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Epigenetics and diagnostic

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https://www.readbyqxmd.com/read/27898666/algorithm-optimization-in-methylation-detection-with-multiple-rt-qpcr
#1
Lele Song, Yuemin Li, Jia Jia, Guangpeng Zhou, Jianming Wang, Qian Kang, Peng Jin, Jianqiu Sheng, Guoxiang Cai, Sanjun Cai, Xiaoliang Han
Epigenetic markers based on differential methylation of DNA sequences are used in cancer screening and diagnostics. Detection of abnormal methylation at specific loci by real-time quantitative polymerase chain reaction (RT-qPCR) has been developed to enable high-throughput cancer screening. For tests that combine the results of multiple PCR replicates into a single reportable result, both individual PCR cutoff and weighting of the individual PCR result are essential to test outcome. In this opportunistic screening study, we tested samples from 1133 patients using the triplicate Epi proColon assay with various algorithms and compared it with the newly developed single replicate SensiColon assay that measures methylation status of the same SEPT9 gene sequence...
2016: PloS One
https://www.readbyqxmd.com/read/27893962/proteopathic-strains-and-the-heterogeneity-of-neurodegenerative-diseases
#2
Lary C Walker
Most age-related neurodegenerative diseases are associated with the misfolding and aberrant accumulation of specific proteins in the nervous system. The proteins self-assemble and spread by a prion-like process of corruptive molecular templating, whereby abnormally folded proteins induce the misfolding and aggregation of like proteins into characteristic lesions. Despite the apparent simplicity of this process at the molecular level, diseases such as Alzheimer's, Parkinson's, Creutzfeldt-Jakob, and others display remarkable phenotypic heterogeneity, both clinically and pathologically...
November 23, 2016: Annual Review of Genetics
https://www.readbyqxmd.com/read/27889782/molecular-pathology-a-requirement-for-precision-medicine-in-cancer
#3
Manfred Dietel
The increasing importance of targeting drugs and check-point inhibitors in the treatment of several tumor entities (breast, colon, lung, malignant melanoma, lymphoma, etc.) and the necessity of a companion diagnostic (HER2, (pan)RAS, EGFR, ALK, BRAF, ROS1, MET, PD-L1, etc.) is leading to new challenges for surgical pathology. Since almost all the biomarkers to be specifically detected are tissue based, a precise and reliable diagnostic is absolutely crucial. To meet this challenge surgical pathology has adapted a number of molecular methods (semi-quantitative immunohistochemistry, fluorescence in situ hybridization, PCR and its multiple variants, (pyro/Sanger) sequencing, next generation sequencing (amplicon, whole exome, whole genome), DNA arrays, methylation analyses, etc...
2016: Oncology Research and Treatment
https://www.readbyqxmd.com/read/27885689/pathogenesis-and-diagnosis-of-placental-disorders-is-related-to-abnormal-methylation-at-promoters-of-placental-vascularization-mediating-genes
#4
Beenish Rahat, Rauf Ahmad Najar, Abid Hamid, Rashmi Bagga, Jyotdeep Kaur
OBJECTIVES: To investigate the role of methylation levels at promoter regions of placental vascularization genes (VEGF, EGFR and c-jun) in pathogenesis and diagnosis of placental disorders. METHODS: We analyzed DNA and histone methylation at promoters of VEGF, EGFR and c-jun via methylation-sensitive high resolution melting and chromatin immunoprecipitation assay in pregnant women with normal pregnancy in first, second and third trimester (n = 30 in each group) and pregnant women with pregnancy complicated with preeclampsia (n = 30) and hydatidiform mole (n = 15)...
November 24, 2016: Prenatal Diagnosis
https://www.readbyqxmd.com/read/27883184/epigenetics-in-reactive-and-reparative-cardiac-fibrogenesis-the-promise-of-epigenetic-therapy
#5
REVIEW
Asish K Ghosh, Rahul Rai, Panagiotis Flevaris, Douglas E Vaughan
Epigenetic changes play a pivotal role in the development of a wide spectrum of human diseases including cardiovascular diseases, cancer, diabetes, and intellectual disabilities. Cardiac fibrogenesis is a common pathophysiological process seen during chronic and stress-induced accelerated cardiac aging. While adequate production of extracellular matrix (ECM) proteins is necessary for post-injury wound healing, excessive synthesis and accumulation of extracellular matrix protein in the stressed or injured hearts causes decreased or loss of lusitropy that leads to cardiac failure...
