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Pehkonen H, Filippou A, Väänänen J, Lindfors I, Vänttinen M, Ianevski P, Mäkelä A, Munne P, Klefström J, Toppila‐Salmi S, Grénman R, Hagström J, Mäkitie AA, Karhemo P, Monni O. Liprin-α1 contributes to oncogenic MAPK signaling by counteracting ERK activity. Mol Oncol 2024; 18:662-676. [PMID: 38264964 PMCID: PMC10920090 DOI: 10.1002/1878-0261.13593] [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: 07/05/2023] [Revised: 12/15/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024] Open
Abstract
PTPRF interacting protein alpha 1 (PPFIA1) encodes for liprin-α1, a member of the leukocyte common antigen-related protein tyrosine phosphatase (LAR-RPTPs)-interacting protein family. Liprin-α1 localizes to adhesive and invasive structures in the periphery of cancer cells, where it modulates migration and invasion in head and neck squamous cell carcinoma (HNSCC) and breast cancer. To study the possible role of liprin-α1 in anticancer drug responses, we screened a library of oncology compounds in cell lines with high endogenous PPFIA1 expression. The compounds with the highest differential responses between high PPFIA1-expressing and silenced cells across cell lines were inhibitors targeting mitogen-activated protein kinase kinase (MEK)/extracellular signal-regulated kinases (ERK) signaling. KRAS proto-oncogene, GTPase (KRAS)-mutated MDA-MB-231 cells were more resistant to trametinib upon PPFIA1 knockdown compared with control cells. In contrast, liprin-α1-depleted HNSCC cells with low RAS activity showed a context-dependent response to MEK/ERK inhibitors. Importantly, we showed that liprin-α1 depletion leads to increased p-ERK1/2 levels in all our studied cell lines independent of KRAS mutational status, suggesting a role of liprin-α1 in the regulation of MAPK oncogenic signaling. Furthermore, liprin-α1 depletion led to more pronounced redistribution of RAS proteins to the cell membrane. Our data suggest that liprin-α1 is an important contributor to oncogenic RAS/MAPK signaling, and the status of liprin-α1 may assist in predicting drug responses in cancer cells in a context-dependent manner.
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Affiliation(s)
- Henna Pehkonen
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiFinland
| | - Artemis Filippou
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiFinland
| | - Juho Väänänen
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiFinland
| | - Iida Lindfors
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiFinland
| | - Mira Vänttinen
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiFinland
| | - Philipp Ianevski
- Institute for Molecular Medicine Finland (FIMM)University of HelsinkiFinland
| | - Anne Mäkelä
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiFinland
| | - Pauliina Munne
- Finnish Cancer Institute, FICAN South Helsinki University Hospital & Translational Cancer Medicine, Medical FacultyUniversity of HelsinkiFinland
| | - Juha Klefström
- Finnish Cancer Institute, FICAN South Helsinki University Hospital & Translational Cancer Medicine, Medical FacultyUniversity of HelsinkiFinland
- iCAN Digital Precision Cancer Medicine FlagshipHelsinkiFinland
| | - Sanna Toppila‐Salmi
- Skin and Allergy HospitalHelsinki University Hospital and University of HelsinkiFinland
- Department of Otorhinolaryngology, Kuopio University Hospital and School of Medicine, Institute of Clinical MedicineUniversity of Eastern FinlandKuopioFinland
| | - Reidar Grénman
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of Turku and Turku University HospitalFinland
| | - Jaana Hagström
- Department of PathologyUniversity of Helsinki and Helsinki University HospitalFinland
- Institute of DentistryUniversity of TurkuFinland
| | - Antti A. Mäkitie
- iCAN Digital Precision Cancer Medicine FlagshipHelsinkiFinland
- Department of Otorhinolaryngology‐Head and Neck Surgery, Research Program in Systems OncologyUniversity of Helsinki and Helsinki University HospitalFinland
| | - Piia‐Riitta Karhemo
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiFinland
- iCAN Digital Precision Cancer Medicine FlagshipHelsinkiFinland
| | - Outi Monni
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiFinland
- iCAN Digital Precision Cancer Medicine FlagshipHelsinkiFinland
- Department of Oncology, Faculty of MedicineUniversity of HelsinkiFinland
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2
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Kucukhuseyin O, Yanar K, Hakan MT, Verim A, Suoglu Y, Atukeren P, Aydin S, Cakatay U, Yılmaz Aydogan H, Yaylim I. Evaluation of advanced protein oxidation and RAGE gene variants in the risk of laryngeal cancer. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2072236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Ozlem Kucukhuseyin
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Karolin Yanar
- Department of Medical Biochemistry, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Mehmet Tolgahan Hakan
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Aysegul Verim
- Department of Otorhinolaryngology/Head and Neck Surgery, Haydarpasa Numune Education and Research Hospital, Istanbul, Turkey
| | - Yusufhan Suoglu
- Department of Otorhinolaryngology, Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Pinar Atukeren
- Department of Medical Biochemistry, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Seval Aydin
- Department of Medical Biochemistry, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Ufuk Cakatay
- Department of Medical Biochemistry, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Hulya Yılmaz Aydogan
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Ilhan Yaylim
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
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3
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Liprins in oncogenic signaling and cancer cell adhesion. Oncogene 2021; 40:6406-6416. [PMID: 34654889 PMCID: PMC8602034 DOI: 10.1038/s41388-021-02048-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/21/2021] [Accepted: 09/28/2021] [Indexed: 12/30/2022]
Abstract
Liprins are a multifunctional family of scaffold proteins, identified by their involvement in several important neuronal functions related to signaling and organization of synaptic structures. More recently, the knowledge on the liprin family has expanded from neuronal functions to processes relevant to cancer progression, including cell adhesion, cell motility, cancer cell invasion, and signaling. These proteins consist of regions, which by prediction are intrinsically disordered, and may be involved in the assembly of supramolecular structures relevant for their functions. This review summarizes the current understanding of the functions of liprins in different cellular processes, with special emphasis on liprins in tumor progression. The available data indicate that liprins may be potential biomarkers for cancer progression and may have therapeutic importance.
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Ustaszewski A, Kostrzewska-Poczekaj M, Janiszewska J, Jarmuz-Szymczak M, Wierzbicka M, Marszal J, Grénman R, Giefing M. Assessing Various Control Samples for Microarray Gene Expression Profiling of Laryngeal Squamous Cell Carcinoma. Biomolecules 2021; 11:biom11040588. [PMID: 33923685 PMCID: PMC8072880 DOI: 10.3390/biom11040588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 01/11/2023] Open
Abstract
Selection of optimal control samples is crucial in expression profiling tumor samples. To address this issue, we performed microarray expression profiling of control samples routinely used in head and neck squamous cell carcinoma studies: human bronchial and tracheal epithelial cells, squamous cells obtained by laser uvulopalatoplasty and tumor surgical margins. We compared the results using multidimensional scaling and hierarchical clustering versus tumor samples and laryngeal squamous cell carcinoma cell lines. A general observation from our study is that the analyzed cohorts separated according to two dominant factors: “malignancy”, which separated controls from malignant samples and “cell culture-microenvironment” which reflected the differences between cultured and non-cultured samples. In conclusion, we advocate the use of cultured epithelial cells as controls for gene expression profiling of cancer cell lines. In contrast, comparisons of gene expression profiles of cancer cell lines versus surgical margin controls should be treated with caution, whereas fresh frozen surgical margins seem to be appropriate for gene expression profiling of tumor samples.
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Affiliation(s)
- Adam Ustaszewski
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznań, Poland; (A.U.); (M.K.-P.); (J.J.); (M.J.-S.); (M.W.)
| | - Magdalena Kostrzewska-Poczekaj
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznań, Poland; (A.U.); (M.K.-P.); (J.J.); (M.J.-S.); (M.W.)
| | - Joanna Janiszewska
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznań, Poland; (A.U.); (M.K.-P.); (J.J.); (M.J.-S.); (M.W.)
| | - Malgorzata Jarmuz-Szymczak
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznań, Poland; (A.U.); (M.K.-P.); (J.J.); (M.J.-S.); (M.W.)
- Department of Oncology, Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, 61-001 Poznań, Poland
| | - Malgorzata Wierzbicka
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznań, Poland; (A.U.); (M.K.-P.); (J.J.); (M.J.-S.); (M.W.)
- Department of Otolaryngology and Laryngological Oncology, Poznań University of Medical Sciences, 60-355 Poznań, Poland;
| | - Joanna Marszal
- Department of Otolaryngology and Laryngological Oncology, Poznań University of Medical Sciences, 60-355 Poznań, Poland;
| | - Reidar Grénman
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Turku and Turku University Hospital, 20520 Turku, Finland;
| | - Maciej Giefing
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznań, Poland; (A.U.); (M.K.-P.); (J.J.); (M.J.-S.); (M.W.)
- Correspondence: ; Tel.: +48-61-6579-138
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Raudenská M, Balvan J, Masařík M. Cell death in head and neck cancer pathogenesis and treatment. Cell Death Dis 2021; 12:192. [PMID: 33602906 PMCID: PMC7893032 DOI: 10.1038/s41419-021-03474-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 12/13/2022]
Abstract
Many cancer therapies aim to trigger apoptosis in cancer cells. Nevertheless, the presence of oncogenic alterations in these cells and distorted composition of tumour microenvironment largely limit the clinical efficacy of this type of therapy. Luckily, scientific consensus describes about 10 different cell death subroutines with different regulatory pathways and cancer cells are probably not able to avoid all of cell death types at once. Therefore, a focused and individualised therapy is needed to address the specific advantages and disadvantages of individual tumours. Although much is known about apoptosis, therapeutic opportunities of other cell death pathways are often neglected. Molecular heterogeneity of head and neck squamous cell carcinomas (HNSCC) causing unpredictability of the clinical response represents a grave challenge for oncologists and seems to be a critical component of treatment response. The large proportion of this clinical heterogeneity probably lies in alterations of cell death pathways. How exactly cells die is very important because the predominant type of cell death can have multiple impacts on the therapeutic response as cell death itself acts as a second messenger. In this review, we discuss the different types of programmed cell death (PCD), their connection with HNSCC pathogenesis and possible therapeutic windows that result from specific sensitivity to some form of PCD in some clinically relevant subgroups of HNSCC.
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Affiliation(s)
- Martina Raudenská
- Department of Physiology, Faculty of Medicine, Masaryk University / Kamenice 5, CZ-625 00, Brno, Czech Republic.,Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic
| | - Jan Balvan
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University / Kamenice 5, CZ-625 00, Brno, Czech Republic
| | - Michal Masařík
- Department of Physiology, Faculty of Medicine, Masaryk University / Kamenice 5, CZ-625 00, Brno, Czech Republic. .,Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic. .,Department of Pathological Physiology, Faculty of Medicine, Masaryk University / Kamenice 5, CZ-625 00, Brno, Czech Republic. .,BIOCEV, First Faculty of Medicine, Charles University, Prumyslova 595, CZ-252 50, Vestec, Czech Republic.
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6
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Tandon V, de la Vega L, Banerjee S. Emerging roles of DYRK2 in cancer. J Biol Chem 2021; 296:100233. [PMID: 33376136 PMCID: PMC7948649 DOI: 10.1074/jbc.rev120.015217] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 12/14/2022] Open
Abstract
Over the last decade, the CMGC kinase DYRK2 has been reported as a tumor suppressor across various cancers triggering major antitumor and proapoptotic signals in breast, colon, liver, ovary, brain, and lung cancers, with lower DYRK2 expression correlated with poorer prognosis in patients. Contrary to this, various medicinal chemistry studies reported robust antiproliferative properties of DYRK2 inhibitors, whereas unbiased 'omics' and genome-wide association study-based studies identified DYRK2 as a highly overexpressed kinase in various patient tumor samples. A major paradigm shift occurred in the last 4 years when DYRK2 was found to regulate proteostasis in cancer via a two-pronged mechanism. DYRK2 phosphorylated and activated the 26S proteasome to enhance degradation of misfolded/tumor-suppressor proteins while also promoting the nuclear stability and transcriptional activity of its substrate, heat-shock factor 1 triggering protein folding. Together, DYRK2 regulates proteostasis and promotes protumorigenic survival for specific cancers. Indeed, potent and selective small-molecule inhibitors of DYRK2 exhibit in vitro and in vivo anti-tumor activity in triple-negative breast cancer and myeloma models. However, with conflicting and contradictory reports across different cancers, the overarching role of DYRK2 remains enigmatic. Specific cancer (sub)types coupled to spatiotemporal interactions with substrates could decide the procancer or anticancer role of DYRK2. The current review aims to provide a balanced and critical appreciation of the literature to date, highlighting top substrates such as p53, c-Myc, c-Jun, heat-shock factor 1, proteasome, or NOTCH1, to discuss DYRK2 inhibitors available to the scientific community and to shed light on this duality of protumorigenic and antitumorigenic roles of DYRK2.
