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Trevisi E, Sessa C, Colombo I. Clinical relevance of circulating tumor DNA in ovarian cancer: current issues and future opportunities. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2024; 5:627-640. [PMID: 38966171 PMCID: PMC11220313 DOI: 10.37349/etat.2024.00239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 03/13/2024] [Indexed: 07/06/2024] Open
Abstract
Ovarian cancer (OC) is the most lethal gynecologic malignancy worldwide. Due to the lack of effective screening and early detection strategies, many patients with OC are diagnosed with advanced disease, where treatment is rarely curative. Moreover, OC is characterized by high intratumor heterogeneity, which represents a major barrier to the development of effective treatments. Conventional tumor biopsy and blood-based biomarkers, such as cancer antigen 125 (CA125), have different limitations. Liquid biopsy has recently emerged as an attractive and promising area of investigation in oncology, due to its minimally invasive, safe, comprehensive, and real-time dynamic nature. Preliminary evidence suggests a potential role of liquid biopsy to refine OC management, by improving screening, early diagnosis, assessment of response to treatment, detection, and profiling of drug resistance. The current knowledge and the potential clinical value of liquid biopsy in OC is discussed in this review to provide an overview of the clinical settings in which its use might support and improve diagnosis and treatment.
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Affiliation(s)
- Elena Trevisi
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland
| | - Cristiana Sessa
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland
| | - Ilaria Colombo
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland
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Habicher J, Sanvido I, Bühler A, Sartori S, Piccoli G, Carl M. The Risk Genes for Neuropsychiatric Disorders negr1 and opcml Are Expressed throughout Zebrafish Brain Development. Genes (Basel) 2024; 15:363. [PMID: 38540422 PMCID: PMC10969947 DOI: 10.3390/genes15030363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 06/14/2024] Open
Abstract
The immunoglobulin LAMP/OBCAM/NTM (IgLON) family of cell adhesion molecules comprises five members known for their involvement in establishing neural circuit connectivity, fine-tuning, and maintenance. Mutations in IgLON genes result in alterations in these processes and can lead to neuropsychiatric disorders. The two IgLON family members NEGR1 and OPCML share common links with several of them, such as schizophrenia, autism, and major depressive disorder. However, the onset and the underlying molecular mechanisms have remained largely unresolved, hampering progress in developing therapies. NEGR1 and OPCML are evolutionarily conserved in teleosts like the zebrafish (Danio rerio), which is excellently suited for disease modelling and large-scale screening for disease-ameliorating compounds. To explore the potential applicability of zebrafish for extending our knowledge on NEGR1- and OPCML-linked disorders and to develop new therapeutic strategies, we investigated the spatio-temporal expression of the two genes during early stages of development. negr1 and opcml are expressed maternally and subsequently in partially distinct domains of conserved brain regions. Other areas of expression in zebrafish have not been reported in mammals to date. Our results indicate that NEGR1 and OPCML may play roles in neural circuit development and function at stages earlier than previously anticipated. A detailed functional analysis of the two genes based on our findings could contribute to understanding the mechanistic basis of related psychiatric disorders.
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Affiliation(s)
- Judith Habicher
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, 38123 Trento, Italy; (J.H.); (I.S.); (A.B.); (S.S.); (G.P.)
| | - Ilaria Sanvido
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, 38123 Trento, Italy; (J.H.); (I.S.); (A.B.); (S.S.); (G.P.)
| | - Anja Bühler
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, 38123 Trento, Italy; (J.H.); (I.S.); (A.B.); (S.S.); (G.P.)
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, 89081 Ulm, Germany
| | - Samuele Sartori
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, 38123 Trento, Italy; (J.H.); (I.S.); (A.B.); (S.S.); (G.P.)
| | - Giovanni Piccoli
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, 38123 Trento, Italy; (J.H.); (I.S.); (A.B.); (S.S.); (G.P.)
| | - Matthias Carl
- Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, 38123 Trento, Italy; (J.H.); (I.S.); (A.B.); (S.S.); (G.P.)
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Liu Z, Wang Z, Wei Y, Shi J, Shi T, Chen X, Li L. Transcriptomic Profiling of Tetrodotoxin-Induced Neurotoxicity in Human Cerebral Organoids. Mar Drugs 2023; 21:588. [PMID: 37999412 PMCID: PMC10672545 DOI: 10.3390/md21110588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023] Open
Abstract
Tetrodotoxin (TTX) is an exceedingly toxic non-protein biotoxin that demonstrates remarkable selectivity and affinity for sodium channels on the excitation membrane of nerves. This property allows TTX to effectively obstruct nerve conduction, resulting in nerve paralysis and fatality. Although the mechanistic aspects of its toxicity are well understood, there is a dearth of literature addressing alterations in the neural microenvironment subsequent to TTX poisoning. In this research endeavor, we harnessed human pluripotent induced stem cells to generate cerebral organoids-an innovative model closely mirroring the structural and functional intricacies of the human brain. This model was employed to scrutinize the comprehensive transcriptomic shifts induced by TTX exposure, thereby delving into the neurotoxic properties of TTX and its potential underlying mechanisms. Our findings revealed 455 differentially expressed mRNAs (DEmRNAs), 212 differentially expressed lncRNAs (DElncRNAs), and 18 differentially expressed miRNAs (DEmiRNAs) in the TTX-exposed group when juxtaposed with the control cohort. Through meticulous Gene Ontology (GO) annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and protein-protein interaction (PPI) analysis, we ascertained that these differential genes predominantly participate in the regulation of voltage-gated channels and synaptic homeostasis. A comprehensive ceRNA network analysis unveiled that DEmRNAs exert control over the expression of ion channels and neurocytokines, suggesting their potential role in mediating apoptosis.
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Affiliation(s)
- Zhanbiao Liu
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China (J.S.)
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian 116600, China
| | - Zhe Wang
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian 116600, China
| | - Yue Wei
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China (J.S.)
| | - Jingjing Shi
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China (J.S.)
| | - Tong Shi
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China (J.S.)
| | - Xuejun Chen
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China (J.S.)
| | - Liqin Li
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China (J.S.)
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Yi J, Wu M, Zheng Z, Zhou Q, Li X, Lu Y, Liu P. Integrated analysis of DNA methylome and transcriptome reveals SFRP1 and LIPG as potential drivers of ovarian cancer metastasis. J Gynecol Oncol 2023; 34:e71. [PMID: 37417299 PMCID: PMC10627750 DOI: 10.3802/jgo.2023.34.e71] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 04/17/2023] [Accepted: 05/13/2023] [Indexed: 07/08/2023] Open
Abstract
OBJECTIVE More than 75% of ovarian cancer patients are diagnosed at advanced stages and die of tumor cell metastasis. This study aimed to identify new epigenetic and transcriptomic alterations associated with ovarian cancer metastasis. METHODS Two cell sublines with low- and high-metastasis potentials were derived from the ovarian cancer cell line A2780. Genome-wide DNA methylome and transcriptome profiling were carried out in these two sublines by Reduced Representation Bisulfite Sequencing and RNA-seq technologies. Cell-based assays were conducted to support the clinical findings. RESULTS There are distinct DNA methylation and gene expression patterns between the two cell sublines with low- and high-metastasis potentials. Integrated analysis identified 33 methylation-induced genes potentially involved in ovarian cancer metastasis. The DNA methylation patterns of two of them (i.e., SFRP1 and LIPG) were further validated in human specimens, indicating that they were hypermethylated and downregulated in peritoneal metastatic ovarian carcinoma compared to primary ovarian carcinoma. Patients with lower SFRP1 and LIPG expression tend to have a worse prognosis. Functionally, knockdown of SFRP1 and LIPG promoted cell growth and migration, whereas their overexpression resulted in the opposite effects. In particular, knockdown of SFRP1 could phosphorylate GSK3β and increase β-catenin expression, leading to deregulated activation of the Wnt/β-catenin signaling. CONCLUSION Many systemic and important epigenetic and transcriptomic alterations occur in the progression of ovarian cancer. In particular, epigenetic silencing of SFRP1 and LIPG is a potential driver event in ovarian cancer metastasis. They can be used as prognostic biomarkers and therapeutic targets for ovarian cancer patients.
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Affiliation(s)
- Jiani Yi
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengting Wu
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhihong Zheng
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Qing Zhou
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Xufan Li
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Lu
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Pengyuan Liu
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China.
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Martinez-Monleon A, Gaarder J, Djos A, Kogner P, Fransson S. Identification of recurrent 3q13.31 chromosomal rearrangement indicates LSAMP as a tumor suppressor gene in neuroblastoma. Int J Oncol 2023; 62:27. [PMID: 36601748 PMCID: PMC9851131 DOI: 10.3892/ijo.2023.5475] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 11/04/2022] [Indexed: 01/04/2023] Open
Abstract
Neuroblastoma (NB) is a childhood malignancy of the sympathetic nervous system. NB is mainly driven by copy number alterations, such as MYCN amplification, large deletions of chromosome arm 11q and gain of chromosome arm 17q, which are all markers of high‑risk disease. Genes targeted by recurrent, smaller, focal alterations include CDKN2A/B, TERT, PTPRD and ATRX. Our previous study on relapsed NB detected recurrent structural alterations centered at limbic system‑associated membrane protein (LSAMP; HUGO Gene Nomenclature Committee: 6705; chromosomal location 3q13.31), which is a gene frequently reported to be deleted or downregulated in other types of cancer. Notably, in cancer, LSAMP has been shown to have tumor‑suppressing functions. The present study performed an expanded investigation using whole genome sequencing of tumors from 35 patients, mainly with high‑risk NB. Focal duplications or deletions targeting LSAMP were detected in six cases (17%), whereas single nucleotide polymorphism‑microarray analysis of 16 NB cell lines detected segmental alterations at 3q13.31 in seven out of the 16 NB cell lines (44%). Furthermore, low expression of LSAMP in NB tumors was significantly associated with poor overall and event‑free survival. In vitro, knockdown of LSAMP in NB cell lines increased cell proliferation, whereas overexpression decreased proliferation and viability. These findings supported a tumor suppressor role for LSAMP in NB. However, the higher incidence of LSAMP aberrations in cell lines and in relapsed NB tumors suggested that these alterations were a late event predominantly in advanced NB with a poor prognosis, indicating a role of LSAMP in tumor progression rather than in tumor initiation. In conclusion, the present study demonstrated recurrent genomic aberrations of chromosomal region 3q13.31 that targeted the LSAMP gene, which encodes a membrane protein involved in cell adhesion, central nervous system development and neurite outgrowth. The frequent aberrations affecting LSAMP, together with functional evidence, suggested an anti‑proliferative role of LSAMP in NB.
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Affiliation(s)
- Angela Martinez-Monleon
- Department of Laboratory Medicine, Sahlgrenska Academy at University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Jennie Gaarder
- Department of Laboratory Medicine, Sahlgrenska Academy at University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Anna Djos
- Department of Laboratory Medicine, Sahlgrenska Academy at University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Per Kogner
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Susanne Fransson
- Department of Laboratory Medicine, Sahlgrenska Academy at University of Gothenburg, SE-405 30 Gothenburg, Sweden,Correspondence to: Dr Susanne Fransson, Department of Laboratory Medicine, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 3B, SE-405 30 Gothenburg, Sweden, E-mail:
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Boni C, Sorio C. The Role of the Tumor Suppressor Gene Protein Tyrosine Phosphatase Gamma in Cancer. Front Cell Dev Biol 2022; 9:768969. [PMID: 35071225 PMCID: PMC8766859 DOI: 10.3389/fcell.2021.768969] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/16/2021] [Indexed: 12/31/2022] Open
Abstract
Members of the Protein Tyrosine Phosphatase (PTPs) family are associated with growth regulation and cancer development. Acting as natural counterpart of tyrosine kinases (TKs), mainly involved in crucial signaling pathways such as regulation of cell cycle, proliferation, invasion and angiogenesis, they represent key parts of complex physiological homeostatic mechanisms. Protein tyrosine phosphatase gamma (PTPRG) is classified as a R5 of the receptor type (RPTPs) subfamily and is broadly expressed in various isoforms in different tissues. PTPRG is considered a tumor-suppressor gene (TSG) mapped on chromosome 3p14-21, a region frequently subject to loss of heterozygosity in various tumors. However, reported mechanisms of PTPRG downregulation include missense mutations, ncRNA gene regulation and epigenetic silencing by hypermethylation of CpG sites on promoter region causing loss of function of the gene product. Inactive forms or total loss of PTPRG protein have been described in sporadic and Lynch syndrome colorectal cancer, nasopharyngeal carcinoma, ovarian, breast, and lung cancers, gastric cancer or diseases affecting the hematopoietic compartment as Lymphoma and Leukemia. Noteworthy, in Central Nervous System (CNS) PTPRZ/PTPRG appears to be crucial in maintaining glioblastoma cell-related neuronal stemness, carving out a pathological functional role also in this tissue. In this review, we will summarize the current knowledge on the role of PTPRG in various human cancers.
