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Biomarker discovery

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https://www.readbyqxmd.com/read/29345617/loss-of-functional-bap1-augments-sensitivity-to-trail-in-cancer-cells
#1
Krishna Kalyan Kolluri, Constantine Alifrangis, Neelam Kumar, Yuki Ishii, Stacey Price, Magali Michaut, Steven Williams, Syd Barthorpe, Howard Lightfoot, Sara Busacca, Annabel Sharkey, Zhenqiang Yuan, Elizabeth K Sage, Sabarinath Vallath, John Le Quesne, David A Tice, Doraid Alrifai, Sylvia von Karstedt, Antonella Montinaro, Naomi Guppy, David A Waller, Apostolos Nakas, Robert Good, Alan Holmes, Henning Walczak, Dean A Fennel, Mathew Garnett, Francesco Iorio, Lodewyk Wessels, Ultan McDermott, Samuel M Janes
Malignant mesothelioma (MM) is poorly responsive to systemic cytotoxic chemotherapy and invariably fatal. Here we describe a screen of 94 drugs in 15 exome-sequenced MM lines and the discovery of a subset defined by loss of function of the nuclear deubiquitinase BRCA associated protein-1 (BAP1) that demonstrate heightened sensitivity to TRAIL (tumour necrosis factor-related apoptosis-inducing ligand). This association is observed across human early passage MM cultures, mouse xenografts and human tumour explants...
January 18, 2018: ELife
https://www.readbyqxmd.com/read/29344888/perseus-a-bioinformatics-platform-for-integrative-analysis-of-proteomics-data-in-cancer-research
#2
Stefka Tyanova, Juergen Cox
Mass spectrometry-based proteomics is a continuously growing field marked by technological and methodological improvements. Cancer proteomics is aimed at pursuing goals such as accurate diagnosis, patient stratification, and biomarker discovery, relying on the richness of information of quantitative proteome profiles. Translating these high-dimensional data into biological findings of clinical importance necessitates the use of robust and powerful computational tools and methods. In this chapter, we provide a detailed description of standard analysis steps for a clinical proteomics dataset performed in Perseus, a software for functional analysis of large-scale quantitative omics data...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344885/microrna-networks-in-breast-cancer-cells
#3
Andliena Tahiri, Miriam R Aure, Vessela N Kristensen
A variety of molecular techniques can be used in order to unravel the molecular composition of cells. In particular, the microarray technology has been used to identify novel biomarkers that may be useful in the diagnosis, prognosis, or treatment of cancer. The microarray technology is ideal for biomarker discovery as it allows for the screening of a large number of molecules at once. In this review, we focus on microRNAs (miRNAs) which are key molecules in cells and regulate gene expression post-transcriptionally...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344854/laser-microdissection-workflow-for-isolating-nucleic-acids-from-fixed-and-frozen-tissue-samples
#4
Yelena G Golubeva, Andrew C Warner
Laser Capture Microdissection has earned a permanent place among modern techniques connecting histology and molecular biology. Laser Capture Microdissection has become an invaluable tool in medical research as a means for collection of specific cell populations isolated from their environment. Such genomic sample enrichment dramatically increases the sensitivity and precision of downstream molecular assays used for biomarker discovery, monitoring disease onset and progression, and in the development of personalized medicine...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29343722/multiplex-glycan-bead-array-for-high-throughput-and-high-content-analyses-of-glycan-binding-proteins
#5
Sharad Purohit, Tiehai Li, Wanyi Guan, Xuezheng Song, Jing Song, Yanna Tian, Lei Li, Ashok Sharma, Boying Dun, David Mysona, Sharad Ghamande, Bunja Rungruang, Richard D Cummings, Peng George Wang, Jin-Xiong She
Glycan-binding proteins (GBPs) play critical roles in diverse cellular functions such as cell adhesion, signal transduction and immune response. Studies of the interaction between GBPs and glycans have been hampered by the availability of high throughput and high-content technologies. Here we report multiplex glycan bead array (MGBA) that allows simultaneous analyses of 384 samples and up to 500 glycans in a single assay. The specificity, sensitivity and reproducibility of MGBA are evaluated using 39 plant lectins, 13 recombinant anti-glycan antibodies, and mammalian GBPs...
