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Biomarker discovery

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https://www.readbyqxmd.com/read/29775619/proteomic-approach-to-profiling-immune-complex-antigens-in-cerebrospinal-fluid-samples-from-patients-with-central-nervous-system-autoimmune-diseases
#1
Nozomi Aibara, Kunihiro Ichinose, Miyako Baba, Hideki Nakajima, Katsuya Satoh, Ryuichiro Atarashi, Naoya Kishikawa, Noriyuki Nishida, Atsushi Kawakami, Naotaka Kuroda, Kaname Ohyama
BACKGROUND: Immune complexes (ICs) may clearly reflect immunological abnormalities caused by disease, especially for autoimmune diseases. Although ICs have been detected in cerebrospinal fluid (CSF) from patients with CNS autoimmune diseases, identities of antigens in such ICs have not been comprehensively determined. METHODS: We used immune complexome analysis, in which nano-liquid chromatography-tandem mass spectrometry is employed to comprehensively identify antigens incorporated into ICs in biological fluids, to characterize ICs in CSF samples from patients with CNS autoimmune diseases, and to find disease-specific IC antigen to a certain CNS autoimmune disease...
May 15, 2018: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/29774017/identifying-group-specific-sequences-for-microbial-communities-using-long-k-mer-sequence-signatures
#2
Ying Wang, Lei Fu, Jie Ren, Zhaoxia Yu, Ting Chen, Fengzhu Sun
Comparing metagenomic samples is crucial for understanding microbial communities. For different groups of microbial communities, such as human gut metagenomic samples from patients with a certain disease and healthy controls, identifying group-specific sequences offers essential information for potential biomarker discovery. A sequence that is present, or rich, in one group, but absent, or scarce, in another group is considered " group-specific " in our study. Our main purpose is to discover group-specific sequence regions between control and case groups as disease-associated markers...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29773267/update-on-research-and-clinical-translation-on-specific-clinical-areas-from-biology-to-bedside-unpacking-the-mysteries-of-juvenile-idiopathic-arthritis-pathogenesis
#3
REVIEW
Jorg van Loosdregt, Femke van Wijk, Berent Prakken, Bas Vastert
In the past decades, we have gained important insights into the mechanisms of disease and therapy underlying chronic inflammation in juvenile idiopathic arthritis (JIA). These insights have resulted in several game-changing therapeutic modalities for many patients. However, additional progress still has to be made with regard to efficacy, cost reduction, minimization of side effects, and dose-tapering and stop strategies of maintenance drugs. Moreover, to really transform the current therapeutic strategies into personalized medicine, we need validated biomarkers to translate increased insights into clinical practice...
August 2017: Best Practice & Research. Clinical Rheumatology
https://www.readbyqxmd.com/read/29772817/computational-convolution-of-seldi-data-for-the-diagnosis-of-alzheimer-s-disease
#4
Destiny E O Anyaiwe, Gautam B Singh, George D Wilson, Timothy J Geddes
Alzheimer's disease is rapidly becoming an endemic for people over the age of 65. A vital path towards reversing this ominous trend is the building of reliable diagnostic devices for definite and early diagnoses in lieu of the longitudinal, usually inconclusive and non-generalize-able methods currently in use. In this article, we present a survey of methods for mining pools of mass spectrometer saliva data in relation to diagnosing Alzheimer's disease. The computational methods provides new approaches for appropriately gleaning latent information from mass spectra data...
May 17, 2018: High-throughput
https://www.readbyqxmd.com/read/29772420/the-search-for-biomarkers-of-hepatocellular-carcinoma-and-the-impact-on-patient-outcome
#5
REVIEW
Alyson P Black, Anand S Mehta
Hepatocellular carcinoma (HCC) is the 5th most common cancer, but the 3rd leading cause of cancer death globally with approximately 700,000 fatalities annually. The severity of this cancer arises from its difficulty to detect and treat. The major etiologies of HCC are liver fibrosis or cirrhosis from chronic viral infections, as well as metabolic conditions. Since most cases arise from prior pathologies, biomarker surveillance in high-risk individuals is an essential approach for early detection and improved patient outcome...