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Affiliation(s)
- Christian Boni
- Department of Medicine, General Pathology Division, University of Verona, Verona, Italy
| | - Claudio Sorio
- Department of Medicine, General Pathology Division, University of Verona, Verona, Italy
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Bellou E, Escott-Price V. Are Alzheimer's and coronary artery diseases genetically related to longevity? Front Psychiatry 2022; 13:1102347. [PMID: 36684006 PMCID: PMC9859055 DOI: 10.3389/fpsyt.2022.1102347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/12/2022] [Indexed: 01/07/2023] Open
Abstract
INTRODUCTION In the last decade researchers have attempted to investigate the shared genetic architecture of longevity and age-related diseases and assess whether the increased longevity in certain people is due to protective alleles in the risk genes for a particular condition or whether there are specific "longevity" genes increasing the lifespan independently of age-related conditions' risk genes. The aim of this study was to investigate the shared genetic component between longevity and two age-related conditions. METHODS We performed a cross-trait meta-analysis of publicly available genome-wide data for Alzheimer's disease, coronary artery disease and longevity using a subset-based approach provided by the R package ASSET. RESULTS Despite the lack of strong genetic correlation between longevity and the two diseases, we identified 38 genome-wide significant lead SNPs across 22 independent genomic loci. Of them 6 were found to be potentially shared among the three traits mapping to genes including DAB2IP, DNM2, FCHO1, CLPTM1, and SNRPD2. We also identified 19 novel genome-wide associations for the individual traits in this study. Functional annotations and biological pathway enrichment analyses suggested that pleiotropic variants are involved in clathrin-mediated endocytosis and plasma lipoprotein and neurotransmitter clearance processes. DISCUSSION In summary, we have been able to advance in the knowledge of the genetic overlap existing among longevity and the two most common age-related disorders.
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Affiliation(s)
- Eftychia Bellou
- UK Dementia Research Institute, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Valentina Escott-Price
- Division of Neuroscience and Mental Health, School of Medicine, Cardiff University, Cardiff, United Kingdom
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Khamko R, Daduang J, Settasatian C, Limpaiboon T. OPCML Exerts Antitumor Effects in Cholangiocarcinoma via AXL/STAT3 Inactivation and Rho GTPase Down-regulation. Cancer Genomics Proteomics 2021; 18:771-780. [PMID: 34697068 DOI: 10.21873/cgp.20296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND/AIM Opioid-binding protein/cell adhesion molecule-like (OPCML) plays a crucial role in the suppression of tumor progression in several cancer types. Nevertheless, the association between OPCML functions and cholangiocarcinoma (CCA) progression remains unknown. We aimed to investigate biological functions of OPCML and related signaling pathways in CCA cell lines. MATERIALS AND METHODS Methylation status and ectopic expression of OPCML were determined in CCA cell lines using methylation-specific polymerase chain reaction and pcDNA3.1+/C-(K)DYK-OPCML, respectively. Cell proliferation, migration and invasion were investigated. RESULTS OPCML was found to be epigenetically silenced by DNA methylation. Ectopic expression of OPCML inhibited CCA proliferation by inducing apoptosis via AXL receptor tyrosine kinase/signal transducer and activator of transcription 3 (AXL/STAT3) inactivation. It also suppressed cell migration and invasion via down-regulation of Rho GTPases, ras homolog family member A (RHOA), Rac family small GTPase 1 (RAC1) and cell division cycle 42 (CDC42). CONCLUSION We are the first to unravel the antitumor effects and the related signaling pathways of OPCML in CCA. The loss of OPCML expression due to promoter hypermethylation can cause a decrease in cell death but increase in cell migration and invasion, which may at least in part contribute to CCA progression.
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Affiliation(s)
- Ricuphan Khamko
- Biomedical Science Program, Graduate School, Khon Kaen University, Khon Kaen, Thailand.,Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Jureerut Daduang
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Chatri Settasatian
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Temduang Limpaiboon
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand; .,Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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Song Y, Lee JK, Lee JO, Kwon B, Seo EJ, Suh DC. Whole Exome Sequencing in Patients with Phenotypically Associated Familial Intracranial Aneurysm. Korean J Radiol 2021; 23:101-111. [PMID: 34668355 PMCID: PMC8743149 DOI: 10.3348/kjr.2021.0467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/17/2021] [Accepted: 08/03/2021] [Indexed: 11/24/2022] Open
Abstract
Objective Familial intracranial aneurysms (FIAs) are found in approximately 6%–20% of patients with intracranial aneurysms (IAs), suggesting that genetic predisposition likely plays a role in its pathogenesis. The aim of this study was to identify possible IA-associated variants using whole exome sequencing (WES) in selected Korean families with FIA. Materials and Methods Among the 26 families in our institutional database with two or more IA-affected first-degree relatives, three families that were genetically enriched (multiple, early onset, or common site involvement within the families) for IA were selected for WES. Filtering strategies, including a family-based approach and knowledge-based prioritization, were applied to derive possible IA-associated variants from the families. A chromosomal microarray was performed to detect relatively large chromosomal abnormalities. Results Thirteen individuals from the three families were sequenced, of whom seven had IAs. We noted three rare, potentially deleterious variants (PLOD3 c.1315G>A, NTM c.968C>T, and CHST14 c.58C>T), which are the most promising candidates among the 11 potential IA-associated variants considering gene-phenotype relationships, gene function, co-segregation, and variant pathogenicity. Microarray analysis did not reveal any significant copy number variants in the families. Conclusion Using WES, we found that rare, potentially deleterious variants in PLOD3, NTM, and CHST14 genes are likely responsible for the subsets of FIAs in a cohort of Korean families.
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Affiliation(s)
- Yunsun Song
- Division of Neurointervention Clinic, Department of Radiology, Neurointervention Clinic, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jong-Keuk Lee
- Asan Institute of Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jin-Ok Lee
- Department of Laboratory Medicine, Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Boseong Kwon
- Division of Neurointervention Clinic, Department of Radiology, Neurointervention Clinic, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Eul-Ju Seo
- Department of Laboratory Medicine, Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
| | - Dae Chul Suh
- Division of Neurointervention Clinic, Department of Radiology, Neurointervention Clinic, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
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Shao Y, Kong J, Xu H, Wu X, Cao Y, Li W, Han J, Li D, Xie K, Wu J. OPCML Methylation and the Risk of Ovarian Cancer: A Meta and Bioinformatics Analysis. Front Cell Dev Biol 2021; 9:570898. [PMID: 33777925 PMCID: PMC7990783 DOI: 10.3389/fcell.2021.570898] [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: 07/01/2020] [Accepted: 02/08/2021] [Indexed: 11/13/2022] Open
Abstract
Background: The association of opioid binding protein cell adhesion molecule-like (OPCML) gene methylation with ovarian cancer risk remains unclear. Methods: We identified eligible studies by searching the PubMed, Web of Science, ScienceDirect, and Wanfang databases. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were used to determine the association of OPCML methylation with ovarian cancer risk. Meta-regression and subgroup analysis were used to assess the sources of heterogeneity. Additionally, we analyzed the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) datasets to validate our findings. Results: Our study included 476 ovarian cancer patients and 385 controls from eight eligible studies. The pooled OR was 33.47 (95% CI = 12.43-90.16) in the cancer group vs. the control group under the random-effects model. The association was still significant in subgroups according to sample type, control type, methods, and sample sizes (all P < 0.05). Sensitivity analysis showed that the finding was robust. No publication bias was observed in Begg's (P = 0.458) and Egger's tests (P = 0.261). We further found that OPCML methylation was related to III/IV (OR = 4.20, 95% CI = 1.59-11.14) and poorly differentiated grade (OR = 4.37; 95% CI = 1.14-16.78). Based on GSE146552 and GSE155760, we validated that three CpG sites (cg16639665, cg23236270, cg15964611) in OPCML promoter region were significantly higher in cancer tissues compared to normal tissues. However, we did not observe the associations of OPCML methylation with clinicopathological parameters and overall survival based on TCGA ovarian cancer data. Conclusion: Our findings support that OPCML methylation is associated with an increased risk of ovarian cancer.
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Affiliation(s)
- Yang Shao
- Nanjing Maternity and Child Health Care Institute, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, China.,The First People's Hospital of Zhangjiagang City, The Zhangjiagang Affiliated Hospital of Soochow University, Suzhou, China
| | - Jing Kong
- Nanjing Maternity and Child Health Care Institute, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, China
| | - Hanzi Xu
- Department of Radiotherapy, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaoli Wu
- Nanjing Maternity and Child Health Care Institute, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, China
| | - YuePeng Cao
- Nanjing Maternity and Child Health Care Institute, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, China
| | - Weijian Li
- Nanjing Maternity and Child Health Care Institute, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, China
| | - Jing Han
- Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Dake Li
- Nanjing Maternity and Child Health Care Institute, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, China
| | - Kaipeng Xie
- Nanjing Maternity and Child Health Care Institute, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, China
| | - Jiangping Wu
- Nanjing Maternity and Child Health Care Institute, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, China
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Lim JH, Beg MMA, Ahmad K, Shaikh S, Ahmad SS, Chun HJ, Choi D, Lee WJ, Jin JO, Kim J, Jan AT, Lee EJ, Choi I. IgLON5 Regulates the Adhesion and Differentiation of Myoblasts. Cells 2021; 10:417. [PMID: 33671182 PMCID: PMC7922608 DOI: 10.3390/cells10020417] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/06/2021] [Accepted: 02/15/2021] [Indexed: 02/07/2023] Open
Abstract
IgLON5 is a cell adhesion protein belonging to the immunoglobulin superfamily and has important cellular functions. The objective of this study was to determine the role played by IgLON5 during myogenesis. We found IgLON5 expression progressively increased in C2C12 myoblasts during transition from the adhesion to differentiation stage. IgLON5 knockdown (IgLON5kd) cells exhibited reduced cell adhesion, myotube formation, and maturation and reduced expressions of different types of genes, including those coding for extracellular matrix (ECM) components (COL1a1, FMOD, DPT, THBS1), cell membrane proteins (ITM2a, CDH15), and cytoskeletal protein (WASP). Furthermore, decreased IgLON5 expression in FMODkd, DPTkd, COL1a1kd, and ITM2akd cells suggested that IgLON5 and these genes mutually control gene expression during myogenesis. IgLON5 immunoneutralization resulted in significant reduction in the protein level of myogenic markers (MYOD, MYOG, MYL2). IgLON5 expression was higher in the CTX-treated gastrocnemius mice muscles (day 7), which confirmed increase expression of IgLON5 during muscle. Collectively, these results suggest IgLON5 plays an important role in myogenesis, muscle regeneration, and that proteins in ECM and myoblast membranes form an interactive network that establishes an essential microenvironment that ensures muscle stem cell survival.
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Affiliation(s)
- Jeong Ho Lim
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (J.H.L.); (M.M.A.B.); (S.S.); (S.S.A.); (H.J.C.); (D.C.); (J.-O.J.); (J.K.)
| | - Mirza Masroor Ali Beg
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (J.H.L.); (M.M.A.B.); (S.S.); (S.S.A.); (H.J.C.); (D.C.); (J.-O.J.); (J.K.)
| | - Khurshid Ahmad
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea;
| | - Sibhghatulla Shaikh
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (J.H.L.); (M.M.A.B.); (S.S.); (S.S.A.); (H.J.C.); (D.C.); (J.-O.J.); (J.K.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea;
| | - Syed Sayeed Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (J.H.L.); (M.M.A.B.); (S.S.); (S.S.A.); (H.J.C.); (D.C.); (J.-O.J.); (J.K.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea;
| | - Hee Jin Chun
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (J.H.L.); (M.M.A.B.); (S.S.); (S.S.A.); (H.J.C.); (D.C.); (J.-O.J.); (J.K.)
| | - Dukhwan Choi
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (J.H.L.); (M.M.A.B.); (S.S.); (S.S.A.); (H.J.C.); (D.C.); (J.-O.J.); (J.K.)
| | - Woo-Jong Lee
- Biomedical Manufacturing Technology Center, Korea Institute of Industrial Technology, Yeongcheon 38822, Korea;
| | - Jun-O Jin
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (J.H.L.); (M.M.A.B.); (S.S.); (S.S.A.); (H.J.C.); (D.C.); (J.-O.J.); (J.K.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea;
| | - Jihoe Kim
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (J.H.L.); (M.M.A.B.); (S.S.); (S.S.A.); (H.J.C.); (D.C.); (J.-O.J.); (J.K.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea;
| | - Arif Tasleem Jan
- School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185234, India;
| | - Eun Ju Lee
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (J.H.L.); (M.M.A.B.); (S.S.); (S.S.A.); (H.J.C.); (D.C.); (J.-O.J.); (J.K.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea;
| | - Inho Choi
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (J.H.L.); (M.M.A.B.); (S.S.); (S.S.A.); (H.J.C.); (D.C.); (J.-O.J.); (J.K.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea;
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12
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Lian B, Li H, Liu Y, Chai D, Gao Y, Zhang Y, Zhou J, Li J. Expression and promoter methylation status of OPCML and its functions in the inhibition of cell proliferation, migration, and invasion in breast cancer. Breast Cancer 2020; 28:448-458. [PMID: 33108608 DOI: 10.1007/s12282-020-01179-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/16/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND Opioid binding protein/cell adhesion molecule-like (OPCML) has been demonstrated to be a tumor suppressor gene, as it has been shown in previous studies to play a tumor-suppressive role in a variety of cancers. However, the role of OPCML in breast tumorigenesis remains unclear. METHODS In this study, we analyzed OPCML expression in breast cancers and adjacent non-tumor tissue samples and examined its molecular function in the breast cancer-derived cell lines MDA-MB-231 and MCF7. RESULTS We found that OPCML was downregulated in most breast cancer samples but that this protein was expressed in most adjacent non-tumor samples. The loss or downregulation of OPCML is associated with hypermethylation of its promoter. Methylation of the OPCML promoter was detected in all breast cancer cell lines and primary tumors but was not detected in surgical margin tissues and normal breast tissues. Furthermore, functional assays showed that ectopic OPCML expression could inhibit breast tumor cell proliferation in vivo and in vitro and further suppresses tumor cell migration and invasion. CONCLUSION Our results show that OPCML exerts its tumor-suppressive functions in human breast cancer cells. Moreover, the promoter-specific hypermethylation of OPCML plays an important role in human breast cancer development.