January 17, 2018: Nature Communications
https://www.readbyqxmd.com/read/29343260/liquid-biomarkers-in-melanoma-detection-and-discovery
#6
REVIEW
Su Yin Lim, Jenny H Lee, Russell J Diefenbach, Richard F Kefford, Helen Rizos
A vast array of tumor-derived genetic, proteomic and cellular components are constantly released into the circulation of cancer patients. These molecules including circulating tumor DNA and RNA, proteins, tumor and immune cells are emerging as convenient and accurate liquid biomarkers of cancer. Circulating cancer biomarkers provide invaluable information on cancer detection and diagnosis, prognosticate patient outcomes, and predict treatment response. In this era of effective molecular targeted treatments and immunotherapies, there is now an urgent need to implement use of these circulating biomarkers in the clinic to facilitate personalized therapy...
January 17, 2018: Molecular Cancer
https://www.readbyqxmd.com/read/29342213/circulating-neutrophil-transcriptome-may-reveal-intracranial-aneurysm-signature
#7
Vincent M Tutino, Kerry E Poppenberg, Kaiyu Jiang, James N Jarvis, Yijun Sun, Ashish Sonig, Adnan H Siddiqui, Kenneth V Snyder, Elad I Levy, John Kolega, Hui Meng
BACKGROUND: Unruptured intracranial aneurysms (IAs) are typically asymptomatic and undetected except for incidental discovery on imaging. Blood-based diagnostic biomarkers could lead to improvements in IA management. This exploratory study examined circulating neutrophils to determine whether they carry RNA expression signatures of IAs. METHODS: Blood samples were collected from patients receiving cerebral angiography. Eleven samples were collected from patients with IAs and 11 from patients without IAs as controls...
2018: PloS One
https://www.readbyqxmd.com/read/29340997/immunohistochemical-biomarkers-of-mesenchymal-neoplasms-in-endocrine-organs-diagnostic-pitfalls-and-recent-discoveries
#8
Yin P Hung, Jason L Hornick
Mesenchymal neoplasms rarely present in or adjacent to endocrine organs. In this context, the recognition of these rare tumor types can be challenging, with significant potential for misdiagnosis as sarcomatoid carcinomas (i.e., anaplastic thyroid carcinoma and sarcomatoid adrenal cortical carcinoma) or neuroendocrine carcinomas, depending upon the dominant histologic patterns. In this review, we address potential pitfalls in diagnosing selected mesenchymal neoplasms arising within or near endocrine organs, including dedifferentiated liposarcoma, synovial sarcoma, angiosarcoma, PEComa, proximal-type epithelioid sarcoma, Ewing sarcoma, and neuroblastoma...
January 16, 2018: Endocrine Pathology
https://www.readbyqxmd.com/read/29340569/associations-of-the-top-20-alzheimer-disease-risk-variants-with-brain-amyloidosis
#9
Liana G Apostolova, Shannon L Risacher, Tugce Duran, Eddie C Stage, Naira Goukasian, John D West, Triet M Do, Jonathan Grotts, Holly Wilhalme, Kwangsik Nho, Meredith Phillips, David Elashoff, Andrew J Saykin
Importance: Late-onset Alzheimer disease (AD) is highly heritable. Genome-wide association studies have identified more than 20 AD risk genes. The precise mechanism through which many of these genes are associated with AD remains unknown. Objective: To investigate the association of the top 20 AD risk variants with brain amyloidosis. Design, Setting, and Participants: This study analyzed the genetic and florbetapir F 18 data from 322 cognitively normal control individuals, 496 individuals with mild cognitive impairment, and 159 individuals with AD dementia who had genome-wide association studies and 18F-florbetapir positron emission tomographic data from the Alzheimer's Disease Neuroimaging Initiative (ADNI), a prospective, observational, multisite tertiary center clinical and biomarker study...
January 16, 2018: JAMA Neurology
https://www.readbyqxmd.com/read/29339835/obtaining-high-quality-transcriptome-data-from-formalin-fixed-paraffin-embedded-diagnostic-prostate-tumor-specimens
#10
Liesel M FitzGerald, Chol-Hee Jung, Ee Ming Wong, JiHoon E Joo, Jodee A Gould, Vivien Vasic, Julie K Bassett, Neil O'Callaghan, Tim Nottle, John Pedersen, Graham G Giles, Melissa C Southey
Prognostic genomic biomarkers that can be measured at diagnosis to aid choice of treatment options are unavailable for most common cancers. This is due in part to the poor quality and quantity of available diagnostic specimens for discovery research and to limitations in genomic technologies. Recent technical advances now enable high-density molecular analyses using suboptimal biological specimens. Here we describe the optimization of a transcriptome-specific protocol for use with formalin-fixed, paraffin-embedded (FFPE) diagnostic prostate cancer (PrCa) specimens...
