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Potential Role of Methylation Marker in Glioma Supporting Clinical Decisions. Int J Mol Sci 2016; 17:ijms17111876. [PMID: 27834917 PMCID: PMC5133876 DOI: 10.3390/ijms17111876] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/27/2016] [Accepted: 11/04/2016] [Indexed: 01/18/2023] Open
Abstract
The IDH1/2 gene mutations, ATRX loss/mutation, 1p/19q status, and MGMT promoter methylation are increasingly used as prognostic or predictive biomarkers of gliomas. However, the effect of their combination on radiation therapy outcome is discussable. Previously, we demonstrated that the IDH1 c.G395A; p.R132H mutation was associated with longer survival in grade II astrocytoma and GBM (Glioblastoma). Here we analyzed the MGMT promoter methylation status in patients with a known mutation status in codon 132 of IDH1, followed by clinical and genetic data analysis based on the two statuses. After a subtotal tumor resection, the patients were treated using IMRT (Intensity-Modulated Radiation Therapy) with 6 MeV photons. The total dose was: 54 Gy for astrocytoma II, 60 Gy for astrocytoma III, 60 Gy for glioblastoma, 2 Gy per day, with 24 h intervals, five days per week. The patients with MGMT promoter methylation and IDH1 somatic mutation (OS = 40 months) had a better prognosis than those with MGMT methylation alone (OS = 18 months). In patients with astrocytoma anaplasticum (n = 7) with the IDH1 p.R132H mutation and hypermethylated MGMT, the prognosis was particularly favorable (median OS = 47 months). In patients with astrocytoma II meeting the above criteria, the prognosis was also better than in those not meeting those criteria. The IDH1 mutation appears more relevant for the prognosis than MGMT methylation. The IDH1 p.R132H mutation combined with MGMT hypermethylation seems to be the most advantageous for treatment success. Patients not meeting those criteria may require more aggressive treatments.
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Subramanyam M, Goyal J. Translational biomarkers: from discovery and development to clinical practice. DRUG DISCOVERY TODAY. TECHNOLOGIES 2016; 21-22:3-10. [PMID: 27978985 DOI: 10.1016/j.ddtec.2016.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/12/2016] [Accepted: 10/31/2016] [Indexed: 06/06/2023]
Abstract
The refinement of disease taxonomy utilizing molecular phenotypes has led to significant improvements in the precision of disease diagnosis and customization of treatment options. This has also spurred efforts to identify novel biomarkers to understand the impact of therapeutically altering the underlying molecular network on disease course, and to support decision-making in drug discovery and development. However, gaps in knowledge regarding disease heterogeneity, combined with the inadequacies of surrogate disease model systems, make it challenging to demonstrate the unequivocal association of molecular and physiological biomarkers to disease pathology. This article will discuss the current landscape in biomarker research and highlight strategies being adopted to increase the likelihood of transitioning biomarkers from discovery to medical practice to enable more objective decision making, and to improve health outcome.
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Affiliation(s)
- Meena Subramanyam
- Global Biomarker Discovery and Development, Biogen, 300 Binney St., Cambridge, MA 02142, United States.
