Gene expression signatures in neutrophils exposed to glucocorticoids a new paradigm to help explain
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非酒精性脂肪性肝病专题.综述•m6A甲基化在非酒精性脂肪性肝病中的作用骆云晨彭永德上海交通大学医学院附属第一人民医院内分泌代谢科200080通信作者:彭永德,Email:pengyongde0908@126. com【摘要】RNA作为基因表达的核心成分,在基因表达过程中通过转录水平或转录后化学修饰参与基因表达的调节。
mRNA N6-甲基腺苷(m6A)修饰在非酒精性脂肪性肝病的发生、发展中发挥重要作用。
甲基转移酶3抑制肝脏胰岛素敏感性并促进脂肪酸合成,去甲基化酶脂肪与肥胖相关蛋白(F T0)可通过改变脂代谢相关基因的表达以及增加氧化应激水平促进脂质蓄积,甲基化阅读蛋白通过m6A甲基化逆转F T0介导的脂肪生成。
探讨m6A甲基化在非酒精性脂肪性肝病中的作用,对其诊断和治疗具有重要的指导意义。
【关键词】RNA甲基化;非酒精性脂肪性肝病;N6-甲基腺苷DOI : 10. 3760/cma. j. cnl21383-20200322-03061Effects of m6A methylation in the progress of nonalcoholic fatty liver disease Luo Yunchen, PengYongde. Department of Endocrinology and Metabolism,Shanghai First People’s Hospital,Medical College,Shanghai Jiaotong University, Shanghai 200080y ChinaCorresponding author:Peng Yongde, Email:**********************【Abstract】As a core component of gene expression, RNA participates in the regulation of gene ex-pression through transcription or post-transcriptional chemical modification during gene expression. mRNAN6-methyladenosine (m6A) modification plays an important role in the occurrence and development of nonalcoholic fatty liver disease. Methyltransferase-like 3 inhibits insulin sensitivity in liver and promotes fattyacid synthesis. Demethylases fat mass and obesity-associated gene(PTO) can promote lipid accumulation viachanging the expression of lipid metabolism-related genes and increasing the level of oxidative stress. Methylation reading protein reverses FTO-mediated adipogenesis through m6A methylation. To explore the researchprogression of m6A methylation in nonalcoholic fatty liver disease is important for the clinical diagnosis andtreatment of this disease.【Key words】RNA methylation; Nonalcoholic fatty liver disease;N6-methyladenosineDOI : 10. 3760/cma. j. cnl21383-20200322-03061随着肥胖症和体重相关代谢性疾病发病率的增 加,非酒精性脂肪性肝病(NAFLD)已成为慢性肝病 的最常见原因之一。
LncRNA H19在肿瘤发病中的作用机制研究进展①朱敏郗雪艳杜伯雨(湖北医药学院基础医学院,十堰442000)中图分类号R735.3文献标志码A文章编号1000-484X(2021)07-0883-05[摘要]随着研究的深入和研究技术的提高,研究者在人类基因组中发现了大量非编码RNA(NcRNA),这类RNA一直受到人们的广泛关注。
越来越多的研究显示,NcRNA可能参与各种基因表达的调控。
目前的研究已证实,长链非编码RNA (LncRNA)在生长调控及生理代谢中发挥重要作用,并且参与肿瘤调控。
LncRNA H19是最早发现的印迹LncRNA,虽然在大多数组织中LncRNA H19的表达在出生后被关闭,但很多研究提示其可在肿瘤发生期间被重新激活或抑制,从而影响肿瘤进展。
本文主要综述近期LncRNA H19在肿瘤发病中作用机制的研究进展,为今后的研究提供参考。
[关键词]LncRNA;H19;肿瘤;作用机制Research progress of mechanism of LncRNA H19in cancer disease development ZHU Min,XI Xue-Yan,DU Bo-Yu.School of Basic Medical Sciences,Hubei University of Medicine,Shiyan 442000,China[Abstract]With the deepening of study and the improvement of research techniques,researchers have found a large number of noncoding RNA(NcRNAs)in human genome,which has been receiving attention.Increasing evidence indicated that NcRNA is likely to involve in the regulation of various gene