January 16, 2018: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/29338886/overweight-and-obesity-status-in-pregnant-women-are-related-to-intestinal-microbiota-and-serum-metabolic-and-inflammatory-profiles
#11
Noora Houttu, Kati Mokkala, Kirsi Laitinen
BACKGROUND: Overweight and obesity may predispose women to clinical complications during their pregnancy. We hypothesize that a higher degree of overweight status is related to a range of aberrations in biomarkers already in early pregnancy. Our objective was to investigate whether intestinal microbiota, serum metabolic and inflammatory profiles differ in relation to the degree of overweight status in pregnant women. METHODS: This study investigated 52 overweight and 47 obese pregnant women in early pregnancy...
December 27, 2017: Clinical Nutrition: Official Journal of the European Society of Parenteral and Enteral Nutrition
https://www.readbyqxmd.com/read/29336696/controlled-adverse-environment-chambers-in-dry-eye-research
#12
Margarita Calonge, Marc Labetoulle, Elisabeth M Messmer, Sunil Shah, Yonca A Akova, Kostas G Boboridis, Jesús Merayo-Lloves, Pasquale Aragona, José Benítez-Del-Castillo, Gerd Geerling, Maurizio Rolando, Christophe Baudouin
Dry eye disease (DED) is a common condition with signs and symptoms that vary depending on a wide range of environmental factors to which people are exposed in their daily lives. Factors such as variable temperature, airflow velocity, relative humidity, seasonality, and pollutants can alter the rate of tear film evaporation, improving or exacerbating symptoms of DED. Results from currently available clinical tests do not always correlate well with patient-reported symptoms, and the continually changing environment and variability in DED symptoms present challenges for the design and conduct of clinical trials...
January 16, 2018: Current Eye Research
https://www.readbyqxmd.com/read/29335596/circulating-microrna-signature-for-the-diagnosis-of-childhood-dilated-cardiomyopathy
#13
Meng Jiao, Hong-Zhao You, Xin-Ying Yang, Hui Yuan, Yu-Lin Li, Wen-Xian Liu, Mei Jin, Jie Du
Circulating miRNAs are proposed as a biomarker of heart disease. This study evaluated whether circulating miRNAs could be used as a biomarker for childhood dilated cardiomyopathy (CDCM). A total of 28 participants were enrolled in a discovery set, including patients with CDCM (n = 16) and healthy children (n = 12). The cardiac function of patients with CDCM was characterized by echocardiography and serum miRNA profiles of all participants were assessed by miRNA sequencing. After miRNA profiling, we quantitatively confirmed 148 regulated miRNAs in patients with CDCM compared with healthy subjects, and none were downregulated...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29333491/multifunctional-bioreactor-system-for-human-intestine-tissues
#14
Wenda Zhou, Ying Chen, Terrence Roh, Yinan Lin, Shengjie Ling, Siwei Zhao, James D Lin, Noor Khalil, Dana M Cairns, Eleana Manousiouthakis, Megan Tse, David L Kaplan
The three-dimensional (3D) cultivation of intestinal cells and tissues in dynamic bioreactor systems to represent in vivo intestinal microenvironments is essential for developing regenerative medicine treatments for intestinal diseases. We have previously developed in vitro human intestinal tissue systems using a 3D porous silk scaffold system with intestinal architectures and topographical features for the adhesion, growth, and differentiation of intestinal cells under static culture conditions. In this study, we designed and fabricated a multifunctional bioreactor system that incorporates pre-epithelialized 3D silk scaffolds in a dynamic culture environment for in vitro engineering of human intestine tissues...
January 8, 2018: ACS Biomaterials Science & Engineering
https://www.readbyqxmd.com/read/29331148/isolation-of-anti-extra-cellular-vesicle-single-domain-antibodies-by-direct-panning-on-vesicle-enriched-fractions
#15
Milica Popovic, Elisa Mazzega, Barbara Toffoletto, Ario de Marco
BACKGROUND: The thorough understanding of the physiological and pathological processes mediated by extracellular vesicles (EVs) is challenged by purification methods which are cumbersome, not reproducible, or insufficient to yield homogeneous material. Chromatography based on both ion-exchange and immune-capture can represent an effective method to improve EV purification and successive analysis. METHODS: Cell culture supernatant was used as a model sample for assessing the capacity of anion-exchange chromatography to separate distinct EV fractions and to isolate nanobodies by direct panning on whole EVs to recover binders specific for the native conformation of EV-surface epitopes and suitable to develop EV immune-capture reagents...
