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https://www.readbyqxmd.com/read/29030865/the-22rv1-prostate-cancer-cell-line-carries-mixed-genetic-ancestry-implications-for-prostate-cancer-health-disparities-research-using-pre-clinical-models
#1
Leanne Woods-Burnham, Anamika Basu, Christina K Cajigas-Du Ross, Arthur Love, Clayton Yates, Marino De Leon, Sourav Roy, Carlos A Casiano
BACKGROUND: Understanding how biological factors contribute to prostate cancer (PCa) health disparities requires mechanistic functional analysis of specific genes or pathways in pre-clinical cellular and animal models of this malignancy. The 22Rv1 human prostatic carcinoma cell line was originally derived from the parental CWR22R cell line. Although 22Rv1 has been well characterized and used in numerous mechanistic studies, no racial identifier has ever been disclosed for this cell line...
October 14, 2017: Prostate
https://www.readbyqxmd.com/read/29026104/cetsa-quantitatively-verifies-in-vivo-target-engagement-of-novel-ripk1-inhibitors-in-various-biospecimens
#2
Tsuyoshi Ishii, Takuro Okai, Misa Iwatani-Yoshihara, Manabu Mochizuki, Satoko Unno, Masako Kuno, Masato Yoshikawa, Sachio Shibata, Masanori Nakakariya, Takatoshi Yogo, Tomohiro Kawamoto
The proof of target engagement (TE) is a key element for evaluating potential investment in drug development. The cellular thermal shift assay (CETSA) is expected to facilitate direct measurement of intracellular TE at all stages of drug development. However, there have been no reports of applying this technology to comprehensive animal and clinical studies. This report demonstrates that CETSA can not only quantitatively evaluate the drug-TE in mouse peripheral blood, but also confirm TE in animal tissues exemplified by using the receptor interacting protein 1 kinase (RIPK1) lead compound we have developed...
October 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29022598/landscape-of-x-chromosome-inactivation-across-human-tissues
#3
Taru Tukiainen, Alexandra-Chloé Villani, Angela Yen, Manuel A Rivas, Jamie L Marshall, Rahul Satija, Matt Aguirre, Laura Gauthier, Mark Fleharty, Andrew Kirby, Beryl B Cummings, Stephane E Castel, Konrad J Karczewski, François Aguet, Andrea Byrnes, Tuuli Lappalainen, Aviv Regev, Kristin G Ardlie, Nir Hacohen, Daniel G MacArthur
X chromosome inactivation (XCI) silences transcription from one of the two X chromosomes in female mammalian cells to balance expression dosage between XX females and XY males. XCI is, however, incomplete in humans: up to one-third of X-chromosomal genes are expressed from both the active and inactive X chromosomes (Xa and Xi, respectively) in female cells, with the degree of 'escape' from inactivation varying between genes and individuals. The extent to which XCI is shared between cells and tissues remains poorly characterized, as does the degree to which incomplete XCI manifests as detectable sex differences in gene expression and phenotypic traits...
October 11, 2017: Nature
https://www.readbyqxmd.com/read/29022597/genetic-effects-on-gene-expression-across-human-tissues
#4
Alexis Battle, Christopher D Brown, Barbara E Engelhardt, Stephen B Montgomery
Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci...
October 11, 2017: Nature
https://www.readbyqxmd.com/read/29022589/dynamic-landscape-and-regulation-of-rna-editing-in-mammals
#5
Meng How Tan, Qin Li, Raghuvaran Shanmugam, Robert Piskol, Jennefer Kohler, Amy N Young, Kaiwen Ivy Liu, Rui Zhang, Gokul Ramaswami, Kentaro Ariyoshi, Ankita Gupte, Liam P Keegan, Cyril X George, Avinash Ramu, Ni Huang, Elizabeth A Pollina, Dena S Leeman, Alessandra Rustighi, Y P Sharon Goh, Ajay Chawla, Giannino Del Sal, Gary Peltz, Anne Brunet, Donald F Conrad, Charles E Samuel, Mary A O'Connell, Carl R Walkley, Kazuko Nishikura, Jin Billy Li
Adenosine-to-inosine (A-to-I) RNA editing is a conserved post-transcriptional mechanism mediated by ADAR enzymes that diversifies the transcriptome by altering selected nucleotides in RNA molecules. Although many editing sites have recently been discovered, the extent to which most sites are edited and how the editing is regulated in different biological contexts are not fully understood. Here we report dynamic spatiotemporal patterns and new regulators of RNA editing, discovered through an extensive profiling of A-to-I RNA editing in 8,551 human samples (representing 53 body sites from 552 individuals) from the Genotype-Tissue Expression (GTEx) project and in hundreds of other primate and mouse samples...