expression.Recent studies have confirmed that long noncoding RNA(LncRNA)plays im‐portant regulator roles in various biological processes,including cancer development.LncRNA H19is the first imprinted gene. Although H19expression is turned off after birth in most tissues,there are many studies demonstrate that it can be reactivated or inhib‐ited during tumorigenesis.This article mainly reviews the recent research progress of the pathogenic mechanism of LncRNA H19in cancer disease development,aimed to provide a reference for future research.[Key words]LncRNA;H19;Cancer;Mechanism1概述由美国国立人类基因组研究院启动的多国联合研究项目计划——DNA元件百科全书(EN‐CODE)项目已证实,基因组中有80%的基因可被转录,然而最终可表达为蛋白质的基因只有不到2%[1]。
J Apoplexy and Nervous Diseases, July 2024, Vol 41,No. 7偏头痛发病机制及生物标志物研究进展毛西京, 朱博驰综述, 于挺敏审校摘要: 偏头痛是一种具有多种亚表型的异质性疾病,其诊断主要基于临床标准,缺乏特异性的生物标志物进行客观评估,影响了偏头痛的精确诊断、治疗选择以及预后评估。
近年来偏头痛在遗传、生化、影像等方面研究取得重大进展,为临床诊断及治疗偏头痛提供了客观的检测指标。
如能在临床工作中选择特异性、敏感性、易检测、可行性高的标志物将推动偏头痛早期诊断、精准化治疗的步伐。
关键词: 偏头痛; 生物标志物; 神经元; 胶质细胞中图分类号:R747.2 文献标识码:A Research advances in the pathogenesis and biomarkers of migraine MAO Xijing ,ZHU Bochi ,YU Tingmin. (The Sec⁃ond Hospital of Jilin University , Changchun 130000, China )Abstract : Migraine is a heterogeneous disease with various subtypes , and the diagnosis of migraine mainly relies on clinical criteria. The lack of specific biomarkers for objective assessment impacts the precise diagnosis , treatment selec⁃tion , and prognostic assessment of migraine. In recent years , great progress has been made in migraine in terms of genet⁃ics , biochemistry ,and imaging , which provides objective indicators for the clinical diagnosis and treatment of migraine. Identifying specific ,sensitive ,easily detectable ,and highly feasible markers in clinical practice will accelerate the early di⁃agnosis and precise treatment of migraine.Key words : Migraine ; Biomarkers ; Neurons ; Glial cells偏头痛的发病机制尚不完全明确,越来越多的研究发现神经元-神经胶质细胞-血管交互作用的炎性病理生理过程参与其中,并且从血液、脑脊液、唾液、影像检查中均发现了有意义的标志物,这些标志物成为偏头痛诊疗的潜在靶点。
gene expression signature 基因表达-回复基因表达(gene expression)在生物学研究中扮演着至关重要的角色。
基因表达指的是基因通过转录和翻译过程将DNA中的遗传信息转化为生物体内功能蛋白的过程。
而基因表达特定的模式或表达水平所构成的基因表达特征,被称为基因表达签名(gene expression signature)。
本文将一步一步回答关于基因表达签名的问题,介绍基因表达签名的意义、方法以及在研究和临床应用中的应用。
第一步:基因表达签名的意义基因表达签名是指在特定条件下,一组基因在其表达水平方面的共同特征。
这些条件可以是不同的组织类型、疾病状态、生理或环境刺激等。
通过对基因表达进行全面的分析,我们可以识别出这些共同特征,从而了解基因调控网络以及细胞功能的变化。
基因表达签名可以提供关于基因变化和相应生物学现象之间的关系的重要线索。
此外,基因表达签名还可以用于疾病诊断、患者分层、预后预测和治疗反应预测等方面的临床应用。
第二步:基因表达签名的分析方法为了生成基因表达签名,研究人员通常需要对大量的基因表达数据进行分析。
最常用的方法是通过高通量基因表达测量技术(如DNA芯片或RNA 测序)获取基因表达数据。
然后,这些数据会被标准化和归一化,以去除技术和样本间的差异。
接下来,可以利用聚类分析、主成分分析和差异表达分析等生物信息学方法来鉴定基因表达的模式,并根据这些模式构建基因表达签名。
此外,机器学习方法如支持向量机、随机森林和神经网络等也可以用于建立预测模型和识别特征基因。
第三步:基因表达签名的应用领域基因表达签名在研究和临床应用中具有广泛的应用。
在基础研究领域,基因表达签名可以用于研究疾病的发生和发展机制,从而揭示潜在的疾病标志物和治疗靶点。
在癌症研究中,基因表达签名已经被用来分类肿瘤亚型、预测患者预后和治疗反应,并指导个体化治疗决策。
此外,基因表达签名也在药物开发和药物筛选中发挥了重要作用。
