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Epigenetics and diagnostic

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https://www.readbyqxmd.com/read/28644958/translating-cancer-epigenomics-into-the-clinic-focus-on-lung-cancer
#1
REVIEW
Josep Mari-Alexandre, Angel Diaz-Lagares, Maria Villalba, Oscar Juan, Ana B Crujeiras, Alfonso Calvo, Juan Sandoval
Epigenetic deregulation is increasingly being recognized as a hallmark of cancer. Recent studies have identified many new epigenetic biomarkers, some of which are being introduced into clinical practice for diagnosis, molecular classification, prognosis or prediction of response to therapies. O-6-methylguanine-DNA methyltransferase gene is the most clinically advanced epigenetic biomarker as it predicts the response to temozolomide and carmustine in gliomas. Therefore, epigenomics may represent a novel and promising tool for precision medicine, and in particular, the detection of epigenomic biomarkers in liquid biopsies will be of great interest for monitoring diseases in patients...
June 2, 2017: Translational Research: the Journal of Laboratory and Clinical Medicine
https://www.readbyqxmd.com/read/28642604/turning-the-tide-in-myelodysplastic-myeloproliferative-neoplasms
#2
REVIEW
Michael W N Deininger, Jeffrey W Tyner, Eric Solary
Myelodysplastic syndromes/myeloproliferative neoplasms (MDS/MPN) are aggressive myeloid malignancies recognized as a distinct category owing to their unique combination of dysplastic and proliferative features. Although current classification schemes still emphasize morphology and exclusionary criteria, disease-defining somatic mutations and/or germline predisposition alleles are increasingly incorporated into diagnostic algorithms. The developing picture suggests that phenotypes are driven mostly by epigenetic mechanisms that reflect a complex interplay between genotype, physiological processes such as ageing and interactions between malignant haematopoietic cells and the stromal microenvironment of the bone marrow...
June 23, 2017: Nature Reviews. Cancer
https://www.readbyqxmd.com/read/28638988/same-day-genomic-and-epigenomic-diagnosis-of-brain-tumors-using-real-time-nanopore-sequencing
#3
Philipp Euskirchen, Franck Bielle, Karim Labreche, Wigard P Kloosterman, Shai Rosenberg, Mailys Daniau, Charlotte Schmitt, Julien Masliah-Planchon, Franck Bourdeaut, Caroline Dehais, Yannick Marie, Jean-Yves Delattre, Ahmed Idbaih
Molecular classification of cancer has entered clinical routine to inform diagnosis, prognosis, and treatment decisions. At the same time, new tumor entities have been identified that cannot be defined histologically. For central nervous system tumors, the current World Health Organization classification explicitly demands molecular testing, e.g., for 1p/19q-codeletion or IDH mutations, to make an integrated histomolecular diagnosis. However, a plethora of sophisticated technologies is currently needed to assess different genomic and epigenomic alterations and turnaround times are in the range of weeks, which makes standardized and widespread implementation difficult and hinders timely decision making...
June 21, 2017: Acta Neuropathologica
https://www.readbyqxmd.com/read/28630300/g9a-drives-hypoxia-mediated-gene-repression-for-breast-cancer-cell-survival-and-tumorigenesis
#4
Francesco Casciello, Fares Al-Ejeh, Greg Kelly, Donal J Brennan, Shin Foong Ngiow, Arabella Young, Thomas Stoll, Karolina Windloch, Michelle M Hill, Mark J Smyth, Frank Gannon, Jason S Lee
G9a is an epigenetic regulator that methylates H3K9, generally causing repression of gene expression, and participates in diverse cellular functions. G9a is genetically deregulated in a variety of tumor types and can silence tumor suppressor genes and, therefore, is important for carcinogenesis. Although hypoxia is recognized to be an adverse factor in tumor growth and metastasis, the role of G9a in regulating gene expression in hypoxia has not been described extensively. Here, we show that G9a protein stability is increased in hypoxia via reduced proline hydroxylation and, hence, inefficient degradation by the proteasome...