November 24, 2016: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/27882306/personalized-proteomics-the-future-of-precision-medicine
#6
Trevor T Duarte, Charles T Spencer
Medical diagnostics and treatment has advanced from a one size fits all science to treatment of the patient as a unique individual. Currently, this is limited solely to genetic analysis. However, epigenetic, transcriptional, proteomic, posttranslational modifications, metabolic, and environmental factors influence a patient's response to disease and treatment. As more analytical and diagnostic techniques are incorporated into medical practice, the personalized medicine initiative transitions to precision medicine giving a holistic view of the patient's condition...
2016: Proteomes
https://www.readbyqxmd.com/read/27874289/epigenetic-changes-as-prognostic-predictors-in-endometrial-carcinomas
#7
Sanja A Farkas, Bengt G Sorbe, Torbjörn K Nilsson
Endometrial carcinoma is one of the most frequent gynecological malignancies of the female. The diagnostic and prognostic markers for the high-risk subgroups with unfavorable prognosis are under intense debate worldwide, and, therefore, the aim of this study was to identify new potential DNA methylation markers for the high-risk groups. We used the Illumina Infinium HumanMethylation450 BeadChip to analyze the DNA methylation pattern and investigated its association with clinicopathological features important for defining the high-risk (FIGO-grade 3) and low-risk (FIGO-grade 1) groups of patients with endometrial cancer (n = 31 and n = 39, respectively)...
November 22, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27874187/performance-of-a-new-hpv-and-biomarker-assay-in-management-of-hrhpv-positive-women-subanalysis-of-the-ongoing-multicenter-trace-clinical-trial-n-6-000-to-evaluate-pou4f3-as-a-potential-biomarker-of-cervical-precancer-and-cancer
#8
Adrienn Kocsis, Tibor Takács, Csaba Jeney, Zsuzsa Schaff, Róbert Koiss, Balázs Járay, Gábor Sobel, Károly Pap, István Székely, Tamás Ferenci, Hung-Cheng Lai, Miklós Nyíri, Márta Benczik
The ongoing TRACE prospective, multicenter study aimed to provide a clinical evaluation of the CONFIDENCE™ assay, which comprises an HPV DNA and a human epigenetic biomarker test. Between 2013 and 2015 over 6,000 women aged 18 or older were recruited in Hungary. Liquid based cytology, hrHPV DNA detection and single target host-gene methylation test of the promoter sequence of the POU4F3 gene by quantitative methylation specific PCR were performed from the same LBC sample. The current analysis is focused on the baseline cross-sectional clinical results of 5,384 LBC samples collected from subjects aged 25 years or older...
November 22, 2016: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/27872267/endophenotypes-epigenetics-polygenicity-and-more-irv-gottesman-s-dynamic-legacy
#9
David L Braff, Carol A Tamminga
First, we describe the hallmark contributions of Irv Gottesman's pioneering scholarship for schizophrenia research including concepts of polygenicity, gene × environment interactions, epigenetics and the endophenotype concept. Gottesman and colleagues' twin studies showed that genes, not social factors, mediate schizophrenia risk. He then showed that schizophrenia is highly polygenic. Next, he introduced the concept of epigenetics into schizophrenia research. Gottesman then introduced the quantitative endophenotype concept...
November 21, 2016: Schizophrenia Bulletin
https://www.readbyqxmd.com/read/27869444/-brca1-and-brca2-pathologists-starting-kit
#10
Petr Škapa
Dysfunction of tumor suppressor genes BRCA1 and BRCA2 is involved in the pathogenesis of malignant tumors, especially breast and ovarian carcinoma. BRCA1/2 genes may be inactivated by germinal and somatic mutations or epigenetic changes. Germinal mutations are responsible for the hereditary breast and ovarian carcinoma syndrome. Defects of BRCA1/2 genes lead to the failure of homologous recombination, the basic mechanism for DNA double strand break repair. The resultant genomic instability is associated with a high risk of malignant transformation of the cell, but it also results in a higher sensitivity of tumors to platinum-based chemotherapeutic compounds which damage DNA structure directly...
2016: Ceskoslovenská Patologie
https://www.readbyqxmd.com/read/27865783/the-modulation-of-inflammatory-parameters-brain-derived-neurotrophic-factor-levels-and-global-histone-h4-acetylation-status-in-peripheral-blood-of-patients-with-gaucher-disease-type-1
#11
Alexandre Silva de Mello, Ivy Reichert Vital da Silva, Gustavo Pereira Reinaldo, Gilson Pires Dorneles, Jaqueline Cé, Pedro Dal Lago, Alessandra Peres, Viviane Rostirola Elsner, Janice Carneiro Coelho
OBJECTIVES: Gaucher's disease type 1 (GD1) pathophysiology includes an imbalance on brain-derived neurotrophic factor (BDNF) levels and in the inflammatory system. However, the pathways involved remain poorly understood. The hypothesis of this study is that epigenetic mechanisms might be involved, at least partially, in this phenomenon. DESIGN AND METHODS: This study investigated the BDNF modulation, global histone H4 acetylation and pro- and anti-inflammatory cytokines levels in the peripheral blood of GD1 patients (n=10) when compared with control samples (CS) (n=11)...