October 11, 2017: Nature
https://www.readbyqxmd.com/read/29022581/the-impact-of-rare-variation-on-gene-expression-across-tissues
#6
Xin Li, Yungil Kim, Emily K Tsang, Joe R Davis, Farhan N Damani, Colby Chiang, Gaelen T Hess, Zachary Zappala, Benjamin J Strober, Alexandra J Scott, Amy Li, Andrea Ganna, Michael C Bassik, Jason D Merker, Ira M Hall, Alexis Battle, Stephen B Montgomery
Rare genetic variants are abundant in humans and are expected to contribute to individual disease risk. While genetic association studies have successfully identified common genetic variants associated with susceptibility, these studies are not practical for identifying rare variants. Efforts to distinguish pathogenic variants from benign rare variants have leveraged the genetic code to identify deleterious protein-coding alleles, but no analogous code exists for non-coding variants. Therefore, ascertaining which rare variants have phenotypic effects remains a major challenge...
October 11, 2017: Nature
https://www.readbyqxmd.com/read/28967885/assessment-of-variation-in-microbial-community-amplicon-sequencing-by-the-microbiome-quality-control-mbqc-project-consortium
#7
Rashmi Sinha, Galeb Abu-Ali, Emily Vogtmann, Anthony A Fodor, Boyu Ren, Amnon Amir, Emma Schwager, Jonathan Crabtree, Siyuan Ma, Christian C Abnet, Rob Knight, Owen White, Curtis Huttenhower
In order for human microbiome studies to translate into actionable outcomes for health, meta-analysis of reproducible data from population-scale cohorts is needed. Achieving sufficient reproducibility in microbiome research has proven challenging. We report a baseline investigation of variability in taxonomic profiling for the Microbiome Quality Control (MBQC) project baseline study (MBQC-base). Blinded specimen sets from human stool, chemostats, and artificial microbial communities were sequenced by 15 laboratories and analyzed using nine bioinformatics protocols...
October 2, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28963102/comprehensive-metabolomic-profiling-and-incident-cardiovascular-disease-a-systematic-review
#8
REVIEW
Miguel Ruiz-Canela, Adela Hruby, Clary B Clish, Liming Liang, Miguel A Martínez-González, Frank B Hu
BACKGROUND: Metabolomics is a promising tool of cardiovascular biomarker discovery. We systematically reviewed the literature on comprehensive metabolomic profiling in association with incident cardiovascular disease (CVD). METHODS AND RESULTS: We searched MEDLINE and EMBASE from inception to January 2016. Studies were eligible if they pertained to adult humans; followed an agnostic and/or comprehensive approach; used serum or plasma (not urine or other biospecimens); conducted metabolite profiling at baseline in the context of examining prospective disease; and included myocardial infarction, stroke, and/or CVD death in the CVD outcome definition...
September 28, 2017: Journal of the American Heart Association
https://www.readbyqxmd.com/read/28922617/training-the-next-generation-of-biobankers-a-two-year-master-s-course-in-the-management-of-biobanks
#9
Emmanuelle Gormally, Isabelle Hardy, Elodie Caboux, Jeanne-Hélène di Donato, Pierre Hainaut, Paul Hofman
The growing complexity of biobanking requires dedicated professional staff who are trained in multiple aspects of the biobanking process, including technical, managerial, regulatory, and ethical aspects, and who have a good understanding of the challenges of biospecimen research, but also of the challenges related to the sustainability of future biobanks. Up to the present, biobanking staff have been trained in an ad-hoc manner, usually through specific short duration courses, for example, summer schools. In this article, we describe the development/establishment of a systematic 2-year training program at the Master level intended for students with a background in life sciences and providing them with a professional qualification as a "Biobank Manager...