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Affiliation(s)
- Bin Lian
- Department of Oncology Surgery, General Hospital of Ningxia Medical University, Yinchuan, 750004, Ningxia, China
| | - Hong Li
- Department of Oncology Surgery, General Hospital of Ningxia Medical University, Yinchuan, 750004, Ningxia, China
| | - Yaobang Liu
- Department of Oncology Surgery, General Hospital of Ningxia Medical University, Yinchuan, 750004, Ningxia, China
| | - Dahai Chai
- Department of Oncology Surgery, General Hospital of Ningxia Medical University, Yinchuan, 750004, Ningxia, China
| | - Yali Gao
- Ningxia Medical University, Yinchuan, 750004, Ningxia, China
| | - Yangyang Zhang
- Ningxia Medical University, Yinchuan, 750004, Ningxia, China
| | - Jia Zhou
- Ningxia Medical University, Yinchuan, 750004, Ningxia, China
| | - Jinping Li
- Department of Oncology Surgery, General Hospital of Ningxia Medical University, Yinchuan, 750004, Ningxia, China.
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13
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Antony J, Zanini E, Birtley JR, Gabra H, Recchi C. Emerging roles for the GPI-anchored tumor suppressor OPCML in cancers. Cancer Gene Ther 2020; 28:18-26. [PMID: 32595215 DOI: 10.1038/s41417-020-0187-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 12/11/2022]
Abstract
OPCML is a highly conserved glycosyl phosphatidylinositol (GPI)-anchored protein belonging to the IgLON family of cell adhesion molecules. OPCML functions as a tumor suppressor and is silenced in over 80% of ovarian cancers by loss of heterozygosity and by epigenetic mechanisms. OPCML inactivation is also observed in many other cancers suggesting a conservation of tumor suppressor function. Although epigenetic silencing and subsequent loss of OPCML expression correlate with poor progression-free and overall patient survival, its mechanism of action is only starting to be fully elucidated. Recent discoveries have demonstrated that OPCML exerts its tumor suppressor effect by inhibiting several cancer hallmark phenotypes in vitro and abrogating tumorigenesis in vivo, by downregulating/inactivating a specific spectrum of Receptor Tyrosine Kinases (RTKs), including EphA2, FGFR1, FGFR3, HER2, HER4, and AXL. This modulation of RTKs can also sensitize ovarian and breast cancers to lapatinib, erlotinib, and anti-AXL therapies. Furthermore, OPCML has also been shown to function in synergy with the tumor suppressor phosphatase PTPRG to inactivate pro-metastatic RTKs such as AXL. Recently, the identification of inactivating point mutations and the elucidation of the crystal structure of OPCML have provided valuable insights into its structure-function relationships, giving rise to its potential as an anti-cancer therapeutic.
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Affiliation(s)
- Jane Antony
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, W12 0NN, UK.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, 94305, USA
| | - Elisa Zanini
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, W12 0NN, UK
| | | | - Hani Gabra
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, W12 0NN, UK
| | - Chiara Recchi
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, W12 0NN, UK.
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14
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Palu RAS, Ong E, Stevens K, Chung S, Owings KG, Goodman AG, Chow CY. Natural Genetic Variation Screen in Drosophila Identifies Wnt Signaling, Mitochondrial Metabolism, and Redox Homeostasis Genes as Modifiers of Apoptosis. G3 (BETHESDA, MD.) 2019; 9:3995-4005. [PMID: 31570502 PMCID: PMC6893197 DOI: 10.1534/g3.119.400722] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/26/2019] [Indexed: 12/22/2022]
Abstract
Apoptosis is the primary cause of degeneration in a number of neuronal, muscular, and metabolic disorders. These diseases are subject to a great deal of phenotypic heterogeneity in patient populations, primarily due to differences in genetic variation between individuals. This creates a barrier to effective diagnosis and treatment. Understanding how genetic variation influences apoptosis could lead to the development of new therapeutics and better personalized treatment approaches. In this study, we examine the impact of the natural genetic variation in the Drosophila Genetic Reference Panel (DGRP) on two models of apoptosis-induced retinal degeneration: overexpression of p53 or reaper (rpr). We identify a number of known apoptotic, neural, and developmental genes as candidate modifiers of degeneration. We also use Gene Set Enrichment Analysis (GSEA) to identify pathways that harbor genetic variation that impact these apoptosis models, including Wnt signaling, mitochondrial metabolism, and redox homeostasis. Finally, we demonstrate that many of these candidates have a functional effect on apoptosis and degeneration. These studies provide a number of avenues for modifying genes and pathways of apoptosis-related disease.
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Affiliation(s)
- Rebecca A S Palu
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Elaine Ong
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Kaitlyn Stevens
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Shani Chung
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Katie G Owings
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Alan G Goodman
- School of Molecular Biosciences, and
- Paul G. Allen School for Global Animal Health, Washington State University College of Veterinary Medicine, Pullman, WA 99164
| | - Clement Y Chow
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112,
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15
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Singh A, Gupta S, Sachan M. Epigenetic Biomarkers in the Management of Ovarian Cancer: Current Prospectives. Front Cell Dev Biol 2019; 7:182. [PMID: 31608277 PMCID: PMC6761254 DOI: 10.3389/fcell.2019.00182] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/19/2019] [Indexed: 12/15/2022] Open
Abstract
Ovarian cancer (OC) causes significant morbidity and mortality as neither detection nor screening of OC is currently feasible at an early stage. Difficulty to promptly diagnose OC in its early stage remains challenging due to non-specific symptoms in the early-stage of the disease, their presentation at an advanced stage and poor survival. Therefore, improved detection methods are urgently needed. In this article, we summarize the potential clinical utility of epigenetic signatures like DNA methylation, histone modifications, and microRNA dysregulation, which play important role in ovarian carcinogenesis and discuss its application in development of diagnostic, prognostic, and predictive biomarkers. Molecular characterization of epigenetic modification (methylation) in circulating cell free tumor DNA in body fluids offers novel, non-invasive approach for identification of potential promising cancer biomarkers, which can be performed at multiple time points and probably better reflects the prevailing molecular profile of cancer. Current status of epigenetic research in diagnosis of early OC and its management are discussed here with main focus on potential diagnostic biomarkers in tissue and body fluids. Rapid and point of care diagnostic applications of DNA methylation in liquid biopsy has been precluded as a result of cumbersome sample preparation with complicated conventional methods of isolation. New technologies which allow rapid identification of methylation signatures directly from blood will facilitate sample-to answer solutions thereby enabling next-generation point of care molecular diagnostics. To date, not a single epigenetic biomarker which could accurately detect ovarian cancer at an early stage in either tissue or body fluid has been reported. Taken together, the methodological drawbacks, heterogeneity associated with ovarian cancer and non-validation of the clinical utility of reported potential biomarkers in larger ovarian cancer populations has impeded the transition of epigenetic biomarkers from lab to clinical settings. Until addressed, clinical implementation as a diagnostic measure is a far way to go.
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Affiliation(s)
- Alka Singh
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
| | - Sameer Gupta
- Department of Surgical Oncology, King George Medical University, Lucknow, India
| | - Manisha Sachan
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
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16
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Birtley JR, Alomary M, Zanini E, Antony J, Maben Z, Weaver GC, Von Arx C, Mura M, Marinho AT, Lu H, Morecroft EVN, Karali E, Chayen NE, Tate EW, Jurewicz M, Stern LJ, Recchi C, Gabra H. Inactivating mutations and X-ray crystal structure of the tumor suppressor OPCML reveal cancer-associated functions. Nat Commun 2019; 10:3134. [PMID: 31316070 PMCID: PMC6637204 DOI: 10.1038/s41467-019-10966-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/06/2019] [Indexed: 11/28/2022] Open
Abstract
OPCML, a tumor suppressor gene, is frequently silenced epigenetically in ovarian and other cancers. Here we report, by analysis of databases of tumor sequences, the observation of OPCML somatic missense mutations from various tumor types and the impact of these mutations on OPCML function, by solving the X-ray crystal structure of this glycoprotein to 2.65 Å resolution. OPCML consists of an extended arrangement of three immunoglobulin-like domains and homodimerizes via a network of contacts between membrane-distal domains. We report the generation of a panel of OPCML variants with representative clinical mutations and demonstrate clear phenotypic effects in vitro and in vivo including changes to anchorage-independent growth, interaction with activated cognate receptor tyrosine kinases, cellular migration, invasion in vitro and tumor growth in vivo. Our results suggest that clinically occurring somatic missense mutations in OPCML have the potential to contribute to tumorigenesis in a variety of cancers.
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Affiliation(s)
- James R Birtley
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, 01655, USA
- UCB Pharma, Bath Road, Slough, SL1 3WE, UK
| | - Mohammad Alomary
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Elisa Zanini
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Jane Antony
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Zachary Maben
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, 01655, USA
| | - Grant C Weaver
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, 01655, USA
| | - Claudia Von Arx
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Manuela Mura
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Aline T Marinho
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Haonan Lu
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Eloise V N Morecroft
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK
- Department of Chemistry, Imperial College London, Wood Lane, London, W12 0BZ, UK
| | - Evdoxia Karali
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Naomi E Chayen
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, SW7 2AZ, UK
| | - Edward W Tate
- Department of Chemistry, Imperial College London, Wood Lane, London, W12 0BZ, UK
| | - Mollie Jurewicz
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, 01655, USA
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, 01655, USA.
| | - Chiara Recchi
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK.
| | - Hani Gabra
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK.
- Clinical Discovery Unit, Early Clinical Development, IMED Biotech Unit, AstraZeneca, Cambridge, SG8 6HB, UK.
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Simovic I, Castaño-Rodríguez N, Kaakoush NO. OPCML: A Promising Biomarker and Therapeutic Avenue. Trends Cancer 2019; 5:463-466. [PMID: 31421903 DOI: 10.1016/j.trecan.2019.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/29/2019] [Accepted: 06/04/2019] [Indexed: 10/26/2022]
Abstract
Opioid-binding protein/cell adhesion molecule (OPCML) is expressed in many tissues and localizes to the plasma membrane. It is a putative tumor suppressor that acts on receptor tyrosine kinases (RTKs), influencing cell cycle arrest, apoptosis, and migration. Its expression is silenced epigenetically in cancer, inferring potential diagnostic, prognostic, and therapeutic roles.
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Affiliation(s)
- Isidora Simovic
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW 2052, Australia
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18
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Cross-Talk between Fibroblast Growth Factor Receptors and Other Cell Surface Proteins. Cells 2019; 8:cells8050455. [PMID: 31091809 PMCID: PMC6562592 DOI: 10.3390/cells8050455] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/08/2019] [Accepted: 05/13/2019] [Indexed: 12/14/2022] Open
Abstract
Fibroblast growth factors (FGFs) and their receptors (FGFRs) constitute signaling circuits that transmit signals across the plasma membrane, regulating pivotal cellular processes like differentiation, migration, proliferation, and apoptosis. The malfunction of FGFs/FGFRs signaling axis is observed in numerous developmental and metabolic disorders, and in various tumors. The large diversity of FGFs/FGFRs functions is attributed to a great complexity in the regulation of FGFs/FGFRs-dependent signaling cascades. The function of FGFRs is modulated at several levels, including gene expression, alternative splicing, posttranslational modifications, and protein trafficking. One of the emerging ways to adjust FGFRs activity is through formation of complexes with other integral proteins of the cell membrane. These proteins may act as coreceptors, modulating binding of FGFs to FGFRs and defining specificity of elicited cellular response. FGFRs may interact with other cell surface receptors, like G-protein-coupled receptors (GPCRs) or receptor tyrosine kinases (RTKs). The cross-talk between various receptors modulates the strength and specificity of intracellular signaling and cell fate. At the cell surface FGFRs can assemble into large complexes involving various cell adhesion molecules (CAMs). The interplay between FGFRs and CAMs affects cell–cell interaction and motility and is especially important for development of the central nervous system. This review summarizes current stage of knowledge about the regulation of FGFRs by the plasma membrane-embedded partner proteins and highlights the importance of FGFRs-containing membrane complexes in pathological conditions, including cancer.
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19
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Wasenang W, Chaiyarit P, Proungvitaya S, Limpaiboon T. Serum cell-free DNA methylation of OPCML and HOXD9 as a biomarker that may aid in differential diagnosis between cholangiocarcinoma and other biliary diseases. Clin Epigenetics 2019; 11:39. [PMID: 30832707 PMCID: PMC6399934 DOI: 10.1186/s13148-019-0634-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 02/18/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Cholangiocarcinoma (CCA) is a fatal cancer of the bile duct epithelial cell lining. The misdiagnosis of CCA and other biliary diseases may occur due to the similarity of clinical manifestations and blood tests resulting in inappropriate or delayed treatment. Thus, an accurate and less-invasive method for differentiating CCA from other biliary diseases is inevitable. METHODS We quantified methylation of OPCML, HOXA9, and HOXD9 in serum cell-free DNA (cfDNA) of CCA patients and other biliary diseases using methylation-sensitive high-resolution melting (MS-HRM). Their potency as differential biomarkers between CCA and other biliary diseases was also evaluated by using receiver operating characteristic (ROC) curves. RESULTS The significant difference of methylation levels of OPCML and HOXD9 was observed in serum cfDNA of CCA compared to other biliary diseases. Assessment of serum cfDNA methylation of OPCML and HOXD9 as differential biomarkers of CCA and other biliary diseases showed the area under curve (AUC) of 0.850 (0.759-0.941) for OPCML which sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy were 80.00%, 90.00%, 88.88%, 81.81%, and 85.00%, respectively. The AUC of HOXD9 was 0.789 (0.686-0.892) with sensitivity, specificity, PPV, NPV, and accuracy of 67.50%, 90.00%, 87.09%, 73.46%, and 78.75%, respectively. The combined marker between OPCML and HOXD9 showed sensitivity, specificity, PPV, and NPV of 62.50%, 100%, 100%, and 72.72%, respectively, which may be helpful to prevent a misdiagnosis between CCA and other biliary diseases. CONCLUSIONS Our findings suggest the application of serum cfDNA methylation of OPCML and HOXD9 for differential diagnosis of CCA and other biliary diseases due to its less invasiveness and clinically practical method which may benefit the patients by preventing the misdiagnosis of CCA and avoiding unnecessary surgical intervention.