| | - Jaya Goyal
- Value Based Medicine, Biogen, 300 Binney St., Cambridge, MA 02142, United States
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103
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Chiantore MV, Mangino G, Iuliano M, Zangrillo MS, De Lillis I, Vaccari G, Accardi R, Tommasino M, Columba Cabezas S, Federico M, Fiorucci G, Romeo G. Human papillomavirus E6 and E7 oncoproteins affect the expression of cancer-related microRNAs: additional evidence in HPV-induced tumorigenesis. J Cancer Res Clin Oncol 2016; 142:1751-63. [PMID: 27300513 DOI: 10.1007/s00432-016-2189-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 06/09/2016] [Indexed: 02/03/2023]
Abstract
PURPOSE Human papillomaviruses (HPVs) are the causative agents of cervical cancer and are also associated with other types of cancers. HPVs can modulate microRNAs (miRNAs) expressed by infected cells. The production of extracellular vesicles is deregulated in cancer, and their cargo delivered to the microenvironment can promote tumorigenesis. The involvement of HPV oncoproteins on miRNA expression in cells and exosomes was analyzed in keratinocytes transduced with E6 and E7 from mucosal HPV-16 or cutaneous HPV-38 (K16 and K38). METHODS MiRNAs were investigated through the TaqMan Array Human MicroRNA Cards, followed by real-time RT-PCR assay for specific miRNAs. Selected miRNA targets were analyzed by Western blot and correlated to the HPV oncoproteins by specifically silencing E6 and E7 expression. Exosomes, isolated from K16 and K38 supernatants by differential centrifugations, were quantified through the vesicle-associated acetylcholinesterase activity. RESULTS MiRNAs deregulated in K16 and K38 cells were identified. HPV-16 and/or HPV-38 E6 and E7 single proteins can modify the expression of selected miRNAs involved in the tumorigenesis, in particular miR-18a, -19a, -34a and -590-5p. The analysis of the content of exosomes isolated from HPV-positive cells revealed the presence of E6 and E7 mRNAs and few miRNAs. MiR-222, a key miRNA deregulated in many cancers, was identified in exosomes from K16 cells. CONCLUSIONS HPV E6 and/or E7 oncoprotein expression can induce the deregulation of some miRNAs. Through the production and function of exosomes, HPV oncogenes as well as HPV-deregulated miRNAs can potentiate the virus oncogenic effects in the tumor cell microenvironment.
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Affiliation(s)
- Maria Vincenza Chiantore
- Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy.
| | - Giorgio Mangino
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, 04100, Latina, Italy
| | - Marco Iuliano
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, 04100, Latina, Italy
| | - Maria Simona Zangrillo
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, 04100, Latina, Italy
| | - Ilaria De Lillis
- Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Gabriele Vaccari
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Rosita Accardi
- Infections and Cancer Biology Group, International Agency for Research on Cancer, 69372, Lyon, France
| | - Massimo Tommasino
- Infections and Cancer Biology Group, International Agency for Research on Cancer, 69372, Lyon, France
| | - Sandra Columba Cabezas
- Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Maurizio Federico
- National AIDS Center, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Gianna Fiorucci
- Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy
- Institute of Molecular Biology and Pathology, Consiglio Nazionale delle Ricerche, 00161, Rome, Italy
| | - Giovanna Romeo
- Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, 04100, Latina, Italy
- Institute of Molecular Biology and Pathology, Consiglio Nazionale delle Ricerche, 00161, Rome, Italy
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104
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Mahgoub A, Steer CJ. MicroRNAs in the Evaluation and Potential Treatment of Liver Diseases. J Clin Med 2016; 5:E52. [PMID: 27171116 PMCID: PMC4882481 DOI: 10.3390/jcm5050052] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 04/18/2016] [Accepted: 04/25/2016] [Indexed: 02/07/2023] Open
Abstract
Acute and chronic liver disease continue to result in significant morbidity and mortality of patients, along with increasing burden on their families, society and the health care system. This in part is due to increased incidence of liver disease associated factors such as metabolic syndrome; improved survival of patients with chronic predisposing conditions such as HIV; as well as advances in the field of transplantation and associated care leading to improved survival. The fact that one disease can result in different manifestations and outcomes highlights the need for improved understanding of not just genetic phenomenon predisposing to a condition, but additionally the role of epigenetic and environmental factors leading to the phenotype of the disease. It is not surprising that providers continue to face daily challenges pertaining to diagnostic accuracy, prognostication of disease severity, progression, and response to therapies. A number of these challenges can be addressed by incorporating a personalized approach of management to the current paradigm of care. Recent advances in the fields of molecular biology and genetics have paved the way to more accurate, individualized and precise approach to caring for liver disease. The study of microRNAs and their role in both healthy and diseased livers is one example of such advances. As these small, non-coding RNAs work on fine-tuning of cellular activities and organ function in a dynamic and precise fashion, they provide us a golden opportunity to advance the field of hepatology. The study of microRNAs in liver disease promises tremendous improvement in hepatology and is likely to lay the foundation towards a personalized approach in liver disease.