September 18, 2017: Biopreservation and Biobanking
https://www.readbyqxmd.com/read/28911955/brief-report-somatic-mutations-and-ancestry-markers-in-hispanic-lung-cancer-patients
#10
Nicholas T Gimbrone, Bhaswati Sarcar, Edna R Gordian, Jason I Rivera, Christian Lopez, Sean J Yoder, Jamie K Teer, Eric A Welsh, Alberto A Chiaporri, Matthew B Schabath, Gary W Reuther, Julie Dutil, Miosotis Garcia, Ronald Ventosilla-Villanueva, Luis Vera-Valdivia, Alejandro Yabar-Berrocal, Rodrigo Motta-Guerrero, Pedro G Santiago-Cardona, Teresita Muñoz-Antonia, W Douglas Cress
INTRODUCTION: To address the lack of genomic data from Hispanic/Latino (H/L) patients with lung cancer, the Latino Lung Cancer Registry was established to collect patient data and biospecimens from these patients. METHODS: This retrospective observational study examined lung cancer tumor samples from 163 H/L patients, and tumor-derived DNA was subjected to targeted-exome sequencing (>1000 genes, including EGFR, KRAS, STK11, and TP53) and ancestry analysis. Mutation frequencies in this H/L cohort were compared with those in a similar cohort of non-Hispanic white (NHW) patients and were correlated with ancestry, sex, smoking status, and tumor histology...
September 11, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28883635/tissue-alkalosis-in-cold-ischemia-time
#11
V Denninghoff, E H R Olivieri, C Fresno, A Uceda, L Mota, A P Suenaga, D M Carraro, V R Martins, A Avagnina, F A Soares, A H J Fróes Marques Campos
The control of pre-analytical-factors in human biospecimens collected for health research is currently required. Only two previous reports using post-mortem brain samples have tried to address the impact of cold-ischemia on tissue pH. Here we report pH variations according to time (third-order polynomial model) in mice for liver, kidney and lung samples. Tissue alkalosis in cold-ischemia time may be an underlying mechanism of gene expression changes. Therefore, tissue-pH regulation after organ removal may minimize biological stress in human tissue samples...
September 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28883167/on-the-fly-query-translation-between-i2b2-and-samply-in-the-german-biobank-node-gbn-prototypes
#12
Sebastian Mate, Patric Vormstein, Dennis Kadioglu, Raphael W Majeed, Martin Lablans, Hans-Ulrich Prokosch, Holger Storf
Information retrieval is a major challenge in medical informatics. Various research projects have worked on this task in recent years on an institutional level by developing tools to integrate and retrieve information. However, when it comes down to querying such data across institutions, the challenge persists due to the high heterogeneity of data and differences in software systems. The German Biobank Node (GBN) project faced this challenge when trying to interconnect four biobanks to enable distributed queries for biospecimens...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28882126/predictors-of-acute-renal-injury-study-paris-among-hiv-positive-individuals-design-and-methods
#13
Celia P Corona-Villalobos, Michael G Shlipak, Adrienne Tin, Chirag Parikh, Richard D Moore, Eric Vittinghoff, Jose Manuel Monroy-Trujillo, Mohamed G Atta, Michelle M Estrella
BACKGROUND: Acute kidney injury (AKI), which is common among HIV-positive individuals, may contribute to the excess burden of chronic kidney disease (CKD) in this patient population; however, conventional clinical methods to detect AKI do not capture kidney injury sufficiently early to prevent irreversible damage. Further, large observational and interventional studies of AKI generally exclude HIV-positive persons in spite of their disproportionate risk. METHODS: The Predictors of Acute Renal Injury Study (PARIS) is a prospective observational cohort study among HIV-positive individuals established to determine the ability of candidate kidney injury biomarkers to predict future hospitalized clinical AKI, to characterize hospitalized subclinical AKI, and to discern the risk of progressive kidney disease following subclinical and clinical AKI...
September 7, 2017: BMC Nephrology
https://www.readbyqxmd.com/read/28873014/impact-of-preanalytical-variations-in-blood-derived-biospecimens-on-omics-studies-toward-precision-biobanking
#14
Jae-Eun Lee, Young-Youl Kim
Research data and outcomes do vary across populations and persons, but this is not always due to experimental or true biological variation. Preanalytical components of experiments, be they biospecimen acquisition, preparation, storage, or transportation to the laboratory, may all contribute to apparent variability in research data, outcomes, and interpretation. The present review article and biobanking innovation analysis offer new insights with a summary of such preanalytical variables, for example, the type of blood collection tube, centrifugation conditions, long-term sample storage temperature, and duration, on output of omics analyses of blood-derived biospecimens: whole blood, serum, plasma, buffy coat, and peripheral blood mononuclear cells...
September 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28865512/radiogenomics-identification-of-genomic-predictors-for-radiation-toxicity
#15
REVIEW
Barry S Rosenstein
The overall goal of radiogenomics is the identification of genomic markers that are predictive for the development of adverse effects resulting from cancer treatment with radiation. The principal rationale for a focus on toxicity in radiogenomics is that for many patients treated with radiation, especially individuals diagnosed with early-stage cancers, the survival rates are high, and therefore a substantial number of people will live for a significant period of time beyond treatment. However, many of these patients could suffer from debilitating complications resulting from radiotherapy...