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Affiliation(s)
- Wiphawan Wasenang
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
- Biomedical Sciences, Graduate School, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Ponlatham Chaiyarit
- Research Group of Chronic Inflammatory Oral Diseases and Systemic Diseases Associated with Oral Health, Department of Oral Diagnosis, Faculty of Dentistry, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Siriporn Proungvitaya
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Temduang Limpaiboon
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand.
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.
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20
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Hentze JL, Høgdall CK, Høgdall EV. Methylation and ovarian cancer: Can DNA methylation be of diagnostic use? Mol Clin Oncol 2019; 10:323-330. [PMID: 30847169 DOI: 10.3892/mco.2019.1800] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 12/04/2018] [Indexed: 12/31/2022] Open
Abstract
Ovarian cancer is a silent killer and, due to late diagnosis and frequent chemo resistance in patients, the primary cause of fatality amongst the various types of gynecological cancer. The discovery of a specific and sensitive biomarker for ovarian cancer could improve early diagnosis, thereby saving lives. Biomarkers could also improve treatment, by predicting which patients will benefit from specific treatment strategies. DNA methylation is an epigenetic mechanism, and 'methylation imbalance' is characteristic of cancer. Previous research suggests that changes in DNA methylation can be used diagnostically, and that they may predict resistance to treatment. This paper gives an up-to-date overview of research investigating the potential of DNA methylation-based markers for diagnostics, prognostics, screening and prediction of drug resistance for ovarian cancer patients. DNA methylation cancer-biomarkers may be useful for cancer treatment, particularly since they are chemically stable and since cancer-associated changes in methylation typically precedes tumor growth. DNA methylation markers could improve diagnosis and treatment and might even be used for screening in the future. Furthermore, DNA methylation biomarkers could facilitate the development of precision medicine. However, at this point no biomarkers for ovarian cancer have a sufficient combination of sensitivity and specificity in a clinical setting. A reason for this is that most studies have focused on a single or a few methylation sites. More large screenings and genome-wide studies must be performed to increase the chance of identifying a DNA methylation marker which can identify ovarian cancer.
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Affiliation(s)
- Julie L Hentze
- Department of Pathology, Herlev Hospital, University of Copenhagen, 2730 Herlev, Denmark
| | - Claus K Høgdall
- Department of Gynecology, The Juliane Marie Centre, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Estrid V Høgdall
- Department of Pathology, Herlev Hospital, University of Copenhagen, 2730 Herlev, Denmark
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21
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OPCML is hypermethylated in a subset of patients with metaplastic changes in their esophagus. Biomark Res 2018; 6:35. [PMID: 30555700 PMCID: PMC6286609 DOI: 10.1186/s40364-018-0150-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/28/2018] [Indexed: 12/17/2022] Open
Abstract
OPCML hypermethylation is considered a promising cancer biomarker. We examined methylation levels in the first exon of OPCML in two patient cohorts within the esophageal adenocarcinoma and gastric adenocarcinoma cascades and in a range of cell-lines using a custom PyroMark CpG assay. Methylation levels were significantly higher in esophageal tissue with histologically confirmed glandular mucosa as compared to tissue from normal esophagi or gastro-esophageal reflux disease. Higher levels of OPCML methylation were absent in the adjacent normal esophageal tissue of patients with glandular mucosa. Higher levels of methylation were confirmed in cell-lines derived from patients with adenocarcinoma, but also detected in two cell-lines with signs of dysplasia. We validated our assay by showing no differences in methylation levels in DNA extracted from blood of patients within the gastric adenocarcinoma cascade. OPCML hypermethylation is present in a subset of patients with metaplastic changes in their esophagus.
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22
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Dong X, Zhang J, Yang F, Wu J, Cai R, Wang T, Zhang J. Effect of luteolin on the methylation status of the OPCML gene and cell growth in breast cancer cells. Exp Ther Med 2018; 16:3186-3194. [PMID: 30214542 DOI: 10.3892/etm.2018.6526] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/24/2018] [Indexed: 02/06/2023] Open
Abstract
The present study aimed to investigate the effect of luteolin on the methylation of opioid binding protein/cell adhesion molecule (OPCML) in breast cancer cells, as well as its underlying mechanism of action. Human breast cancer cell lines BT474 and MCF-7 were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum. The cells were treated with 0-30 µmol/l luteolin prior to investigation. Reverse transcription-quantitative polymerase chain reaction and western blot analysis were used to determine the mRNA and protein expression, respectively. High performance liquid chromatography and electrosprary ionization-mass spectrometry was used to analyze the methylation of the OPCML promoter region and whole genome. The methylation activity in the cell nucleus was determined using a DNA methyltransferase catalytic test. ELISA analysis was used to detect changes in the activity of transcription factors Sp1 and nuclear factor (NF)-κB. An MTT assay was performed to determine cell proliferation, while flow cytometry was used to detect cell cycle stage and apoptosis. Luteolin effectively upregulated the expression of OPCML in breast cancer cells. Luteolin activated OPCML by reducing intracellular methylation levels. Luteolin downregulated intracellular methylation levels by decreasing Sp1 and NF-κB activities. Luteolin affected the expression of DNMT1 and OPCML by downregulating Sp1 activity. Luteolin inhibited the proliferation and induced the apoptosis of BT474 and MCF-7 cells. The results of the present study suggest that luteolin inhibits the growth of breast cancer cells by decreasing the methylation and upregulating the expression of the OPCML gene.
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Affiliation(s)
- Xinmin Dong
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China.,Department of Oncology, The Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia 010010, P.R. China
| | - Jian Zhang
- Department of Radiotherapy, The Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia 010017, P.R. China
| | - Fan Yang
- Department of Basic Medicine, Xiangnan University, Chenzhou, Hunan 423000, P.R. China
| | - Jing Wu
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
| | - Rui Cai
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
| | - Tian Wang
- Department of Hematology and Oncology, Yan'an People's Hospital, Yan'an, Shaanxi 716000, P.R. China
| | - Jiren Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, P.R. China
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24
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Antony J, Zanini E, Kelly Z, Tan TZ, Karali E, Alomary M, Jung Y, Nixon K, Cunnea P, Fotopoulou C, Paterson A, Roy-Nawathe S, Mills GB, Huang RYJ, Thiery JP, Gabra H, Recchi C. The tumour suppressor OPCML promotes AXL inactivation by the phosphatase PTPRG in ovarian cancer. EMBO Rep 2018; 19:embr.201745670. [PMID: 29907679 DOI: 10.15252/embr.201745670] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 05/14/2018] [Accepted: 05/23/2018] [Indexed: 01/22/2023] Open
Abstract
In ovarian cancer, the prometastatic RTK AXL promotes motility, invasion and poor prognosis. Here, we show that reduced survival caused by AXL overexpression can be mitigated by the expression of the GPI-anchored tumour suppressor OPCML Further, we demonstrate that AXL directly interacts with OPCML, preferentially so when AXL is activated by its ligand Gas6. As a consequence, AXL accumulates in cholesterol-rich lipid domains, where OPCML resides. Here, phospho-AXL is brought in proximity to the lipid domain-restricted phosphatase PTPRG, which de-phosphorylates the RTK/ligand complex. This prevents AXL-mediated transactivation of other RTKs (cMET and EGFR), thereby inhibiting sustained phospho-ERK signalling, induction of the EMT transcription factor Slug, cell migration and invasion. From a translational perspective, we show that OPCML enhances the effect of the phase II AXL inhibitor R428 in vitro and in vivo We therefore identify a novel mechanism by which two spatially restricted tumour suppressors, OPCML and PTPRG, coordinate to repress AXL-dependent oncogenic signalling.
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Affiliation(s)
- Jane Antony
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, UK.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
| | - Elisa Zanini
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, UK
| | - Zoe Kelly
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, UK
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Evdoxia Karali
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, UK
| | - Mohammad Alomary
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, UK
| | - Youngrock Jung
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, UK
| | - Katherine Nixon
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, UK
| | - Paula Cunnea
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, UK
| | - Christina Fotopoulou
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, UK
| | - Andrew Paterson
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, UK
| | - Sushmita Roy-Nawathe
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, UK
| | - Gordon B Mills
- Division of Basic Science Research, Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ruby Yun-Ju Huang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Obstetrics and Gynecology, National University Health System, Singapore, Singapore
| | - Jean Paul Thiery
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore.,Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Hani Gabra
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, UK .,Early Clinical Development, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Chiara Recchi
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, UK
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Zanini E, Louis LS, Antony J, Karali E, Okon IS, McKie AB, Vaughan S, El-Bahrawy M, Stebbing J, Recchi C, Gabra H. The Tumor-Suppressor Protein OPCML Potentiates Anti-EGFR- and Anti-HER2-Targeted Therapy in HER2-Positive Ovarian and Breast Cancer. Mol Cancer Ther 2017; 16:2246-2256. [PMID: 28775148 DOI: 10.1158/1535-7163.mct-17-0081] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 05/22/2017] [Accepted: 07/14/2017] [Indexed: 11/16/2022]
Abstract
Opioid-binding protein/cell adhesion molecule-like (OPCML) is a tumor-suppressor gene that is frequently inactivated in ovarian cancer and many other cancers by somatic methylation. We have previously shown that OPCML exerts its suppressor function by negatively regulating a spectrum of receptor tyrosine kinases (RTK), such as ErbB2/HER2, FGFR1, and EphA2, thus attenuating their related downstream signaling. The physical interaction of OPCML with this defined group of RTKs is a prerequisite for their downregulation. Overexpression/gene amplification of EGFR and HER2 is a frequent event in multiple cancers, including ovarian and breast cancers. Molecular therapeutics against EGFR/HER2 or EGFR only, such as lapatinib and erlotinib, respectively, were developed to target these receptors, but resistance often occurs in relapsing cancers. Here we show that, though OPCML interacts only with HER2 and not with EGFR, the interaction of OPCML with HER2 disrupts the formation of the HER2-EGFR heterodimer, and this translates into a better response to both lapatinib and erlotinib in HER2-expressing ovarian and breast cancer cell lines. Also, we show that high OPCML expression is associated with better response to lapatinib therapy in breast cancer patients and better survival in HER2-overexpressing ovarian cancer patients, suggesting that OPCML co-therapy could be a valuable sensitizing approach to RTK inhibitors. Mol Cancer Ther; 16(10); 2246-56. ©2017 AACR.
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Affiliation(s)
- Elisa Zanini
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Louay S Louis
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Jane Antony
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Evdoxia Karali
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Imoh S Okon
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Center for Molecular and Translational Medicine, Georgia State University, Atlanta, Georgia
| | - Arthur B McKie
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Department of Medical Genetics, University of Cambridge, Addenbrooke's Treatment Centre, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Sebastian Vaughan
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Mona El-Bahrawy
- Department of Histopathology, Imperial College London, London, United Kingdom
| | - Justin Stebbing
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Chiara Recchi
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, United Kingdom.
| | - Hani Gabra
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, United Kingdom.
- Clinical Discovery Unit, Early Clinical Development, AstraZeneca, Cambridge, United Kingdom
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Wang B, Yu L, Luo X, Huang L, Li QS, Shao XS, Liu Y, Fan Y, Yang GZ. Detection of OPCML methylation, a possible epigenetic marker, from free serum circulating DNA to improve the diagnosis of early-stage ovarian epithelial cancer. Oncol Lett 2017; 14:217-223. [PMID: 28693156 PMCID: PMC5494804 DOI: 10.3892/ol.2017.6111] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 01/17/2017] [Indexed: 01/08/2023] Open
Abstract
The aim of the present study was to identify the appropriate DNA sequence and design high-quality primers for methylation-specific polymerase chain reaction (MSP). These primers may be used to examine and identify patients with early-stage epithelial ovarian carcinoma (EOC). Opioid binding protein/cell adhesion molecule like (OPCML), Runt-related transcription factor 3 and tissue factor pathway inhibitor 2 were selected as possible molecular markers. MSP primer sets were designed to monitor the methylation of the three markers. Free circulating DNA (fcDNA) from 194 patients with epithelial ovarian carcinoma and healthy donors were templates in the nested MSP. OPCML MSP was effective with respect to screening methylated fcDNA. One-way ANOVA P-values indicated that the difference in cancer antigen 125 (CA125), a biomarker for EOC diagnosis, level between early EOC and healthy donors was not significant. The methylation of OPCML was significantly altered in early-stage EOC compared with healthy donors (P<0.0001), and this supported the hypothesis that specific fcDNA methylation was able to distinguish patients with early-stage EOC from healthy donors. With respect to detecting early EOC, compared with the results of the CA125 test, MSP increased the κ coefficient from 0.140 to 0.757. Therefore, OPCML combined with fcDNA may be used to establish an improved clinical assay compared with the current CA125 test.