January 13, 2018: Microbial Cell Factories
https://www.readbyqxmd.com/read/29329282/induction-of-high-mobility-group-box-1-in-vitro-and-in-vivo-by-respiratory-syncytial-virus
#16
Sara Manti, Terri J Harford, Carmelo Salpietro, Fariba Rezaee, Giovanni Piedimonte
BACKGROUND: Despite decades have passed since its discovery, accurate biomarkers of Respiratory syncytial virus (RSV) disease activity and effective therapeutic strategies are still lacking. The high mobility group box type 1 (HMGB1) protein has been proposed as a possible link between RSV and immune system, but only limited information is currently available to support this hypothesis. METHODS: Expression of HMGB1 gene and protein were analyzed by quantitative PCR, ELISA, Western blot, immunocytochemistry, and confocal microscopy in immortalized and primary human bronchial epithelial cells, as well as in rat pup lungs...
January 12, 2018: Pediatric Research
https://www.readbyqxmd.com/read/29328463/construction-and-investigation-of-lncrna-associated-cerna-regulatory-network-in-papillary-thyroid-cancer
#17
Yangjing Zhao, Hui Wang, Chengjiang Wu, Meina Yan, Haojie Wu, Jingzhe Wang, Xinxin Yang, Qixiang Shao
Increasing evidence has experimentally proved the competitive endogenous RNA (ceRNA) hypothesis that long non-coding RNA (lncRNA) can affect the expression of RNA targets by competitively combining microRNA (miRNA) via miRNA response elements. However, an extensive ceRNA network of thyroid carcinoma in a large cohort has not been evaluated. We analyzed the RNAseq and miRNAseq data of 348 cases of primary papillary thyroid cancer (PTC) patients with clinical information downloaded from The Cancer Genome Atlas (TCGA) project to search for potential biomarkers or therapeutic targets...
January 10, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29327732/a-mirna-signature-suggestive-of-nodal-metastases-from-laryngeal-carcinoma
#18
F Ricciardiello, R Capasso, H Kawasaki, T Abate, F Oliva, A Lombardi, G Misso, D Ingrosso, C A Leone, M Iengo, M Caraglia
The discovery that miRNAs are frequently deregulated in tumours offers the opportunity to identify them as prognostic and diagnostic markers. The aim of this multicentric study is to identify a miRNA expression profile specific for laryngeal cancer. The secondary endpoint was to identify specific deregulated miRNAs with potential as prognostic biomarkers for tumour spread and nodal involvement, and specifically to search for a miRNA pattern pathognomonic for N+ laryngeal cancer and for N- tissues. We identified 20 miRNAs specific for laryngeal cancer and a tissue-specific miRNA signature that is predictive of lymph node metastases in laryngeal carcinoma characterised by 11 miRNAs, seven of which are overexpressed (upregulated) and four downregulated...
December 2017: Acta Otorhinolaryngologica Italica
https://www.readbyqxmd.com/read/29327610/the-44th-congress-of-the-international-society-of-oncology-and-biomarkers-rio-de-janeiro-brazil-7-10-september-2017
#19
Judita Kinkorová
The 44th Congress of the International Society of Oncology and Biomarkers: Rio de Janeiro, Brazil, 7-10 September 2017 The 44th congress followed the previous one of  International Society of Oncology and Biomarkers (ISOBM) that took place in Chicago (USA) in 2016. The title of the 44th Annual congress was: 'Biomarkers in oncology: new horizons and challenges in the diagnosis and treatment of cancer' [ 1 ]. The congress was co-organized by ISOBM, European Group on Tumor Markers (EGTM) and Brazilian Society of Clinical Pathology SBPC/ML...
January 12, 2018: Biomarkers in Medicine
https://www.readbyqxmd.com/read/29325451/expression-of-sestrin-genes-in-radiotherapy-for-prostate-cancer-and-its-association-with-fatigue-a-proof-of-concept-study
#20
Velda J Gonzalez, Farnoosh Abbas-Aghababazadeh, Brooke L Fridley, Tomar Ghansah, Leorey N Saligan
Genetic factors that influence inflammation and energy production/expenditure in cells may affect patient outcomes following treatment with external beam radiation therapy (EBRT). Sestrins, stress-inducible genes with antioxidant properties, have recently been implicated in several behaviors including fatigue. This proof-of-concept study explored whether the sestrin family of genes ( SESN1, SESN2, and SESN3) were differentially expressed from baseline to the midpoint of EBRT in a sample of 26 Puerto Rican men with nonmetastatic prostate cancer...
January 1, 2018: Biological Research for Nursing
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