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Affiliation(s)
- Amar Mahgoub
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Minnesota Medical School, Veterans of Foreign Wars Cancer Research Center, 406 Harvard Street, S.E., Minneapolis, MN 55455, USA.
| | - Clifford J Steer
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Minnesota Medical School, Veterans of Foreign Wars Cancer Research Center, 406 Harvard Street, S.E., Minneapolis, MN 55455, USA.
- Department of Genetics, Cell Biology and Development, University of Minnesota Medical School, Veterans of Foreign Wars Cancer Research Center, 406 Harvard Street, S.E., Minneapolis, MN 55455, USA.
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105
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Beltran-Sarmiento E, Floriano-Sánchez E, Bandala C, Lara-Padilla E, Cárdenas-Rodríguez N. Association of CYP8A1 (Prostacyclin I2 synthase) polymorphism rs5602 with breast cancer in Mexican woman. Am J Cancer Res 2016; 6:341-349. [PMID: 27186408 PMCID: PMC4859665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 12/07/2015] [Indexed: 06/05/2023] Open
Abstract
Breast cancer (BCa) is the most common cancer in Mexican women. Certain risk factors, such as environmental and lifestyle factors have been implicated in BCa initiation and progression. Moreover, genetic factors, such as single nucleotide polymorphisms (SNPs) of the P450 system, have been reported in BCa. In this report, and for the first time in the literature, we analyzed the rs5602 (67730 T > C) polymorphism in the CYP8A1 in patients with BCa and in healthy Mexican women to identify a potential risk between this polymorphism and BCa. Leukocyte cells from 38 control patients and tissue from radical mastectomy surgeries in 64 BCa patients were used for polymorphism analysis using an allelic discrimination assay with TaqMan probes. Links with clinic-pathological characteristics were also analyzed. Statistical analysis was performed using the standard χ(2) or Fisher exact test statistic. All CYP8A1 genotypes were detected in patients with BCa and the controls. Significant differences were observed in the distribution of CYP8A1 genotypes between the patients and controls (P=0.0008) and allele C was significantly associated with BCa risk (OR 2.08, 95% CI 1.166-3.72, P=0.0178). All polymorphism frequencies were in Hardy-Weinberg Equilibrium (HWE) in the controls (P > 0.05). We found that variant 67730 T > C was significantly associated with an increased risk of BCa (P < 0.05). We not observed an association of the TT and TC + CC genotypes with the clinical stage, BIRADS, estrogen receptor (ER) status, progesterone receptor (PR) status, HER2 status, p53 status, CD34 status, metastasis or therapy use. These results indicate that the CYP8A1 rs5602 SNP is a possible risk factor for BCa in Mexican women. This study showed an association between the CYP8A1 polymorphism and BCa risk in a Mexican population.
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Affiliation(s)
| | - Esaú Floriano-Sánchez
- Multidisciplinary Research Laboratory, Military School of Graduate of Health, SEDENA México 11200, D.F., México
| | - Cindy Bandala
- Department of Neuroscience, National Rehabilitation Institute México 14389, D.F., México
| | - Eleazar Lara-Padilla
- Section of Research and Graduate Studies, National Polytechnic Institute México 11340, D.F., México
| | - Noemí Cárdenas-Rodríguez
- Laboratory of Neurosciences (Neurochemistry), National Institute of Pediatrics México 04530, D.F., México
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Abstract
Diagnostics of inflammatory bowel diseases (IBDs) currently relies on a combination of biological and morphological tests. The current method of diagnostic remains a critical challenge for physicians in part due to their invasiveness and also for their limitations in term of diagnosis, prognosis, disease activity and severity assessment, and therapeutic outcomes. Laboratory biomarkers can be used in the diagnosis and management of IBD, but none of them has been proven to be ideal. Increasing efforts are being made to discover new biomarkers that can discriminate between the types of IBD, predict future responses to treatment, and aid in differential diagnosis, treatment planning, and prognosis prediction. This review addresses the potential for current biomarkers and the emergence of the concept of biomarker signatures in IBD diagnostic and personalized medicine.