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Affiliation(s)
- Vasudha Tandon
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Laureano de la Vega
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Sourav Banerjee
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee, United Kingdom.
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Dwivedi R, Pandey R, Chandra S, Mehrotra D. Apoptosis and genes involved in oral cancer - a comprehensive review. Oncol Rev 2020; 14:472. [PMID: 32685111 PMCID: PMC7365992 DOI: 10.4081/oncol.2020.472] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 03/20/2020] [Indexed: 12/24/2022] Open
Abstract
Oral cancers needs relentless research due to high mortality and morbidity associated with it. Despite of the comparable ease in accessibility to these sites, more than 2/3rd cases are diagnosed in advanced stages. Molecular/genetic studies augment clinical assessment, classification and prediction of malignant potential of oral lesions, thereby reducing its incidence and increasing the scope for early diagnosis and treatment of oral cancers. Herein we aim to review the role of apoptosis and genes associated with it in oral cancer development in order to aid in early diagnosis, prediction of malignant potential and evaluation of possible treatment targets in oral cancer. An internet-based search was done with key words apoptosis, genes, mutations, targets and analysis to extract 72 articles after considering inclusion and exclusion criteria. The knowledge of genetics and genomics of oral cancer is of utmost need in order to stop the rising prevalence of oral cancer. Translational approach and interventions at the early stage of oral cancer, targeted destruction of cancerous cells by silencing or promoting involved genes should be the ideal intervention.
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Affiliation(s)
- Ruby Dwivedi
- DHR-MRU & Department of Oral and Maxillofacial Surgery, Faculty of Dental Sciences, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Rahul Pandey
- DHR-MRU & Department of Oral and Maxillofacial Surgery, Faculty of Dental Sciences, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Shaleen Chandra
- DHR-MRU & Department of Oral and Maxillofacial Surgery, Faculty of Dental Sciences, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Divya Mehrotra
- DHR-MRU & Department of Oral and Maxillofacial Surgery, Faculty of Dental Sciences, King George's Medical University, Lucknow, Uttar Pradesh, India
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8
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Li D, Wang X, Lu S, Wang P, Wang X, Yin W, Zhu W, Li S. Integrated analysis revealing genome-wide chromosomal copy number variation in supraglottic laryngeal squamous cell carcinoma. Oncol Lett 2020; 20:1201-1212. [PMID: 32724360 PMCID: PMC7377034 DOI: 10.3892/ol.2020.11653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/27/2020] [Indexed: 01/22/2023] Open
Abstract
Laryngeal squamous cell carcinoma (LSCC) is a genetically complex tumor type and one of the leading causes of cancer-associated disability and mortality. Genetic instability, such as chromosomal instability, is associated with the tumorigenesis of LSCC. Copy number variations (CNVs) have been demonstrated to contribute to the genetic diversity of tumor pathogenesis. Comparative genomic hybridization (CGH) has emerged as a high-throughput genomic technology that facilitates the aggregation of high-resolution data of cancer-associated genomic imbalances. In the present study, a total of 38 primary supraglottic LSCC cases were analyzed by high-resolution array-based CGH (aCGH) to improve the understanding of the genetic alterations in LSCC. Additionally, integration with bioinformatic analysis of microarray expression profiling data from the Gene Expression Omnibus (GEO) database provided a fundamental method for the identification of putative target genes. Genomic CNVs were detected in all cases. The size of net genomic imbalances per case ranged between a loss of 682.3 Mb (~24% of the genome) and a gain of 1,958.6 Mb (~69% of the genome). Recurrent gains included 2pter-q22.1, 3q26.1-qter, 5pter-p12, 7p22.3p14.1, 8p12p11.22, 8q24.13q24.3, 11q13.2q13.4, 12pter-p12.2, 18pter-p11.31 and 20p13p12.1, whereas recurrent losses included 3pter-p21.32, 4q28.1-q35.2, 5q13.2-qter, 9pter-p21.3 and monosomy 13. Gains of 3q26.1-qter were associated with tumor stage, poor differentiation and smoking history. Additionally, through integration with bioinformatic analysis of data from the GEO database, putative target oncogenes, including sex-determining region Y-box 2, eukaryotic translation initiation factor 4 gamma 1, fragile X-related gene 1, disheveled segment polarity protein 3, defective n cullin neddylation 1 domain containing 1, insulin like growth factor 2 mRNA binding protein 2 and CCDC26 long non-coding RNA, and tumor suppressor genes, such as CUB and sushi multiple domains 1, cyclin dependent kinase inhibitor 2A, protocadherin 20, serine peptidase inhibitor Kazal type 5 and Nei like DNA glycosylase 3, were identified in supraglottic LSCC. Supraglottic LSCC is a genetically complex tumor type and aCGH was demonstrated to be effective in the determination of molecular profiles with higher resolution. The present results enable the identification of putative target oncogenes and tumor suppressor gene mapping in supraglottic LSCC.
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Affiliation(s)
- Dongjie Li
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Xianfu Wang
- Department of Pediatrics, Genetics Laboratory, University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA
| | - Shunfei Lu
- Department of Clinical Medicine, Lishui College of Medicine, Lishui, Zhejiang 323000, P.R. China
| | - Ping Wang
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Xin Wang
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Wanzhong Yin
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Wei Zhu
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Shibo Li
- Department of Pediatrics, Genetics Laboratory, University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA
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Ribeiro IP, Caramelo F, Ribeiro M, Machado A, Miguéis J, Marques F, Carreira IM, Melo JB. Upper aerodigestive tract carcinoma: Development of a (epi)genomic predictive model for recurrence and metastasis. Oncol Lett 2020; 19:3459-3468. [PMID: 32269619 PMCID: PMC7115117 DOI: 10.3892/ol.2020.11459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 12/31/2019] [Indexed: 12/02/2022] Open
Abstract
Despite the increased molecular knowledge and the diagnostic and therapeutic improvements, the survival of patients with upper aerodigestive tract carcinoma remains poor. The identification of early diagnostic and prognostic biomarkers and the development of molecular models to distinguish patients that will recur and/or develop metastasis after treatment as well as to benefit with target therapies can be important to decrease mortality, improve survival rates and improve the quality of life of these patients. The current study analyzed 21 upper aerodigestive tract carcinomas through array comparative genomic hybridization and methylation-specific multiplex ligation-dependent probe amplification techniques. A number of chromosomal regions and genes were observed with copy number alterations and methylation. A predictive (epi)genomic model that comprises the 3p chromosomal region and WT1, VHL and THBS1 genes was built, highlighting a molecular signature with possible clinical use. The current study may aid in the development of a more individualized patient management and targeted drug design. The power of this genomic and epigenetic model to predict the recurrence and metastasis development should be evaluated and validated in future larger cohort study.
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Affiliation(s)
- Ilda Patrícia Ribeiro
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal.,iCBR-CIMAGO-Coimbra Institute for Clinical and Biomedical Research/Center of Investigation on Environment Genetics and Oncobiology-Faculty of Medicine, University of Coimbra, 3001-301 Coimbra, Portugal
| | - Francisco Caramelo
- iCBR-CIMAGO-Coimbra Institute for Clinical and Biomedical Research/Center of Investigation on Environment Genetics and Oncobiology-Faculty of Medicine, University of Coimbra, 3001-301 Coimbra, Portugal.,Laboratory of Biostatistics and Medical Informatics, IBILI-Institute for Biomedical Imaging and Life Sciences, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Margarida Ribeiro
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Ana Machado
- Department of Otorhinolaryngology-Head and Neck Surgery, Coimbra Hospital and University Centre, CHUC-Coimbra Hospital and University Centre, EPE, 3000-075 Coimbra, Portugal
| | - Jorge Miguéis
- Department of Otorhinolaryngology-Head and Neck Surgery, Coimbra Hospital and University Centre, CHUC-Coimbra Hospital and University Centre, EPE, 3000-075 Coimbra, Portugal
| | - Francisco Marques
- iCBR-CIMAGO-Coimbra Institute for Clinical and Biomedical Research/Center of Investigation on Environment Genetics and Oncobiology-Faculty of Medicine, University of Coimbra, 3001-301 Coimbra, Portugal.,Department of Dentistry, Faculty of Medicine, University of Coimbra, 3000-075 Coimbra, Portugal.,Stomatology Unit, Coimbra Hospital and University Centre, CHUC-Coimbra Hospital and University Centre, EPE, 3000-075 Coimbra, Portugal
| | - Isabel Marques Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal.,iCBR-CIMAGO-Coimbra Institute for Clinical and Biomedical Research/Center of Investigation on Environment Genetics and Oncobiology-Faculty of Medicine, University of Coimbra, 3001-301 Coimbra, Portugal
| | - Joana Barbosa Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal.,iCBR-CIMAGO-Coimbra Institute for Clinical and Biomedical Research/Center of Investigation on Environment Genetics and Oncobiology-Faculty of Medicine, University of Coimbra, 3001-301 Coimbra, Portugal
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Yalcin E, Kara G, Celik E, Pinarli FA, Saylam G, Sucularli C, Ozturk S, Yilmaz E, Bayir O, Korkmaz MH, Denkbas EB. Preparation and characterization of novel albumin-sericin nanoparticles as siRNA delivery vehicle for laryngeal cancer treatment. Prep Biochem Biotechnol 2019; 49:659-670. [DOI: 10.1080/10826068.2019.1599395] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Eda Yalcin
- Nanoscience and Nanomedicine Division, Hacettepe University, Ankara, Turkey
| | - Goknur Kara
- Department of Chemistry, Biochemistry Division, Hacettepe University, Ankara, Turkey
| | - Ekin Celik
- Bioengineering Division, Hacettepe University, Ankara, Turkey
| | - Ferda Alpaslan Pinarli
- Department of Stem Cell and Genetic Diagnostic Center, Diskapi Yildirim Beyazit Training and Research Hospital, Ankara, Turkey
| | - Guleser Saylam
- Department of Otolaryngology, Head and Neck Surgery, Diskapi Yildirim Beyazit Training and Research Hospital, Ankara, Turkey
| | - Ceren Sucularli
- Department of Bioinformatics, Institute of Health Sciences, Hacettepe University, Ankara, Turkey
| | - Serhat Ozturk
- Department of Chemistry, Biochemistry Division, Hacettepe University, Ankara, Turkey
| | - Esin Yilmaz
- Advanced Technologies Application& Research Center, Hacettepe University, Ankara, Turkey
| | - Omer Bayir
- Department of Otolaryngology, Head and Neck Surgery, Diskapi Yildirim Beyazit Training and Research Hospital, Ankara, Turkey
| | - Mehmet Hakan Korkmaz
- Department of Otolaryngology, Head and Neck Surgery, Yildirim Beyazit University Medical School, Ankara, Turkey
| | - Emir Baki Denkbas
- Department of Chemistry, Biochemistry Division, Hacettepe University, Ankara, Turkey
- Faculty of Engineering, Department of Biomedical Engineering, Başkent University, Ankara, Turkey
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11
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Wintergerst L, Selmansberger M, Maihoefer C, Schüttrumpf L, Walch A, Wilke C, Pitea A, Woischke C, Baumeister P, Kirchner T, Belka C, Ganswindt U, Zitzelsberger H, Unger K, Hess J. A prognostic mRNA expression signature of four 16q24.3 genes in radio(chemo)therapy-treated head and neck squamous cell carcinoma (HNSCC). Mol Oncol 2018; 12:2085-2101. [PMID: 30259648 PMCID: PMC6275282 DOI: 10.1002/1878-0261.12388] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 08/13/2018] [Accepted: 09/12/2018] [Indexed: 01/28/2023] Open
Abstract
Previously, we have shown that copy number gain of the chromosomal band 16q24.3 is associated with impaired clinical outcome of radiotherapy‐treated head and neck squamous cell carcinoma (HNSCC) patients. We set out to identify a prognostic mRNA signature from genes located on 16q24.3 in radio(chemo)therapy‐treated HNSCC patients of the TCGA (The Cancer Genome Atlas, n = 99) cohort. We applied stepwise forward selection using expression data of 41 16q24.3 genes. The resulting optimal Cox‐proportional hazards regression model included the genes APRT, CENPBD1, CHMP1A, and GALNS. Afterward, the prognostic value of the classifier was confirmed in an independent cohort of HNSCC patients treated by adjuvant radio(chemo)therapy (LMU‐KKG cohort). The signature significantly differentiated high‐ and low‐risk patients with regard to overall survival (HR = 2.01, 95% CI 1.10–3.70; P = 0.02125), recurrence‐free survival (HR = 1.84, 95% CI 1.01–3.34; P = 0.04206), and locoregional recurrence‐free survival (HR = 1.87, 95% CI 1.03–3.40; P = 0.03641). The functional impact of the four signature genes was investigated after reconstruction of a gene association network from transcriptome data of the TCGA HNSCC cohort using a partial correlation approach. Subsequent pathway enrichment analysis of the network neighborhood (first and second) of the signature genes suggests involvement of HNSCC‐associated signaling pathways such as apoptosis, cell cycle, cell adhesion, EGFR, JAK‐STAT, and mTOR. Furthermore, a detailed analysis of the first neighborhood revealed a cluster of co‐expressed genes located on chromosome 16q, substantiating the impact of 16q24.3 alterations in poor clinical outcome of HNSCC. The reported gene expression signature represents a prognostic marker in HNSCC patients following postoperative radio(chemo)therapy.
