Multiple Loci Modulate Opioid Therapy Response for Cancer Pain
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A Gene-Level Methylome-Wide Association Analysis Identifies Novel
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.13.201376; this version posted July 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 A gene-level methylome-wide association analysis identifies novel 2 Alzheimer’s disease genes 1 1 2 3 4 3 Chong Wu , Jonathan Bradley , Yanming Li , Lang Wu , and Hong-Wen Deng 1 4 Department of Statistics, Florida State University; 2 5 Department of Biostatistics & Data Science, University of Kansas Medical Center; 3 6 Population Sciences in the Pacific Program, University of Hawaii Cancer center; 4 7 Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, 8 Tulane University School of Medicine 9 Corresponding to: Chong Wu, Assistant Professor, Department of Statistics, Florida State 10 University, email: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.13.201376; this version posted July 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 11 Abstract 12 Motivation: Transcriptome-wide association studies (TWAS) have successfully facilitated the dis- 13 covery of novel genetic risk loci for many complex traits, including late-onset Alzheimer’s disease 14 (AD). However, most existing TWAS methods rely only on gene expression and ignore epige- 15 netic modification (i.e., DNA methylation) and functional regulatory information (i.e., enhancer- 16 promoter interactions), both of which contribute significantly to the genetic basis ofAD. -
Genome-Wide Association Study in Collaborative Cross Mice Revealed a Skeletal
bioRxiv preprint doi: https://doi.org/10.1101/094698; this version posted December 16, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Title Genome-wide association study in Collaborative Cross mice revealed a skeletal role for Rhbdf2 Authors Roei Levy1,2, Clemence Levet3, Keren Cohen1, Matthew Freeman3, Richard Mott4, Fuad Iraqi5, Yankel Gabet1 Affiliations 1 Department of Anatomy and Anthropology, 2 Department of Human Molecular Genetics and Biochemistry, and 5 Department of Clinical Microbiology and Immunology, Sackler Medical School, Tel Aviv University. 3 Dunn School of Pathology, South Parks Road, Oxford OX1 3RE. 4 UCL Genetics Institute, University College London, Gower St., London, WC1E 6BT, UK. Abstract A growing concern that overshadows the increased life expectancy developed countries have been witnessing during the last decades is an accompanying bone loss, which often manifests as osteoporosis. Despite ongoing efforts in utilizing genomic data to fully map the genes responsible for bone remodeling, a detailed picture remains to be desired. Here we took advantage of the phenotypic and genetic diversity innate in Collaborative Cross (CC) mice to identify genetic variants associated with microstructural bone characteristics. 1 bioRxiv preprint doi: https://doi.org/10.1101/094698; this version posted December 16, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
Genetic Deletion of Amphiregulin Restores the Normal Skin Phenotype in a Mouse Model of the Human Skin Disease Tylosis Vishnu Hosur*, Benjamin E
© 2017. Published by The Company of Biologists Ltd | Biology Open (2017) 6, 1174-1179 doi:10.1242/bio.026260 RESEARCH ARTICLE Genetic deletion of amphiregulin restores the normal skin phenotype in a mouse model of the human skin disease tylosis Vishnu Hosur*, Benjamin E. Low, Leonard D. Shultz and Michael V. Wiles ABSTRACT mutations in human RHBDF2 lead to enhanced AREG secretion In humans, gain-of-function (GOF) mutations in RHBDF2 cause the and tylosis. We provide evidence that Rhbdf2 GOF mutations skin disease tylosis. We generated a mouse model of human tylosis enhance AREG secretion to cause hyperplasia and hyperkeratosis. and show that GOF mutations in RHBDF2 cause tylosis by enhancing In addition, we show that genetic ablation of AREG attenuates skin P159L/P159L the amount of amphiregulin (AREG) secretion. Furthermore, we show disease in the Rhbdf2 mouse model of human tylosis. that genetic disruption of AREG ameliorates skin pathology in mice Together, our data strongly suggest that inhibition