May 14, 2018: Current Opinion in Pharmacology
https://www.readbyqxmd.com/read/29769539/integrated-analysis-of-hepatic-mrna-and-mirna-profiles-identified-molecular-networks-and-potential-biomarkers-of-nafld
#6
Mingzhe Zhu, Qianlei Wang, Wenjun Zhou, Tao Liu, Lili Yang, Peiyong Zheng, Li Zhang, Guang Ji
To enhance our understanding of molecular mechanisms and mine novel biomarkers of non-alcoholic fatty liver disease (NAFLD), RNA sequencing was performed to gain hepatic expression profiles of mRNAs and miRNAs in NAFLD and normal rats. Using DESeq with thresholds of a two-fold change and a false discovery rate (FDR) less than 0.05, 336 mRNAs and 21 miRNAs were identified as differentially expressed. Among those, 17 miRNAs (e.g., miR-144-3p, miR-99a-3p, miR-200b-3p, miR-200b-5p, miR-200c-3p, etc.) might serve as novel biomarkers of NAFLD...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29769011/evolving-strategies-for-the-treatment-of-t-cell-lymphoma-a-systematic-review-and-recent-patents
#7
Kamel Laribi, Mustapha Alani, Catherine Truong, Alix Baugier de Materre
OBJECTIVE: Mature T-cell lymphomas are a heterogeneous group of T-cell malignancies with a poor outcome. The discovery of new molecular biomarkers has led to the emergence of new drugs in recent years that target various signaling pathways. METHOD: We examined all pertinent published patents through 2015 that analyzed novel methods for the diagnosis and treatment of T cell lymphoma, as well as related published and unpublished studies. Selection criteria were established before data collection...
May 16, 2018: Recent Patents on Anti-cancer Drug Discovery
https://www.readbyqxmd.com/read/29767973/discovery-of-orally-bioavailable-quinoline-based-aldehyde-dehydrogenase-1a1-aldh1a1-inhibitors-with-potent-cellular-activity
#8
Shyh-Ming Yang, Natalia J Martinez, Adam Yasgar, Carina Danchik, Catrine Johansson, Yuhong Wang, Bolormaa Baljinnyam, Amy Q Wang, Xin Xu, Pranav Shah, Dorian Cheff, Xinran S Wang, Jacob Roth, Madhu Lal-Nag, James Edward Dunford, Udo C T Oppermann, Vasilis Vasiliou, Anton Simeonov, Ajit Jadhav, David J Maloney
Aldehyde dehydrogenases (ALDHs) are responsible for the metabolism of aldehydes (exogenous and endogenous) and possess vital physiological and toxicological functions in areas such as CNS, inflammation, metabolic disorders, and cancers. Overexpression of certain ALDHs (e.g. ALDH1A1) are important biomarkers in cancers and cancer stem cells (CSCs) indicating the potential need for the identification and development of small molecule ALDH inhibitors. Herein, a newly designed series of quinoline-based analogs of ALDH1A1 inhibitors is described...
May 16, 2018: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29767355/overview-of-gene-expression-analysis-transcriptomics
#9
Nalini Raghavachari, Natàlia Garcia-Reyero
Currently, the study of the transcriptome is widely used to interpret the functional elements of the genome and molecular constituents of cells and tissues in an effort to unravel biological pathways associated with development and disease. The advent of technologies is now enabling the study of such comprehensive transcriptional characterization of mRNA, miRNA, lncRNA, and small RNA in a robust and successful manner. Transcriptomic strategies are gaining momentum across diverse areas of biological, plant sciences, medical, clinical, and pharmaceutical research for biomarker discovery, and disease diagnosis and prognosis...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29766684/neuromyelitis-optica-review-and-utility-of-testing-aquaporin-4-antibody-in-typical-optic-neuritis
#10
Meagan Seay, Janet C Rucker
Neuromyelitis optica (NMO) is an autoimmune, inflammatory demyelinating disorder often leading to severe vision impairment and disability. The discovery of a diagnostic biomarker, the aquaporin-4 antibody (AQP4-IgG), transformed the clinical diagnosis and treatment of NMO and broadened the spectrum of disease [NMO spectrum disorders (NMOSD)]. Though the antibody is highly sensitive and specific to NMOSD, routine testing in patients with typical optic neuritis is considered controversial. This article will provide a brief review of NMOSD and highlight the pros and cons of routine testing in typical optic neuritis...