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Affiliation(s)
- Ludmila Wintergerst
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer', Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Martin Selmansberger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Cornelius Maihoefer
- Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer', Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Germany
| | - Lars Schüttrumpf
- Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer', Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Germany
| | - Axel Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Christina Wilke
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Adriana Pitea
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | | | - Philipp Baumeister
- Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer', Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital, LMU Munich, Germany
| | - Thomas Kirchner
- Institute of Pathology, Faculty of Medicine, LMU Munich, Germany
| | - Claus Belka
- Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer', Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany
| | - Ute Ganswindt
- Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer', Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Germany.,Department of Therapeutic Radiology and Oncology, Innsbruck Medical University, Austria
| | - Horst Zitzelsberger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer', Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Germany
| | - Kristian Unger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer', Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Germany
| | - Julia Hess
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy in Head and Neck Cancer', Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Germany
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12
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Liprin-α1 modulates cancer cell signaling by transmembrane protein CD82 in adhesive membrane domains linked to cytoskeleton. Cell Commun Signal 2018; 16:41. [PMID: 30005669 PMCID: PMC6045882 DOI: 10.1186/s12964-018-0253-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 07/10/2018] [Indexed: 12/26/2022] Open
Abstract
Background PPFIA1 is located at the 11q13 region commonly amplified in cancer. The protein liprin-α1 encoded by PPF1A1 contributes to the adhesive and invasive structures of cytoskeletal elements and is located at the invadosomes in cancer cells. However, the precise mechanism of liprin-α1 function in cancer progression has remained elusive. Methods Invasion regulating activity of liprin-α1 was examined by analyzing the functions of squamous cell carcinoma of head and neck (HNSCC) cell lines in three-dimensional collagen I after RNAi mediated gene knockdown. Transcriptome profiling and Gene Set Enrichment Analysis from HNSCC and breast cancer cells were used to identify expression changes relevant to specific cellular localizations, biological processes and signaling pathways after PPFIA1 knockdown. The significance of the results was assessed by relevant statistical methods (Wald and Benjamini-Hochberg). Localization of proteins associated to liprin-α1 was studied by immunofluorescence in 2D and 3D conditions. The association of PPFIA1 amplification to HNSCC patient survival was explored using The Cancer Genome Atlas data. Results In this study, we show that liprin-α1 regulates biological processes related to membrane microdomains in breast carcinoma, as well as protein trafficking, cell-cell and cell-substrate contacts in HNSCC cell lines cultured in three-dimensional matrix. Importantly, we show that in all these cancer cells liprin-α1 knockdown leads to the upregulation of transmembrane protein CD82, which is a suppressor of metastasis in several solid tumors. Conclusions Our results provide novel information regarding the function of liprin-α1 in biological processes essential in cancer progression. The results reveal liprin-α1 as a novel regulator of CD82, linking liprin-α1 to the cancer cell invasion and metastasis pathways. Electronic supplementary material The online version of this article (10.1186/s12964-018-0253-y) contains supplementary material, which is available to authorized users.
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13
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Lepikhova T, Karhemo PR, Louhimo R, Yadav B, Murumägi A, Kulesskiy E, Kivento M, Sihto H, Grénman R, Syrjänen SM, Kallioniemi O, Aittokallio T, Wennerberg K, Joensuu H, Monni O. Drug-Sensitivity Screening and Genomic Characterization of 45 HPV-Negative Head and Neck Carcinoma Cell Lines for Novel Biomarkers of Drug Efficacy. Mol Cancer Ther 2018; 17:2060-2071. [DOI: 10.1158/1535-7163.mct-17-0733] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 12/15/2017] [Accepted: 06/21/2018] [Indexed: 11/16/2022]
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14
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Byzia E, Soloch N, Bodnar M, Szaumkessel M, Kiwerska K, Kostrzewska-Poczekaj M, Jarmuz-Szymczak M, Szylberg L, Wierzbicka M, Bartochowska A, Kalinowicz E, Grenman R, Szyfter K, Marszalek A, Giefing M. Recurrent transcriptional loss of the PCDH17 tumor suppressor in laryngeal squamous cell carcinoma is partially mediated by aberrant promoter DNA methylation. Mol Carcinog 2018; 57:878-885. [PMID: 29566279 DOI: 10.1002/mc.22808] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/06/2018] [Accepted: 03/20/2018] [Indexed: 12/18/2022]
Abstract
Protocadherins are cell-cell adhesion molecules encoded by a large family of genes. Recent reports demonstrate recurrent silencing of protocadherin genes in tumors and provide strong arguments for their tumor supresor functionality. Loss of protocadherins may contribute to cancer development not only by altering cell-cell adhesion, that is a hallmark of cancer, but also by enhancing proliferation and epithelial mesenchymal transition of cells via deregulation of the WNT signaling pathway. In this study we have further corroborated our previous findings on the involvement of PCDH17 in laryngeal squamous cell carcinoma (LSCC). We used bisulfite pyrosequencing to analyze a cohort of primary LSCC tumors for alterations in PCDH17 promoter DNA methylation as an alternative gene inactivation mechanism to the homozygous deletions reported earlier. Moreover, we analyzed primary LSCC samples by immunohistochemistry for PCDH17 protein loss. We identified recurrent elevation of PCDH17 promoter DNA methylation in 32/81 (40%) primary tumors (P < 0.001) and therein hypermethylation of 12 (15%) cases in contrast to no tumor controls (n = 24) that were all unmethylated. Importantly, DNA demethylation by decitabine has restored low level PCDH17 expression in LSCC cell lines. In conclusion, we provide a mechanistic explanation of recurrently observed PCDH17 silencing in LSCC by demonstrating the role of promoter methylation in this process. In light of these findings and recent reports showing that PCDH17 methylation is detectable in serum of cancer patients we suggest that testing PCDH17 DNA methylation might serve as a potential biomarker in LSCC.
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Affiliation(s)
- Ewa Byzia
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Natalia Soloch
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Magdalena Bodnar
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland.,Department of Otolaryngology and Laryngological Oncology, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Katarzyna Kiwerska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland.,Department of Tumor Pathology, Greater Poland Cancer Center, Poznan, Poland
| | | | - Malgorzata Jarmuz-Szymczak
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland.,Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Lukasz Szylberg
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Malgorzata Wierzbicka
- Department of Otolaryngology and Laryngological Oncology, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Bartochowska
- Department of Otolaryngology and Laryngological Oncology, Poznan University of Medical Sciences, Poznan, Poland
| | - Ewelina Kalinowicz
- Department of Otolaryngology and Laryngological Oncology, Poznan University of Medical Sciences, Poznan, Poland
| | - Reidar Grenman
- Department of Otorhinolaryngology, -Head and Neck Surgery, Turku University Central Hospital and Turku University, Turku, Finland.,Department of Medical Biochemistry, Turku University Central Hospital and Turku University, Turku, Finland
| | - Krzysztof Szyfter
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Andrzej Marszalek
- Department of Tumor Pathology and Prophylaxis, Poznan University of Medical Sciences and Greater Poland Cancer Center, Poznan, Poland
| | - Maciej Giefing
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland.,Department of Otolaryngology and Laryngological Oncology, Poznan University of Medical Sciences, Poznan, Poland
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15
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Tokar T, Pastrello C, Ramnarine VR, Zhu CQ, Craddock KJ, Pikor LA, Vucic EA, Vary S, Shepherd FA, Tsao MS, Lam WL, Jurisica I. Differentially expressed microRNAs in lung adenocarcinoma invert effects of copy number aberrations of prognostic genes. Oncotarget 2018; 9:9137-9155. [PMID: 29507679 PMCID: PMC5823624 DOI: 10.18632/oncotarget.24070] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 01/02/2018] [Indexed: 12/30/2022] Open
Abstract
In many cancers, significantly down- or upregulated genes are found within chromosomal regions with DNA copy number alteration opposite to the expression changes. Generally, this paradox has been overlooked as noise, but can potentially be a consequence of interference of epigenetic regulatory mechanisms, including microRNA-mediated control of mRNA levels. To explore potential associations between microRNAs and paradoxes in non-small-cell lung cancer (NSCLC) we curated and analyzed lung adenocarcinoma (LUAD) data, comprising gene expressions, copy number aberrations (CNAs) and microRNA expressions. We integrated data from 1,062 tumor samples and 241 normal lung samples, including newly-generated array comparative genomic hybridization (aCGH) data from 63 LUAD samples. We identified 85 “paradoxical” genes whose differential expression consistently contrasted with aberrations of their copy numbers. Paradoxical status of 70 out of 85 genes was validated on sample-wise basis using The Cancer Genome Atlas (TCGA) LUAD data. Of these, 41 genes are prognostic and form a clinically relevant signature, which we validated on three independent datasets. By meta-analysis of results from 9 LUAD microRNA expression studies we identified 24 consistently-deregulated microRNAs. Using TCGA-LUAD data we showed that deregulation of 19 of these microRNAs explains differential expression of the paradoxical genes. Our results show that deregulation of paradoxical genes is crucial in LUAD and their expression pattern is maintained epigenetically, defying gene copy number status.
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Affiliation(s)
- Tomas Tokar
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Chiara Pastrello
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Varune R Ramnarine
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,The Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, Canada
| | - Chang-Qi Zhu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Kenneth J Craddock
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Larrisa A Pikor
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
| | - Emily A Vucic
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
| | - Simon Vary
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,Mathematical Institute, University of Oxford, Oxford, United Kingdom.,Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava, Slovakia
| | - Frances A Shepherd
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Wan L Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
| | - Igor Jurisica
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Department of Computer Science, University of Toronto, Toronto, Canada.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
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16
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Combined deletion and DNA methylation result in silencing of FAM107A gene in laryngeal tumors. Sci Rep 2017; 7:5386. [PMID: 28710449 PMCID: PMC5511162 DOI: 10.1038/s41598-017-05857-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 06/05/2017] [Indexed: 12/13/2022] Open
Abstract
Larynx squamous cell carcinoma (LSCC) is characterized by complex genotypes, with numerous abnormalities in various genes. Despite the progress in diagnosis and treatment of this disease, 5-year survival rates remain unsatisfactory. Therefore, the extended studies are conducted, with the aim to find genes, potentially implicated in this cancer. In this study, we focus on the FAM107A (3p14.3) gene, since we found its significantly reduced expression in LSCC by microarray profiling (Affymetrix U133 Plus 2.0 array). By RT-PCR we have confirmed complete FAM107A downregulation in laryngeal cancer cell lines (15/15) and primary tumors (21/21) and this finding was further supported by FAM107A protein immunohistochemistry (15/15). We further demonstrate that a combined two hit mechanism including loss of 3p and hypermethylation of FAM107A promoter region (in 9/15 cell lines (p < 0.0001) and in 15/21 primary tumors (p < 0.0001)) prevails in the gene transcriptional loss. As a proof of principle, we show that Decitabine - a hypomethylating agent – restores FAM107A expression (5 to 6 fold increase) in the UT-SCC-29 cell line, characterized by high DNA methylation. Therefore, we report the recurrent inactivation of FAM107A in LSCC, what may suggest that the gene is a promising tumor suppressor candidate involved in LSCC development.