November 16, 2016: Clinical Biochemistry
https://www.readbyqxmd.com/read/27853465/epigenetic-dna-methylation-profiling-with-msre-a-quantitative-ngs-approach-using-a-parkinson-s-disease-test-case
#12
Adam G Marsh, Matthew T Cottrell, Morton F Goldman
Epigenetics is a rapidly developing field focused on deciphering chemical fingerprints that accumulate on human genomes over time. As the nascent idea of precision medicine expands to encompass epigenetic signatures of diagnostic and prognostic relevance, there is a need for methodologies that provide high-throughput DNA methylation profiling measurements. Here we report a novel quantification methodology for computationally reconstructing site-specific CpG methylation status from next generation sequencing (NGS) data using methyl-sensitive restriction endonucleases (MSRE)...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27849631/reduced-h3k27me3-expression-is-common-in-nodular-melanomas-of-childhood-associated-with-congenital-melanocytic-nevi-but-not-in-proliferative-nodules
#13
Klaus J Busam, Kara N Shah, Pedram Gerami, Thomas Sitzman, Achim A Jungbluth, Veronica Kinsler
The formation of a nodule within a congenital melanocytic nevus (CMN) raises concerns about possible melanoma. Most new nodular growths that develop during childhood, however, are benign proliferative nodules (PN); melanoma is very rare. The distinction of melanoma from PN can at times be difficult clinically and histopathologically, requiring ancillary molecular tests for diagnosis. Although the application of molecular methods has revealed new insights into the mutational and genomic landscape of childhood melanomas, little is known about epigenetic events that may drive the growth of a melanoma or PN in a CMN...
November 15, 2016: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/27846723/-novel-approaches-in-dna-methylation-studies-ms-hrm-analysis-and-electrochemistry
#14
M Bartošík, E Ondroušková
Cytosine methylation in DNA is an epigenetic mechanism regulating gene expression and plays a vital role in cell differentiation or proliferation. Tumor cells often exhibit aberrant DNA methylation, e.g. hypermethylation of tumor suppressor gene promoters. New methods, capable of determining methylation status of specific DNA sequences, are thus being developed. Among them, MS-HRM (methylation-specific high resolution melting) and electrochemistry offer relatively inexpensive instrumentation, fast assay times and possibility of screening multiple samples/DNA regions simultaneously...
2016: Klinická Onkologie: Casopis Ceské a Slovenské Onkologické Spolecnosti
https://www.readbyqxmd.com/read/27845777/newer-insights-into-the-role-of-mirna-a-tiny-genetic-tool-in-psychiatric-disorders-focus-on-post-traumatic-stress-disorder
#15
REVIEW
V V Giridharan, R A Thandavarayan, G R Fries, C Walss-Bass, T Barichello, N J Justice, M K Reddy, J Quevedo
Post-traumatic stress disorder (PTSD) is a mental disorder occurring in about 2-9% of individuals after their exposure to life-threatening events, such as severe accidents, sexual abuse, combat or a natural catastrophe. Because PTSD patients are exposed to trauma, it is likely that epigenetic modifications have an important role in disease development and prognosis. For the past two decades, abnormal expression of the epigenetic regulators microRNAs (miRs) and miR-mediated gene regulation have been given importance in a variety of human diseases, such as cancer, heart disease and viral infection...
November 15, 2016: Translational Psychiatry
https://www.readbyqxmd.com/read/27843535/insights-for-hepatitis-c-virus-related-hepatocellular-carcinoma-genetic-biomarkers-early-diagnosis-and-therapeutic-intervention
#16
REVIEW
Wafaa M Ezzat, Khalda Sayed Amr
The current review explores the role of emerging molecular contributing factors in liver carcinogenesis on top of hepatitis C virus (HCV). Here we will try to discuss the role genetic and epigenetic factors in pathogenesis of hepatocellular carcinoma. Understanding the role of these factors will help in discovering the mystery of liver carcinogenesis on top of chronic HCV infection. Moreover, use of the studied molecular factors will provide the hepatologists with tailored diagnostic promising biomarkers and flatten the way for establishment of emerging molecular treatment based on exploring the molecular subscription of this aggressive liver cancer...