doi:10.3969/j.issn.1000-484X.2024.03.025·论著/临床免疫学·痛风基因表达谱的差异基因表达及免疫细胞浸润分析陈锋1李华南2章晓云1黄慧莲3陈跃平1任国武1(1.广西中医药大学附属瑞康医院骨科,南宁530011;2.江西中医药大学附属医院,南昌330006;3.江西中医药大学,南昌330004)中图分类号R589.7 文献标志码 A 文章编号1000-484X(2024)03-0592-07[摘要]目的:研究痛风患者的差异基因表达及免疫细胞浸润情况,寻找痛风发病的关键基因及免疫细胞,探究免疫细胞与痛风的关系。
方法:从GEO数据库下载痛风的芯片GSE160170,借助R语言筛选差异基因,随后采用STRING数据库对差异基因进行分析,并借助Cytoscape软件筛选关键基因,再对其进行富集分析,同时对免疫细胞浸润情况进行分析。
结果:研究发现IL-6、IL-1β、TNF、CCL3、CXCL8和CXCL1为痛风发病的关键基因,主要通过IL-17、Toll样受体、NOD样受体、NF-κB等信号通路发挥细胞对脂多糖、细菌来源分子及生物刺激的反应等过程导致疾病发生;免疫浸润结果表明记忆性B细胞、活化的NK细胞、活化的树突状细胞、活化的肥大细胞和嗜酸性粒细胞在痛风患者中表达显著;免疫细胞间的相关性分析结果表明滤泡辅助性T细胞与活化的肥大细胞表达呈正相关,未活化的NK细胞与单核细胞表达呈负相关。
结论:关键基因和差异表达的免疫细胞与痛风发病机制密切相关,为痛风的免疫机制研究提供了新思路。
[关键词]痛风;单钠尿酸盐;生物信息学;免疫细胞;细胞浸润Differential gene expression and immune cell infiltration analysis of gout gene expression profileCHEN Feng1, LI Huanan2, ZHANG Xiaoyun1, HUANG Huilian3, CHEN Yueping1, REN Guowu1. 1. Department of Orthopaedics,Ruikang Hospital Affiliated to Guangxi University of Traditional Chinese Medicine,Nanning 530011, China; 2. Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang 330006,China; 3. Jiangxi University of Chinese Medicine, Nanchang 330004, China[Abstract]Objective:To study the differential gene expression and immune cell infiltration of gout patients, to find the key genes and immune cells of gout pathogenesis, and to explore the relationship between immune cells and gout. Methods:The gout chip GSE160170 was downloaded from the GEO database, and the differential gene expression analysis was carried out with the help of R language. Then, the STRING database was used to analyze the differential gene, and the Cytoscape software was used to screen the key genes,and then carry out enrichment analysis. At the same time,the infiltration of immune cells were analyzed. Results:The study found that IL-6, IL-1β, TNF, CCL3, CXCL8 and CXCL1 were key genes in the pathogenesis of gout, which were mainly exerted by IL-17, Toll-like receptor, NOD-like receptor, NF-κB and other signaling pathways. Processes such as cellular responses to lipo‑polysaccharides, bacteria-derived molecules, and biological stimuli lead to disease; immune infiltration results indicate that memory B cells, activated NK cells, activated dendritic cells, activated mast cells and eosinophils were involved in the disease. It was signifi‑cantly expressed in gout patients; the correlation analysis between immune cells showed that the expression of follicular helper T cells were positively correlated with the expression of activated mast cells, and the expression of unactivated NK cells and monocyte were negatively correlated. Conclusion:Key genes and differentially expressed immune cells are closely related to the pathogenesis of gout,providing new ideas for the study of the molecular mechanism of gout.[Key words]Gout;Monosodium urate;Bioinformatics;Immune cells;Cellular infiltration基金项目:国家自然科学基金项目(81860857,82060871,82160792);江西省自然科学基金项目(20202BAB206071);江西省教育厅科学技术研究项目(GJJ190582);2020年度江西省中医药管理局科技计划项目(2020B0333);江西省第二届国医大师邓运明名医工作室(赣人社[2021]201号文)。