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17
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Szaumkessel M, Wojciechowska S, Janiszewska J, Zemke N, Byzia E, Kiwerska K, Kostrzewska-Poczekaj M, Ustaszewski A, Jarmuz-Szymczak M, Grenman R, Wierzbicka M, Bartochowska A, Szyfter K, Giefing M. Recurrent epigenetic silencing of the PTPRD tumor suppressor in laryngeal squamous cell carcinoma. Tumour Biol 2017; 39:1010428317691427. [DOI: 10.1177/1010428317691427] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cellular processes like differentiation, mitotic cycle, and cell growth are regulated by tyrosine kinases with known oncogenic potential and tyrosine phosphatases that downmodulate the first. Therefore, tyrosine phosphatases are recurrent targets of gene alterations in human carcinomas. We and others suggested recently a tumor suppressor function of the PTPRD tyrosine phosphatase and reported homozygous deletions of the PTPRD locus in laryngeal squamous cell carcinoma. In this study, we investigated other gene-inactivating mechanisms potentially targeting PTPRD, including loss-of-function mutations and also epigenetic alterations like promoter DNA hypermethylation. We sequenced the PTPRD gene in eight laryngeal squamous cell carcinoma cell lines but did not identify any inactivating mutations. In contrast, by bisulfite pyrosequencing of the gene promoter region, we identified significantly higher levels of methylation (p = 0.001 and p = 0.0002, respectively) in 9/14 (64%) laryngeal squamous cell carcinoma cell lines and 37/79 (47%) of primary laryngeal squamous cell carcinoma tumors as compared to normal epithelium of the upper aerodigestive tract. There was also a strong correlation (p = 0.0001) between methylation and transcriptional silencing for the PTPRD gene observed in a cohort of 497 head and neck tumors from The Cancer Genome Atlas dataset suggesting that DNA methylation is the main mechanism of PTPRD silencing in these tumors. In summary, our data provide further evidence of the high incidence of PTPRD inactivation in laryngeal squamous cell carcinoma. We suggest that deletions and loss-of-function mutations are responsible for PTPRD loss only in a fraction of cases, whereas DNA methylation is the dominating mechanism of PTPRD inactivation.
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Affiliation(s)
| | | | | | - Natalia Zemke
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Ewa Byzia
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | | | - Adam Ustaszewski
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | - Reidar Grenman
- Department of Otorhinolaryngology—Head and Neck Surgery, Turku University Hospital and University of Turku, Turku, Finland
- Department of Medical Biochemistry and Genetics, University of Turku, Turku, Finland
| | - Malgorzata Wierzbicka
- Department of Otolaryngology and Laryngological Oncology, K. Marcinkowski University of Medical Sciences, Poznan, Poland
| | - Anna Bartochowska
- Department of Otolaryngology and Laryngological Oncology, K. Marcinkowski University of Medical Sciences, Poznan, Poland
| | - Krzysztof Szyfter
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
- Department of Phoniatrics and Audiology, K. Marcinkowski University of Medical Sciences, Poznan, Poland
| | - Maciej Giefing
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
- Department of Otolaryngology and Laryngological Oncology, K. Marcinkowski University of Medical Sciences, Poznan, Poland
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18
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Okuda T, Taki T, Nishida K, Chinen Y, Nagoshi H, Sakakura C, Taniwaki M. Molecular heterogeneity in the novel fusion gene APIP-FGFR2: Diversity of genomic breakpoints in gastric cancer with high-level amplifications at 11p13 and 10q26. Oncol Lett 2016; 13:215-221. [PMID: 28123544 PMCID: PMC5244987 DOI: 10.3892/ol.2016.5386] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 09/28/2016] [Indexed: 01/14/2023] Open
Abstract
Several novel fusion transcripts were identified by next-generation sequencing in gastric cancer; however, the breakpoint junctions have yet to be characterized. The present study characterized a plethora of APIP-FGFR2 genomic breakpoints in the SNU-16 gastric cancer cell line, which harbored homogeneously staining regions (hsrs) and double minute chromosomes. Oligonucleotide microarrays revealed high-level amplifications at chromosomes 8q24.1 (0.8 Mb region), 10q26 (1.1 Mb) and 11p13 (1.1 Mb). These amplicons contained MYC and PVT1 at chromosome 8q24.1, BRWD2, FGFR2 and ATE1 at chromosome 10q26, and 24 genes, including APIP, CD44, RAG1 and RAG2, at chromosome 11p13. Based on these findings, reverse transcription-polymerase chain reaction (PCR) was performed using various candidate gene primers to detect possible fusion transcripts, and several products using primer sets for the APIP and FGFR2 genes were detected. Eventually, three in-frame and two out-of-frame fusion transcripts were detected. Notably, PCR analysis of the entire genomic DNA detected three distinct genomic junctions. The breakpoints were within intron 5 of APIP, which contained three distinct breakpoints, and introns 5, 7 and 9 of FGFR2. Fluorescence in situ hybridization showed several fusion signals within hsrs using two short probes (~10-kb segments of a bacterial artificial chromosome clone) containing exons 2–5 of APIP or exons 11–13 of FGFR2. Although, for any given fusion, a multiplicity of transcripts is thought to be created by alternative splicing of one rearranged allele, the results of the present study suggested that genomic fusions of APIP and FGFR2 are generated in hsrs with a diversity of breakpoints that are then faithfully transcribed.
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Affiliation(s)
- Takashi Okuda
- Department of Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602-8566, Japan; Department of Hematology and Oncology, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602-8566, Japan
| | - Tomohiko Taki
- Department of Molecular Diagnostics and Therapeutics, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602-8566, Japan
| | - Kazuhiro Nishida
- Department of Hematology and Oncology, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602-8566, Japan
| | - Yoshiaki Chinen
- Department of Hematology and Oncology, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602-8566, Japan
| | - Hisao Nagoshi
- Department of Hematology and Oncology, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602-8566, Japan
| | - Chouhei Sakakura
- Department of Digestive Surgery, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602-8566, Japan
| | - Masafumi Taniwaki
- Department of Hematology and Oncology, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602-8566, Japan
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19
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Callegari CC, Cavalli IJ, Lima RS, Jucoski TS, Torresan C, Urban CA, Kuroda F, Anselmi KF, Cavalli LR, Ribeiro EM. Copy number and expression analysis of FOSL1, GSTP1, NTSR1, FADD and CCND1 genes in primary breast tumors with axillary lymph node metastasis. Cancer Genet 2016; 209:331-9. [DOI: 10.1016/j.cancergen.2016.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 05/02/2016] [Accepted: 06/06/2016] [Indexed: 12/20/2022]
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20
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Liu F, Du J, Liu J, Wen B. Identification of key target genes and pathways in laryngeal carcinoma. Oncol Lett 2016; 12:1279-1286. [PMID: 27446427 PMCID: PMC4950495 DOI: 10.3892/ol.2016.4750] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 04/08/2016] [Indexed: 02/05/2023] Open
Abstract
The purpose of the present study was to screen the key genes associated with laryngeal carcinoma and to investigate the molecular mechanism of laryngeal carcinoma progression. The gene expression profile of GSE10935 [Gene Expression Omnibus (GEO) accession number], including 12 specimens from laryngeal papillomas and 12 specimens from normal laryngeal epithelia controls, was downloaded from the GEO database. Differentially expressed genes (DEGs) were screened in laryngeal papillomas compared with normal controls using Limma package in R language, followed by Gene Ontology (GO) enrichment analysis and pathway enrichment analysis. Furthermore, the protein-protein interaction (PPI) network of DEGs was constructed using Cytoscape software and modules were analyzed using MCODE plugin from the PPI network. Furthermore, significant biological pathway regions (sub-pathway) were identified by using iSubpathwayMiner analysis. A total of 67 DEGs were identified, including 27 up-regulated genes and 40 down-regulated genes and they were involved in different GO terms and pathways. PPI network analysis revealed that Ras association (RalGDS/AF-6) domain family member 1 (RASSF1) was a hub protein. The sub-pathway analysis identified 9 significantly enriched sub-pathways, including glycolysis/gluconeogenesis and nitrogen metabolism. Genes such as phosphoglycerate kinase 1 (PGK1), carbonic anhydrase II (CA2), and carbonic anhydrase XII (CA12) whose node degrees were >10 were identified in the disease risk sub-pathway. Genes in the sub-pathway, such as RASSF1, PGK1, CA2 and CA12 were presumed to serve critical roles in laryngeal carcinoma. The present study identified DEGs and their sub-pathways in the disease, which may serve as potential targets for treatment of laryngeal carcinoma.
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Affiliation(s)
- Feng Liu
- Department of Otorhinolaryngology, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Jintao Du
- Department of Otorhinolaryngology, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Jun Liu
- Department of Otorhinolaryngology, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Bei Wen
- Department of Otorhinolaryngology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, P.R. China
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21
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Liprin-α1 is a regulator of vimentin intermediate filament network in the cancer cell adhesion machinery. Sci Rep 2016; 6:24486. [PMID: 27075696 PMCID: PMC4830931 DOI: 10.1038/srep24486] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/30/2016] [Indexed: 12/13/2022] Open
Abstract
PPFIA1 is located at the 11q13 region, which is one of the most commonly amplified regions in several epithelial cancers including head and neck squamous cell carcinoma and breast carcinoma. Considering the location of PPFIA1 in this amplicon, we examined whether protein encoded by PPFIA1, liprin-α1, possesses oncogenic properties in relevant carcinoma cell lines. Our results indicate that liprin-α1 localizes to different adhesion and cytoskeletal structures to regulate vimentin intermediate filament network, thereby altering the invasion and growth properties of the cancer cells. In non-invasive cells liprin-α1 promotes expansive growth behavior with limited invasive capacity, whereas in invasive cells liprin-α1 has significant impact on mesenchymal cancer cell invasion in three-dimensional collagen. Current results identify liprin-α1 as a novel regulator of the tumor cell intermediate filaments with differential oncogenic properties in actively proliferating or motile cells.
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22
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Bodnar M, Luczak M, Bednarek K, Szylberg L, Marszalek A, Grenman R, Szyfter K, Jarmuz-Szymczak M, Giefing M. Proteomic profiling identifies the inorganic pyrophosphatase (PPA1) protein as a potential biomarker of metastasis in laryngeal squamous cell carcinoma. Amino Acids 2016; 48:1469-76. [PMID: 26948660 PMCID: PMC4875942 DOI: 10.1007/s00726-016-2201-8] [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: 09/18/2015] [Accepted: 02/12/2016] [Indexed: 01/29/2023]
Abstract
Relapse and metastasis are the main causes of unfavorable outcome in head and neck cancers. Whereas, understanding of the molecular background of these processes is far from being complete. Therefore, in this study we aimed to identify potential biomarker candidates of relapse and metastasis in laryngeal squamous cell carcinoma (LSCC) by combining the 2D electrophoresis based protein screen and immunohistochemical analysis of candidate proteins. We screened three groups of LSCC cell lines derived from primary tumors, recurrent tumors and metastases and identified seven proteins that differed significantly in relative abundance between the analyzed groups. Among the identified proteins were the heat shock proteins HSP60 and HSP70 that were significantly downregulated both in recurrences- and metastases-derived cell lines but not in primary tumor-derived cell lines. Moreover, we identified significant upregulation of the annexin V, calreticulin and the inorganic pyrophosphatase (PPA1) exclusively in the metastases-derived cell lines. As these upregulated proteins could potentially become novel biomarkers of metastasis, we have compared their abundance in primary tumor LSCC N(0) cases, primary tumor LSCC N(+) cases as well as in LSCC metastases N(+). Our results show an intense increase of cytoplasmic PPA1 abundance in the N(+) (p = 0.000042) compared to the N(0) group. In summary, we show a group of proteins deregulated in recurrences and metastases of LSCC. Moreover, we suggest the PPA1 protein as a potential new biomarker for metastasis in this cancer.