October 28, 2016: World Journal of Hepatology
https://www.readbyqxmd.com/read/27843151/a-dna-methylation-biomarker-of-alcohol-consumption
#17
C Liu, R E Marioni, Å K Hedman, L Pfeiffer, P-C Tsai, L M Reynolds, A C Just, Q Duan, C G Boer, T Tanaka, C E Elks, S Aslibekyan, J A Brody, B Kühnel, C Herder, L M Almli, D Zhi, Y Wang, T Huan, C Yao, M M Mendelson, R Joehanes, L Liang, S-A Love, W Guan, S Shah, A F McRae, A Kretschmer, H Prokisch, K Strauch, A Peters, P M Visscher, N R Wray, X Guo, K L Wiggins, A K Smith, E B Binder, K J Ressler, M R Irvin, D M Absher, D Hernandez, L Ferrucci, S Bandinelli, K Lohman, J Ding, L Trevisi, S Gustafsson, J H Sandling, L Stolk, A G Uitterlinden, I Yet, J E Castillo-Fernandez, T D Spector, J D Schwartz, P Vokonas, L Lind, Y Li, M Fornage, D K Arnett, N J Wareham, N Sotoodehnia, K K Ong, J B J van Meurs, K N Conneely, A A Baccarelli, I J Deary, J T Bell, K E North, Y Liu, M Waldenberger, S J London, E Ingelsson, D Levy
The lack of reliable measures of alcohol intake is a major obstacle to the diagnosis and treatment of alcohol-related diseases. Epigenetic modifications such as DNA methylation may provide novel biomarkers of alcohol use. To examine this possibility, we performed an epigenome-wide association study of methylation of cytosine-phosphate-guanine dinucleotide (CpG) sites in relation to alcohol intake in 13 population-based cohorts (ntotal=13 317; 54% women; mean age across cohorts 42-76 years) using whole blood (9643 European and 2423 African ancestries) or monocyte-derived DNA (588 European, 263 African and 400 Hispanic ancestry) samples...
November 15, 2016: Molecular Psychiatry
https://www.readbyqxmd.com/read/27826838/the-role-of-dna-methylation-in-cancer
#18
Ranjani Lakshminarasimhan, Gangning Liang
The malignant transformation of normal cells is driven by both genetic and epigenetic changes. With the advent of next-generation sequencing and large-scale multinational consortium studies, it has become possible to profile the genomes and epigenomes of thousands of primary tumors from nearly every cancer type. From these genome-wide studies, it became clear that the dynamic regulation of DNA methylation is a critical epigenetic mechanism of cancer initiation, maintenance, and progression. Proper control of DNA methylation is not only crucial for regulating gene transcription, but its broader consequences include maintaining the integrity of the genome and modulating immune response...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27826568/pax1-and-sox1-methylation-as-an-initial-screening-method-for-cervical-cancer-a-meta-analysis-of-individual-studies-in-asians
#19
Yan Chen, Zhaolei Cui, Zhenzhou Xiao, Minhua Hu, Chuanhui Jiang, Yingying Lin, Yansong Chen
BACKGROUND: Epigenetic alterations of gene or DNA methylation have been highlighted as promising biomarkers for early cervical cancer screening. Herein, we evaluated the diagnostic performance of paired boxed gene 1 (PAX1) and sex determining region Y-box 1 (SOX1) methylation for cervical cancer detection. METHODS: Eligible studies were retrieved by searching the electronic databases. Study quality was assessed according to the Quality Assessment of Diagnostic Accuracy Studies (QUADAS) checklist...
October 2016: Annals of Translational Medicine
https://www.readbyqxmd.com/read/27822313/quantitative-analysis-of-chip-seq-data-uncovers-dynamic-and-sustained-h3k4me3-and-h3k27me3-modulation-in-cancer-cells-under-hypoxia
#20
Michiel E Adriaens, Peggy Prickaerts, Michelle Chan-Seng-Yue, Twan van den Beucken, Vivian E H Dahlmans, Lars M Eijssen, Timothy Beck, Bradly G Wouters, Jan Willem Voncken, Chris T A Evelo
BACKGROUND: A comprehensive assessment of the epigenetic dynamics in cancer cells is the key to understanding the molecular mechanisms underlying cancer and to improving cancer diagnostics, prognostics and treatment. By combining genome-wide ChIP-seq epigenomics and microarray transcriptomics, we studied the effects of oxygen deprivation and subsequent reoxygenation on histone 3 trimethylation of lysine 4 (H3K4me3) and lysine 27 (H3K27me3) in a breast cancer cell line, serving as a model for abnormal oxygenation in solid tumors...
2016: Epigenetics & Chromatin
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