基因英语词汇翻译Aactivation domain 活化结构域adapters 连接物adenine 腺嘌呤adenosine 腺ADP (adenosine diphosphate) 腺二磷酸affinity column 亲和柱AFLP (amplified fragment length polymorphisms) 增值性断片长度多态现象agrobacterium 农杆菌属alanine 丙氨酸allele 等位基因amber mutation 琥珀型突变AMP (adenosine monophosphate) 腺一磷酸ampicillin 氨?青霉素anchor primer 锚状引物annealing 退火annealing temperature 退火温度anticodon 反密码子AP-PCR (arbitrarily primed PCR) 任意引物聚合?链反应arbitrary primer 任意引物ATP (adenosine triphosphate) 腺三磷酸autosome 常染色体腺苷脱氨酶缺乏症 adenosine deaminasedeficiency (ADA) 腺病毒 adenovirusAlagille综合征 Alagille syndrome等位基因 allele氨基酸 amino acids动物模型 animal model抗体 antibody凋亡 apoptosis路-巴综合征ataxia-telangiectasia常染色体显性autosomal dominant常染色体 autosomeBbaculovirus 杆状病毒base pair ..基对base sequence ..基顺序beta-galactosidase ..-半乳糖? beta-glucuronidase ..-葡糖醛酸糖? bioluminescence 生物发光bioremediation 生物降解biotechnology 生物技术blotting 印迹法blue-white selection 蓝白斑筛选细菌人工染色体 bacterial artificial chromosome (BAC)碱基对 base pair先天缺陷birth defect骨髓移植bone marrow transplantation blunt end 平(整末)端Ccatalyst 催化剂cDNA library 反向转录DNA库centromere 着丝体centrosome 中心体chemiluminescence 化学发光chiasma 交叉chromomere 染色粒chromoplast 有色体chromosomal aberration 染色体畸变chromosomal duplication 染色体复制chromosomal fibre 染色体牵丝chromosome 染色体chromosome complement 染色体组chromosome map 染色体图chromosome mutation 染色体突变clone 克隆cloning 无性繁殖系化codon 密码子codon degeneracy 密码简并codon usage 密码子选择cohesive end 黏性末端complementary DNA (cDNA) 反向转录DNA complementary gene 互补基因consensus sequence 共有序列construct 组成cosmids 黏性质粒crossing over 互换cyclic AMP (cAMP) 环腺酸cytosine 胞嘧啶癌 cancer后选基因 candidate gene癌 carcinomacDNA文库 cDNA library 细胞cell染色体 chromosome克隆 cloning密码 codon天生的 congenital重叠群 contig囊性纤维化 cystic fibrosis 细胞遗传图 cytogenetic mapDdark band 暗带deamination 脱氨基作用decarboxylation 脱羧基作用degenerate code 简并密码degenerate PCR 退化性聚合?链反应dehydrogenase 脱氢?denaturation 变性deoxyribonucleoside diphospahte 脱氧核糖核一磷酸deoxyribonucleoside monophospahte 脱氧核糖核二磷酸deoxyribonucleoside triphospahte 脱氧核糖核三磷酸deoxyribose 去(脱)氧核糖dicarboxylic acid 二羧酸digoxigenin 洋地黄毒diploid 二倍体DNA (deoxyribonucleic acid) 去(脱)氧核糖核酸DNA binding domain DNA结合性结构域DNA fingerprinting DNA指纹图谱DNA helicase DNA解螺旋?DNA kinase DNA激?DNA ligase DNA连接?DNA polymer DNA聚合物DNA polymerase DNA聚合?double helix 双螺旋double-strand 双链缺失 deletion脱氧核糖核酸 deoxyribonucleic acid (DNA) 糖尿病 diabetes mellitus二倍体 diploidDNA复制 DNA replicationDNA测序 DNA sequencing显性的 dominant双螺旋 double helix复制 duplicationEelectroporation 电穿孔endonuclease 内切核酸? enhancer 增强子enterokinase 肠激? episome 游离基因ethidium bromide 溴乙锭eukaryotic 真核生物的euploid 整倍体exonuclease 外切核酸?expressed-sequence tags 表达的序列标记片段extron 外含子电泳electrophoresis 酶enzyme外显子exonFF factor