May 16, 2018: Asia-Pacific Journal of Ophthalmology
https://www.readbyqxmd.com/read/29764892/intense-exercise-for-survival-among-men-with-metastatic-castrate-resistant-prostate-cancer-interval-gap4-a-multicentre-randomised-controlled-phase-iii-study-protocol
#11
Robert U Newton, Stacey A Kenfield, Nicolas H Hart, June M Chan, Kerry S Courneya, James Catto, Stephen P Finn, Rosemary Greenwood, Daniel C Hughes, Lorelei Mucci, Stephen R Plymate, Stephan F E Praet, Emer M Guinan, Erin L Van Blarigan, Orla Casey, Mark Buzza, Sam Gledhill, Li Zhang, Daniel A Galvão, Charles J Ryan, Fred Saad
INTRODUCTION: Preliminary evidence supports the beneficial role of physical activity on prostate cancer outcomes. This phase III randomised controlled trial (RCT) is designed to determine if supervised high-intensity aerobic and resistance exercise increases overall survival (OS) in patients with metastatic castrate-resistant prostate cancer (mCRPC). METHODS AND ANALYSIS: Participants (n=866) must have histologically documented metastatic prostate cancer with evidence of progressive disease on androgen deprivation therapy (defined as mCRPC)...
May 14, 2018: BMJ Open
https://www.readbyqxmd.com/read/29763860/ants-and-their-nests-as-indicators-for-industrial-heavy-metal-contamination
#12
Oksana Skaldina, Sirpa Peräniemi, Jouni Sorvari
Ants accumulate heavy metals and respond to pollution with modification in species composition, community structure, altered behaviour and immunity. However, the levels of heavy metals in ants' nests and explicit individual-level responses towards heavy metals have not been revealed. We found that red wood ants Formica lugubris accumulate high and correlated values of such heavy metals as Al, Cd, Co, Cu, Fe, Ni, Pb and Zn both in ants and nest material near cobalt smelter in Finland. Relative differences in metal concentrations were higher in nests than in ants...
May 12, 2018: Environmental Pollution
https://www.readbyqxmd.com/read/29763839/salivary-fingerprint-of-simple-obesity
#13
Anna Lehmann-Kalata, Izabela Miechowicz, Katarzyna Korybalska, Ewelina Swora-Cwynar, Natasza Czepulis, Joanna Łuczak, Zofia Orzechowska, Marian Grzymisławski, Anna Surdacka, Janusz Witowski
BACKGROUND: The nature of a link between poor oral health and obesity is not fully understood. It is also unclear if saliva contributes to it and whether the properties of saliva change as a result of an increase in body mass or rather as a consequence of obesity-associated comorbidities. This pilot study was undertaken in an attempt to determine if salivary biomarkers can identify obesity per se. METHODS: Whole mixed saliva was analysed for 16 soluble parameters covering 4 categories (inflammation, oxidative stress, endothelial dysfunction, adipokines)...
May 11, 2018: Cytokine
https://www.readbyqxmd.com/read/29762666/discovery-and-validation-of-methylation-biomarkers-for-ulcerative-colitis-associated-neoplasia
#14
Andrew D Beggs, Jonathan James, Germaine Caldwell, Toby Prout, Mark P Dilworth, Phillipe Taniere, Tariq Iqbal, Dion G Morton, Glenn Matthews
Background and aims: Ulcerative colitis (UC) is associated with a higher background risk of dysplasia and/or neoplasia due to chronic inflammation. There exist few biomarkers for identification of patients with dysplasia, and targeted biopsies in this group of patients are inaccurate in reliably identifying dysplasia. We aimed to examine the epigenome of UC dysplasia and to identify and validate potential biomarkers. Methods: Colonic samples from patients with UC-associated dysplasia or neoplasia underwent epigenome-wide analysis on the Illumina 450K methylation array...
May 14, 2018: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/29762635/an-epigenome-wide-association-study-ewas-of-obesity-related-traits
#15
Klodian Dhana, Kim V E Braun, Jana Nano, Trudy Voortman, Ellen W Demerath, Weihua Guan, Myriam Fornage, Joyce B J van Meurs, Andre G Uitterlinden, Albert Hofman, Oscar H Franco, Abbas Dehghan
We conducted an epigenome-wide association study on obesity-related traits. We used data from two prospective, population-based cohort studies: the Rotterdam Study (RS) (2006-2013) and the Atherosclerosis Risk in Communities (ARIC) Study (1990-1992). We used RS (n = 1,454) as the discovery panel and ARIC (n = 2,097) as replication panel. Linear mixed-effect models were used to assess the cross-sectional association between genome-wide DNA methylation in leukocytes with body mass index (BMI) and waist circumference (WC) adjusting for sex, age, smoking, leukocyte proportions, array number and position on array...
