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https://www.readbyqxmd.com/read/27933110/profiling-lung-adenocarcinoma-by-liquid-biopsy-can-one-size-fit-all
#1
Harry W Clifford, Amy P Cassidy, Courtney Vaughn, Evaline S Tsai, Bianka Seres, Nirmesh Patel, Hannah L O'Neill, Emil Hewage, John W Cassidy
BACKGROUND: Cancer is first and foremost a disease of the genome. Specific genetic signatures within a tumour are prognostic of disease outcome, reflect subclonal architecture and intratumour heterogeneity, inform treatment choices and predict the emergence of resistance to targeted therapies. Minimally invasive liquid biopsies can give temporal resolution to a tumour's genetic profile and allow the monitoring of treatment response through levels of circulating tumour DNA (ctDNA). However, the detection of ctDNA in repeated liquid biopsies is currently limited by economic and time constraints associated with targeted sequencing...
2016: Cancer Nanotechnology
https://www.readbyqxmd.com/read/27925336/non-exponential-growth-of-mycobacterium-leprae-thai-53-strain-cultured-in-vitro
#2
Kazunobu Amako, Ken-Ichiro Iida, Mitsumasa Saito, Yoshitosi Ogura, Tetsuya Hayashi, Shin-Ichi Yoshida
To determine why cultivation of Mycobacterium leprae in vitro has not been successful, we attempted to culture this bacterium in media supplemented with a variety of biological materials. We observed a slight increase in the number of cells in medium supplemented with human blood plasma and an extract of nude mouse tissue after more than 3 months of cultivation at 30°C. To ascertain whether this increase was real growth, we analyzed the growth by droplet digital PCR. The analysis had the following two results: the slow increase in the copy number of cell-associated DNA and the release of a large amount of DNA into the culture medium from bacterial cells during cultivation...
December 7, 2016: Microbiology and Immunology
https://www.readbyqxmd.com/read/27922678/a-novel-rapid-point-of-care-test-for-lung-cancer-patients-to-detect-epidermal-growth-factor-receptor-gene-mutations-by-using-real-time-droplet-pcr-and-fresh-liquid-cytology-specimens
#3
Shiho Asaka, Akihiko Yoshizawa, Kazuyuki Matsuda, Akemi Yamaguchi, Hiroshi Yamamoto, Takayuki Shiina, Rie Nakata, Kaoru Ogawa, Meng Zhang, Takayuki Honda
Epidermal growth factor receptor gene (EGFR) mutations are associated with response to tyrosine kinase inhibitors (TKIs) in patients with non-small cell lung cancer (NSCLC). We developed a novel, rapid EGFR mutation assay using a real-time droplet-polymerase chain reaction machine (EGFR d-PCR assay). The purpose of this study was to validate the performance of the EGFR d-PCR assay using fresh liquid cytology specimens. We analyzed three major EGFR mutations (L858R in exon 21, E746_A750del in exon 19 and T790M in exon 20) in 80 fresh liquid cytology specimens of adenocarcinoma (ADC) or NSCLC-not otherwise specified (NOS) via the EGFR d-PCR assay and conventional real-time PCR assay using the therascreen® EGFR RGQ PCR kit (Therascreen assay)...
December 2, 2016: Oncology Reports
https://www.readbyqxmd.com/read/27921220/increased-cell-free-mitochondrial-dna-is-a-marker-of-ongoing-inflammation-and-better-neurocognitive-function-in-virologically-suppressed-hiv-infected-individuals
#4
Josué Pérez-Santiago, Michelli F De Oliveira, Susanna R Var, Tyler R C Day, Steven P Woods, Sara Gianella, Sanjay R Mehta
Cell-free mitochondrial DNA (mtDNA) is a highly immunogenic molecule that is associated with several inflammatory conditions and with neurocognitive impairment during untreated HIV infection. Here, we investigate how cell-free mtDNA in cerebrospinal fluid (CSF) is associated with inflammation, neuronal damage, and neurocognitive functioning in the context of long-term suppressive antiretroviral therapy (ART). We quantified the levels of cell-free mtDNA in the CSF from 41 HIV-infected individuals with completely suppressed HIV RNA levels in blood plasma (<50 copies/mL) by droplet digital PCR...
December 5, 2016: Journal of Neurovirology
https://www.readbyqxmd.com/read/27919855/uncoupling-protein-2-deficiency-reduces-proliferative-capacity-of-murine-pancreatic-stellate-cells
#5
Sarah Muller, Sandra Maria Klingbeil, Andreea Sandica, Robert Jaster
BACKGROUND: Uncoupling protein 2 (UCP2) has been suggested to inhibit mitochondrial production of reactive oxygen species (ROS) by decreasing the mitochondrial membrane potential. Experimental acute pancreatitis is associated with increased UCP2 expression, whereas UCP2 deficiency retards regeneration of aged mice from acute pancreatitis. Here, we have addressed biological and molecular functions of UCP2 in pancreatic stellate cells (PSCs), which are involved in pancreatic wound repair and fibrogenesis...