of AREG could carrying the human tylosis disease mutation. Collectively, our data have potential therapeutic value in the treatment of tylosis. suggest that RHBDF2 plays a critical role in regulating EGFR signaling and its downstream events, including development of RESULTS AND DISCUSSION tylosis, by facilitating enhanced secretion of AREG. Thus, targeting The human tylosis disease mutation enhances AREG AREG could have therapeutic benefit in the treatment of tylosis. secretion Autosomal dominant mutations in the human RHBDF2 gene cause KEY WORDS: CRISPR/Cas9, EGFR, RHBDF2, Amphiregulin, Tylosis tylosis (Blaydon et al., 2012; Saarinen et al., 2012). Substantial evidence implicates the involvement of AREG-induced constitutive INTRODUCTION activation of the EGFR pathway (Blaydon et al., 2012; Brooke et al., The role of RHBDF2 in enhancing amphiregulin (AREG) secretion, 2014; Hosur et al., 2014) in human tylosis. -
Multiple Loci Modulate Opioid Therapy Response for Cancer Pain
Published OnlineFirst May 27, 2011; DOI: 10.1158/1078-0432.CCR-10-3028 Clinical Cancer Predictive Biomarkers and Personalized Medicine Research Multiple Loci Modulate Opioid Therapy Response for Cancer Pain Antonella Galvan1, Frank Skorpen2,Pal Klepstad2,3, Anne Kari Knudsen2, Torill Fladvad2, Felicia S. Falvella1, Alessandra Pigni1, Cinzia Brunelli1, Augusto Caraceni1,2, Stein Kaasa2,4, and Tommaso A. Dragani1 Abstract Purpose: Patients treated with opioid drugs for cancer pain experience different relief responses, raising the possibility that genetic factors play a role in opioid therapy outcome. In this study, we tested the hypothesis that genetic variations may control individual response to opioid drugs in cancer patients. Experimental Design: We tested 1 million single-nucleotide polymorphisms (SNP) in European cancer patients, selected in a first series, for extremely poor (pain relief 40%; n ¼ 145) or good (pain relief 90%; n ¼ 293) responses to opioid therapy using a DNA-pooling approach. Candidate SNPs identified by SNP- array were genotyped in individual samples constituting DNA pools as well as in a second series of 570 patients. Results: Association analysis in 1,008 cancer patients identified eight SNPs significantly associated with À pain relief at a statistical threshold of P < 1.0 Â 10 3, with rs12948783, upstream of the RHBDF2 gene, À showing the best statistical association (P ¼ 8.1 Â 10 9). Functional annotation analysis of SNP-tagged genes suggested the involvement of genes acting on processes of the neurologic system. Conclusion: Our results indicate that the identified SNP panel can modulate the response of cancer patients to opioid therapy and may provide a new tool for personalized therapy of cancer pain. -
Collagen-Induced Arthritis Analysis in Rhbdf2 Knockout Mouse
Original Article Biomol Ther 26(3), 298-305 (2018) Collagen-Induced Arthritis Analysis in Rhbdf2 Knockout Mouse MinYoung Lee1,2, JuSeong Kang1, RyeoEun Go2, YongSub Byun1, Young Jin Wi3, KyungA Hwang2, JaeHoon Choi3, HyoungChin Kim1, KyungChul Choi2,* and KiHoan Nam1,* 1Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Cheongwon 28116, 2Laboratory of Biochemistry and Immunology, College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, 3Department of Life Science, College of Natureal Sciences, Research Institute of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea Abstract Rhomboid family member 2 gene (Rhbdf2) is an inactive homologue lacking essential catalytic residues of rhomboid intramem- brane serine proteases. The protein is necessary for maturation of tumor necrosis factor-alpha (TNF-α) converting enzyme, which is the molecule responsible for the release of TNF-α. In this study, Rhbdf2 knockout (KO) mice were produced by CRISPR/CAS9. To see the effects of the failure of TNF-α release induced by Rhbdf2 gene KO, collagen-induced arthritis (CIA), which is the rep- resentative TNF-α related disease, was induced in the Rhbdf2 mutant mouse using chicken collagen type II. The severity of the CIA was measured by traditional clinical scores and histopathological analysis of hind limb joints. A rota-rod test and grip strength test were employed to evaluate the severity of CIA based on losses of physical functions. The results indicated that Rhbdf2 mutant mice showed clear alleviation of the clinical severity of CIA as demonstrated by the significantly lower severity indexes. -