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Affiliation(s)
- Magdalena Bodnar
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Magdalena Luczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Institute of Chemical Technology and Engineering, Poznan University of Technology, Poznan, Poland
| | - Kinga Bednarek
- Department of Cancer Genetics, Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Lukasz Szylberg
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Andrzej Marszalek
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland.,Chair of Oncologic Pathology and Epidemiology, Poznan University of Medical Sciences and Greater Poland Cancer Center, Poznan, Poland
| | - Reidar Grenman
- Department of Otorhinolaryngology, Head and Neck Surgery, Turku University Hospital and University of Turku, Turku, Finland.,Department of Medical Biochemistry, Turku University Hospital and University of Turku, Turku, Finland
| | - Krzysztof Szyfter
- Department of Cancer Genetics, Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland.,Department of Audiology and Phoniatrics, Poznan University of Medical Sciences, Poznan, Poland
| | - Malgorzata Jarmuz-Szymczak
- Department of Cancer Genetics, Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland.,Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Maciej Giefing
- Department of Cancer Genetics, Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland. .,Department of Otolaryngology and Laryngeal Oncology, Poznan University of Medical Sciences, Poznan, Poland.
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23
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Janiszewska J, Szaumkessel M, Kostrzewska-Poczekaj M, Bednarek K, Paczkowska J, Jackowska J, Grenman R, Szyfter K, Wierzbicka M, Giefing M, Jarmuz-Szymczak M. Global miRNA Expression Profiling Identifies miR-1290 as Novel Potential oncomiR in Laryngeal Carcinoma. PLoS One 2015; 10:e0144924. [PMID: 26694163 PMCID: PMC4692263 DOI: 10.1371/journal.pone.0144924] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 10/21/2015] [Indexed: 12/30/2022] Open
Abstract
Background Laryngeal squamous cell carcinoma (LSCC) is the most common group among head and neck cancers. LSCC is characterized by a high incidence in Europe. With the aim of better understanding its genetic background we performed global miRNA expression profiling of LSCC cell lines and primary specimens. By this approach we identified a cohort of 33 upregulated and 9 downregulated miRNA genes in LSCC as compared to epithelial no tumor controls. Results Within this group we identified overexpression of the novel miR-1290 gene not reported in the context of LSCC before. Using a combined bioinformatical approach in connection with functional analysis we delineated two putative target genes of miR-1290 namely ITPR2 and MAF which are significantly downregulated in LSCC. They are interesting candidates for tumor suppressor genes as they are implicated in apoptosis and other processes deregulated in cancer. Conclusion Taken together, we propose miR-1290 as the new oncomiR involved in LSCC pathogenesis. Additionally, we suggest that the oncogenic potential of miR-1290 might be expressed by the involvement in downregulation of its target genes MAF and ITPR2.
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Affiliation(s)
- Joanna Janiszewska
- Institute of Human Genetics, Polish Academy of Sciences, Department of Cancer Genetics, Poznan, Poland
- * E-mail:
| | - Marcin Szaumkessel
- Institute of Human Genetics, Polish Academy of Sciences, Department of Cancer Genetics, Poznan, Poland
| | | | - Kinga Bednarek
- Institute of Human Genetics, Polish Academy of Sciences, Department of Cancer Genetics, Poznan, Poland
| | - Julia Paczkowska
- Institute of Human Genetics, Polish Academy of Sciences, Department of Cancer Genetics, Poznan, Poland
| | - Joanna Jackowska
- Department of Otolaryngology and Laryngological Oncology, University of Medical Sciences, Poznan, Poland
| | - Reidar Grenman
- Department of Otorhinolaryngology, Head and Neck Surgery and Department of Medical Biochemistry, Turku University Hospital and University of Turku, Turku, Finland
| | - Krzysztof Szyfter
- Institute of Human Genetics, Polish Academy of Sciences, Department of Cancer Genetics, Poznan, Poland
- Department of Audiology and Phoniatry, University of Medical Sciences, Poznan, Poland
| | - Malgorzata Wierzbicka
- Department of Otolaryngology and Laryngological Oncology, University of Medical Sciences, Poznan, Poland
| | - Maciej Giefing
- Institute of Human Genetics, Polish Academy of Sciences, Department of Cancer Genetics, Poznan, Poland
- Department of Otolaryngology and Laryngological Oncology, University of Medical Sciences, Poznan, Poland
| | - Malgorzata Jarmuz-Szymczak
- Institute of Human Genetics, Polish Academy of Sciences, Department of Cancer Genetics, Poznan, Poland
- Department of Hematology, K. Marcinkowski University of Medical Sciences, Poznan, Poland
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24
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Xiong Y, Wu S, Du Q, Wang A, Wang Z. Integrated analysis of gene expression and genomic aberration data in osteosarcoma (OS). Cancer Gene Ther 2015; 22:524-9. [PMID: 26427513 DOI: 10.1038/cgt.2015.48] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 08/28/2015] [Accepted: 08/30/2015] [Indexed: 12/15/2022]
Abstract
Cytogenetic analyses have revealed that complex karyotypes with numerous and highly variable genomic aberrations including single-nucleotide polymorphisms (SNPs) and copy number variants (CNVs), are observed in most of the conventional osteosarcomas (OSs). Several genome-wide studies have reported that the dysregulated expression of many genes is correlated with genomic aberrations in OS. We first compared OS gene expression in Gene Expression Omnibus (GEO) data sets and genomic aberrations in International Cancer Genome Consortium (ICGC) database to identify differentially expressed genes (DEGs) associated with SNPs or CNVs in OS. Then the function annotation of SNP- or CNV-associated DEGs was performed in terms of gene ontology analysis, pathway analysis and protein-protein interactions (PPIs). Finally, the expression of genes correlated with both SNPs and CNVs were confirmed by quantitative reverse-transcription PCR. Eight publicly available GEO data sets were obtained, and a set of 979 DEGs were identified (472 upregulated and 507 downregulated DEGs). Moreover, we obtained 1039 SNPs mapped in 938 genes, and 583 CNV sites mapped in 2915 genes. Comparing genomic aberrations and DGEs, we found 41 SNP-associated DEGs and 124 CNV-associated DEGs, in which 7 DGEs were associated with both SNPs and CNVs, including WWP1, EXT1, LDHB, C8orf59, PLEKHA5, CCT3 and VWF. The result of function annotation showed that ossification, bone development and skeletal system development were the significantly enriched terms of biological processes for DEGs. PPI network analysis showed that CCT3, COPS3 and WWP1 were the significant hub proteins. We conclude that these genes, including CCT3, COPS3 and WWP1 are candidate driver genes of importance in OS tumorigenesis.
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Affiliation(s)
- Y Xiong
- Department of Orthopedics, Daping Hospital, Third Military Medical University, Chongqing, China
| | - S Wu
- Department of Orthopedics, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Q Du
- Department of Orthopedics, Daping Hospital, Third Military Medical University, Chongqing, China
| | - A Wang
- Department of Orthopedics, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Z Wang
- Department of Orthopedics, Daping Hospital, Third Military Medical University, Chongqing, China
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25
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Clausen MJAM, Melchers LJ, Mastik MF, Slagter-Menkema L, Groen HJM, van der Laan BFAM, van Criekinge W, de Meyer T, Denil S, Wisman GBA, Roodenburg JLN, Schuuring E. Identification and validation of WISP1 as an epigenetic regulator of metastasis in oral squamous cell carcinoma. Genes Chromosomes Cancer 2015; 55:45-59. [PMID: 26391330 DOI: 10.1002/gcc.22310] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 08/19/2015] [Indexed: 12/29/2022] Open
Abstract
Lymph node (LN) metastasis is the most important prognostic factor in oral squamous cell carcinoma (OSCC) patients. However, in approximately one third of OSCC patients nodal metastases remain undetected, and thus are not adequately treated. Therefore, clinical assessment of LN metastasis needs to be improved. The purpose of this study was to identify DNA methylation biomarkers to predict LN metastases in OSCC. Genome wide methylation assessment was performed on six OSCC with (N+) and six without LN metastases (N0). Differentially methylated sequences were selected based on the likelihood of differential methylation and validated using an independent OSCC cohort as well as OSCC from The Cancer Genome Atlas (TCGA). Expression of WISP1 using immunohistochemistry was analyzed on a large OSCC cohort (n = 204). MethylCap-Seq analysis revealed 268 differentially methylated markers. WISP1 was the highest ranking annotated gene that showed hypomethylation in the N+ group. Bisulfite pyrosequencing confirmed significant hypomethylation within the WISP1 promoter region in N+ OSCC (P = 0.03) and showed an association between WISP1 hypomethylation and high WISP1 expression (P = 0.01). Both these results were confirmed using 148 OSCC retrieved from the TCGA database. In a large OSCC cohort, high WISP1 expression was associated with LN metastasis (P = 0.05), disease-specific survival (P = 0.022), and regional disease-free survival (P = 0.027). These data suggest that WISP1 expression is regulated by methylation and WISP1 hypomethylation contributes to LN metastasis in OSCC. WISP1 is a potential biomarker to predict the presence of LN metastases.
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Affiliation(s)
- Martijn J A M Clausen
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Oral and Maxillofacial Surgery, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Lieuwe J Melchers
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Oral and Maxillofacial Surgery, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mirjam F Mastik
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Lorian Slagter-Menkema
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Otorhinolaryngology/Head & Neck Surgery, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Harry J M Groen
- Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Bernard F A M van der Laan
- Otorhinolaryngology/Head & Neck Surgery, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Wim van Criekinge
- Department of Mathematical Modelling Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - Tim de Meyer
- Department of Mathematical Modelling Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - Simon Denil
- Department of Mathematical Modelling Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - G Bea A Wisman
- Gynecologic Oncology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jan L N Roodenburg
- Oral and Maxillofacial Surgery, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ed Schuuring
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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26
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Guan GF, Zheng Y, Wen LJ, Zhang DJ, Yu DJ, Lu YQ, Zhao Y, Zhang H. Gene expression profiling via bioinformatics analysis reveals biomarkers in laryngeal squamous cell carcinoma. Mol Med Rep 2015; 12:2457-64. [PMID: 25936657 PMCID: PMC4464462 DOI: 10.3892/mmr.2015.3701] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 02/20/2015] [Indexed: 12/16/2022] Open
Abstract
The present study aimed to identify key genes and relevant microRNAs (miRNAs) involved in laryngeal squamous cell carcinoma (LSCC). The gene expression profiles of LSCC tissue samples were analyzed with various bioinformatics tools. A gene expression data set (GSE51985), including ten laryngeal squamous cell carcinoma (LSCC) tissue samples and ten adjacent non-neoplastic tissue samples, was downloaded from the Gene Expression Omnibus. Differential analysis was performed using software package limma of R. Functional enrichment analysis was applied to the differentially expressed genes (DEGs) using the Database for Annotation, Visualization and Integrated Discovery. Protein-protein interaction (PPI) networks were constructed for the protein products using information from the Search Tool for the Retrieval of Interacting Genes/Proteins. Module analysis was performed using ClusterONE (a software plugin from Cytoscape). MicroRNAs (miRNAs) regulating the DEGs were predicted using WebGestalt. A total of 461 DEGs were identified in LSCC, 297 of which were upregulated and 164 of which were downregulated. Cell cycle, proteasome and DNA replication were significantly over-represented in the upregulated genes, while the ribosome was significantly over-represented in the downregulated genes. Two PPI networks were constructed for the up- and downregulated genes. One module from the upregulated gene network was associated with protein kinase. Numerous miRNAs associated with LSCC were predicted, including miRNA (miR)-25, miR-32, miR-92 and miR-29. In conclusion, numerous key genes and pathways involved in LSCC were revealed, which may aid the advancement of current knowledge regarding the pathogenesis of LSCC. In addition, relevant miRNAs were also identified, which may represent potential biomarkers for use in the diagnosis or treatment of the disease.