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107
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Valdespino V, Valdespino PM. Potential of epigenetic therapies in the management of solid tumors. Cancer Manag Res 2015; 7:241-51. [PMID: 26346546 PMCID: PMC4529253 DOI: 10.2147/cmar.s70358] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Cancer is a complex disease with both genetic and epigenetic origins. The growing field of epigenetics has contributed to our understanding of oncogenesis and tumor progression, and has allowed the development of novel therapeutic drugs. First-generation epigenetic inhibitor drugs have obtained modest clinical results in two types of hematological malignancy. Second-generation epigenetic inhibitors are in development, and have intrinsically greater selectivity for their molecular targets. Solid tumors are more genetic and epigenetically complex than hematological malignancies, but the transcriptome and epigenome biomarkers have been identified for many of these malignancies. This solid tumor molecular aberration profile may be modified using specific or quasi-specific epidrugs together with conventional and innovative anticancer treatments. In this critical review, we briefly analyze the strategies to select the targeted epigenetic changes, enumerate the second-generation epigenetic inhibitors, and describe the main signs indicating the potential of epigenetic therapies in the management of solid tumors. We also highlight the work of consortia or academic organizations that support the undertaking of human epigenetic therapeutic projects as well as some examples of transcriptome/epigenome profile determination in clinical assessment of cancer patients treated with epidrugs. There is a good chance that epigenetic therapies will be able to be used in patients with solid tumors in the future. This may happen soon through collaboration of diverse scientific groups, making the selection of targeted epigenetic aberration(s) more rapid, the design and probe of drug candidates, accelerating in vitro and in vivo assays, and undertaking new cancer epigenetic-therapy clinical trails.
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Affiliation(s)
- Victor Valdespino
- Health Attention Department, Universidad Autónoma Metropolitana, Mexico
| | - Patricia M Valdespino
- Bacterial Ecology and Epigenetics Laboratory, Universidad Nacional Autónoma de México, Mexico
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108
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Punaro M. Use of microarrays in the clinical practice of pediatric rheumatology: the future is now? Curr Opin Rheumatol 2015; 26:585-91. [PMID: 25014037 DOI: 10.1097/bor.0000000000000095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PURPOSE OF REVIEW Systems immunology is an integrative approach that leverages high throughput technologies as well as mathematical and computational tools to investigate complex immunologic diseases by looking at the state of a system on a comprehensive scale. Gene expression profiling, also known as transcriptomics, measures the expression level of mRNAs (transcripts) in a given cell population at a specific time. Over the past decade, several major gene expression discoveries have been made in pediatric rheumatology, most notably the alpha interferon signature of systemic lupus erythematosus and the interleukin-1 signature in systemic onset juvenile idiopathic arthritis. This article reviews these discoveries, their clinical implications and the recent associated literature. RECENT FINDINGS Interferon-α has been exploited as a therapeutic target in lupus. Interleukin-1 blockade has been utilized to treat systemic onset juvenile idiopathic arthritis and related autoinflammatory diseases. SUMMARY Current gene expression studies extend our understanding of the disease pathogenesis of lupus and systemic onset juvenile idiopathic arthritis as well as related conditions. This knowledge has translated to the bedside with implications for clinical practice and direct therapeutic targeting.