F因子FAD (flavine adenine dinucleotide) 黄素腺嘌呤二(双)核酸feedback control 反馈控制feedback inhibition 反馈抑制feedback mechanism 反馈机制first filial (F1) generation 第一子代FISH (fluoresence in situ hybridization) 荧光原位杂交forward mutation 正向突变F-pilus F纤毛functional complementation 功能性互补作用fusion protein 融合蛋白家族性地中海热familial Mediterraneanfever 荧光原位杂交fluorescence in situhybridization (FISH) 脆性X染色体综合征Fragile X syndromeGgel electrophoresis 凝胶电泳gene 基因gene cloning 基因克隆gene conversion 基因转变gene duplication 基因复制gene flow 基因流动gene gun 基因枪gene interaction 基因相互作用gene locus 基因位点gene mutation 基因突变gene regulation 基因调节gene segregation 基因分离gene therapy 基因治疗geneome 基因组/ 染色体组genetic map 基因图genetic modified foods (GM foods) 基因食物genetics 遗传学genetypic ratio 基因型比/ 基因型比值genome 基因组/ 染色体组genomic library 基因组文库genotype 基因型giant chromosome 巨染色体globulin 球蛋白glucose-6-phosphate dehydrogenase 6-磷酸葡萄糖脱氢?GP (glycerate phosphate) 磷酸甘油酸脂GTP (guanine triphosphate) 鸟三磷酸guanine 鸟嘌呤基因扩增gene amplification基因表达gene expression基因图谱gene mapping基因库gene pool基因治疗gene therapy基因转移gene transfer遗传密码genetic code (A TGC)遗传咨询genetic counseling遗传图genetic map遗传标记genetic marker遗传病筛查genetic screening基因组genome基因型genotype种系germ lineHhaploid 单倍体haploid generation 单倍世代heredity 遗传heterochromatin 异染色质Hfr strain 高频重组菌株holoenzyme 全?homologous 同源的housekeeping gene 家务基因hybridization 杂交单倍体haploid造血干细胞hematopoietic stem cell 血友病hemophilia 杂合子heterozygous高度保守序列highly conserved sequence Hirschsprung病Hirschsprung's disease纯合子homozygous人工染色体human artificial chromosome (HAC)人类基因组计划Human Genome Project human immunodeficiency virus (HIV)/ 人类免疫缺陷病毒acquired immunodeficiency syndrome (AIDS) 获得性免疫缺陷综合征huntington舞蹈病Huntington's diseaseIimmunoglobulin 免疫球蛋白in vitro 在体外/ 在试管内in vivio 在体内independent assortment 独立分配induced mutation 诱发性突变induction 诱导initiation codon 起始密码子inosine 次黄insert 插入片段insertional inactivation 插入失活interference 干扰intergenic 基因间的interphase 间期intragenic 基因内的intron 内含子inversion 倒位isocaudarner 同尾酸isoschizomer 同切点?Kkanamycin 卡那毒素klenow fragment 克列诺夫片段Llac operon 乳糖操纵子ligase 连接? ligation 连接作用light band 明带linker 连接体liposome 脂质体locus 位点Mmap distance 图距离map unit 图距单位mature transcript 成熟转录物metaphase 中期methylase 甲基化? methylation 甲基化作用microarray 微列microinjection 微注射missense mutation 错差突变molecular genetics 分子遗传学monoploid 单倍体monosome 单染色体messenger RNA (mRNA) 信使RNA multiple alleles 复(多)等位基因mutagen 诱变剂mutagenesis 诱变mutant 突变体mutant gene 突变基因mutant strain 突变株mutation 突变mutation rate 突变率muton 突变子畸形malformation描图mapping标记marker黑色素瘤melanoma孟德尔Mendel, Johann (Gregor)孟德尔遗传Mendelian inheritance信使RNA messenger RNA (mRNA)[分裂]中期metaphase微阵技术microarray technology线立体DNA mitochondrial DNA单体性monosomy小鼠模型mouse model多发性内分泌瘤病multiple endocrine neoplasia, type 1 (MEN1)NNAD (nicotinamide adenine dinucleotide) 烟醯胺腺嘌呤二核酸NADP (nicotinamide adenine dinucleotide phosphate) 烟醯胺腺嘌呤二核酸磷酸nicking activity 切割活性nonsense