPK pathway for viability. SIGNIFICANCE Intensification of mutant RAS signaling through copy-number imbalances is commonly associated with transformation. We show that NF2/merlin inactivation augments mutant RAS signaling by promoting YAP/TEAD-driven transcription of oncogenic and wild-type RAS, resulting in greater MAPK output and increased sensitivity to MEK inhibitors.
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MESH Headings
- Animals
- Binding Sites
- Cell Cycle Proteins
- Cell Line, Tumor
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Chromosome Deletion
- Chromosomes, Human, Pair 22
- DNA Copy Number Variations
- Disease Models, Animal
- Drug Resistance, Neoplasm/genetics
- Gene Deletion
- Gene Expression Regulation, Neoplastic/drug effects
- Gene Order
- Gene Targeting
- Genes, ras
- Humans
- Mice
- Mice, Transgenic
- Mitogen-Activated Protein Kinases/antagonists & inhibitors
- Models, Biological
- Neoplasm Staging
- Neurofibromin 2/genetics
- Nuclear Proteins/metabolism
- Nucleotide Motifs
- Position-Specific Scoring Matrices
- Promoter Regions, Genetic
- Protein Binding
- Protein Kinase Inhibitors/pharmacology
- Signal Transduction/drug effects
- Thyroid Neoplasms/drug therapy
- Thyroid Neoplasms/genetics
- Thyroid Neoplasms/metabolism
- Thyroid Neoplasms/pathology
- Transcription Factors/metabolism
- Transcriptional Activation
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Affiliation(s)
| | - Julio C Ricarte-Filho
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Brian R Untch
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York. Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Iňigo Landa
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jeffrey A Knauf
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York. Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Francesca Voza
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vicki E Smith
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ian Ganly
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Barry S Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York. Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yogindra Persaud
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gisele Oler
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yuqiang Fang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Suresh C Jhanwar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Agnes Viale
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Adriana Heguy
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kety H Huberman
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Filippo Giancotti
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York. Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Ronald Ghossein
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James A Fagin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York. Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York. Department of Medicine, Weill Cornell Medical College, New York, New York.
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43
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Jin DH, Park SE, Lee J, Kim KM, Kim S, Kim DH, Park J. Copy Number Gains at 8q24 and 20q11-q13 in Gastric Cancer Are More Common in Intestinal-Type than Diffuse-Type. PLoS One 2015; 10:e0137657. [PMID: 26360582 PMCID: PMC4567330 DOI: 10.1371/journal.pone.0137657] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 08/19/2015] [Indexed: 12/21/2022] Open
Abstract
The present study was aimed at discovering DNA copy number alterations (CNAs) involved in the carcinogenesis of stomach and at understanding their clinicopathological significances in the Korean population. DNA copy numbers were analyzed using Agilent 244K or 400K array comparative genomic hybridization (aCGH) in fresh-frozen tumor and matched normal tissues from 40 gastric cancer patients. Some of the detected CNA regions were validated using multiplex ligation-dependent probe amplification (MLPA) in six of the 40 patients and customized Agilent 60K aCGH in an independent set of 48 gastric cancers. The mRNA levels of genes at common CNA regions were analyzed using quantitative real-time PCR. Copy number gains were more common than losses across the entire genome in tumor tissues compared to matched normal tissues. The mean number of alterations per case was 64 for gains and 40 for losses, and the median aberration length was 44016 bp for gains and 4732 bp for losses. Copy number gains were frequently detected at 7p22.1 (20%), 8q24.21 (27%-30%), 8q24.3 (22%-48%), 13q34 (20%-31%), and 20q11-q13 (25%-30%), and losses at 3p14.2 (43%), 4q35.2 (27%), 6q26 (23%), and 17p13.3 (20%-23%). CNAs at 7p22.1, 13q34, and 17p13.3 have not been reported in other populations. Most of the copy number losses were associated with down-regulation of mRNA levels, but the correlation between copy number gains and mRNA expression levels varied in a gene-dependent manner. In addition, copy number gains tended to occur more commonly in intestinal-type cancers than in diffuse-type cancers. In conclusion, the present study suggests that copy number gains at 8q24 and 20q11-q13 and losses at 3p14.2 may be common events in gastric cancer but CNAs at 7p22.1, 13q34, and 17p13.3 may be Korean-specific.