May 14, 2018: American Journal of Epidemiology
https://www.readbyqxmd.com/read/29760869/metabolic-alterations-in-urine-extracellular-vesicles-are-associated-to-prostate-cancer-pathogenesis-and-progression
#16
Marc Clos-Garcia, Ana Loizaga-Iriarte, Patricia Zuñiga-Garcia, Pilar Sánchez-Mosquera, Ana Rosa Cortazar, Esperanza González, Verónica Torrano, Cristina Alonso, Miriam Pérez-Cormenzana, Aitziber Ugalde-Olano, Isabel Lacasa-Viscasillas, Azucena Castro, Felix Royo, Miguel Unda, Arkaitz Carracedo, Juan M Falcón-Pérez
Urine contains extracellular vesicles (EVs) that concentrate molecules and protect them from degradation. Thus, isolation and characterisation of urinary EVs could increase the efficiency of biomarker discovery. We have previously identified proteins and RNAs with differential abundance in urinary EVs from prostate cancer (PCa) patients compared to benign prostate hyperplasia (BPH). Here, we focused on the analysis of the metabolites contained in urinary EVs collected from patients with PCa and BPH. Targeted metabolomics analysis of EVs was performed by ultra-high-performance liquid chromatography-mass spectrometry...
2018: Journal of Extracellular Vesicles
https://www.readbyqxmd.com/read/29760435/biomarkers-as-drug-development-tools-discovery-validation-qualification-and-use
#17
REVIEW
Virginia B Kraus
The 21st Century Cures Act, approved in the USA in December 2016, has encouraged the establishment of the national Precision Medicine Initiative and the augmentation of efforts to address disease prevention, diagnosis and treatment on the basis of a molecular understanding of disease. The Act adopts into law the formal process, developed by the FDA, of qualification of drug development tools, including biomarkers and clinical outcome assessments, to increase the efficiency of clinical trials and encourage an era of molecular medicine...
May 14, 2018: Nature Reviews. Rheumatology
https://www.readbyqxmd.com/read/29758944/the-conundrum-of-gsk3-inhibitors-is-it-the-dawn-of-a-new-beginning
#18
Ratan V Bhat, Ulf Andersson, Shalini Andersson, Laurent Knerr, Udo Bauer, Anna Sundgren Andersson
Spanning over three decades of extensive drug discovery research, the efforts to develop a potent and selective GSK3 inhibitor as a therapeutic for the treatment of type 2 diabetes, Alzheimer's disease (AD), bipolar disorders and cancer have been futile. Since its initial discovery in 1980 and subsequent decades of research, one cannot underscore the importance of the target and the promise of a game changing disease modifier. Several pharmaceutical companies, biotech companies, and academic institutions raged in a quest to unravel the biology and discover potent and selective GSK3 inhibitors, some of which went through clinical trials...
May 11, 2018: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/29756991/the-immune-landscape-of-non-small-cell-lung-cancer-utility-of-cytologic-and-histologic-samples-obtained-through-minimally-invasive-pulmonary-procedures
#19
Jason Beattie, Lonny Yarmus, Momen Wahidi, M Patricia Rivera, Christopher Gilbert, Fabien Maldonado, Kasia Czarnecka, Angela Argento, Alexander Chen, Felix Herth, Daniel H Sterman
The success of immune checkpoint inhibitors and the discovery of useful biomarkers to predict response to these agents has shifted much of the focus of personalized care for advanced non-small cell lung cancer towards harnessing the immune response. With further advancement, more effective immunotherapy options will emerge along with more useful biomarkers. For patients with advanced disease, minimally invasive techniques will remain most appropriate for acquisition of tissue. This is in contrast to default gold-standard large tissue specimens obtained through surgical resection...
May 14, 2018: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/29755696/the-use-of-long-non-coding-rnas-as-prognostic-biomarkers-and-therapeutic-targets-in-prostate-cancer
#20
REVIEW
Cristian Arriaga-Canon, Inti Alberto De La Rosa-Velázquez, Rodrigo González-Barrios, Rogelio Montiel-Manríquez, Diego Oliva-Rico, Francisco Jiménez-Trejo, Carlo Cortés-González, Luis A Herrera
Prostate cancer is the most common cancer in men and the second leading cause of cancer-related deaths. The most used biomarker to detect prostate cancer is Prostate Specific Antigen (PSA), whose levels are measured in serum. However, it has been recently established that molecular markers of cancer should not be based solely on genes and proteins but should also reflect other genomic traits; long non-coding RNAs (lncRNAs) serve this purpose. lncRNAs are transcripts of >200 bases that do not encode proteins and that have been shown to display abnormal expression profiles in different types of cancer...
April 17, 2018: Oncotarget
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