Sex-Specific Transcriptome Differences in Human Adipose
G C A T T A C G G C A T genes Article Sex-Specific Transcriptome Differences in Human Adipose Mesenchymal Stem Cells 1, 2, 3 1,3 Eva Bianconi y, Raffaella Casadei y , Flavia Frabetti , Carlo Ventura , Federica Facchin 1,3,* and Silvia Canaider 1,3 1 National Laboratory of Molecular Biology and Stem Cell Bioengineering of the National Institute of Biostructures and Biosystems (NIBB)—Eldor Lab, at the Innovation Accelerator, CNR, Via Piero Gobetti 101, 40129 Bologna, Italy; [email protected] (E.B.); [email protected] (C.V.); [email protected] (S.C.) 2 Department for Life Quality Studies (QuVi), University of Bologna, Corso D’Augusto 237, 47921 Rimini, Italy; [email protected] 3 Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy; fl[email protected] * Correspondence: [email protected]; Tel.: +39-051-2094114 These authors contributed equally to this work. y Received: 1 July 2020; Accepted: 6 August 2020; Published: 8 August 2020 Abstract: In humans, sexual dimorphism can manifest in many ways and it is widely studied in several knowledge fields. It is increasing the evidence that also cells differ according to sex, a correlation still little studied and poorly considered when cells are used in scientific research. Specifically, our interest is on the sex-related dimorphism on the human mesenchymal stem cells (hMSCs) transcriptome. A systematic meta-analysis of hMSC microarrays was performed by using the Transcriptome Mapper (TRAM) software. This bioinformatic tool was used to integrate and normalize datasets from multiple sources and allowed us to highlight chromosomal segments and genes differently expressed in hMSCs derived from adipose tissue (hADSCs) of male and female donors. -
The Mutational Landscape of Human Olfactory G Protein-Coupled Receptors
Jimenez et al. BMC Biology (2021) 19:21 https://doi.org/10.1186/s12915-021-00962-0 RESEARCH ARTICLE Open Access The mutational landscape of human olfactory G protein-coupled receptors Ramón Cierco Jimenez1,2, Nil Casajuana-Martin1, Adrián García-Recio1, Lidia Alcántara1, Leonardo Pardo1, Mercedes Campillo1 and Angel Gonzalez1* Abstract Background: Olfactory receptors (ORs) constitute a large family of sensory proteins that enable us to recognize a wide range of chemical volatiles in the environment. By contrast to the extensive information about human olfactory thresholds for thousands of odorants, studies of the genetic influence on olfaction are limited to a few examples. To annotate on a broad scale the impact of mutations at the structural level, here we analyzed a compendium of 119,069 natural variants in human ORs collected from the public domain. Results: OR mutations were categorized depending on their genomic and protein contexts, as well as their frequency of occurrence in several human populations. Functional interpretation of the natural changes was estimated from the increasing knowledge of the structure and function of the G protein-coupled receptor (GPCR) family, to which ORs belong. Our analysis reveals an extraordinary diversity of natural variations in the olfactory gene repertoire between individuals and populations, with a significant number of changes occurring at the structurally conserved regions. A particular attention is paid to mutations in positions linked to the conserved GPCR activation mechanism that could imply phenotypic variation in the olfactory perception. An interactive web application (hORMdb, Human Olfactory Receptor Mutation Database) was developed for the management and visualization of this mutational dataset. -
Science Advances | Research Article