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Affiliation(s)
- Dong-Hao Jin
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 135–710, Korea
| | - Seong-Eun Park
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 135–710, Korea
| | - Jeeyun Lee
- Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 135–710, Korea
| | - Kyung-Mi Kim
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, 135–710, Seoul, Korea
| | - Sung Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 135–710, Korea
| | - Duk-Hwan Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 135–710, Korea
| | - Joobae Park
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 135–710, Korea
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44
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Arnedos M, Vicier C, Loi S, Lefebvre C, Michiels S, Bonnefoi H, Andre F. Precision medicine for metastatic breast cancer—limitations and solutions. Nat Rev Clin Oncol 2015. [DOI: 10.1038/nrclinonc.2015.123] [Citation(s) in RCA: 223] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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45
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Cross-species DNA copy number analyses identifies multiple 1q21-q23 subtype-specific driver genes for breast cancer. Breast Cancer Res Treat 2015; 152:347-56. [PMID: 26109346 PMCID: PMC4491106 DOI: 10.1007/s10549-015-3476-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 06/15/2015] [Indexed: 11/17/2022]
Abstract
A large number of DNA copy number alterations (CNAs) exist in human breast cancers, and thus characterizing the most frequent CNAs is key to advancing therapeutics because it is likely that these regions contain breast tumor ‘drivers’ (i.e., cancer causal genes). This study aims to characterize the genomic landscape of breast cancer CNAs and identify potential subtype-specific drivers using a large set of human breast tumors and genetically engineered mouse (GEM) mammary tumors. Using a novel method called SWITCHplus, we identified subtype-specific DNA CNAs occurring at a 15 % or greater frequency, which excluded many well-known breast cancer-related drivers such as amplification of ERBB2, and deletions of TP53 and RB1. A comparison of CNAs between mouse and human breast tumors identified regions with shared subtype-specific CNAs. Additional criteria that included gene expression-to-copy number correlation, a DawnRank network analysis, and RNA interference functional studies highlighted candidate driver genes that fulfilled these multiple criteria. Numerous regions of shared CNAs were observed between human breast tumors and GEM mammary tumor models that shared similar gene expression features. Specifically, we identified chromosome 1q21-23 as a Basal-like subtype-enriched region with multiple potential driver genes including PI4KB, SHC1, and NCSTN. This step-wise computational approach based on a cross-species comparison is applicable to any tumor type for which sufficient human and model system DNA copy number data exist, and in this instance, highlights that a single region of amplification may in fact harbor multiple driver genes.
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46
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Newman S. Interactive analysis of large cancer copy number studies with Copy Number Explorer. Bioinformatics 2015; 31:2874-6. [PMID: 25957352 PMCID: PMC4547619 DOI: 10.1093/bioinformatics/btv298] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/05/2015] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED Copy number abnormalities (CNAs) such as somatically-acquired chromosomal deletions and duplications drive the development of cancer. As individual tumor genomes can contain tens or even hundreds of large and/or focal CNAs, a major difficulty is differentiating between important, recurrent pathogenic changes and benign changes unrelated to the subject's phenotype. Here we present Copy Number Explorer, an interactive tool for mining large copy number datasets. Copy Number Explorer facilitates rapid visual and statistical identification of recurrent regions of gain or loss, identifies the genes most likely to drive CNA formation using the cghMCR method and identifies recurrently broken genes that may be disrupted or fused. The software also allows users to identify recurrent CNA regions that may be associated with differential survival. AVAILABILITY AND IMPLEMENTATION Copy Number Explorer is available under the GNU public license (GPL-3). Source code is available at: https://sourceforge.net/projects/copynumberexplorer/ CONTACT scott.newman@emory.edu.
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Affiliation(s)
- Scott Newman
- Biostatistics & Bioinformatics Shared Resource, Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
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47
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Dixon-McIver A. Emerging technologies in paediatric leukaemia. Transl Pediatr 2015; 4:116-24. [PMID: 26835367 PMCID: PMC4729090 DOI: 10.3978/j.issn.2224-4336.2015.03.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Genetic changes, in particular chromosomal aberrations, are a hallmark of acute lymphoblastic lymphoma (ALL) and accurate detection of them is important in ensuring assignment to the appropriate drug protocol. Our ability to detect these genetic changes has been somewhat limited in the past due to the necessity to analyse mitotically active cells by conventional G-banded metaphase analysis and by mutational analysis of individual genes. Advances in technology include high resolution, microarray-based techniques that permit examination of the whole genome. Here we will review the current available methodology and discuss how the technology is being integrated into the diagnostic setting.