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Affiliation(s)
- Bi Wang
- School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China.,Department of Obstetrics and Gynecology, Guiyang Maternal and Child Health-Care Hospital, Guiyang, Guizhou 550003, P.R. China
| | - Lei Yu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510630, P.R. China.,Prenatal Diagnostic Center, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Xin Luo
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510630, P.R. China
| | - Lin Huang
- Prenatal Diagnostic Center, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Qin-Shan Li
- School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Xiao-Shan Shao
- Department of Obstetrics and Gynecology, Guiyang Maternal and Child Health-Care Hospital, Guiyang, Guizhou 550003, P.R. China
| | - Yi Liu
- Department of Obstetrics and Gynecology, Guiyang Maternal and Child Health-Care Hospital, Guiyang, Guizhou 550003, P.R. China
| | - Yu Fan
- Department of Obstetrics and Gynecology, Guiyang Maternal and Child Health-Care Hospital, Guiyang, Guizhou 550003, P.R. China
| | - Guo-Zhen Yang
- School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China.,Prenatal Diagnostic Center, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
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27
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Xing X, Cai W, Ma S, Wang Y, Shi H, Li M, Jiao J, Yang Y, Liu L, Zhang X, Chen M. Down-regulated expression of OPCML predicts an unfavorable prognosis and promotes disease progression in human gastric cancer. BMC Cancer 2017; 17:268. [PMID: 28407749 PMCID: PMC5391589 DOI: 10.1186/s12885-017-3203-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 03/17/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND OPCML belongs to the IgLON family of Ig domain-containing GPI-anchored cell adhesion molecules and was recently found to be involved in carcinogenesis, while its role in gastric cancer remains unclear. METHODS We assessed expression and biological behavior of OPCML in gastric cancer. RESULTS OPCML expression was markedly reduced in tumor tissues and cancer cell lines. Decreased OPCML expression had a significant association with unfavorable tumor stage (p = 0.007) and grading (p < 0.001). Furthermore, the results revealed that OPCML was an independent prognostic factor for overall survival in gastric cancer (p = 0.002). In addition, ectopic expression of OPCML in cancer cells significantly inhibited cell viability (p < 0.01) and colony formation (p < 0.001), arrest cell cycle in G0/G1 phase and induced apoptosis, and suppressed tumor formation in nude mice. The alterations of phosphorylation status of AKT and its substrate GSK3β, up-regulation of pro-apoptotic regulators including caspase-3, caspase-9 and PARP, and up-regulation of cell cycle regulator p27, were implicated in the biological activity of OPCML in cancer cells. CONCLUSION Down-regulated OPCML expression might serve as an independent predictor for unfavorable prognosis of patients, and the biological behavior supports its role as a tumor suppressor in gastric cancer.
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Affiliation(s)
- Xiangbin Xing
- Department of Gastroenterology, the First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan II Road, Guangzhou, 510080 China
| | - Weibin Cai
- Department of Biochemistry, Zhongshan Medical School, Sun Yat-sen University, Guangzhou, 510089 China
| | - Sanmei Ma
- Department of Biotechnology, Jinan University, Guangzhou, 510632 China
| | - Yongfei Wang
- Department of Biotechnology, Jinan University, Guangzhou, 510632 China
| | - Huijuan Shi
- Department of Pathology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080 China
| | - Ming Li
- Department of Gastroenterology, the First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan II Road, Guangzhou, 510080 China
- Department of Biotechnology, Jinan University, Guangzhou, 510632 China
| | - Jinxia Jiao
- Department of Gastroenterology, the First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan II Road, Guangzhou, 510080 China
- Department of Biotechnology, Jinan University, Guangzhou, 510632 China
| | - Yang Yang
- Department of Gastroenterology, the First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan II Road, Guangzhou, 510080 China
- Department of Biotechnology, Jinan University, Guangzhou, 510632 China
| | - Longshan Liu
- Department of Laboratory of General Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080 China
| | - Xiangliang Zhang
- Department of Abdominal Surgery (Section 2), Affiliated Cancer Hospital of Guangzhou Medical University, Guangzhou, 510095 China
| | - Minhu Chen
- Department of Gastroenterology, the First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan II Road, Guangzhou, 510080 China
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28
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Declerck K, Remy S, Wohlfahrt-Veje C, Main KM, Van Camp G, Schoeters G, Vanden Berghe W, Andersen HR. Interaction between prenatal pesticide exposure and a common polymorphism in the PON1 gene on DNA methylation in genes associated with cardio-metabolic disease risk-an exploratory study. Clin Epigenetics 2017; 9:35. [PMID: 28396702 PMCID: PMC5382380 DOI: 10.1186/s13148-017-0336-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 03/30/2017] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Prenatal environmental conditions may influence disease risk in later life. We previously found a gene-environment interaction between the paraoxonase 1 (PON1) Q192R genotype and prenatal pesticide exposure leading to an adverse cardio-metabolic risk profile at school age. However, the molecular mechanisms involved have not yet been resolved. It was hypothesized that epigenetics might be involved. The aim of the present study was therefore to investigate whether DNA methylation patterns in blood cells were related to prenatal pesticide exposure level, PON1 Q192R genotype, and associated metabolic effects observed in the children. METHODS Whole blood DNA methylation patterns in 48 children (6-11 years of age), whose mothers were occupationally unexposed or exposed to pesticides early in pregnancy, were determined by Illumina 450 K methylation arrays. RESULTS A specific methylation profile was observed in prenatally pesticide exposed children carrying the PON1 192R-allele. Differentially methylated genes were enriched in several neuroendocrine signaling pathways including dopamine-DARPP32 feedback (appetite, reward pathways), corticotrophin releasing hormone signaling, nNOS, neuregulin signaling, mTOR signaling, and type II diabetes mellitus signaling. Furthermore, we were able to identify possible candidate genes which mediated the associations between pesticide exposure and increased leptin level, body fat percentage, and difference in BMI Z score between birth and school age. CONCLUSIONS DNA methylation may be an underlying mechanism explaining an adverse cardio-metabolic health profile in children carrying the PON1 192R-allele and prenatally exposed to pesticides.
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Affiliation(s)
- Ken Declerck
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, Belgium
| | - Sylvie Remy
- Department of Epidemiology and Social Medicine, Antwerp University, Universiteitsplein 1, Antwerp, Belgium.,Flemish Institute for Technological Research (VITO), Unit Environmental Risk and Health, Boeretang 200, Mol, Belgium
| | - Christine Wohlfahrt-Veje
- Department of Growth and Reproduction, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark
| | - Katharina M Main
- Department of Growth and Reproduction, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark
| | - Guy Van Camp
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Greet Schoeters
- Flemish Institute for Technological Research (VITO), Unit Environmental Risk and Health, Boeretang 200, Mol, Belgium.,Department of Biomedical Sciences, Antwerp University, Universiteitsplein 1, Antwerp, Belgium.,Environmental Medicine, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, Belgium
| | - Helle R Andersen
- Environmental Medicine, Institute of Public Health, University of Southern Denmark, Odense, Denmark
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Vanaveski T, Singh K, Narvik J, Eskla KL, Visnapuu T, Heinla I, Jayaram M, Innos J, Lilleväli K, Philips MA, Vasar E. Promoter-Specific Expression and Genomic Structure of IgLON Family Genes in Mouse. Front Neurosci 2017; 11:38. [PMID: 28210208 PMCID: PMC5288359 DOI: 10.3389/fnins.2017.00038] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 01/19/2017] [Indexed: 01/20/2023] Open
Abstract
IgLON family is composed of five genes: Lsamp, Ntm, Opcml, Negr1, and Iglon5; encoding for five highly homologous neural adhesion proteins that regulate neurite outgrowth and synapse formation. In the current study we performed in silico analysis revealing that Ntm and Opcml display similar genomic structure as previously reported for Lsamp, characterized by two alternative promotors 1a and 1b. Negr1 and Iglon5 transcripts have uniform 5′ region, suggesting single promoter. Iglon5, the recently characterized family member, shares high level of conservation and structural qualities characteristic to IgLON family such as N-terminal signal peptide, three Ig domains, and GPI anchor binding site. By using custom 5′-isoform-specific TaqMan gene-expression assay, we demonstrated heterogeneous expression of IgLON transcripts in different areas of mouse brain and several-fold lower expression in selected tissues outside central nervous system. As an example, the expression of IgLON transcripts in urogenital and reproductive system is in line with repeated reports of urogenital tumors accompanied by mutations in IgLON genes. Considering the high levels of intra-family homology shared by IgLONs, we investigated potential compensatory effects at the level of IgLON isoforms in the brains of mice deficient of one or two family members. We found that the lack of IgLONs is not compensated by a systematic quantitative increase of the other family members. On the contrary, the expression of Ntm 1a transcript and NEGR1 protein was significantly reduced in the frontal cortex of Lsamp-deficient mice suggesting that the expression patterns within IgLON family are balanced coherently. The actions of individual IgLONs, however, can be antagonistic as demonstrated by differential expression of Syp in deletion mutants of IgLONs. In conclusion, we show that the genomic twin-promoter structure has impact on both anatomical distribution and intra-family interactions of IgLON family members. Remarkable variety in the activity levels of 1a and 1b promoters both in the brain and in other tissues, suggests complex functional regulation of IgLONs by alternative signal peptides driven by 1a and 1b promoters.
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Affiliation(s)
- Taavi Vanaveski
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu Tartu, Estonia
| | - Katyayani Singh
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu Tartu, Estonia
| | - Jane Narvik
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu Tartu, Estonia
| | - Kattri-Liis Eskla
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu Tartu, Estonia
| | - Tanel Visnapuu
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of TartuTartu, Estonia; Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of HelsinkiHelsinki, Finland
| | - Indrek Heinla
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu Tartu, Estonia
| | - Mohan Jayaram
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu Tartu, Estonia
| | - Jürgen Innos
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu Tartu, Estonia
| | - Kersti Lilleväli
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu Tartu, Estonia
| | - Mari-Anne Philips
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu Tartu, Estonia
| | - Eero Vasar
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu Tartu, Estonia
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30
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Song MA, Brasky TM, Marian C, Weng DY, Taslim C, Dumitrescu RG, Llanos AA, Freudenheim JL, Shields PG. Racial differences in genome-wide methylation profiling and gene expression in breast tissues from healthy women. Epigenetics 2016; 10:1177-87. [PMID: 26680018 DOI: 10.1080/15592294.2015.1121362] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Breast cancer is more common in European Americans (EAs) than in African Americans (AAs) but mortality from breast cancer is higher among AAs. While there are racial differences in DNA methylation and gene expression in breast tumors, little is known whether such racial differences exist in breast tissues of healthy women. Genome-wide DNA methylation and gene expression profiling was performed in histologically normal breast tissues of healthy women. Linear regression models were used to identify differentially-methylated CpG sites (CpGs) between EAs (n = 61) and AAs (n = 22). Correlations for methylation and expression were assessed. Biological functions of the differentially-methylated genes were assigned using the Ingenuity Pathway Analysis. Among 485 differentially-methylated CpGs by race, 203 were hypermethylated in EAs, and 282 were hypermethylated in AAs. Promoter-related differentially-methylated CpGs were more frequently hypermethylated in EAs (52%) than AAs (27%) while gene body and intergenic CpGs were more frequently hypermethylated in AAs. The differentially-methylated CpGs were enriched for cancer-associated genes with roles in cell death and survival, cellular development, and cell-to-cell signaling. In a separate analysis for correlation in EAs and AAs, different patterns of correlation were found between EAs and AAs. The correlated genes showed different biological networks between EAs and AAs; networks were connected by Ubiquitin C. To our knowledge, this is the first comprehensive genome-wide study to identify differences in methylation and gene expression between EAs and AAs in breast tissues from healthy women. These findings may provide further insights regarding the contribution of epigenetic differences to racial disparities in breast cancer.