October 2017: Seminars in Radiation Oncology
https://www.readbyqxmd.com/read/28859290/racial-differences-in-pam50-subtypes-in-the-carolina-breast-cancer-study
#16
Melissa A Troester, Xuezheng Sun, Emma H Allott, Joseph Geradts, Stephanie M Cohen, Chiu-Kit Tse, Erin L Kirk, Leigh B Thorne, Michelle Mathews, Yan Li, Zhiyuan Hu, Whitney R Robinson, Katherine A Hoadley, Olufunmilayo I Olopade, Katherine E Reeder-Hayes, H Shelton Earp, Andrew F Olshan, Lisa A Carey, Charles M Perou
Background: African American breast cancer patients have lower frequency of hormone receptor-positive (HR+)/human epidermal growth factor receptor 2 (HER2)-negative disease and higher subtype-specific mortality. Racial differences in molecular subtype within clinically defined subgroups are not well understood. Methods: Using data and biospecimens from the population-based Carolina Breast Cancer Study (CBCS) Phase 3 (2008-2013), we classified 980 invasive breast cancers using RNA expression-based PAM50 subtype and recurrence (ROR) score that reflects proliferation and tumor size...
February 1, 2018: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/28852559/clinical-genomics-big-data-and-electronic-medical-records-reconciling-patient-rights-with-research-when-privacy-and-science-collide
#17
Jennifer Kulynych, Henry T Greely
Widespread use of medical records for research, without consent, attracts little scrutiny compared to biospecimen research, where concerns about genomic privacy prompted recent federal proposals to mandate consent. This paper explores an important consequence of the proliferation of electronic health records (EHRs) in this permissive atmosphere: with the advent of clinical gene sequencing, EHR-based secondary research poses genetic privacy risks akin to those of biospecimen research, yet regulators still permit researchers to call gene sequence data 'de-identified', removing such data from the protection of the federal Privacy Rule and federal human subjects regulations...
April 2017: Journal of Law and the Biosciences
https://www.readbyqxmd.com/read/28851229/the-california-hiv-aids-research-program-history-impact-and-hiv-cure-initiative
#18
Lisa Loeb Stanga, Laura Packel, Tyler Martz, George Lemp
This Special Issue of AIDS Research and Human Retroviruses features results from the HIV Cure Initiative, funded by the California HIV/AIDS Research Program (CHRP). As a publicly-funded grant maker, CHRP has served for more than three decades as a unique resource for innovative researchers in California whose work seeks to address all aspects of the HIV epidemic and the communities affected by it. Early initiatives at CHRP pioneered what would become enduring cornerstones of HIV science: isolation of the virus; efficacy and toxicities of the first HIV treatments; the emergence of drug resistance; the first biospecimen banks for HIV-related research; the first community-based laboratory service for HIV diagnostic serology; and the first population-based longitudinal cohort study of persons living with HIV - The Gay Men's Health Study...
August 29, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28843646/characterizing-the-effect-of-endocrine-disruptors-on-human-health-the-role-of-epidemiological-cohorts
#19
Rémy Slama, Céline Vernet, Feiby L Nassan, Russ Hauser, Claire Philippat
Research on endocrine disruptors (EDs) developed from numerous disciplines. In this concert of disciplines, epidemiology is central to inform on the relevance for humans of mechanisms and dose-response functions identified in animals, to characterize the health impact (number of attributable disease cases), the cost associated with ED exposure, and the efficiency of the measures taken to limit exposure. Here, we present epidemiological tools to draw valid inference regarding effects of potential EDs. Epidemiology is generally observational, requiring care to control confounding bias...
August 23, 2017: Comptes Rendus Biologies
https://www.readbyqxmd.com/read/28814312/rationale-and-design-of-the-brigham-cohort-for-psoriasis-and-psoriatic-arthritis-registry-coppar
#20
Maria Schneeweiss, Joseph F Merola, Elizabeth W Karlson, Daniel H Solomon
BACKGROUND: Psoriasis (PsO) and psoriatic arthritis (PsA) are related conditions with poorly defined transition among them, risk factors for progression, complex treatment algorithms, and biomarkers for treatment response and long-term outcomes. We describe the development of a PsO/PsA registry at an academic medical center. METHODS: We developed a single-center PsO/PsA longitudinal disease registry including biorepository that captures relevant disease markers and treatment choices in a circumscribed population with a defined catchment area...
August 16, 2017: BMC Dermatology
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