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Affiliation(s)
- Guo-Fang Guan
- Department of Otolaryngology, Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
| | - Ying Zheng
- Department of Otolaryngology, Head and Neck Surgery, Tumor Hospital of Jilin Province, Changchun, Jilin 130012, P.R. China
| | - Lian-Ji Wen
- Department of Otolaryngology, Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
| | - De-Jun Zhang
- Department of Otolaryngology, Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
| | - Duo-Jiao Yu
- Department of Otolaryngology, Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
| | - Yan-Qing Lu
- Department of Otolaryngology, Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
| | - Yan Zhao
- Department of Otolaryngology, Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
| | - Hui Zhang
- Department of Otolaryngology, Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
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27
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Laurila K, Autio R, Kong L, Närvä E, Hussein S, Otonkoski T, Lahesmaa R, Lähdesmäki H. Integrative genomics and transcriptomics analysis of human embryonic and induced pluripotent stem cells. BioData Min 2014; 7:32. [PMID: 25649046 PMCID: PMC4298950 DOI: 10.1186/s13040-014-0032-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 12/04/2014] [Indexed: 11/13/2022] Open
Abstract
Background Human genomic variations, including single nucleotide polymorphisms (SNPs) and copy number variations (CNVs), are associated with several phenotypic traits varying from mild features to hereditary diseases. Several genome-wide studies have reported genomic variants that correlate with gene expression levels in various tissue and cell types. Results We studied human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs) measuring the SNPs and CNVs with Affymetrix SNP 6 microarrays and expression values with Affymetrix Exon microarrays. We computed the linear relationships between SNPs and expression levels of exons, transcripts and genes, and the associations between gene CNVs and gene expression levels. Further, for a few of the resulted genes, the expression value was associated with both CNVs and SNPs. Our results revealed altogether 217 genes and 584 SNPs whose genomic alterations affect the transcriptome in the same cells. We analyzed the enriched pathways and gene ontologies within these groups of genes, and found out that the terms related to alternative splicing and development were enriched. Conclusions Our results revealed that in the human pluripotent stem cells, the expression values of several genes, transcripts and exons were affected due to the genomic variation. Electronic supplementary material The online version of this article (doi:10.1186/s13040-014-0032-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kirsti Laurila
- Department of Information and Computer Science, Aalto University School of Science, Espoo, Finland
| | - Reija Autio
- Department of Signal Processing, Tampere University of Technology, Tampere, Finland.,School of Health Sciences, University of Tampere, Tampere, Finland
| | - Lingjia Kong
- Department of Signal Processing, Tampere University of Technology, Tampere, Finland.,Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Elisa Närvä
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Samer Hussein
- Samuel Lunenfeld Research Institute, Toronto, Canada.,Research Program Unit, Molecular Neurology, Biomedicum Stem Cell Center, University of Helsinki, Helsinki, Finland
| | - Timo Otonkoski
- Research Program Unit, Molecular Neurology, Biomedicum Stem Cell Center, University of Helsinki, Helsinki, Finland
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Harri Lähdesmäki
- Department of Information and Computer Science, Aalto University School of Science, Espoo, Finland.,Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
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28
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Brauze D, Fijalkiewicz K, Szaumkessel M, Kiwerska K, Bednarek K, Rydzanicz M, Richter J, Grenman R, Jarmuz-Szymczak M. Diversified expression of aryl hydrocarbon receptor dependent genes in human laryngeal squamous cell carcinoma cell lines treated with β-naphthoflavone. Toxicol Lett 2014; 231:99-107. [DOI: 10.1016/j.toxlet.2014.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 08/08/2014] [Accepted: 09/05/2014] [Indexed: 02/05/2023]
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29
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Szyfter K, Wierzbicka M, Hunt JL, Rinaldo A, Rodrigo JP, Takes RP, Ferlito A. Frequent chromosomal aberrations and candidate genes in head and neck squamous cell carcinoma. Eur Arch Otorhinolaryngol 2014; 273:537-45. [PMID: 25355032 DOI: 10.1007/s00405-014-3339-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 10/14/2014] [Indexed: 12/21/2022]
Abstract
The knowledge of the biology of head and neck squamous cell carcinoma (HNSCC) has had relatively little impact on the improvement in oncologic outcome up to date. However, the identification of oncogenes and tumor suppressor genes (TSGs) involved in cancer progression contributes to the understanding of the molecular pathways involved in oncogenesis and could contribute to individual risk assessment and provide tools for improvement of treatment and targets for therapy based on the alterations in these pathways. The aim of this article is to review the chromosomal aberrations commonly found in HNSCC, to identify the genes in these chromosomal regions suggested to act as (candidate) oncogenes or TSGs, and to discuss the molecular mechanisms modulating their expression.
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Affiliation(s)
- Krzysztof Szyfter
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Malgorzata Wierzbicka
- Department of Otolaryngology and Laryngeal Oncology, K. Marcinkowski University of Medical Sciences, Poznan, Poland
| | - Jennifer L Hunt
- Department of Pathology and Laboratory Services, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Juan P Rodrigo
- Department of Otolaryngology, Hospital Universitario Central de Asturias, Oviedo, Spain.,Instituto Universitario de Oncología del Principado de Asturias, Oviedo, Spain
| | - Robert P Takes
- Department of Otolaryngology Head and Neck Surgery, Radboud University Medicine Center, Nijmegen, The Netherlands
| | - Alfio Ferlito
- University of Udine School of Medicine, Udine, Italy.
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30
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Gollin SM. Cytogenetic alterations and their molecular genetic correlates in head and neck squamous cell carcinoma: a next generation window to the biology of disease. Genes Chromosomes Cancer 2014; 53:972-90. [PMID: 25183546 DOI: 10.1002/gcc.22214] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Accepted: 08/15/2014] [Indexed: 01/14/2023] Open
Abstract
Cytogenetic alterations underlie the development of head and neck squamous cell carcinoma (HNSCC), whether tobacco and alcohol use, betel nut chewing, snuff or human papillomavirus (HPV) causes the disease. Many of the molecular genetic aberrations in HNSCC result from these cytogenetic alterations. This review presents a brief introduction to the epidemiology of HNSCC, and discusses the role of HPV in the disease, cytogenetic alterations and their frequencies in HNSCC, their molecular genetic and The Cancer Genome Atlas (TCGA) correlates, prognostic implications, and possible therapeutic considerations. The most frequent cytogenetic alterations in HNSCC are gains of 5p14-15, 8q11-12, and 20q12-13, gains or amplifications of 3q26, 7p11, 8q24, and 11q13, and losses of 3p, 4q35, 5q12, 8p23, 9p21-24, 11q14-23, 13q12-14, 18q23, and 21q22. To understand their effects on tumor cell biology and response to therapy, the cytogenetic findings in HNSCC are increasingly being examined in the context of the biochemical pathways they disrupt. The goal is to minimize morbidity and mortality from HNSCC using cytogenetic abnormalities to identify valuable diagnostic biomarkers for HNSCC, prognostic biomarkers of tumor behavior, recurrence risk, and outcome, and predictive biomarkers of therapeutic response to identify the most efficacious treatment for each individual patient's tumor, all based on a detailed understanding of the next generation biology of HNSCC.
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Affiliation(s)
- Susanne M Gollin
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA; Departments of Otolaryngology and Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA; University of Pittsburgh Cancer Institute, Pittsburgh, PA
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31
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Newton R, Wernisch L. A meta-analysis of multiple matched copy number and transcriptomics data sets for inferring gene regulatory relationships. PLoS One 2014; 9:e105522. [PMID: 25148247 PMCID: PMC4141782 DOI: 10.1371/journal.pone.0105522] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/21/2014] [Indexed: 12/25/2022] Open
Abstract
Inferring gene regulatory relationships from observational data is challenging. Manipulation and intervention is often required to unravel causal relationships unambiguously. However, gene copy number changes, as they frequently occur in cancer cells, might be considered natural manipulation experiments on gene expression. An increasing number of data sets on matched array comparative genomic hybridisation and transcriptomics experiments from a variety of cancer pathologies are becoming publicly available. Here we explore the potential of a meta-analysis of thirty such data sets. The aim of our analysis was to assess the potential of in silico inference of trans-acting gene regulatory relationships from this type of data. We found sufficient correlation signal in the data to infer gene regulatory relationships, with interesting similarities between data sets. A number of genes had highly correlated copy number and expression changes in many of the data sets and we present predicted potential trans-acted regulatory relationships for each of these genes. The study also investigates to what extent heterogeneity between cell types and between pathologies determines the number of statistically significant predictions available from a meta-analysis of experiments.
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Affiliation(s)
- Richard Newton
- Biostatistics Unit, Medical Research Council, Cambridge, United Kingdom
- * E-mail:
| | - Lorenz Wernisch
- Biostatistics Unit, Medical Research Council, Cambridge, United Kingdom
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32
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Mäkitie AA, Monni O. Molecular profiling of laryngeal cancer. Expert Rev Anticancer Ther 2014; 9:1251-60. [DOI: 10.1586/era.09.102] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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33
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Heterogeneity of 11q13 region rearrangements in laryngeal squamous cell carcinoma analyzed by microarray platforms and fluorescence in situ hybridization. Mol Biol Rep 2013; 40:4161-71. [PMID: 23652995 DOI: 10.1007/s11033-013-2496-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Accepted: 04/24/2013] [Indexed: 10/26/2022]
Abstract
We reinvestigated rearrangements occurring in region q13 of chromosome 11 aiming to: (i) describe heterogeneity of the observed structural alterations, (ii) estimate amplicon size and (iii) identify of oncogenes involved in laryngeal cancer progression as potential targets for therapy. The study included 17 cell lines derived from laryngeal cancers and 34 specimens from primary laryngeal tumors. The region 11q13 was analyzed by fluorescence in situ hybridization (FISH), array comparative genomic hybridization (aCGH) and gene expression microarray. Next, quantitative real time PCR was used for chosen genes to confirm results from aCGH and gene expression microarray. The observed pattern of aberrations allows to distinguish three ways, in which gain and amplification involving 11q13 region may occur: formation of a homogeneously staining region; breakpoints in/near 11q13, which lead to the three to sevenfold increase of the copy number of 11q13 region; the presence of additional copies of the whole chromosome 11. The minimal altered region of gain and/or amplification was limited to ~1.8 Mb (chr.11:69,395,184-71,209,568) and comprised mostly 11q13.3 band which contain 12 genes. Five, out of these genes (CCND1, ORAOV1, FADD, PPFIA1, CTTN) had higher expression levels in comparison to healthy controls. Apart from CCND1 gene, which has an established role in pathogenesis of head and neck cancers, CTTN, ORAOV1 and FADD genes appear to be oncogene-candidates in laryngeal cancers, while a function of PPFIA1 requires further studies.
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Blessmann M, Al-Dam A, Hanken H, Assaf AT, Riecke B, Klatt J, Simon R, Sauter G, Heiland M, Kluwe L, Gröbe A. Amplification of the PPFIA1 gene region on 11q13 in oral squamous cell carcinomas (OSCC). J Craniomaxillofac Surg 2013; 41:845-9. [PMID: 23453270 DOI: 10.1016/j.jcms.2013.01.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 01/05/2013] [Accepted: 01/07/2013] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Analyzing chromosomal amplifications delivers valuable information for identification of oncogenes. For carcinomas of the oral cavity only few genes have been identified in amplified regions. The aim of this study was to search genes in amplified regions as possible biomarkers and targets for novel therapies. MATERIAL AND METHODS DNA from 10 carcinomas of the floor of the oral cavity was examined using a 500K Array GeneChip (Affymetrix 6.0) to detect chromosomal losses, gains or amplifications. Suspicious alterations were validated on tissue microarrays using fluorescence in situ hybridization (FISH) with respective probes. RESULTS FISH-validation on tissue arrays confirmed PPFIA1 amplifications as one of the most frequent events (32.6%). High (10-20 signals) and low (<10 signals) amplification of PPFIA1 was found in 10.9% (5/46) and 21.7% (10/46) tumours, respectively. Fine mapping with overlapping FISH probes showed co-amplification of PPFIA1 and the Cyclin D1 gene which are approximately 600 kb apart from each other, likely in the same amplicon. DISCUSSION PPFIA1 was frequently co-amplified with the Cyclin D1 gene in oral carcinomas and could present a biomarker as well as a novel target for specific gene therapy. Further studies are necessary to investigate the role of PPFIA1 in development and pathogenesis of oral carcinomas.
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Affiliation(s)
- Marco Blessmann
- Department of Oral and Maxillofacial Surgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
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Renkonen S, Kankainen M, Hagström J, Haglund C, Monni O, Mäkitie AA. Systems-level analysis of clinically different phenotypes of juvenile nasopharyngeal angiofibromas. Laryngoscope 2012; 122:2728-35. [PMID: 22965421 DOI: 10.1002/lary.23592] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 05/02/2012] [Accepted: 06/22/2012] [Indexed: 12/12/2022]
Abstract
OBJECTIVES/HYPOTHESIS To explore the molecular genetic background of juvenile nasopharyngeal angiofibromas and to identify biological processes and putative factors determining the different growth patterns of these tumors. STUDY DESIGN By comparing copy number and gene expression level changes of two clinically different phenotypes of juvenile nasopharyngeal angiofibromas, we aimed to find processes essential in the growth and development of these tumors. Based on the results and prior knowledge of the proteins significance for growth, we studied the expression of tyrosine kinase SYK in 27 tumor samples. METHODS Comparative genomic hybridization and gene expression analyses were performed for the two tumor samples, and protein expression of SYK was studied in 27 samples by immunohistochemical staining. RESULTS Between low- and high-stage juvenile nasopharyngeal angiofibromas, 1,245 genes showed at least a two-fold change in expression. The corresponding proteins of these transcripts were enriched in different biological processes. Protein kinase SYK was expressed in all 27 samples, and its intensity significantly correlated with tumor stage. CONCLUSIONS Because the molecular genetic background of juvenile nasopharyngeal angiofibroma is unknown, our aim was to investigate genomic alterations that could associate to low- and high-stage tumors. We were able to identify gene expression changes that relate to particular biological processes, but assessing clinically relevant molecular profiles still requires further characterization. Due to the low incidence of juvenile angiofibroma, in the future a combination of molecular profiling data from several studies would be useful in understanding the molecular background of the disease.