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Affiliation(s)
- Min-Ae Song
- a Comprehensive Cancer Center; The Ohio State University and James Cancer Hospital ; Columbus , Ohio , USA
| | - Theodore M Brasky
- a Comprehensive Cancer Center; The Ohio State University and James Cancer Hospital ; Columbus , Ohio , USA
| | - Catalin Marian
- a Comprehensive Cancer Center; The Ohio State University and James Cancer Hospital ; Columbus , Ohio , USA.,b Biochemistry and Pharmacology Department ; Victor Babes University of Medicine and Pharmacy ; 300041 Timisoara , Romania
| | - Daniel Y Weng
- a Comprehensive Cancer Center; The Ohio State University and James Cancer Hospital ; Columbus , Ohio , USA
| | - Cenny Taslim
- a Comprehensive Cancer Center; The Ohio State University and James Cancer Hospital ; Columbus , Ohio , USA
| | | | - Adana A Llanos
- d Department of Epidemiology ; Rutgers School of Public Health and Rutgers Cancer Institute of New Jersey ; New Brunswick , NJ 08903 , USA
| | - Jo L Freudenheim
- e Department of Epidemiology and Environmental Health; School of Public Health and Health Professions ; University at Buffalo ; Buffalo , NY 14214 , USA
| | - Peter G Shields
- a Comprehensive Cancer Center; The Ohio State University and James Cancer Hospital ; Columbus , Ohio , USA
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Verma SS, Cooke Bailey JN, Lucas A, Bradford Y, Linneman JG, Hauser MA, Pasquale LR, Peissig PL, Brilliant MH, McCarty CA, Haines JL, Wiggs JL, Vrabec TR, Tromp G, Ritchie MD. Epistatic Gene-Based Interaction Analyses for Glaucoma in eMERGE and NEIGHBOR Consortium. PLoS Genet 2016; 12:e1006186. [PMID: 27623284 PMCID: PMC5021356 DOI: 10.1371/journal.pgen.1006186] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/22/2016] [Indexed: 12/22/2022] Open
Abstract
Primary open angle glaucoma (POAG) is a complex disease and is one of the major leading causes of blindness worldwide. Genome-wide association studies have successfully identified several common variants associated with glaucoma; however, most of these variants only explain a small proportion of the genetic risk. Apart from the standard approach to identify main effects of variants across the genome, it is believed that gene-gene interactions can help elucidate part of the missing heritability by allowing for the test of interactions between genetic variants to mimic the complex nature of biology. To explain the etiology of glaucoma, we first performed a genome-wide association study (GWAS) on glaucoma case-control samples obtained from electronic medical records (EMR) to establish the utility of EMR data in detecting non-spurious and relevant associations; this analysis was aimed at confirming already known associations with glaucoma and validating the EMR derived glaucoma phenotype. Our findings from GWAS suggest consistent evidence of several known associations in POAG. We then performed an interaction analysis for variants found to be marginally associated with glaucoma (SNPs with main effect p-value <0.01) and observed interesting findings in the electronic MEdical Records and GEnomics Network (eMERGE) network dataset. Genes from the top epistatic interactions from eMERGE data (Likelihood Ratio Test i.e. LRT p-value <1e-05) were then tested for replication in the NEIGHBOR consortium dataset. To replicate our findings, we performed a gene-based SNP-SNP interaction analysis in NEIGHBOR and observed significant gene-gene interactions (p-value <0.001) among the top 17 gene-gene models identified in the discovery phase. Variants from gene-gene interaction analysis that we found to be associated with POAG explain 3.5% of additional genetic variance in eMERGE dataset above what is explained by the SNPs in genes that are replicated from previous GWAS studies (which was only 2.1% variance explained in eMERGE dataset); in the NEIGHBOR dataset, adding replicated SNPs from gene-gene interaction analysis explain 3.4% of total variance whereas GWAS SNPs alone explain only 2.8% of variance. Exploring gene-gene interactions may provide additional insights into many complex traits when explored in properly designed and powered association studies. The complex nature of primary-open angle glaucoma (POAG) has left researchers exploring the genetic architecture and searching for the missing heritability using a number of different study designs. Over the past decade, many studies have been conducted to explain the etiology of POAG; however, a high proportion of estimated heritability still remains unexplained. GWA studies for POAG have identified significant associations but these associations have only explained a small proportion of the genetic risk (odds ratios range between 1–3). In this paper, we sought to confirm the primary genome-wide significant associations that have been discovered so far for glaucoma in phenotypes developed from EMR data in an effort to show that EMR data can be a powerful resource for finding genetic variants influencing POAG susceptibility. Next, we tested for statistical interactions, which can be presented as an important tool in an attempt to explain POAG heritability. We used a reduced list of variants filtered by marginal main effect analysis to look for epistatic interactions. We present our results from replication of gene-based interaction analyses performed in eMERGE and the NEIGHBOR consortium data. Using expression data and annotations from various publicly available databases, the most significant genes that replicated in our analyses show expression in the eye and trabecular meshwork. Analysis for estimation of genetic variance explained by significant associations from previous GWAS and replicated variants from gene-based interactions suggest that these explain 5.6% of variance in eMERGE dataset and also explain 3.4% variance in NEIGHBOR dataset.
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Affiliation(s)
- Shefali Setia Verma
- Department of Biomedical and Translational Informatics, Geisinger Health System, Danville, Pennsylvania, United States of America
- The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Jessica N. Cooke Bailey
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Anastasia Lucas
- Department of Biomedical and Translational Informatics, Geisinger Health System, Danville, Pennsylvania, United States of America
| | - Yuki Bradford
- Department of Biomedical and Translational Informatics, Geisinger Health System, Danville, Pennsylvania, United States of America
| | - James G. Linneman
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, Wisconsin, United States of America
| | - Michael A. Hauser
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Louis R. Pasquale
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, United States of America
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Peggy L. Peissig
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, Wisconsin, United States of America
| | - Murray H. Brilliant
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, Wisconsin, United States of America
| | | | - Jonathan L. Haines
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Janey L. Wiggs
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, United States of America
| | - Tamara R. Vrabec
- Department of Ophthalmology, Geisinger Health System, Danville, Pennsylvania, United States of America
| | - Gerard Tromp
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Marylyn D. Ritchie
- Department of Biomedical and Translational Informatics, Geisinger Health System, Danville, Pennsylvania, United States of America
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
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Shah AD, Inder KL, Shah AK, Cristino AS, McKie AB, Gabra H, Davis MJ, Hill MM. Integrative Analysis of Subcellular Quantitative Proteomics Studies Reveals Functional Cytoskeleton Membrane-Lipid Raft Interactions in Cancer. J Proteome Res 2016; 15:3451-3462. [PMID: 27384440 DOI: 10.1021/acs.jproteome.5b01035] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Lipid rafts are dynamic membrane microdomains that orchestrate molecular interactions and are implicated in cancer development. To understand the functions of lipid rafts in cancer, we performed an integrated analysis of quantitative lipid raft proteomics data sets modeling progression in breast cancer, melanoma, and renal cell carcinoma. This analysis revealed that cancer development is associated with increased membrane raft-cytoskeleton interactions, with ∼40% of elevated lipid raft proteins being cytoskeletal components. Previous studies suggest a potential functional role for the raft-cytoskeleton in the action of the putative tumor suppressors PTRF/Cavin-1 and Merlin. To extend the observation, we examined lipid raft proteome modulation by an unrelated tumor suppressor opioid binding protein cell-adhesion molecule (OPCML) in ovarian cancer SKOV3 cells. In agreement with the other model systems, quantitative proteomics revealed that 39% of OPCML-depleted lipid raft proteins are cytoskeletal components, with microfilaments and intermediate filaments specifically down-regulated. Furthermore, protein-protein interaction network and simulation analysis showed significantly higher interactions among cancer raft proteins compared with general human raft proteins. Collectively, these results suggest increased cytoskeleton-mediated stabilization of lipid raft domains with greater molecular interactions as a common, functional, and reversible feature of cancer cells.
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Affiliation(s)
- Anup D Shah
- The University of Queensland Diamantina Institute, The University of Queensland , Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - Kerry L Inder
- The University of Queensland Diamantina Institute, The University of Queensland , Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - Alok K Shah
- The University of Queensland Diamantina Institute, The University of Queensland , Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - Alexandre S Cristino
- The University of Queensland Diamantina Institute, The University of Queensland , Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - Arthur B McKie
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London Hammersmith Campus , London W12 0NN, United Kingdom
| | - Hani Gabra
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London Hammersmith Campus , London W12 0NN, United Kingdom
| | - Melissa J Davis
- Division of Bioinformatics, The Walter and Eliza Hall Institute of Medical Research , 1G Royal Parade, Parkville Victoria 3052, Australia
| | - Michelle M Hill
- The University of Queensland Diamantina Institute, The University of Queensland , Translational Research Institute, Brisbane, Queensland 4102, Australia
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Sabater L, Planagumà J, Dalmau J, Graus F. Cellular investigations with human antibodies associated with the anti-IgLON5 syndrome. J Neuroinflammation 2016; 13:226. [PMID: 27586161 PMCID: PMC5007989 DOI: 10.1186/s12974-016-0689-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/18/2016] [Indexed: 12/29/2022] Open
Abstract
Background Antibodies against IgLON5, a neuronal adhesion protein of unknown function, are markers of a novel neurological disorder termed anti-IgLON5 syndrome. The disorder shows a remarkable association with the HLA-DQB1*0501 and HLA-DRB1*1001 alleles, and postmortem studies demonstrate a novel neuronal tauopathy predominantly involving the hypothalamus and tegmentum of the brainstem. The role of IgLON5 antibodies in the pathogenesis of the disease is currently unknown. Here, we have determined the target epitopes of IgLON5 antibodies, the effects of the IgLON5 antibodies in rat hippocampal neurons, and the IgG subclass responsible for these effects. Methods HEK293 cells expressing several deletion constructs of IgLON5 were used to determine the epitopes recognized by the serum of 15 patients with anti-IgLON5 syndrome. The role of glycosylation in immunogenicity was tested with PNGase F treatment of transfected cells. Dissociated hippocampal neuronal cultures were used to test by immunocytochemistry the effects of total IgG, IgG1, and IgG4 subclasses of IgLON5 antibodies. Results Patients’ antibodies reacted with the immunoglobulin-like domain 2 of IgLON5. Glycosylation was not required for immunoreactivity. The predominant subclass of IgLON5 antibodies was IgG4 but all patients also had IgG1. The mean percentage of specific IgLON5 IgG4 and IgG1 of the samples analyzed by flow cytometry was 64 and 33 %, respectively. In cultures of hippocampal neurons, patients’ antibodies caused a decrease of cell surface IgLON5 clusters that was not reversed after IgLON5 antibodies were removed from the media. The decrease of surface IgLON5 clusters correlated with the rate of antibody internalization. These effects were observed with purified IgG1 but not with the IgG4 antibodies. Conclusions IgLON5 antibodies recognize the immunoglobulin-like domain 2 of the antigen, and the reactivity is not dependent on glycosylation. The effects observed on hippocampal neuronal cultures indicate an irreversible antibody-mediated internalization of surface IgLON5. These effects were mediated by specific IgLON5 IgG1 antibodies and suggest a pathogenic role of these antibodies in the disease. Electronic supplementary material The online version of this article (doi:10.1186/s12974-016-0689-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lidia Sabater
- Neuroimmunology Program, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
| | - Jesús Planagumà
- Neuroimmunology Program, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Josep Dalmau
- Neuroimmunology Program, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Department of Neurology, University of Pennsylvania, Philadelphia, USA
| | - Francesc Graus
- Neuroimmunology Program, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Service of Neurology, Hospital Clínic, University of Barcelona, Barcelona, Spain
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Szajnik M, Czystowska-Kuźmicz M, Elishaev E, Whiteside TL. Biological markers of prognosis, response to therapy and outcome in ovarian carcinoma. Expert Rev Mol Diagn 2016; 16:811-26. [PMID: 27268121 DOI: 10.1080/14737159.2016.1194758] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Ovarian cancer (OvCa) is among the most common types of cancer and is the leading cause of death from gynecological malignancies in western countries. Cancer biomarkers have a potential for improving the management of OvCa patients at every point from screening and detection, diagnosis, prognosis, follow up, response to therapy and outcome. AREAS COVERED The literature search has indicated a number of candidate biomarkers have recently emerged that could facilitate the molecular definition of OvCa, providing information about prognosis and predicting response to therapy. These potentially promising biomarkers include immune cells and their products, tumor-derived exosomes, nucleic acids and epigenetic biomarkers. Expert commentary: Although most of the biomarkers available today require prospective validation, the development of noninvasive liquid biopsy-based monitoring promises to improve their utility for evaluations of prognosis, response to therapy and outcome in OvCa.
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Affiliation(s)
- Marta Szajnik
- a Department of Gynecology and Gynecologic Oncology , Military Institute of Medicine , Warsaw , Poland.,b Department of Immunology, Centre of Biostructure Research , Medical University of Warsaw , Warsaw , Poland
| | | | - Esther Elishaev
- c Department of Pathology , University of Pittsburgh, School of Medicine , Pittsburgh , PA , USA
| | - Theresa L Whiteside
- c Department of Pathology , University of Pittsburgh, School of Medicine , Pittsburgh , PA , USA.,d University of Pittsburgh Cancer Institute , Pittsburgh , PA , USA
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Klimczak PF, Ventury DH, Faucz FR, Settas N, Machado de Souza C, Sotomaior VS. Association of a PARK2 Germline Variant and Epithelial Ovarian Cancer in a Southern Brazilian Population. Oncology 2016; 91:101-5. [PMID: 27286703 DOI: 10.1159/000446657] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/28/2016] [Indexed: 01/14/2023]
Abstract
Ovarian cancer (OC) is the eighth most common cancer among women in Brazil and seventh in the world population. OC has a high mortality rate and is difficult to diagnose. Currently, OC detection most often occurs at an advanced stage of the disease due to its silent progression, which contributes to the high mortality rate. Available genetic markers are not considered specifically enough for an initial and definite diagnosis. The association with new genes involved with OC can provide a better understanding of this pathology as well as contribute to the development of a marker scenario, providing an improvement in the treatment and survival of patients. The aim of this study was to examine the potential association between the PARK2 gene and epithelial ovarian cancer (EOC). Accordingly, we conducted a study for which 25 patients and 87 controls were recruited. Linkage disequilibrium analysis showed that the four studied tag SNPs (rs2803073, rs6930532, rs1040079, and rs2276201) were independent. Our results using the multivariate analysis between the additive and dominant model demonstrated that tag SNP rs2803073 of PARK2 is associated with susceptibility to EOC (p = 0.018, OR = 0.42). These findings suggest that hereditary variation in the PARK2 gene could influence EOC development mechanisms.