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48
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Cooperative loss of RAS feedback regulation drives myeloid leukemogenesis. Nat Genet 2015; 47:539-43. [PMID: 25822087 PMCID: PMC4414804 DOI: 10.1038/ng.3251] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/24/2015] [Indexed: 01/15/2023]
Abstract
RAS network activation is common in human cancers and, in acute myeloid leukemia (AML), achieved mainly through gain-of-function mutations in KRAS, NRAS, or the FLT3 receptor tyrosine kinase1. In mice, we show that premalignant myeloid cells harboring a KrasG12D allele retain low Ras signaling owing to a negative feedback involving Spry4 that prevents transformation. In humans, SPRY4 is located on chromosome 5q, a region affected by large heterozygous deletion that are associated with an aggressive disease in which gain-of-function RAS pathway mutations are rare. These 5q deletions often co-occur with chromosome 17 alterations involving deletion of NF1 - another RAS negative regulator - and TP53. Accordingly, combined suppression of Spry4, Nf1 and Trp53 produces high Ras signaling and drives AML in mice. Therefore, SPRY4 is a 5q tumor suppressor whose disruption contributes to a lethal AML subtype that appears to acquire RAS pathway activation through loss of negative regulators.
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49
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Cohen H, Ben-Hamo R, Gidoni M, Yitzhaki I, Kozol R, Zilberberg A, Efroni S. Shift in GATA3 functions, and GATA3 mutations, control progression and clinical presentation in breast cancer. Breast Cancer Res 2014; 16:464. [PMID: 25410484 PMCID: PMC4303202 DOI: 10.1186/s13058-014-0464-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 10/14/2014] [Indexed: 02/03/2023] Open
Abstract
Introduction GATA binding protein 3 (GATA3) is a regulator of mammary luminal cell differentiation, and an estrogen receptor (ER) associated marker in breast cancer. Tumor suppressor functions of GATA3 have been demonstrated primarily in basal-like breast cancers. Here, we focused on its function in luminal breast cancer, where GATA3 is frequently mutated, and its levels are significantly elevated. Methods GATA3 target genes were identified in normal- and luminal cancer- mammary cells by ChIP-seq, followed by examination of the effects of GATA3 expressions and mutations on tumorigenesis-associated genes and processes. Additionally, mutations and expression data of luminal breast cancer patients from The Cancer Genome Atlas were analyzed to characterize genetic signatures associated with GATA3 mutations. Results We show that some GATA3 effects shift from tumor suppressing to tumor promoting during tumorigenesis, with deregulation of three genes, BCL2, DACH1, THSD4, representing major GATA3-controlled processes in cancer progression. In addition, we identify an altered activity of mutant GATA3, and distinct associated genetic signatures. These signatures depend on the functional domain mutated; and, for a specific subgroup, are shared with basal-like breast cancer patients, who are a clinical group with regard to considerations of mode of treatment. Conclusions The GATA3 dependent mechanisms may call for special considerations for proper prognosis and treatment of patients. Electronic supplementary material The online version of this article (doi:10.1186/s13058-014-0464-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Helit Cohen
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan, 52900, Israel.
| | - Rotem Ben-Hamo
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan, 52900, Israel.
| | - Moriah Gidoni
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan, 52900, Israel.
| | - Ilana Yitzhaki
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan, 52900, Israel.
| | - Renana Kozol
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan, 52900, Israel.
| | - Alona Zilberberg
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan, 52900, Israel.
| | - Sol Efroni
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan, 52900, Israel.
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50
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McCole RB, Fonseka CY, Koren A, Wu CT. Abnormal dosage of ultraconserved elements is highly disfavored in healthy cells but not cancer cells. PLoS Genet 2014; 10:e1004646. [PMID: 25340765 PMCID: PMC4207606 DOI: 10.1371/journal.pgen.1004646] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 08/04/2014] [Indexed: 12/17/2022] Open
Abstract
Ultraconserved elements (UCEs) are strongly depleted from segmental duplications and copy number variations (CNVs) in the human genome, suggesting that deletion or duplication of a UCE can be deleterious to the mammalian cell. Here we address the process by which CNVs become depleted of UCEs. We begin by showing that depletion for UCEs characterizes the most recent large-scale human CNV datasets and then find that even newly formed de novo CNVs, which have passed through meiosis at most once, are significantly depleted for UCEs. In striking contrast, CNVs arising specifically in cancer cells are, as a rule, not depleted for UCEs and can even become significantly enriched. This observation raises the possibility that CNVs that arise somatically and are relatively newly formed are less likely to have established a CNV profile that is depleted for UCEs. Alternatively, lack of depletion for UCEs from cancer CNVs may reflect the diseased state. In support of this latter explanation, somatic CNVs that are not associated with disease are depleted for UCEs. Finally, we show that it is possible to observe the CNVs of induced pluripotent stem (iPS) cells become depleted of UCEs over time, suggesting that depletion may be established through selection against UCE-disrupting CNVs without the requirement for meiotic divisions.
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Affiliation(s)
- Ruth B. McCole
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Chamith Y. Fonseka
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Biological and Biomedical Sciences PhD program, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Amnon Koren
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - C.-ting Wu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
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