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Affiliation(s)
- Suvi Renkonen
- Department of Otorhinolaryngology-Head and Neck Surgery, Haartman Institute and HusLab, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland.
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Jun KH, Kim SY, Yoon JH, Song JH, Park WS. Amplification of the UQCRFS1 Gene in Gastric Cancers. J Gastric Cancer 2012; 12:73-80. [PMID: 22792519 PMCID: PMC3392327 DOI: 10.5230/jgc.2012.12.2.73] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 05/07/2012] [Accepted: 05/09/2012] [Indexed: 11/28/2022] Open
Abstract
Purpose The specific aim of this study is to unravel a DNA copy number alterations, and to search for novel genes that are associated with the development of Korean gastric cancer. Materials and Methods We investigated a DNA copy number changes in 23 gastric adenocarcinomas by array-comparative genomic hybridization and quantitative real-time polymerase chain reaction analyses. Besides, the expression of UQCRFS1, which shows amplification in array-CGH, was examined in 186 gastric cancer tissues by an immunohistochemistry, and in 9 gastric cancer cell lines, as well as 24 gastric cancer tissues by immunoblotting. Results We found common gains at 48 different loci, and a common loss at 19 different loci. Amplification of UQCRFS1 gene at 19q12 was found in 5 (21.7%) of the 23 gastric cancers in an array-comparative genomic hybridization and DNA copy number were increased in 5 (20.0%) out of the 25 gastric cancer in quantitative real-time polymerase chain reaction. In immunohistochemistry, the overexpression of the protein was detected in 105 (56.5%) out of the 186 gastric cancer tissues. Statistically, there was no significant relationship between the overexpression of UQCRFS1 and clinicopathologic parameters (P>0.05). In parallel, the overexpression of UQCRFS1 protein was confirmed in 6 (66.7%) of the 9 gastric cancer cell lines, and 12 (50.0%) of the 24 gastric cancer tissues by immunoblotting. Conclusions These results suggest that the overexpression of UQCRFS1 gene may contribute to the development and/or progression of gastric cancer, and further supported that mitochondrial change may serve as a potential cancer biomarker.
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Affiliation(s)
- Kyong Hwa Jun
- Department of General Surgery, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Ambatipudi S, Gerstung M, Pandey M, Samant T, Patil A, Kane S, Desai RS, Schäffer AA, Beerenwinkel N, Mahimkar MB. Genome-wide expression and copy number analysis identifies driver genes in gingivobuccal cancers. Genes Chromosomes Cancer 2011; 51:161-73. [PMID: 22072328 DOI: 10.1002/gcc.20940] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 09/20/2011] [Accepted: 09/21/2011] [Indexed: 01/27/2023] Open
Abstract
The molecular mechanisms contributing to the development and progression of gingivobuccal complex (GBC) cancers-a sub-site of oral cancer, comprising the buccal mucosa, the gingivobuccal sulcus, the lower gingival region, and the retromolar trigone-remain poorly understood. Identifying the GBC cancer-related gene expression signature and the driver genes residing on the altered chromosomal regions is critical for understanding the molecular basis of its pathogenesis. Genome-wide expression profiling of 27 GBC cancers with known chromosomal alterations was performed to reveal differentially expressed genes. Putative driver genes were identified by integrating copy number and gene expression data. A total of 315 genes were found differentially expressed (P ≤ 0.05, logFC > 2.0) of which 11 genes were validated by real-time quantitative reverse transcriptase-PCR (qRT-PCR) in tumors (n = 57) and normal GBC tissues (n = 18). Overexpression of LY6K, in chromosome band 8q24.3, was validated by immunohistochemical (IHC) analysis. We found that 78.5% (2,417/3,079) of the genes located in regions of recurrent chromosomal alterations show copy number dependent expression indicating that copy number alteration has a direct effect on global gene expression. The integrative analysis revealed BIRC3 in 11q22.2 as a candidate driver gene associated with poor clinical outcome. Our study identified previously unreported differentially expressed genes in a homogeneous subtype of oral cancer and the candidate driver genes that may contribute to the development and progression of the disease. © 2011 Wiley Periodicals, Inc.
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Affiliation(s)
- Srikant Ambatipudi
- Cancer Research Institute (CRI), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Navi Mumbai, India
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Huang N, Shah PK, Li C. Lessons from a decade of integrating cancer copy number alterations with gene expression profiles. Brief Bioinform 2011; 13:305-16. [PMID: 21949216 DOI: 10.1093/bib/bbr056] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Over the last decade, multiple functional genomic datasets studying chromosomal aberrations and their downstream effects on gene expression have accumulated for several cancer types. A vast majority of them are in the form of paired gene expression profiles and somatic copy number alterations (CNA) information on the same patients identified using microarray platforms. In response, many algorithms and software packages are available for integrating these paired data. Surprisingly, there has been no serious attempt to review the currently available methodologies or the novel insights brought using them. In this work, we discuss the quantitative relationships observed between CNA and gene expression in multiple cancer types and biological milestones achieved using the available methodologies. We discuss the conceptual evolution of both, the step-wise and the joint data integration methodologies over the last decade. We conclude by providing suggestions for building efficient data integration methodologies and asking further biological questions.
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Affiliation(s)
- Norman Huang
- Department of Biostatistics and Computational Biology, CLS-11075, Dana-Farber Cancer Institute, Harvard School of Public Health, CLS-11075 3 Blackfan Circle, Boston, MA 02115, USA
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Kuroda A, Tsukamoto Y, Nguyen LT, Noguchi T, Takeuchi I, Uchida M, Uchida T, Hijiya N, Nakada C, Okimoto T, Kodama M, Murakami K, Matsuura K, Seto M, Ito H, Fujioka T, Moriyama M. Genomic profiling of submucosal-invasive gastric cancer by array-based comparative genomic hybridization. PLoS One 2011; 6:e22313. [PMID: 21811585 PMCID: PMC3141024 DOI: 10.1371/journal.pone.0022313] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 06/19/2011] [Indexed: 12/28/2022] Open
Abstract
Genomic copy number aberrations (CNAs) in gastric cancer have already been extensively characterized by array comparative genomic hybridization (array CGH) analysis. However, involvement of genomic CNAs in the process of submucosal invasion and lymph node metastasis in early gastric cancer is still poorly understood. In this study, to address this issue, we collected a total of 59 tumor samples from 27 patients with submucosal-invasive gastric cancers (SMGC), analyzed their genomic profiles by array CGH, and compared them between paired samples of mucosal (MU) and submucosal (SM) invasion (23 pairs), and SM invasion and lymph node (LN) metastasis (9 pairs). Initially, we hypothesized that acquisition of specific CNA(s) is important for these processes. However, we observed no significant difference in the number of genomic CNAs between paired MU and SM, and between paired SM and LN. Furthermore, we were unable to find any CNAs specifically associated with SM invasion or LN metastasis. Among the 23 cases analyzed, 15 had some similar pattern of genomic profiling between SM and MU. Interestingly, 13 of the 15 cases also showed some differences in genomic profiles. These results suggest that the majority of SMGCs are composed of heterogeneous subpopulations derived from the same clonal origin. Comparison of genomic CNAs between SMGCs with and without LN metastasis revealed that gain of 11q13, 11q14, 11q22, 14q32 and amplification of 17q21 were more frequent in metastatic SMGCs, suggesting that these CNAs are related to LN metastasis of early gastric cancer. In conclusion, our data suggest that generation of genetically distinct subclones, rather than acquisition of specific CNA at MU, is integral to the process of submucosal invasion, and that subclones that acquire gain of 11q13, 11q14, 11q22, 14q32 or amplification of 17q21 are likely to become metastatic.
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Affiliation(s)
- Akiko Kuroda
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
- Department of General Medicine, Faculty of Medicine, Oita University, Oita, Japan
| | - Yoshiyuki Tsukamoto
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
- * E-mail:
| | - Lam Tung Nguyen
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
- Department of General Medicine, Faculty of Medicine, Oita University, Oita, Japan
| | - Tsuyoshi Noguchi
- Department of Gastrointestinal Surgery, Faculty of Medicine, Oita University, Oita, Japan
| | - Ichiro Takeuchi
- Department of Computer Science/Scientific and Engineering Simulation, Nagoya Institute of Technology, Nagoya, Japan
| | - Masahiro Uchida
- Department of Gastroenterology, Faculty of Medicine, Oita University, Oita, Japan
| | - Tomohisa Uchida
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
| | - Naoki Hijiya
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
| | - Chisato Nakada
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
| | - Tadayoshi Okimoto
- Department of General Medicine, Faculty of Medicine, Oita University, Oita, Japan
- Department of Gastroenterology, Faculty of Medicine, Oita University, Oita, Japan
| | - Masaaki Kodama
- Department of General Medicine, Faculty of Medicine, Oita University, Oita, Japan
- Department of Gastroenterology, Faculty of Medicine, Oita University, Oita, Japan
| | - Kazunari Murakami
- Department of General Medicine, Faculty of Medicine, Oita University, Oita, Japan
- Department of Gastroenterology, Faculty of Medicine, Oita University, Oita, Japan
| | - Keiko Matsuura
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
| | - Masao Seto
- Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Hisao Ito
- Division of Organ Pathology, Department of Microbiology and Pathology, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Toshio Fujioka
- Department of General Medicine, Faculty of Medicine, Oita University, Oita, Japan
- Department of Gastroenterology, Faculty of Medicine, Oita University, Oita, Japan
| | - Masatsugu Moriyama
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
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Mirisola V, Mora R, Esposito AI, Guastini L, Tabacchiera F, Paleari L, Amaro A, Angelini G, Dellepiane M, Pfeffer U, Salami A. A prognostic multigene classifier for squamous cell carcinomas of the larynx. Cancer Lett 2011; 307:37-46. [PMID: 21481529 DOI: 10.1016/j.canlet.2011.03.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Revised: 01/28/2011] [Accepted: 03/17/2011] [Indexed: 10/18/2022]
Abstract
Survival after diagnosis of laryngeal cancer has not improved over the last 20 years. Selection of patients for radio- and chemotherapy or surgery or follow-up strategies based on a prognostic classifier could improve survival without unduly extending radical surgery. We performed microarray gene expression analysis and developed a four-gene classifier for laryngeal cancer using Prediction Analysis of Microarray and leave-one-out cross validation. A four-gene classifier containing the non-coding gene H19, the histone HIST1H3F and the two small nucleolar RNAs, SNORA16A and SNORD14C was developed that assigns cases to low and high risk classes. The high risk class has a relative risk of 6.5 (CI=1.817-23.258, Fisher exact test p<0.0001). The maternally imprinted gene H19 is the top classifier gene.
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Affiliation(s)
- Valentina Mirisola
- Integrated Molecular Pathology, National Cancer Research Institute, Genova, Italy
| | - Renzo Mora
- ENT Department, University of Genova, Italy
| | | | | | - Flavia Tabacchiera
- Integrated Molecular Pathology, National Cancer Research Institute, Genova, Italy
| | - Laura Paleari
- Integrated Molecular Pathology, National Cancer Research Institute, Genova, Italy
| | - Adriana Amaro
- Integrated Molecular Pathology, National Cancer Research Institute, Genova, Italy
| | - Giovanna Angelini
- Integrated Molecular Pathology, National Cancer Research Institute, Genova, Italy
| | | | - Ulrich Pfeffer
- Integrated Molecular Pathology, National Cancer Research Institute, Genova, Italy.