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Affiliation(s)
- Phamela Ferreira Klimczak
- Graduate Program in Health Sciences, School of Medicine, Pontifx00ED;cia Universidade Catx00F3;lica do Paranx00E1; (PUCPR), Curitiba, Brazil
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36
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Wu Y, Davison J, Qu X, Morrissey C, Storer B, Brown L, Vessella R, Nelson P, Fang M. Methylation profiling identified novel differentially methylated markers including OPCML and FLRT2 in prostate cancer. Epigenetics 2016; 11:247-58. [PMID: 26890304 DOI: 10.1080/15592294.2016.1148867] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
To develop new methods to distinguish indolent from aggressive prostate cancers (PCa), we utilized comprehensive high-throughput array-based relative methylation (CHARM) assay to identify differentially methylated regions (DMRs) throughout the genome, including both CpG island (CGI) and non-CGI regions in PCa patients based on Gleason grade. Initially, 26 samples, including 8 each of low [Gleason score (GS) 6] and high (GS ≥7) grade PCa samples and 10 matched normal prostate tissues, were analyzed as a discovery cohort. We identified 3,567 DMRs between normal and cancer tissues, and 913 DMRs distinguishing low from high-grade cancers. Most of these DMRs were located at CGI shores. The top 5 candidate DMRs from the low vs. high Gleason comparison, including OPCML, ELAVL2, EXT1, IRX5, and FLRT2, were validated by pyrosequencing using the discovery cohort. OPCML and FLRT2 were further validated in an independent cohort consisting of 20 low-Gleason and 33 high-Gleason tissues. We then compared patients with biochemical recurrence (n=70) vs. those without (n=86) in a third cohort, and they showed no difference in methylation at these DMR loci. When GS 3+4 cases and GS 4+3 cases were compared, OPCML-DMR methylation showed a trend of lower methylation in the recurrence group (n=30) than in the no-recurrence (n=52) group. We conclude that whole-genome methylation profiling with CHARM revealed distinct patterns of differential DNA methylation between normal prostate and PCa tissues, as well as between different risk groups of PCa as defined by Gleason scores. A panel of selected DMRs may serve as novel surrogate biomarkers for Gleason score in PCa.
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Affiliation(s)
- Yu Wu
- a Fred Hutchinson Cancer Research Center , Seattle , WA
| | - Jerry Davison
- a Fred Hutchinson Cancer Research Center , Seattle , WA
| | - Xiaoyu Qu
- a Fred Hutchinson Cancer Research Center , Seattle , WA
| | | | - Barry Storer
- a Fred Hutchinson Cancer Research Center , Seattle , WA
| | | | - Robert Vessella
- b University of Washington , Seattle , WA.,c Puget Sound VA Health Care System , Seattle , WA
| | - Peter Nelson
- a Fred Hutchinson Cancer Research Center , Seattle , WA.,b University of Washington , Seattle , WA
| | - Min Fang
- a Fred Hutchinson Cancer Research Center , Seattle , WA.,b University of Washington , Seattle , WA
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Kaur M, Singh A, Singh K, Gupta S, Sachan M. Development of a multiplex MethyLight assay for the detection of DAPK1 and SOX1 methylation in epithelial ovarian cancer in a north Indian population. Genes Genet Syst 2016; 91:175-181. [DOI: 10.1266/ggs.15-00051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Manpreet Kaur
- Department of Biotechnology, Motilal Nehru National Institute of Technology
| | - Alka Singh
- Department of Biotechnology, Motilal Nehru National Institute of Technology
| | - Kiran Singh
- Department of Molecular Human Genetics, Banaras Hindu University
| | - Sameer Gupta
- Department of Surgical Oncology, King George Medical University
| | - Manisha Sachan
- Department of Biotechnology, Motilal Nehru National Institute of Technology
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Chai L, Li J, Lv Z. An integrated analysis of cancer genes in thyroid cancer. Oncol Rep 2015; 35:962-70. [PMID: 26718127 DOI: 10.3892/or.2015.4466] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 10/16/2015] [Indexed: 11/06/2022] Open
Abstract
Cancer driver genes are commonly mutationally disrupted in cancer, which confers a growth advantage to tumor cells. Recent studies preferentially search for recurrently mutated driver genes across multiple tumor samples, leading to the neglect of low-frequency mutated cancer genes. The present study was conducted to identify cancer‑driving genes in thyroid cancer with two distinct tools, OncodriveFM and Dendrix, which aim to detect neglected driver genes with low mutation frequency. A total of 23,620 somatic mutations generated by whole‑exome sequencing of 446 tumor/normal pairs of thyroid cancer were obtained from TCGA. Variant classification was conducted with Ensembl Variant Effect Predictor (VEP). OncodriveFM and Dendrix were applied to detect driver genes and pathways with statistical evidence. In addition, we analyzed DNA‑methylation status, copy number variation, expression levels and fusion genes among these driver candidates. In total, non‑synonymous mutations accounted for over 55% (13,091/23,620) of the total variants; 53 and 3 driver genes were determined by OncodriveFM and Dendrix, respectively, including 6 recurrently mutated driver genes, such as BRAF, NRAS, HRAS, EIF1AX, KRAS and 47 new genes. A total of 75 pathways with high function impact bias were identified by OncodriveFM. Two genes, FHOD3 and SRP72, were hypomethylated, overexpressed and involved in major deletions in thyroid cancer. Moreover, we identified 91 pairs of fusion genes, 89 of which were new fusion pairs in thyroid cancer. In conclusion, we successfully identified a list of new cancer genes, pathways and fusion genes, providing better insight into the tumorigenesis of thyroid cancer.
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Affiliation(s)
- Li Chai
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University, School of Medicine, Shanghai 200072, P.R. China
| | - Jia Li
- Department of Thyroid and Breast, Shanghai Tenth People's Hospital, Tongji University, School of Medicine, Shanghai 200072, P.R. China
| | - Zhongwei Lv
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University, School of Medicine, Shanghai 200072, P.R. China
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Maruani A, Huguet G, Beggiato A, ElMaleh M, Toro R, Leblond CS, Mathieu A, Amsellem F, Lemière N, Verloes A, Leboyer M, Gillberg C, Bourgeron T, Delorme R. 11q24.2-25 micro-rearrangements in autism spectrum disorders: Relation to brain structures. Am J Med Genet A 2015; 167A:3019-30. [DOI: 10.1002/ajmg.a.37345] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 08/12/2015] [Indexed: 01/24/2023]
Affiliation(s)
- Anna Maruani
- Human Genetics and Cognitive Functions; Institut Pasteur; Paris France
- CNRS URA 2182; Institut Pasteur; Paris France
- Department of Child Psychiatry; Robert Debré Hospital, APHP; Paris France
| | - Guillaume Huguet
- Human Genetics and Cognitive Functions; Institut Pasteur; Paris France
- CNRS URA 2182; Institut Pasteur; Paris France
| | - Anita Beggiato
- Human Genetics and Cognitive Functions; Institut Pasteur; Paris France
- CNRS URA 2182; Institut Pasteur; Paris France
- Department of Child Psychiatry; Robert Debré Hospital, APHP; Paris France
| | - Monique ElMaleh
- Department of Radiology; Robert Debré Hospital, APHP; Paris France
| | - Roberto Toro
- Human Genetics and Cognitive Functions; Institut Pasteur; Paris France
- CNRS URA 2182; Institut Pasteur; Paris France
| | - Claire S. Leblond
- Human Genetics and Cognitive Functions; Institut Pasteur; Paris France
- CNRS URA 2182; Institut Pasteur; Paris France
| | - Alexandre Mathieu
- Human Genetics and Cognitive Functions; Institut Pasteur; Paris France
- CNRS URA 2182; Institut Pasteur; Paris France
| | | | - Nathalie Lemière
- Human Genetics and Cognitive Functions; Institut Pasteur; Paris France
- CNRS URA 2182; Institut Pasteur; Paris France
| | - Alain Verloes
- Department of Human Genetics; Robert Debré Hospital, APHP; Paris France
| | - Marion Leboyer
- INSERM U955, Team 15; Faculty of Medicine; Creteil France
- Department of Adult Psychiatry; Henri Mondor-Albert Chenevier Hospitals AP-HP; Creteil France
- Fondation FondaMental; French National Science Foundation; Creteil France
| | - Christopher Gillberg
- Gillberg Neuropsychiatry Centre; Gothenburg University; Göteborg Sweden
- Saint George's Hospital Medical School; London United Kingdom
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions; Institut Pasteur; Paris France
- CNRS URA 2182; Institut Pasteur; Paris France
- Diderot Paris 7; University Paris; Paris France
| | - Richard Delorme
- Human Genetics and Cognitive Functions; Institut Pasteur; Paris France
- CNRS URA 2182; Institut Pasteur; Paris France
- Department of Child Psychiatry; Robert Debré Hospital, APHP; Paris France
- Fondation FondaMental; French National Science Foundation; Creteil France
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Lesser-Known Molecules in Ovarian Carcinogenesis. BIOMED RESEARCH INTERNATIONAL 2015; 2015:321740. [PMID: 26339605 PMCID: PMC4538335 DOI: 10.1155/2015/321740] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 06/14/2015] [Accepted: 07/07/2015] [Indexed: 12/23/2022]
Abstract
Currently, the deciphering of the signaling pathways brings about new advances in the understanding of the pathogenic mechanism of ovarian carcinogenesis, which is based on the interaction of several molecules with different biochemical structure that, consequently, intervene in cell metabolism, through their role as regulators in proliferation, differentiation, and cell death. Given that the ensemble of biomarkers in OC includes more than 50 molecules the interest of the researchers focuses on the possible validation of each one's potential as prognosis markers and/or therapeutic targets. Within this framework, this review presents three protein molecules: ALCAM, c-FLIP, and caveolin, motivated by the perspectives provided through the current limited knowledge on their role in ovarian carcinogenesis and on their potential as prognosis factors. Their structural stability, once altered, triggers the initiation of the sequences characteristic for ovarian carcinogenesis, through their role as modulators for several signaling pathways, contributing to the disruption of cellular junctions, disturbance of pro-/antiapoptotic equilibrium, and alteration of transmission of the signals specific for the molecular pathways. For each molecule, the text is built as follows: (i) general remarks, (ii) structural details, and (iii) particularities in expression, from different tumors to landmarks in ovarian carcinoma.
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Niskakoski A, Kaur S, Staff S, Renkonen-Sinisalo L, Lassus H, Järvinen HJ, Mecklin JP, Bützow R, Peltomäki P. Epigenetic analysis of sporadic and Lynch-associated ovarian cancers reveals histology-specific patterns of DNA methylation. Epigenetics 2015; 9:1577-87. [PMID: 25625843 PMCID: PMC4622692 DOI: 10.4161/15592294.2014.983374] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Diagnosis and treatment of epithelial ovarian cancer is challenging due to the poor understanding of the pathogenesis of the disease. Our aim was to investigate epigenetic mechanisms in ovarian tumorigenesis and, especially, whether tumors with different histological subtypes or hereditary background (Lynch syndrome) exhibit differential susceptibility to epigenetic inactivation of growth regulatory genes. Gene candidates for epigenetic regulation were identified from the literature and by expression profiling of ovarian and endometrial cancer cell lines treated with demethylating agents. Thirteen genes were chosen for methylation-specific multiplex ligation-dependent probe amplification assays on 104 (85 sporadic and 19 Lynch syndrome-associated) ovarian carcinomas. Increased methylation (i.e., hypermethylation) of variable degree was characteristic of ovarian carcinomas relative to the corresponding normal tissues, and hypermethylation was consistently more prominent in non-serous than serous tumors for individual genes and gene sets investigated. Lynch syndrome-associated clear cell carcinomas showed the highest frequencies of hypermethylation. Among endometrioid ovarian carcinomas, lower levels of promoter methylation of RSK4, SPARC, and HOXA9 were significantly associated with higher tumor grade; thus, the methylation patterns showed a shift to the direction of high-grade serous tumors. In conclusion, we provide evidence of a frequent epigenetic inactivation of RSK4, SPARC, PROM1, HOXA10, HOXA9, WT1-AS, SFRP2, SFRP5, OPCML, and MIR34B in the development of non-serous ovarian carcinomas of Lynch and sporadic origin, as compared to serous tumors. Our findings shed light on the role of epigenetic mechanisms in ovarian tumorigenesis and identify potential targets for translational applications.
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Affiliation(s)
- Anni Niskakoski
- a Department of Medical Genetics; Biomedicum Helsinki ; University of Helsinki ; Helsinki , Finland
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Tiezzi F, Parker-Gaddis KL, Cole JB, Clay JS, Maltecca C. A genome-wide association study for clinical mastitis in first parity US Holstein cows using single-step approach and genomic matrix re-weighting procedure. PLoS One 2015; 10:e0114919. [PMID: 25658712 PMCID: PMC4319771 DOI: 10.1371/journal.pone.0114919] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 11/01/2014] [Indexed: 11/18/2022] Open
Abstract
Clinical mastitis (CM) is one of the health disorders with large impacts on dairy farming profitability and animal welfare. The objective of this study was to perform a genome-wide association study (GWAS) for CM in first-lactation Holstein. Producer-recorded mastitis event information for 103,585 first-lactation cows were used, together with genotype information on 1,361 bulls from the Illumina BovineSNP50 BeadChip. Single-step genomic-BLUP methodology was used to incorporate genomic data into a threshold-liability model. Association analysis confirmed that CM follows a highly polygenic mode of inheritance. However, 10-adjacent-SNP windows showed that regions on chromosomes 2, 14 and 20 have impacts on genetic variation for CM. Some of the genes located on chromosome 14 (LY6K, LY6D, LYNX1, LYPD2, SLURP1, PSCA) are part of the lymphocyte-antigen-6 complex (LY6) known for its neutrophil regulation function linked to the major histocompatibility complex. Other genes on chromosome 2 were also involved in regulating immune response (IFIH1, LY75, and DPP4), or are themselves regulated in the presence of specific pathogens (ITGB6, NR4A2). Other genes annotated on chromosome 20 are involved in mammary gland metabolism (GHR, OXCT1), antibody production and phagocytosis of bacterial cells (C6, C7, C9, C1QTNF3), tumor suppression (DAB2), involution of mammary epithelium (OSMR) and cytokine regulation (PRLR). DAVID enrichment analysis revealed 5 KEGG pathways. The JAK-STAT signaling pathway (cell proliferation and apoptosis) and the 'Cytokine-cytokine receptor interaction' (cytokine and interleukines response to infectious agents) are co-regulated and linked to the 'ABC transporters' pathway also found here. Gene network analysis performed using GeneMania revealed a co-expression network where 665 interactions existed among 145 of the genes reported above. Clinical mastitis is a complex trait and the different genes regulating immune response are known to be pathogen-specific. Despite the lack of information in this study, candidate QTL for CM were identified in the US Holstein population.