June 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28627779/new-horizon-for-breast-cancer-biomarker-discoveries-what-might-the-liquid-biopsy-of-nipple-aspirate-fluid-hold
#5
Ferdinando Mannello
The existence of cellular, molecular and biochemical heterogeneity of human breast cancers reveals the intricacy of biomarkers complexity, stimulating studies on new approaches (like "liquid biopsies") for the improvements in precision medicine. Breast cancer is recognized as a leading cause of morbidity and mortality worldwide with tumors significantly diverse and containing many types of cells showing different genetic and epigenetic profiles. In this field, the technology of Liquid Biopsy (applied to a fluid produced by breast gland, named nipple aspirate fluids, NAF) highlights the power of combining basic and clinical research...
June 19, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28624979/new-insights-into-the-pathogenesis-of-iga-nephropathy
#6
REVIEW
See Cheng Yeo, Chee Kay Cheung, Jonathan Barratt
IgA nephropathy is the most common form of glomerulonephritis in many parts of the world and remains an important cause of end-stage renal disease. Current evidence suggests that IgA nephropathy is not due to a single pathogenic insult, but rather the result of multiple sequential pathogenic "hits". An abnormally increased level of circulating poorly O-galactosylated IgA1 and the production of O-glycan-specific antibodies leads to the formation of IgA1-containing immune complexes, and their subsequent mesangial deposition results in inflammation and glomerular injury...
June 17, 2017: Pediatric Nephrology: Journal of the International Pediatric Nephrology Association
https://www.readbyqxmd.com/read/28624579/epigenome-wide-association-study-identifies-methylation-sites-associated-with-liver-enzymes-and-hepatic-steatosis
#7
Jana Nano, Mohsen Ghanbari, Wenshi Wang, Paul S de Vries, Klodian Dhana, Taulant Muka, André G Uitterlinden, Joyce B J van Meurs, Albert Hofman, Oscar H Franco, Qiuwei Pan, Sarwa Darwish Murad, Abbas Dehghan
BACKGROUND & AIMS: Epigenetic mechanisms might be involved in the regulation of liver enzyme level. We aimed to identify CpG sites at which DNA methylation levels are associated with blood levels of liver enzymes and hepatic steatosis. METHODS: We conducted an epigenome-wide association study in whole blood for liver enzymes levels including gamma-glutamyl transferase (GGT), alanine aminotransferase (ALT), and aspartate aminotransferase (AST), among a discovery set of 731 participants of the Rotterdam Study and sought replication in a non-overlapping sample of 719 individuals...
June 14, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28624296/a-refined-dna-methylation-detection-method-using-mspji-coupled-quantitative-pcr
#8
Christopher J Petell, Gilbert Loiseau, Ryan Gandy, Sriharsa Pradhan, Humaira Gowher
DNA methylation is a highly conserved epigenetic modification with critical roles ranging from protection against phage infection in bacteria to the regulation of gene expression in mammals. DNA methylation at specific sequences can be measured by using methylation dependent or sensitive restriction enzymes coupled to semi- or quantitative PCR (MD-qPCR). This study reports a refined MD-qPCR method for detecting gain or loss of DNA methylation at specific sites through the specific use of MspJI or HpaII, respectively...
June 15, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28623159/epigenetic-biomarkers-and-cardiovascular-disease-circulating-micrornas
#9
David de Gonzalo-Calvo, Eduardo Iglesias-Gutiérrez, Vicenta Llorente-Cortés
MicroRNAs (miRNAs) are a class of small noncoding RNA (20-25 nucleotides) involved in gene regulation. In recent years, miRNAs have emerged as a key epigenetic mechanism in the development and physiology of the cardiovascular system. These molecular species regulate basic functions in virtually all cell types, and are therefore directly associated with the pathophysiology of a large number of cardiovascular diseases. Since their relatively recent discovery in extracellular fluids, miRNAs have been studied as potential biomarkers of disease...
June 13, 2017: Revista Española de Cardiología
https://www.readbyqxmd.com/read/28623138/hp1%C3%AE-is-highly-expressed-in-glioma-cells-and-facilitates-cell-proliferation-and-survival
#10
Xianliang Lai, Zhifeng Deng, Hua Guo, Xingen Zhu, Wei Tu
Epigenetic alteration plays critical roles in gliomagenesis by regulating gene expression through modifications of Histones and DNA. Trimethylation of H3K9, an essential repressed transcription mark, and one of its methyltransferase, SUV39H1, are implicated in glioma pathogenesis and progression. We find that the protein level of HP1α, a reader of H3K9me3 is elevated in cultured glioma cell lines and glioma tissues. H3K9me3 is also upregulated. Depletion of HP1α and SUV39H1 weakens glioma cell proliferation capacity and results in apoptosis of cells...