SCIENCE ADVANCES | RESEARCH ARTICLE NEUROSCIENCE Copyright © 2019 The Authors, some rights reserved; Sleep fragmentation, microglial aging, and exclusive licensee American Association cognitive impairment in adults with and without for the Advancement of Science. No claim to Alzheimer’s dementia original U.S. Government Kirusanthy Kaneshwaran1, Marta Olah2, Shinya Tasaki3,4, Lei Yu3,4, Works. Distributed 2 3,4 3,4 under a Creative Elizabeth M. Bradshaw , Julie A. Schneider , Aron S. Buchman , Commons Attribution 3,4 2 1 David A. Bennett , Philip L. De Jager , Andrew S. P. Lim * NonCommercial License 4.0 (CC BY-NC). Sleep disruption is associated with cognitive decline and dementia in older adults; however, the underlying mechanisms are unclear. In rodents, sleep disruption causes microglial activation, inhibition of which improves cognition. However, data from humans are lacking. We studied participants in two cohort studies of older persons—the Rush Memory and Aging Project and the Religious Orders Study. We assessed sleep fragmentation by actigraphy and related this to cognitive function, to neocortical microglial marker gene expression measured by RNA sequencing, and to the neocortical density of microglia assessed by immunohistochemistry. Greater Downloaded from sleep fragmentation was associated with higher neocortical expression of genes characteristic of aged microglia, and a higher proportion of morphologically activated microglia, independent of chronological age- and dementia-related neuropathologies. Furthermore, these were, in turn, associated with worse cognition. This suggests that sleep fragmentation is accompanied by accelerated microglial aging and activation, which may partially underlie its association with cognitive impairment. http://advances.sciencemag.org/ INTRODUCTION development of therapies to mitigate the deleterious impact of sleep Cognitive impairment and dementia constitute a growing public disruption on cognition and dementia. -
Biological Pathways, Candidate Genes, and Molecular Markers Associated with Quality-Of-Life Domains: an Update
Qual Life Res (2014) 23:1997–2013 DOI 10.1007/s11136-014-0656-1 REVIEW Biological pathways, candidate genes, and molecular markers associated with quality-of-life domains: an update Mirjam A. G. Sprangers • Melissa S. Y. Thong • Meike Bartels • Andrea Barsevick • Juan Ordon˜ana • Qiuling Shi • Xin Shelley Wang • Pa˚l Klepstad • Eddy A. Wierenga • Jasvinder A. Singh • Jeff A. Sloan Accepted: 19 February 2014 / Published online: 7 March 2014 Ó Springer International Publishing Switzerland 2014 Abstract (depressed mood) and positive (well-being/happiness) Background There is compelling evidence of a genetic emotional functioning, social functioning, and overall foundation of patient-reported quality of life (QOL). Given QOL. the rapid development of substantial scientific advances in Methods We followed a purposeful search algorithm of this area of research, the current paper updates and extends existing literature to capture empirical papers investigating reviews published in 2010. the relationship between biological pathways and molecu- Objectives The objective was to provide an updated lar markers and the identified QOL domains. overview of the biological pathways, candidate genes, and Results Multiple major pathways are involved in each molecular markers involved in fatigue, pain, negative QOL domain. The inflammatory pathway has the strongest evidence as a controlling mechanism underlying fatigue. Inflammation and neurotransmission are key processes On behalf of the GeneQol Consortium. involved in pain perception, and the catechol-O-methyl- transferase (COMT) gene is associated with multiple sorts Electronic supplementary material The online version of this article (doi:10.1007/s11136-014-0656-1) contains supplementary of pain. The neurotransmitter and neuroplasticity theories material, which is available to authorized users. -
A Concise Review of Human Brain Methylome During Aging and Neurodegenerative Diseases