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Affiliation(s)
- Marilynn Punaro
- Texas Scottish Rite Hospital, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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109
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Bai J, Zhang Z, Li X, Liu H. MicroRNA-365 inhibits growth, invasion and metastasis of malignant melanoma by targeting NRP1 expression. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:4913-4922. [PMID: 26191184 PMCID: PMC4503056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 03/23/2015] [Indexed: 06/04/2023]
Abstract
OBJECTIVE The role of miR-365 in cancer cells seemed controversial in previous studies. We thereby in this article aimed to define the role of miR-365 in malignant melanoma (MM) pathogenesis. METHODS We detected miR-365 expression in malignant melanoma cell lines and then investigated the effects of miR-365 on the metastasis and malignancy of melanoma cells. The correlation between miR-365 level and NRP1 (neuropilin1) was further investigated in clinical malignant melanoma specimens. RESULTS MiR-365 was strongly down-regulated in malignant melanoma (MM) tissues and cell lines, and its expression levels were associated with lymph node metastasis and clinical stage, as well as overall survival and replase-free survival of MM. We also found that ectopic expression of miR-365 inhibited MM cell proliferation and MM metastasis in vitro and in vivo. We further identified a novel mechanism of miR-365 to suppress MM growth and metastasis. NRP1 was proved to be a direct target of miR-365, using luciferase assay and western blot. NRP1 over-expression in miR-365 expressing cells could rescue invasion and growth defects of miR-365. In addition, miR-365 expression inversely correlated with NRP1 protein levels in MM. CONCLUSION Our data suggest that miR-365 functions as a tumor suppressor in MM development and progression, and holds promise as a prognostic biomarker and potential therapeutic target for MM.
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Affiliation(s)
- Juanjuan Bai
- Plastic Surgery, The 1st Affiliated Hospital of Zhengzhou University Zhengzhou, China
| | - Zhongling Zhang
- Plastic Surgery, The 1st Affiliated Hospital of Zhengzhou University Zhengzhou, China
| | - Xing Li
- Plastic Surgery, The 1st Affiliated Hospital of Zhengzhou University Zhengzhou, China
| | - Huifan Liu
- Plastic Surgery, The 1st Affiliated Hospital of Zhengzhou University Zhengzhou, China
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110
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Abstract
Cancer is a group of diseases characterized by the uncontrolled growth and spread of abnormal cells and oncology is a branch of medicine that deals with tumors. The last decade has seen significant advances in the development of biomarkers in oncology that play a critical role in understanding molecular and cellular mechanisms which drive tumor initiation, maintenance and progression. Clinical molecular diagnostics and biomarker discoveries in oncology are advancing rapidly as we begin to understand the complex mechanisms that transform a normal cell into an abnormal one. These discoveries have fueled the development of novel drug targets and new treatment strategies. The standard of care for patients with advanced-stage cancers has shifted away from an empirical treatment strategy based on the clinical-pathological profile to one where a biomarker driven treatment algorithm based on the molecular profile of the tumor is used. Recent advances in multiplex genotyping technologies and high-throughput genomic profiling by next-generation sequencing make possible the rapid and comprehensive analysis of the cancer genome of individual patients even from very little tumor biopsy material. Predictive (diagnostic) biomarkers are helpful in matching targeted therapies with patients and in preventing toxicity of standard (systemic) therapies. Prognostic biomarkers identify somatic germ line mutations, changes in DNA methylation, elevated levels of microRNA (miRNA) and circulating tumor cells (CTC) in blood. Predictive biomarkers using molecular diagnostics are currently in use in clinical practice of personalized oncotherapy for the treatment of five diseases: chronic myeloid leukemia, colon, breast, lung cancer and melanoma and these biomarkers are being used successfully to evaluate benefits that can be achieved through targeted therapy. Examples of these molecularly targeted biomarker therapies are: tyrosine kinase inhibitors in chronic myeloid leukemia and gastrointestinal tumors; anaplastic lymphoma kinase (ALK) inhibitors in lung cancer with EML4-ALk fusion; HER2/neu blockage in HER2/neu-positive breast cancer; and epidermal growth factor receptors (EGFR) inhibition in EGFR-mutated lung cancer. This review presents the current state of our knowledge of biomarkers in five selected cancers: chronic myeloid leukemia, colorectal cancer, breast cancer, non-small cell lung cancer and melanoma.