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Wierinckx A, Roche M, Raverot G, Legras-Lachuer C, Croze S, Nazaret N, Rey C, Auger C, Jouanneau E, Chanson P, Trouillas J, Lachuer J. Integrated genomic profiling identifies loss of chromosome 11p impacting transcriptomic activity in aggressive pituitary PRL tumors. Brain Pathol 2011; 21:533-43. [PMID: 21251114 DOI: 10.1111/j.1750-3639.2011.00476.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Integrative genomics approaches associating DNA structure and transcriptomic analysis should allow the identification of cascades of events relating to tumor aggressiveness. While different genome alterations have been identified in pituitary tumors, none have ever been correlated with the aggressiveness. This study focused on one subtype of pituitary tumor, the prolactin (PRL) pituitary tumors, to identify molecular events associated with the aggressive and malignant phenotypes. We combined a comparative genomic hybridization and transcriptomic analysis of 13 PRL tumors classified as nonaggressive or aggressive. Allelic loss within the p arm region of chromosome 11 was detected in five of the aggressive tumors. Allelic loss in the 11q arm was observed in three of these five tumors, all three of which were considered as malignant based on the occurrence of metastases. Comparison of genomic and transcriptomic data showed that allelic loss impacted upon the expression of genes located in the imbalanced region. Data filtering allowed us to highlight five deregulated genes (DGKZ, CD44, TSG101, GTF2H1, HTATIP2), within the missing 11p region, potentially responsible for triggering the aggressive and malignant phenotypes of PRL tumors. Our combined genomic and transcriptomic analysis underlines the importance of chromosome allelic loss in determining the aggressiveness and malignancy of tumors.
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Ortiz-Estevez M, De Las Rivas J, Fontanillo C, Rubio A. Segmentation of genomic and transcriptomic microarrays data reveals major correlation between DNA copy number aberrations and gene–loci expression. Genomics 2011; 97:86-93. [DOI: 10.1016/j.ygeno.2010.10.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 10/20/2010] [Accepted: 10/22/2010] [Indexed: 11/26/2022]
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Astro V, Asperti C, Cangi MG, Cangi G, Doglioni C, de Curtis I. Liprin-α1 regulates breast cancer cell invasion by affecting cell motility, invadopodia and extracellular matrix degradation. Oncogene 2010; 30:1841-9. [PMID: 21151172 DOI: 10.1038/onc.2010.562] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Migration of cells and degradation of the extracellular matrix (ECM) are required for efficient tumor cell invasion, but the underlying molecular mechanisms are only partially known. The PPFIA1 gene for liprin-α1 is frequently amplified in human breast cancers. We recently demonstrated that liprin-α1 is an important regulator of cell edge dynamics during motility. We show, herein, that the liprin-α1 protein is highly expressed in human breast tumors. Functional analysis shows that liprin-α1 is specifically required for the migration and invasion of highly invasive human breast cancer MDA-MB-231 cells. We used time-lapse analysis to demonstrate defects in the motility of liprin-α1-depleted cells that include a striking instability of the lamellipodia. Liprin-α1 levels altered by either RNA interference or overexpression affected also cell spreading and the number of invadopodia per cell, but not the density of invadopodia per unit of surface area. On the other hand, silencing of liprin-α1 inhibited the degradation of the ECM, whereas its overexpression enhanced degradation, resulting in significant negative or positive effects, respectively, on the area of degradation per invadopodium. Transfection of fluorescent-labeled cortactin revealed that depletion of liprin-α1 also affected the assembly and disassembly of invadopodia, with decrease of their lifetime. Our results strongly support a novel important role of liprin-α1 in the regulation of human tumor cell invasion.
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Affiliation(s)
- V Astro
- Cell Adhesion Unit, Division of Neurosciences, San Raffaele Scientific Institute and San Raffaele University, Milano, Italy
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44
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Giefing M, Zemke N, Brauze D, Kostrzewska-Poczekaj M, Luczak M, Szaumkessel M, Pelinska K, Kiwerska K, Tönnies H, Grenman R, Figlerowicz M, Siebert R, Szyfter K, Jarmuz M. High resolution ArrayCGH and expression profiling identifies PTPRD and PCDH17/PCH68 as tumor suppressor gene candidates in laryngeal squamous cell carcinoma. Genes Chromosomes Cancer 2010; 50:154-66. [PMID: 21213369 DOI: 10.1002/gcc.20840] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Accepted: 10/22/2010] [Indexed: 12/21/2022] Open
Abstract
Many classical tumor suppressor genes (TSG) were identified by delineation of bi-allelic losses called homozygous deletions. To identify systematically homozygous deletions in laryngeal squamous cell carcinoma (LSCC) and to unravel novel putative tumor suppressor genes, we screened 10 LSCC cell lines using high resolution array comparative genomic hybridization (arrayCGH) and array based expression analysis. ArrayCGH identified altogether 113 regions harboring protein coding genes that showed strong reduction in copy number indicating a potential homozygous deletion. Out of the 113 candidate regions, 22 novel homozygous deletions that affected the coding sequences of 15 genes were confirmed by multiplexPCR. Three genes were homozygously lost in two cell lines: PCDH17/PCH68, PRR20, and PTPRD. For the 15 homozygously deleted genes, four showed statistically significant downregulation of expression in LSCC cell lines as compared with normal human laryngeal controls. These were ATG7 (1/10 cell line), ZMYND11 (BS69) (1/10 cell line), PCDH17/PCH68 (9/10 cell lines), and PTPRD (7/10 cell lines). Quantitative real-time PCR was used to confirm the downregulation of the candidate genes in 10 expression array-studied cell lines and an additional cohort of cell lines; statistical significant downregulation of PCDH17/PCH68 and PTPRD was observed. In line with this also Western blot analyses demonstrated a complete absence of the PCDH17 and PTPRD proteins. Thus, expression profiling confirmed recurrent alterations of two genes identified primarily by delineation of homozygous deletions. These were PCDH17/PCH68, the protocadherin gene, and the STAT3 inhibiting receptor protein tyrosine phosphatase gene PTPRD. These genes are good candidates for novel TSG in LSCC.
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Affiliation(s)
- Maciej Giefing
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland.
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Oh M, Song B, Lee H. CAM: a web tool for combining array CGH and microarray gene expression data from multiple samples. Comput Biol Med 2010; 40:781-5. [PMID: 20728879 DOI: 10.1016/j.compbiomed.2010.07.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2009] [Revised: 05/06/2010] [Accepted: 07/30/2010] [Indexed: 11/16/2022]
Abstract
We develop a web-based tool for Combining Array CGH copy number aberration data and Microarray gene expression data (CAM). This tool analyzes these two data sets from multiple samples to detect genes having both DNA copy number aberrations (CNAs) and gene expression changes. CAM provides several statistical methods for identifying CNAs, which are consistent across multiple samples. Identified CNAs and their correlated gene expression changes are then visualized along the chromosomes. As a result, CAM is a useful tool for identifying disease related genes when these two types of data sets are available. To illustrate the various analysis outputs of CAM, we subsequently provide ten sets of example data from seven cancer types.
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Affiliation(s)
- Mira Oh
- Department of Information and Communications, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
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High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity. Nat Biotechnol 2010; 28:371-7. [PMID: 20351689 DOI: 10.1038/nbt.1615] [Citation(s) in RCA: 216] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Accepted: 02/16/2010] [Indexed: 11/08/2022]
Abstract
Prolonged culture of human embryonic stem cells (hESCs) can lead to adaptation and the acquisition of chromosomal abnormalities, underscoring the need for rigorous genetic analysis of these cells. Here we report the highest-resolution study of hESCs to date using an Affymetrix SNP 6.0 array containing 906,600 probes for single nucleotide polymorphisms (SNPs) and 946,000 probes for copy number variations (CNVs). Analysis of 17 different hESC lines maintained in different laboratories identified 843 CNVs of 50 kb-3 Mb in size. We identified, on average, 24% of the loss of heterozygosity (LOH) sites and 66% of the CNVs changed in culture between early and late passages of the same lines. Thirty percent of the genes detected within CNV sites had altered expression compared to samples with normal copy number states, of which >44% were functionally linked to cancer. Furthermore, LOH of the q arm of chromosome 16, which has not been observed previously in hESCs, was detected.
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47
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Junnila S, Kokkola A, Karjalainen-Lindsberg ML, Puolakkainen P, Monni O. Genome-wide gene copy number and expression analysis of primary gastric tumors and gastric cancer cell lines. BMC Cancer 2010; 10:73. [PMID: 20187983 PMCID: PMC2837868 DOI: 10.1186/1471-2407-10-73] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Accepted: 03/01/2010] [Indexed: 12/26/2022] Open
Abstract
Background Gastric cancer is one of the most common malignancies worldwide and the second most common cause of cancer related death. Gene copy number alterations play an important role in the development of gastric cancer and a change in gene copy number is one of the main mechanisms for a cancer cell to control the expression of potential oncogenes and tumor suppressor genes. Methods To highlight genes of potential biological and clinical relevance in gastric cancer, we carried out a systematic array-based survey of gene expression and copy number levels in primary gastric tumors and gastric cancer cell lines and validated the results using an affinity capture based transcript analysis (TRAC assay) and real-time qRT-PCR. Results Integrated microarray analysis revealed altogether 256 genes that were located in recurrent regions of gains or losses and had at least a 2-fold copy number- associated change in their gene expression. The expression levels of 13 of these genes, ALPK2, ASAP1, CEACAM5, CYP3A4, ENAH, ERBB2, HHIPL2, LTB4R, MMP9, PERLD1, PNMT, PTPRA, and OSMR, were validated in a total of 118 gastric samples using either the qRT-PCR or TRAC assay. All of these 13 genes were differentially expressed between cancerous samples and nonmalignant tissues (p < 0.05) and the association between copy number and gene expression changes was validated for nine (69.2%) of these genes (p < 0.05). Conclusion In conclusion, integrated gene expression and copy number microarray analysis highlighted genes that may be critically important for gastric carcinogenesis. TRAC and qRT-PCR analyses validated the microarray results and therefore the role of these genes as potential biomarkers for gastric cancer.
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Affiliation(s)
- Siina Junnila
- Institute of Biomedicine, Medical Biochemistry and Developmental Biology, Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
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Dancau AM, Wuth L, Waschow M, Holst F, Krohn A, Choschzick M, Terracciano L, Politis S, Kurtz S, Lebeau A, Friedrichs K, Wencke K, Monni O, Simon R. PPFIA1andCCND1are frequently coamplified in breast cancer. Genes Chromosomes Cancer 2010; 49:1-8. [PMID: 19787783 DOI: 10.1002/gcc.20713] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Ana-Maria Dancau
- Department of General, Visceral and Thoracic Surgery, University Medical Centre Hamburg Eppendorf, Hamburg, Germany
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Schäfer M, Schwender H, Merk S, Haferlach C, Ickstadt K, Dugas M. Integrated analysis of copy number alterations and gene expression: a bivariate assessment of equally directed abnormalities. ACTA ACUST UNITED AC 2009; 25:3228-35. [PMID: 19828576 DOI: 10.1093/bioinformatics/btp592] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
MOTIVATION The analysis of a number of different genetic features like copy number (CN) variation, gene expression (GE) or loss of heterocygosity has considerably increased in recent years, as well as the number of available datasets. This is particularly due to the success of microarray technology. Thus, to understand mechanisms of disease pathogenesis on a molecular basis, e.g. in cancer research, the challenge of analyzing such different data types in an integrated way has become increasingly important. In order to tackle this problem, we propose a new procedure for an integrated analysis of two different data types that searches for genes and genetic regions which for both inputs display strong equally directed deviations from the reference median. We employ this approach, based on a modified correlation coefficient and an explorative Wilcoxon test, to find DNA regions of such abnormalities in GE and CN (e.g. underexpressed genes accompanied by a loss of DNA material). RESULTS In an application to acute myeloid leukemia, our procedure is able to identify various regions on different chromosomes with characteristic abnormalities in GE and CN data and shows a higher sensitivity to differences in abnormalities than standard approaches. While the results support various findings of previous studies, some new interesting DNA regions can be identified. In a simulation study, our procedure also shows more reliable results than standard approaches. AVAILABILITY Code and data available as R packages edira and ediraAMLdata from http://www.statistik.tu-dortmund.de/~schaefer/ CONTACT martin.schaefer@udo.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Martin Schäfer
- Collaborative Research Center 475, TU Dortmund University, Dortmund, Germany.
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Metal-proteinase ADAM12, kinesin 14 and checkpoint suppressor 1 as new molecular markers of laryngeal carcinoma. Eur Arch Otorhinolaryngol 2009; 266:1501-7. [DOI: 10.1007/s00405-009-1019-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Accepted: 06/10/2009] [Indexed: 12/12/2022]
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