December 2016: Hepatobiliary & Pancreatic Diseases International: HBPD INT
https://www.readbyqxmd.com/read/27919468/somatic-gnaq-mutation-is-enriched-in-brain-endothelial-cells-in%C3%A2-sturge-weber-syndrome
#6
Lan Huang, Javier A Couto, Anna Pinto, Sanda Alexandrescu, Joseph R Madsen, Arin K Greene, Mustafa Sahin, Joyce Bischoff
BACKGROUND: Sturge-Weber syndrome (SWS) is a rare congenital neurocutaneous disorder characterized by facial and extracraniofacial capillary malformations and capillary-venule malformations in the leptomeninges. A somatic mosaic mutation in GNAQ (c.548G>A; p.R183Q) was found in SWS brain and skin capillary malformations. Our laboratory showed endothelial cells in skin capillary malformations are enriched for the GNAQ mutation. The purpose of this study is to determine whether the GNAQ mutation is also enriched in endothelial cells in affected SWS brain...
October 21, 2016: Pediatric Neurology
https://www.readbyqxmd.com/read/27917295/circulating-human-papillomavirus-dna-detected-using-droplet-digital-pcr-in-the-serum-of-patients-diagnosed-with-early-stage-human-papillomavirus-associated-invasive-carcinoma
#7
Emmanuelle Jeannot, Véronique Becette, Maura Campitelli, Marie-Ange Calméjane, Emmanuelle Lappartient, Evelyne Ruff, Stéphanie Saada, Allyson Holmes, Dominique Bellet, Xavier Sastre-Garau
Specific human papillomavirus genotypes are associated with most ano-genital carcinomas and a large subset of oro-pharyngeal carcinomas. Human papillomavirus DNA is thus a tumour marker that can be detected in the blood of patients for clinical monitoring. However, data concerning circulating human papillomavirus DNA in cervical cancer patients has provided little clinical value, due to insufficient sensitivity of the assays used for the detection of small sized tumours. Here we took advantage of the sensitive droplet digital PCR method to identify circulating human papillomavirus DNA in patients with human papillomavirus-associated carcinomas...
October 2016: Journal of Pathology. Clinical Research
https://www.readbyqxmd.com/read/27913434/a-study-of-tp53-rna-splicing-illustrates-pitfalls-of-rna-seq-methodology
#8
Sunali Mehta, Peter Tsai, Annette Lasham, Hamish Campbell, Roger Reddel, Antony Braithwaite, Cristin Print
TP53 undergoes multiple RNA-splicing events, resulting in at least nine mRNA transcripts encoding at least 12 functionally different protein isoforms. Antibodies specific to p53 protein isoforms have proven difficult to develop, thus researchers must rely on the transcript information to infer isoform abundance. In this study, we used deep RNA-seq, droplet digital PCR (ddPCR), and real-time quantitative reverse transcriptase PCR (RT-qPCR) from nine human cell lines and RNA-seq data available for tumors in The Cancer Genome Atlas to analyze TP53 splice variant expression...
October 20, 2016: Cancer Research
https://www.readbyqxmd.com/read/27908228/detection-of-mutations-in-mitochondrial-dna-by-droplet-digital-pcr
#9
J K Sofronova, Y Y Ilinsky, K E Orishchenko, E G Chupakhin, E A Lunev, I O Mazunin
Mutations in mitochondrial DNA (mtDNA) may result in various pathological processes. Detection of mutant mtDNAs is a problem for diagnostic practice that is complicated by heteroplasmy - a phenomenon of the inferring presence of at least two allelic variants of the mitochondrial genome. Also, the level of heteroplasmy largely determines the profile and severity of clinical manifestations. Here we discuss detection of mutations in heteroplasmic mtDNA using up-to-date methods that have not yet been introduced as routine clinical assays...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27906039/peering-below-the-diffraction-limit-robust-and-specific-sorting-of-viruses-with-flow-cytometry
#10
Shea T Lance, David J Sukovich, Kenneth M Stedman, Adam R Abate
BACKGROUND: Viruses are incredibly diverse organisms and impact all forms of life on Earth; however, individual virions are challenging to study due to their small size and mass, precluding almost all direct imaging or molecular analysis. Moreover, like microbes, the overwhelming majority of viruses cannot be cultured, impeding isolation, replication, and study of interesting new species. Here, we introduce PCR-activated virus sorting, a method to isolate specific viruses from a heterogeneous population...