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MESH Headings
- Biomarkers, Tumor/analysis
- Biomarkers, Tumor/genetics
- Breast Neoplasms
- Carcinoma, Non-Small-Cell Lung
- Colorectal Neoplasms
- Cytochrome P-450 CYP2D6/analysis
- Cytochrome P-450 CYP2D6/genetics
- Dihydrouracil Dehydrogenase (NADP)/analysis
- Dihydrouracil Dehydrogenase (NADP)/genetics
- ErbB Receptors/analysis
- ErbB Receptors/genetics
- Female
- Gene Expression Profiling
- Genes, ras
- Glucuronosyltransferase/analysis
- Glucuronosyltransferase/genetics
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive
- Lung Neoplasms
- Medical Oncology/methods
- Medical Oncology/standards
- Medical Oncology/trends
- Melanoma
- Molecular Targeted Therapy
- Neoplasms/chemistry
- Precision Medicine/methods
- Precision Medicine/trends
- Predictive Value of Tests
- Proto-Oncogene Proteins B-raf/analysis
- Proto-Oncogene Proteins B-raf/genetics
- Receptor, ErbB-2/analysis
- Receptor, ErbB-2/genetics
- Receptors, Estrogen/analysis
- Receptors, Estrogen/genetics
- Receptors, Progesterone/analysis
- Receptors, Progesterone/genetics
- Skin Neoplasms
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Affiliation(s)
- Madhu Kalia
- Thomas Jefferson University, Philadelphia PA 19107.
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111
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Identification of long-range epigenetic silencing on chromosome 15q25 and its clinical implication in gastric cancer. THE AMERICAN JOURNAL OF PATHOLOGY 2015; 185:666-78. [PMID: 25576785 DOI: 10.1016/j.ajpath.2014.11.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 10/19/2014] [Accepted: 11/04/2014] [Indexed: 12/12/2022]
Abstract
Recent genome-wide epigenomic and transcription profiling studies have demonstrated that epigenetic silencing can encompass multiple neighboring genes, termed as long-range epigenetic silencing (LRES). Herein, we identified a novel LRES region by comparing gene expression of human colon cancer HCT116 cells with their DNA methyltransferase 1 and DNA methyltransferase 3B double-knockout derivative double-knockout cells. Ten consecutive genes spanning 3 Mb of chromosome 15q25 were coordinately silenced, with eight genes showing promoter CpG island hypermethylation and enrichment of repressive histone marks, which were evaluated by bisulfite sequencing analysis and chromatin immunoprecipitation assay. Comparison of primary gastric tumor specimens with normal tissue confirmed that the long-range silencing of this region was tumor specific. Methylation of genes within the LRES region was evaluated in 190 gastric tumor tissues using the MethyLight assay, and their association with clinicopathological features, such as older age, high-grade differentiation, and diffuse or mixed-type histology, was determined. LRES-positive gastric cancer patients (six or more methylated genes) showed lower recurrence and better survival. Our findings emphasize the differential dynamics of DNA methylation and histone modification, indicating the importance of studying the relationship of each epigenetic modification in the context of chromatin domains. Patients with LRES showed lower recurrence and better prognosis, indicating that stratifying patients according to underlying molecular features, such as LRES regions, may better predict recurrence and survival.