June 13, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28620608/a-path-to-implement-precision-child-health-cardiovascular-medicine
#11
REVIEW
Marlin Touma, Brian Reemtsen, Nancy Halnon, Juan Alejos, J Paul Finn, Stanley F Nelson, Yibin Wang
Congenital heart defects (CHDs) affect approximately 1% of live births and are a major source of childhood morbidity and mortality even in countries with advanced healthcare systems. Along with phenotypic heterogeneity, the underlying etiology of CHDs is multifactorial, involving genetic, epigenetic, and/or environmental contributors. Clear dissection of the underlying mechanism is a powerful step to establish individualized therapies. However, the majority of CHDs are yet to be clearly diagnosed for the underlying genetic and environmental factors, and even less with effective therapies...
2017: Frontiers in Cardiovascular Medicine
https://www.readbyqxmd.com/read/28612612/-molecular-aspects-of-thyroid-tumors-with-emphasis-on-microrna-and-their-clinical-implications
#12
M Ludvíková, I Kholová, D Kalfeřt
BACKGROUND: Central to neoplastic transformation and tumor progression is alteration of the signaling pathways that control cell proliferation and apoptosis. The key mechanisms for this neoplastic process are genetic changes (mutations of cancer-related genes) and recently identified epigenetic changes that involve DNA methylation, chromatin remodeling (which has a profound effect on the control of gene expression), and noncoding, regulatory RNA (notably, microRNA - miRNA). MiRNAs control expression of their target gene post-transcriptionally...
2017: Klinická Onkologie: Casopis Ceské a Slovenské Onkologické Spolecnosti
https://www.readbyqxmd.com/read/28607134/dysfunctional-diversity-of-p53-proteins-in-adult-acute-myeloid-leukemia-projections-on-diagnostic-work-up-and-therapy
#13
Miron Prokocimer, Alina Molchadsky, Varda Rotter
The heterogeneous nature of Acute Myeloid Leukemia (AML) and its poor prognosis necessitate therapeutic improvement. Current advances in AML research yield important insights regarding AML genetic, epigenetic, evolutional, and clinical diversity, all in which dysfunctional p53 plays a key role. As p53 is central to hematopoietic stem cell functions, its aberrations affect AML evolution, biology and therapy response, and usually predict poor prognosis. While in human solid tumors TP53 is mutated in more than half of cases, TP53 mutations occur in less than a tenth of de-novo AML cases...
June 12, 2017: Blood
https://www.readbyqxmd.com/read/28602111/genetics-of-polycystic-ovary-syndrome
#14
Kateryna Mykhalchenko, Daria Lizneva, Tatiana Trofimova, Walidah Walker, Larisa Suturina, Michael P Diamond, Ricardo Azziz
Polycystic ovary syndrome (PCOS) is a hormonal and metabolic disorder affecting 5 to 20% of reproductive-aged women worldwide that results in androgen excess, menstrual dysfunction and oligo-ovulatory subfertility, with increased risks for type 2 diabetes, endometrial adenocarcinoma, and potentially vascular disease, among other morbidities. PCOS is a complex genetic trait with strong heritability accounting for as high as 70% of the development of the disorder. Areas covered: The authors summarize the historical and recent findings of genetic studies of PCOS, such as familial studies, twin studies, and molecular genetic studies, including the results of recent genome wide associated studies...
July 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28598237/homocysteine-as-a-diagnostic-and-etiopathogenic-factor-in-children-with-autism-spectrum-disorder
#15
Jan Józefczuk, Wiktoria Kasprzycka, Rafał Czarnecki, Alfreda Graczyk, Paweł Józefczuk, Krzysztof Magda, Urszula Lampart
Substantial characteristics of autism are cognitive and psychophysical disorders. Etiopathogenetic factors are thought to be responsible for development of autism in children with genetic predisposition as well as have their effect on the severity of the disorders. The main problem of early identification of patients affected by autism spectrum disorder is that there are no clear diagnostic criteria. The aim of our study was assessment of hair magnesium and serum homocysteine concentrations in children with autism...