December 1, 2016: Virology Journal
https://www.readbyqxmd.com/read/27899805/circulating-tumour-dna-analysis-demonstrates-spatial-mutational-heterogeneity-that-coincides-with-disease-relapse-in-myeloma
#11
S Mithraprabhu, T Khong, M Ramachandran, A Chow, D Klarica, L Mai, S Walsh, D Broemeling, A Marziali, M Wiggin, J Hocking, A Kalff, B Durie, A Spencer
Mutational characterisation in multiple myeloma (MM) currently relies on bone marrow (BM) biopsy, which fails to capture the putative spatial and genetic heterogeneity of this multi-focal disease. Analysis of plasma (PL)-derived circulating free tumour DNA (ctDNA) as an adjunct to BM biopsy, for mutational characterisation and tracking disease progression, was evaluated. Paired BM MM cell DNA and ctDNA from 33 relapsed [RR] and 15 newly diagnosed [ND] patients were analysed for KRAS, NRAS, BRAF and TP53 mutations using the OnTarget™ Mutation Detection (OMD) platform...
November 30, 2016: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/27898590/reactivation-of-simian-immunodeficiency-virus-reservoirs-in-the-brain-of-virally-suppressed-macaques
#12
Lucio Gama, Celina M Abreu, Erin N Shirk, Sarah L Price, Ming Li, Greg M Laird, Kelly A Metcalf Pate, Stephen W Wietgrefe, Shelby L O'Connor, Luiz Pianowski, Ashley T Haase, Carine Van Lint, Robert F Siliciano, Janice E Clements
OBJECTIVE: Resting CD4 T cells have been recognized as the major cell reservoir of latent HIV-1 during antiretroviral therapy (ART). Using an simian immunodeficiency virus (SIV)/macaque model for AIDS and HIV-related neurocognitive disorders we assessed the contribution of the brain to viral latency and reactivation. DESIGN: Pigtailed macaques were dual inoculated with SIVDeltaB670 and SIV17E-Fr and treated with an efficacious central nervous system-penetrant ART...
January 2, 2017: AIDS
https://www.readbyqxmd.com/read/27895698/combinations-of-bio-active-dietary-constituents-affect-human-white-adipocyte-function-in-vitro
#13
Ines Warnke, Johan W E Jocken, Rotraut Schoop, Christine Toepfer, Regina Goralczyk, Joseph Schwager
BACKGROUND: Specific bio-active dietary compounds modulate numerous metabolic processes in adipose tissue (AT), including pre-adipocyte proliferation and differentiation. AT dysfunction, rather than an increased fat mass per se, is strongly associated with the development of insulin resistance and is characterized by impaired adipogenesis, hypertrophic adipocytes, inflammation, and impairments in substrate metabolism. A better understanding of mechanisms underlying AT dysfunction may provide new strategies for the treatment of obesity-associated metabolic diseases...
2016: Nutrition & Metabolism
https://www.readbyqxmd.com/read/27894866/transcriptional-regulation-of-the-sodium-channel-gene-scn5a-by-gata4-in-human-heart
#14
Anna Tarradas, Mel Lina Pinsach-Abuin, Carlos Mackintosh, Oriol Llorà-Batlle, Alexandra Pérez-Serra, Montserrat Batlle, Félix Pérez-Villa, Thomas Zimmer, Ivan Garcia-Bassets, Ramon Brugada, Pedro Beltran-Alvarez, Sara Pagans
Aberrant expression of the sodium channel gene (SCN5A) has been proposed to disrupt cardiac action potential and cause human cardiac arrhythmias, but the mechanisms of SCN5A gene regulation and dysregulation still remain largely unexplored. To gain insight into the transcriptional regulatory networks of SCN5A, we surveyed the promoter and first intronic regions of the SCN5A gene, predicting the presence of several binding sites for GATA transcription factors (TFs). Consistent with this prediction, chromatin immunoprecipitation (ChIP) and sequential ChIP (Re-ChIP) assays show co-occupancy of cardiac GATA TFs GATA4 and GATA5 on promoter and intron 1 SCN5A regions in fresh-frozen human left ventricle samples...
November 25, 2016: Journal of Molecular and Cellular Cardiology
https://www.readbyqxmd.com/read/27892470/vertical-magnetic-separation-of-circulating-tumor-cells-for-somatic-genomic-alteration-analysis-in-lung-cancer-patients
#15
Chang Eun Yoo, Jong-Myeon Park, Hui-Sung Moon, Je-Gun Joung, Dae-Soon Son, Hyo-Jeong Jeon, Yeon Jeong Kim, Kyung-Yeon Han, Jong-Mu Sun, Keunchil Park, Donghyun Park, Woong-Yang Park
Efficient isolation and genetic analysis of circulating tumor cells (CTCs) from cancer patients' blood is a critical step for clinical applications using CTCs. Here, we report a novel CTC-isolation method and subsequent genetic analysis. CTCs from the blood were complexed with magnetic beads coated with antibodies against the epithelial cell adhesion molecule (EpCAM) and separated vertically on a density-gradient medium in a modified well-plate. The recovery rate of model CTCs was reasonable and the cell purity was enhanced dramatically when compared to those parameters obtained using a conventional magnetic isolation method...