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Affiliation(s)
- Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, United States of America
- * E-mail:
| | - Kristen L. Parker-Gaddis
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, United States of America
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705–2350, United States of America
| | - John B. Cole
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705–2350, United States of America
| | - John S. Clay
- Dairy Records Management Systems, Raleigh, NC, 27603, United States of America
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, United States of America
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DNA methylation level of OPCML and SFRP1: a potential diagnostic biomarker of cholangiocarcinoma. Tumour Biol 2015; 36:4973-8. [PMID: 25652468 DOI: 10.1007/s13277-015-3147-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 01/26/2015] [Indexed: 12/27/2022] Open
Abstract
Cholangiocarcinoma (CCA) is a malignancy of the bile duct epithelium which is caused by liver fluke infection. The clinical symptoms of CCA were revealed as the disease progresses to advanced stage. Thus, specific diagnostic biomarkers are important for this fatal disease. We applied methylation-sensitive high-resolution melting (MS-HRM) to quantify DNA methylation levels of opioid binding protein/cell adhesion molecule-like gene (OPCML) and Secreted frizzled-related protein 1 (SFRP1) in 73 primary CCA and 10 adjacent normal tissues and evaluated the sensitivity, specificity, and accuracy of the assay. The median methylation level of OPCML in CCA was 38.7 % (ranged from 0 to 82.2 %) and of SFRP1 was 31.5 % (ranged from 0 to 86.2 %). Methylation cutoff values of OPCML and SFRP1 derived from adjacent normal tissue were 6.90 and 10.44 %, respectively. With these cutoff values, the area under curve (AUC) of OPCML was 0.932 (95 % CI 0.878-0.986) and of SFRP1 was 0.951 (95 % CI 0.905-0.996). The sensitivity, specificity, and accuracy of OPCML were 89.04, 100, and 90.36 %, respectively, and of SFRP1 were 83.56, 100, and 85.54 %, respectively. In conclusion, the DNA methylation levels of OPCML and SFRP1 could be potential biomarkers for diagnosis of CCA with high specificity, sensitivity, and accuracy, in particular for biopsy specimens. Further validation in noninvasive samples such as serum or plasma is warranted for clinical applicability, especially as early diagnostic biomarkers.
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44
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Decitabine, a new star in epigenetic therapy: the clinical application and biological mechanism in solid tumors. Cancer Lett 2014; 354:12-20. [DOI: 10.1016/j.canlet.2014.08.010] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/05/2014] [Accepted: 08/06/2014] [Indexed: 11/23/2022]
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45
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Fang F, Munck J, Tang J, Taverna P, Wang Y, Miller DFB, Pilrose J, Choy G, Azab M, Pawelczak KS, VanderVere-Carozza P, Wagner M, Lyons J, Matei D, Turchi JJ, Nephew KP. The novel, small-molecule DNA methylation inhibitor SGI-110 as an ovarian cancer chemosensitizer. Clin Cancer Res 2014; 20:6504-16. [PMID: 25316809 DOI: 10.1158/1078-0432.ccr-14-1553] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE To investigate SGI-110 as a "chemosensitizer" in ovarian cancer and to assess its effects on tumor suppressor genes (TSG) and chemoresponsiveness-associated genes silenced by DNA methylation in ovarian cancer. EXPERIMENTAL DESIGN Several ovarian cancer cell lines were used for in vitro and in vivo platinum resensitization studies. Changes in DNA methylation and expression levels of TSG and other cancer-related genes in response to SGI-110 were measured by pyrosequencing and RT-PCR. RESULTS We demonstrate in vitro that SGI-110 resensitized a range of platinum-resistant ovarian cancer cells to cisplatin (CDDP) and induced significant demethylation and reexpression of TSG, differentiation-associated genes, and putative drivers of ovarian cancer cisplatin resistance. In vivo, SGI-110 alone or in combination with CDDP was well tolerated and induced antitumor effects in ovarian cancer xenografts. Pyrosequencing analyses confirmed that SGI-110 caused both global (LINE1) and gene-specific hypomethylation in vivo, including TSGs (RASSF1A), proposed drivers of ovarian cancer cisplatin resistance (MLH1 and ZIC1), differentiation-associated genes (HOXA10 and HOXA11), and transcription factors (STAT5B). Furthermore, DNA damage induced by CDDP in ovarian cancer cells was increased by SGI-110, as measured by inductively coupled plasma-mass spectrometry analysis of DNA adduct formation and repair of cisplatin-induced DNA damage. CONCLUSIONS These results strongly support further investigation of hypomethylating strategies in platinum-resistant ovarian cancer. Specifically, SGI-110 in combination with conventional and/or targeted therapeutics warrants further development in this setting.
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Affiliation(s)
- Fang Fang
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana
| | | | - Jessica Tang
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana
| | | | - Yinu Wang
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana
| | - David F B Miller
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana
| | - Jay Pilrose
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana
| | - Gavin Choy
- Astex Pharmaceuticals Inc., Dublin, California
| | | | - Katherine S Pawelczak
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Pamela VanderVere-Carozza
- Department of Medicine, Division of Hematology/Oncology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Michael Wagner
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana
| | - John Lyons
- Astex Pharmaceuticals Inc., Dublin, California
| | - Daniela Matei
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana. Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana. VA Roudebush Hospital, Indianapolis, Indiana. Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, Indiana. Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana.
| | - John J Turchi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana. Department of Medicine, Division of Hematology/Oncology, Indiana University School of Medicine, Indianapolis, Indiana.
| | - Kenneth P Nephew
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana. Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana. Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, Indiana. Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, Indiana.
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Ye M, Parente F, Li X, Perryman MB, Zelante L, Wynshaw-Boris A, Chen J, Grossfeld P. Gene-targeted deletion ofOPCMLandNeurotriminin mice does not yield congenital heart defects. Am J Med Genet A 2014; 164A:966-74. [DOI: 10.1002/ajmg.a.36441] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 12/26/2013] [Indexed: 01/20/2023]
Affiliation(s)
- Maoqing Ye
- Key Laboratory of Arrhythmia, Ministry of Education, East Hospital; Tongji University School of Medicine; Shanghai China
- Department of Pediatrics; UCSD School of Medicine; San Diego California
| | - Fabienne Parente
- Department of Medicine; UCSD School of Medicine; San Diego California
| | - Xiaodong Li
- Department of Medicine; UCSD School of Medicine; San Diego California
| | | | - Leopoldo Zelante
- Medical Genetics Service; IRCCS-CSS Hospital; San Giovanni Rotondo Italy
| | | | - Ju Chen
- Department of Medicine; UCSD School of Medicine; San Diego California
| | - Paul Grossfeld
- Department of Pediatrics; UCSD School of Medicine; San Diego California
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Khoury T, Hu Q, Liu S, Wang J. Intracystic papillary carcinoma of breast: interrelationship with in situ and invasive carcinoma and a proposal of pathogenesis: array comparative genomic hybridization study of 14 cases. Mod Pathol 2014; 27:194-203. [PMID: 23907150 PMCID: PMC4389629 DOI: 10.1038/modpathol.2013.136] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 06/03/2013] [Accepted: 06/04/2013] [Indexed: 12/22/2022]
Abstract
Classifying intracystic papillary carcinoma under invasive or in situ ductal carcinoma is still a matter of debate. The purpose of this study was to explore the genomic relationship of this tumor to its concurrent invasive ductal carcinoma and ductal carcinoma in situ using array comparative genomic hybridization. Intracystic papillary carcinoma cases were classified into three categories: pure, with concurrent ductal carcinoma in situ or with concurrent invasive ductal carcinoma. Each component was dissected using laser capture microdissection. DNA was extracted and array comparative genomic hybridization was performed. The test of difference in copy number changes among the three tumors was carried out using CGHMultiArray. Intracystic papillary carcinoma clustered with four of five concurrent ductal carcinoma in situ cases and with two of two invasive ductal carcinoma cases. Intracystic papillary carcinoma showed the highest proportions of genome copy number aberration, followed by ductal carcinoma in situ, and then by invasive ductal carcinoma (P=0.06). Comparing intracystic papillary carcinoma with invasive ductal carcinoma vs without invasive ductal carcinoma, the former had 11q22.1-23.3 loss (P=0.031) and chr5 gain (P=0.085), and was enriched with matrix metalloproteinase genes. Comparing intracystic papillary carcinoma with ductal carcinoma in situ vs without ductal carcinoma in situ, the former had gain in 5q35.3 (P=0.041), 8q24.3 (P=0.041) and 21q13.2 to 21q13.31 (P=0.011). Comparing intracystic papillary carcinoma with ductal carcinoma in situ, the latter acquired a group of genes involved in cell adhesion and motility, whereas intracystic papillary carcinoma differentially expressed genes that are involved in papillary carcinomas of other organs (thyroid and kidney). We conclude that the overall molecular change in intracystic papillary carcinoma is closer to ductal carcinoma in situ than to invasive ductal carcinoma, which may explain the indolent behavior of this tumor. We offer herein a proposal of intracystic papillary carcinoma pathogenesis through its relation to invasive ductal carcinoma and ductal carcinoma in situ.
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Affiliation(s)
- Thaer Khoury
- Department of Pathology, Roswell Park Cancer Institute, Buffalo, NY
| | - Qiang Hu
- Department of Biostatistics, Roswell Park Cancer Institute, Buffalo, NY
| | - Song Liu
- Department of Biostatistics, Roswell Park Cancer Institute, Buffalo, NY
| | - Jianmin Wang
- Department of Biostatistics, Roswell Park Cancer Institute, Buffalo, NY, Co-corresponding author: Jianmin Wang PhD Roswell Park Cancer Institute Elm & Carlton streets Buffalo, NY 14263 Tel: (716) 845-1499
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48
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Gloss BS, Samimi G. Epigenetic biomarkers in epithelial ovarian cancer. Cancer Lett 2014; 342:257-63. [DOI: 10.1016/j.canlet.2011.12.036] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 12/08/2011] [Accepted: 12/12/2011] [Indexed: 12/31/2022]
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49
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Zhang J, Xing B, Song J, Zhang F, Nie C, Jiao L, Liu L, Lv F, Wang S. Associated Analysis of DNA Methylation for Cancer Detection Using CCP-Based FRET Technique. Anal Chem 2013; 86:346-50. [DOI: 10.1021/ac402720g] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jiangyan Zhang
- Beijing National
Laboratory for Molecular Sciences, Key Laboratory of Organic Solids,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Baoling Xing
- Department
of Pathology, Changzhou Women and Children Health Hospital, Changzhou 213003, P. R. China
| | - Jinzhao Song
- Beijing National
Laboratory for Molecular Sciences, Key Laboratory of Organic Solids,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Feng Zhang
- Department
of Pathology, Changzhou Women and Children Health Hospital, Changzhou 213003, P. R. China
| | - Chenyao Nie
- Beijing National
Laboratory for Molecular Sciences, Key Laboratory of Organic Solids,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Lian Jiao
- Department
of Pathology, Changzhou Women and Children Health Hospital, Changzhou 213003, P. R. China
| | - Libing Liu
- Beijing National
Laboratory for Molecular Sciences, Key Laboratory of Organic Solids,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Fengting Lv
- Beijing National
Laboratory for Molecular Sciences, Key Laboratory of Organic Solids,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Shu Wang
- Beijing National
Laboratory for Molecular Sciences, Key Laboratory of Organic Solids,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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50
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Liao YP, Chen LY, Huang RL, Su PH, Chan MWY, Chang CC, Yu MH, Wang PH, Yen MS, Nephew KP, Lai HC. Hypomethylation signature of tumor-initiating cells predicts poor prognosis of ovarian cancer patients. Hum Mol Genet 2013; 23:1894-906. [PMID: 24256813 DOI: 10.1093/hmg/ddt583] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
DNA methylation contributes to tumor formation, development and metastasis. Epigenetic dysregulation of stem cells is thought to predispose to malignant development. The clinical significance of DNA methylation in ovarian tumor-initiating cells (OTICs) remains unexplored. We analyzed the methylomic profiles of OTICs (CP70sps) and their derived progeny using a human methylation array. qRT-PCR, quantitative methylation-specific PCR (qMSP) and pyrosequencing were used to verify gene expression and DNA methylation in cancer cell lines. The methylation status of genes was validated quantitatively in cancer tissues and correlated with clinicopathological factors. ATG4A and HIST1H2BN were hypomethylated in OTICs. Methylation analysis of ATG4A and HIST1H2BN by qMSP in 168 tissue samples from patients with ovarian cancer showed that HIST1H2BN methylation was a significant and independent predictor of progression-free survival (PFS) and overall survival (OS). Multivariate Cox regression analysis showed that patients with a low level of HIST1H2BN methylation had poor PFS (hazard ratio (HR), 4.5; 95% confidence interval (CI), 1.4-14.8) and OS (HR, 4.3; 95% CI, 1.3-14.0). Hypomethylation of both ATG4A and HIST1H2BN predicted a poor PFS (HR, 1.8; 95% CI, 1.0-3.6; median, 21 months) and OS (HR, 1.7; 95% CI, 1.0-3.0; median, 40 months). In an independent cohort of ovarian tumors, hypomethylation predicted early disease recurrence (HR, 1.7; 95% CI, 1.1-2.5) and death (HR, 1.4; 95% CI, 1.0-1.9). The demonstration that expression of ATG4A in cells increased their stem properties provided an indication of its biological function. Hypomethylation of ATG4A and HIST1H2BN in OTICs predicts a poor prognosis for ovarian cancer patients.
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