BMB Rep. 2019; 52(10): 577-588 BMB www.bmbreports.org Reports Invited Mini Review A concise review of human brain methylome during aging and neurodegenerative diseases Renuka Prasad G & Eek-hoon Jho* Department of Life Science, University of Seoul, Seoul 02504, Korea DNA methylation at CpG sites is an essential epigenetic mark position of carbon in the cytosine within CG dinucleotides that regulates gene expression during mammalian development with resultant formation of 5mC. The symmetrical CG and diseases. Methylome refers to the entire set of methylation dinucleotides are also called as CpG, due to the presence of modifications present in the whole genome. Over the last phosphodiester bond between cytosine and guanine. The several years, an increasing number of reports on brain DNA human genome contains short lengths of DNA (∼1,000 bp) in methylome reported the association between aberrant which CpG is commonly located (∼1 per 10 bp) in methylation and the abnormalities in the expression of critical unmethylated form and referred as CpG islands; they genes known to have critical roles during aging and neuro- commonly overlap with the transcription start sites (TSSs) of degenerative diseases. Consequently, the role of methylation genes. In human DNA, 5mC is present in approximately 1.5% in understanding neurodegenerative diseases has been under of the whole genome and CpG base pairs are 5-fold enriched focus. This review outlines the current knowledge of the human in CpG islands than other regions of the genome (3, 4). CpG brain DNA methylomes during aging and neurodegenerative islands have the following salient features. In the human diseases. -
IPP17 Carcinoma IPMN Gene Symbol Transcript Accession Nucleotide
IPP17 Carcinoma IPMN Gene Transcript Amino Gene Transcript Amino Allele Nucleotide change Consequence Allele Frequency Nucleotide change Consequence Symbol Accession Acid Symbol Accession Acid Frequency ACAP2 CCDS33924.1 chr3: 195063234 C>T C165Y Missense 19 ADCY8 CCDS33924.1 chr8: 131964235 C>T V374M Missense 29 ADAMTS1 CCDS33524.1 chr21: 28212054 T>G E627A Missense 11 ASH1L CCDS6363.1 chr1: 155307924 T>C N2920S Missense 16 ADCY8 CCDS6363.1 chr8: 131964235 C>T V374M Missense 36 CLNK CCDS1113.2 chr4: 10542196 G>T P175H Missense 14 AR CCDS14387.1 chrX: 66765158 T>A L57Q Missense 15 CLU CCDS47024.1 chr1: 155307924 T>C R127H Missense 23 ARL11 CCDS9419.1 chr13: 50204931 delCTT F117del In-frame deletion 10 CPN1 CCDS47832.1 chr10: 101816891 T>A Y297F In-frame deletion 13 ASH1L CCDS1113.2 chr1: 155307924 T>C N2920S Missense 16 CSRNP2 CCDS7486.1 chr12: 51458139 delTCT E340del In-frame deletion 13 C7orf26 CCDS5353.1 chr7: 6647641 C>T A400V Missense 13 CTNNB1 CCDS8807.1 chr3: 41266136 T>C S45P Missense 11 CLNK CCDS47024.1 chr4: 10542196 G>T P175H Missense 14 ERF CCDS2694.1 chr19: 42752892 G>A R458C Missense 15 COMT CCDS13770.1 chr22: 19951169 G>A V124M Missense 11 FBP2 CCDS12600.1 chr9: 97325736 C>A S238I Missense 13 CORIN CCDS3477.1 chr4: 47645243 G>C A663G Missense 14 HOXB3 CCDS6711.1 chr17: 46629769 C>T G23D Missense 13 CPN1 CCDS8807.1 chr10: 101816891 T>A Y297F In-frame deletion 9 KRTAP13 CCDS11528.1 chr21: 31797951 T>C T94A Missense 14 CSRNP2 CCDS2694.1 chr12: 51458139 delTCT E340del In-frame deletion 17 MAGEB4 CCDS13591.1 chrX: 30260590 C>T -
The Hypothalamus As a Hub for SARS-Cov-2 Brain Infection and Pathogenesis
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.08.139329; this version posted June 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. The hypothalamus as a hub for SARS-CoV-2 brain infection and pathogenesis Sreekala Nampoothiri1,2#, Florent Sauve1,2#, Gaëtan Ternier1,2ƒ, Daniela Fernandois1,2 ƒ, Caio Coelho1,2, Monica ImBernon1,2, Eleonora Deligia1,2, Romain PerBet1, Vincent Florent1,2,3, Marc Baroncini1,2, Florence Pasquier1,4, François Trottein5, Claude-Alain Maurage1,2, Virginie Mattot1,2‡, Paolo GiacoBini1,2‡, S. Rasika1,2‡*, Vincent Prevot1,2‡* 1 Univ. Lille, Inserm, CHU Lille, Lille Neuroscience & Cognition, DistAlz, UMR-S 1172, Lille, France 2 LaBoratorY of Development and PlasticitY of the Neuroendocrine Brain, FHU 1000 daYs for health, EGID, School of Medicine, Lille, France 3 Nutrition, Arras General Hospital, Arras, France 4 Centre mémoire ressources et recherche, CHU Lille, LiCEND, Lille, France 5 Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and ImmunitY of Lille (CIIL), Lille, France. # and ƒ These authors contriButed equallY to this work. ‡ These authors directed this work *Correspondence to: [email protected] and [email protected] Short title: Covid-19: the hypothalamic hypothesis 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.08.139329; this version posted June 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.