November 28, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27888686/integration-of-isothermal-amplification-methods-in-microfluidic-devices-recent-advances
#16
REVIEW
Maria Chiara Giuffrida, Giuseppe Spoto
The integration of nucleic acids detection assays in microfluidic devices represents a highly promising approach for the development of convenient, cheap and efficient diagnostic tools for clinical, food safety and environmental monitoring applications. Such tools are expected to operate at the point-of-care and in resource-limited settings. The amplification of the target nucleic acid sequence represents a key step for the development of sensitive detection protocols. The integration in microfluidic devices of the most popular technology for nucleic acids amplifications, polymerase chain reaction (PCR), is significantly limited by the thermal cycling needed to obtain the target sequence amplification...
November 19, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27878529/association-between-copy-number-variation-on-metabolic-phenotypes-and-hdl-c-levels-in-patients-with-polycystic-ovary-syndrome
#17
Birgit Knebel, Stefan Lehr, Onno E Janssen, Susanne Hahn, Sylvia Jacob, Ulrike Nitzgen, Dirk Müller-Wieland, Jorg Kotzka
Polygenic diseases with a broad phenotypic spectrum, such as polycystic ovary syndrome (PCOS), present a particular challenge in terms of identifying the underlying genetic mechanisms, nevertheless genetic variants have impact on the individual phenotype. We aimed to determine if next to genetic variations like SNPs further mechanisms might play a role in the pathogenesis of PCOS. We examined the effect of copy-number variations (CNVs) on metabolic phenotypes in PCOS. The intragenic rs1244979, rs2815752 in NEGR1 gene, and rs780094 in GCKR gene were genotyped and CNVs were determined by droplet digital polymerase chain reaction (ddPCR) in PCOS patients (n = 153) and controls without metabolic syndrome (n = 142)...
November 22, 2016: Molecular Biology Reports
https://www.readbyqxmd.com/read/27866884/microrna-biomarkers-of-pancreatic-injury-in-a-canine-model
#18
Rodney Rouse, Barry Rosenzweig, Katie Shea, Alan Knapton, Sharron Stewart, Lin Xu, Ashok Chockalingam, Leah Zadrozny, Karol Thompson
Pancreas-enriched microRNAs have been experimentally investigated in rodents as candidate serum biomarkers of pancreatic injury with several different acute pancreatic injury models. In the present study, temporal and magnitude responses of exocrine pancreas-enriched miR-216a, miR-216b, and miR-217 and endocrine-enriched miR-375 and miR-148a were measured by droplet digital PCR in serum in a caerulein model of pancreatic injury in the dog. All 5 microRNAs followed a similar time course that mirrored the responses of the conventional serum pancreatic injury biomarkers, amylase and lipase...
November 17, 2016: Experimental and Toxicologic Pathology: Official Journal of the Gesellschaft Für Toxikologische Pathologie
https://www.readbyqxmd.com/read/27866824/detection-of-her2-overexpressing-cancer-cells-using-keyhole-shaped-chamber-array-employing-a-magnetic-droplet-handling-system
#19
Mina Okochi, Shinji Koike, Masayoshi Tanaka, Hiroyuki Honda
An on-chip gene expression analysis compartmentalized in droplets was developed for detection of cancer cells at a single-cell level. The chip consists of a keyhole-shaped reaction chamber with hydrophobic modification employing a magnetic bead-droplet-handling system with a gate for bead separation. Using three kinds of water-based droplets in oil, a droplet with sample cells, a lysis buffer with magnetic beads, and RT-PCR buffer, parallel magnetic manipulation and fusion of droplets were performed using a magnet-handling device containing small external magnet patterns in an array...
November 11, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27866520/-research-advancement-on-egfr-mutation-detection-of-cell-free-dna-and-tumor-cell-in-peripheral-blood-of-patients-with-non-small-cell-lung-cancer
#20
Yu Zhang, Yan Xu, Mengzhao Wang
Non-small cell lung cancer (NSCLC) is the most common type of lung cancer. Epideral growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) are the most important treatments currently for advanced NSCLC patients harboring activating EGFR gene mutations, and achieve significant clinical efficacy. T790M mutation occurs in half of NSCLC patents with acquired EGFR-TKI resistance. Screening for EGFR gene mutations in histological and/or circulating tumor cell or DNA samples of NSCLC patients can identify patients who would have a response to EGFR-TKIs or acquire resistance during the treatment...
November 20, 2016: Zhongguo Fei Ai za Zhi, Chinese Journal of Lung Cancer
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