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112
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Hunt EA, Broyles D, Head T, Deo SK. MicroRNA Detection: Current Technology and Research Strategies. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2015; 8:217-37. [PMID: 25973944 DOI: 10.1146/annurev-anchem-071114-040343] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The relatively new field of microRNA (miR) has experienced rapid growth in methodology associated with its detection and bioanalysis as well as with its role in -omics research, clinical diagnostics, and new therapeutic strategies. The breadth of this area of research and the seemingly exponential increase in number of publications on the subject can present scientists new to the field with a daunting amount of information to evaluate. This review aims to provide a collective overview of miR detection methods by relating conventional, established techniques [such as quantitative reverse transcription polymerase chain reaction (RT-qPCR), microarray, and Northern blotting (NB)] and relatively recent advancements [such as next-generation sequencing (NGS), highly sensitive biosensors, and computational prediction of microRNA/targets] to common miR research strategies. This should guide interested readers toward a more focused study of miR research and the surrounding technology.
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Affiliation(s)
- Eric A Hunt
- Department of Biochemistry and Molecular Biology, University of Miami, Miami, Florida 33136;
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113
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Cao Q, Lu K, Dai S, Hu Y, Fan W. Clinicopathological and prognostic implications of the miR-200 family in patients with epithelial ovarian cancer. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2014; 7:2392-2401. [PMID: 24966949 PMCID: PMC4069884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 03/28/2014] [Indexed: 06/03/2023]
Abstract
The aim of the present study was to investigate the association of the expression of members in the miR-200 family with clinicopathological characteristics and their impacts on overall survival in patients with epithelial ovarian cancer (EOC). Expression levels of members in the miR-200 family, including miR-200a, miR-200b, miR-200c, miR-141, and miR-429, were detected by using miRNA qRT-PCR and in situ hybridization. Associations of their expression with clinicopathological factors and overall survival were statistically evaluated. Among five members in the miR-200 family, the expression levels of miR-200a, miR-200b and miR-200c were significantly higher in EOC tissues than those in normal surface ovarian epithelium tissues, in line with the findings ofin situ hybridization analysis. In addition, tumors with high miR-200a and miR-200 bexpressionwere both more likely to have advanced stage (both P=0.006) and higher grade (P=0.01 and 0.02), whilehighmiR-200 cexpression was onlysignificantly associated with advanced stage disease (P=0.01). Moreover, univariate analysis showed that the patients with high miR-200a, miR-200b and miR-200c expression all correlated with shorter overall survival in EOC patients (all P<0.001). Multivariate statistical analysis further identified miR-200a, miR-200b and miR-200c asindependent prognostic factorsfor EOC (all P=0.01). In conclusion, these findings suggest that miR-200a, miR-200b and miR-200c overexpression may promote the aggressive tumor progression and be recognized as reliable markers to predict the survival in patients with EOCs. The three miRNAs could be attractive therapeutic targets in patients with advanced-stage EOCs.
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Affiliation(s)
- Qing Cao
- Department of Obstetrics and Gynecology, The 180th Hospital of Chinese People's Liberation Army Hua-Yuan Road No.180, Quanzhou City, Fujian Province, 362000 China
| | - Kunlin Lu
- Department of Obstetrics and Gynecology, The 180th Hospital of Chinese People's Liberation Army Hua-Yuan Road No.180, Quanzhou City, Fujian Province, 362000 China
| | - Suiping Dai
- Department of Obstetrics and Gynecology, The 180th Hospital of Chinese People's Liberation Army Hua-Yuan Road No.180, Quanzhou City, Fujian Province, 362000 China
| | - Yan Hu
- Department of Obstetrics and Gynecology, The 180th Hospital of Chinese People's Liberation Army Hua-Yuan Road No.180, Quanzhou City, Fujian Province, 362000 China
| | - Weifang Fan
- Department of Obstetrics and Gynecology, The 180th Hospital of Chinese People's Liberation Army Hua-Yuan Road No.180, Quanzhou City, Fujian Province, 362000 China
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