June 9, 2017: Journal of Medicinal Food
https://www.readbyqxmd.com/read/28596419/intra-tumor-heterogeneity-novel-approaches-for-resolving-genomic-architecture-and-clonal-evolution
#16
Ravi G Gupta, Robert A Somer
High-throughput genomic technologies have revealed a remarkably complex portrait of intra-tumor heterogeneity in cancer and have shown that tumors evolve through a reiterative process of genetic diversification and clonal selection. This discovery has challenged the classical paradigm of clonal dominance and brought attention to subclonal tumor cell populations that contribute to the cancer phenotype. Dynamic evolutionary models may explain how these populations grow within the ecosystem of tissues, including linear, branching, neutral and punctuated patterns...
June 8, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28596259/morphologic-and-molecular-characteristics-of-de-novo-aml-with-jak2-v617f-mutation
#17
Juliana E Hidalgo-López, Rashmi Kanagal-Shamanna, L Jeffrey Medeiros, Zeev Estrov, C Cameron Yin, Srdan Verstovsek, Sergej Konoplev, Jeffrey L Jorgensen, Mohammad M Mohammad, Roberto N Miranda, Chong Zhao, John Lee, Zhuang Zuo, Carlos E Bueso-Ramos
Background:JAK2 V617F mutation (mut) in acute myeloid leukemia (AML) is rare. We describe the clinicopathologic findings of a single-institution series of 11 de novo AML cases with JAK2 V617. Methods: We identified cases of de novo AML with JAK2 V617F over a 10-year period. We reviewed diagnostic peripheral blood and bone marrow (BM) morphologic, cytogenetic, and molecular studies, including next-generation sequencing. The control group consisted of 12 patients with JAK2 wild-type (wt) AML matched for age, sex, and diagnosis...
June 2017: Journal of the National Comprehensive Cancer Network: JNCCN
https://www.readbyqxmd.com/read/28592764/multiple-myeloma-pathophysiology-and-progress-in-management
#18
Junya Kuroda, Yoshiaki Chinen
There have been dramatic recent advances in understanding the basic pathophysiology and treatment strategies for multiple myeloma (MM). Research has shown both a high inter-patient diversity and intra-clonal heterogeneity even in a single patient in terms of cytogenetic/molecular abnormalities, and has also identified marked diversity in the immunological factors involved in tumor surveillance among MM patients. In the presence of a variety of novel agents, including molecular-targeted agents, immunomodulatory agents, and monoclonal antibodies, the optimal translation of current knowledge on both molecular and immunologic findings into clinical use is crucial for managing MM...
2017: [Rinshō Ketsueki] the Japanese Journal of Clinical Hematology
https://www.readbyqxmd.com/read/28580304/significance-of-inactivated-genes-in-leukemia-pathogenesis-and-prognosis
#19
REVIEW
Nazanin Heidari, Saeid Abroun, Jessika Bertacchini, Tina Vosoughi, Fakher Rahim, Najmaldin Saki
Epigenetic and genetic alterations are two mechanisms participating in leukemia, which can inactivate genes involved in leukemia pathogenesis or progression. The purpose of this review was to introduce various inactivated genes and evaluate their possible role in leukemia pathogenesis and prognosis. By searching the mesh words "Gene, Silencing AND Leukemia" in PubMed website, relevant English articles dealt with human subjects as of 2000 were included in this study. Gene inactivation in leukemia is largely mediated by promoter's hypermethylation of gene involving in cellular functions such as cell cycle, apoptosis, and gene transcription...
2017: Cell Journal
https://www.readbyqxmd.com/read/28578013/paradoxical-roles-of-dual-oxidases-in-cancer-biology
#20
REVIEW
Andrew C Little, Arvis Sulovari, Karamatullah Danyal, David E Heppner, David J Seward, Albert van der Vliet
Dysregulated oxidative metabolism is a well-recognized aspect of cancer biology, and many therapeutic strategies are based on targeting cancers by altering cellular redox pathways. The NADPH oxidases (NOXes) present an important enzymatic source of biological oxidants, and the expression and activation of several NOX isoforms are frequently dysregulated in many cancers. Cell-based studies have demonstrated a role for several NOX isozymes in controlling cell proliferation and/or cell migration, further supporting a potential contributing role for NOX in promoting cancer...
May 31, 2017: Free Radical Biology & Medicine
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