codon 无意义密码子nonsense mutation 无意义突变Northern blot Northern印迹法nuclear DNA 核DNAnuclear gene 核基因nuclease 核酸?nucleic acid 核酸nucleoside 核nucleoside triphosphate 核三磷酸nucleotidase 核酸?nucleotide 核酸nucleotide sequence 核酸序列神经纤维瘤病neurofibromatosis尼曼-皮克病Niemann-Pick disease, type C (NPC)RNA印记Northern blot核苷酸nucleotide神经核nucleusOoligonucleotide 寡核酸one gene one polypeptide hypothesis 一个基因学说operon 操纵子oxidative decarboxylation 氧化脱羧作用oxidative phosphorylation 氧化磷酸化作用寡核苷酸oligo癌基因oncogenePpeptide ? peptide bond ?键phagemids 噬菌粒phosphorylation 磷酸化作用physical map 物理图谱plasmid 质粒point mutation 点突变poly(A) tail poly(A)尾polymerase 聚合?polyploid 多倍体positional cloning 位置性无性繁殖系化primary transcript 初级转录物primer 引物probe 探针prokaryotic 原核的promoter 启动子protease 蛋白?purine 嘌呤pyrimidine 嘧啶Parkinson病Parkinson's disease血系/谱系pedigree表型phenotype物理图谱physical map多指畸形/多趾畸形polydactyly聚合酶链反应polymerase chain reaction (PCR)多态性polymorphism定位克隆positional cloning原发性免疫缺陷primary immunodeficiency 原核pronucleus前列腺癌prostate cancerRrandom segregation 随机分离RAPD (rapid amplified polymorphic DNA) 快速扩增多态DNAreading frame 阅读码框recessive gene 隐性基因recombinant 重组体recombinant DNA technology 重组DNA技术recombination 重组regulator (gene) 调控基因replica 复制物/ 印模replica plating 复制平皿(板)培养法replication 复制replication origin 复制起点reporter gene 报道基因repression 阻遏repressor 阻遏物repressor gene 阻遏基因resistance strain 抗药性菌株restriction 限制作用restriction enzyme 限制性内切? restriction mapping 限制性内切?图谱retrovirus 反转录病毒reverse transcription 反转录作用RFLP (restricted fragment length polymorphisms) 限制性断片长度多态现象ribonucleotide 核糖核酸ribose 核糖ribosomal RNA (rRNA) 核糖体RNA ribosome 核糖体RNA (ribonucleic acid) 核糖核酸RNA polymerase I RNA聚合?IRNA polymerase II RNA聚合?IIRNA polymerase III RNA聚合?IIIR-plasmid R质粒/ 抗药性质粒隐性recessive逆转录病毒retrovirus核糖核酸ribonucleic acid (RNA)核糖体ribosomeSsecond filial (F2) generation 第二子代self-ligation 自我连接作用shuttle vectors 穿梭载体sigma factor ..因子single nucleotide polymorphism 单核酸多态性single-stranded DNA 单链DNAsister chromatid 姊妹染色单体sister chromosome 姊妹染色体site-directed mutagenesis 定点诱变somatic cell 体细胞Southern blot Southern印迹法splice 拼接star activity 星号活性stationary phase 静止生长期sticky end 黏性末端stop codon 终止密码子structural gene 结构基因supernatant 上层清液supressor 抑制基因序列标记位点sequence-tagged site (STS) 联合免疫缺陷severe combined immunodeficiency (SCID)性染色体sex chromosome伴性的sex-linked体细胞somatic cellsDNA印记Southern blot光谱核型spectral karyotype (SKY)替代substitution自杀基因suicide gene综合征syndromeTtelophase 末期template 模板terminator 终止子tetracycline 四环素thymine 胸腺嘧啶tissue culture 组织培养transcription 转录作用transfer RNA (tRNA) 转移RNA transformation 转化作用transgene 转基因translation 翻译/ 平移transmembrane 跨膜triplet 三联体triplet code 三联体密码triploid 三倍体技术转让technology transfer转基因的transgenic易位translocation三体型trisomy肿瘤抑制基因tumor suppressor geneVvector 载体WWestern blot Western印迹法Wolfram综合征Wolfram syndromeY 酵母人工染色体yeast artificial chromosome (YAC)。
gene expression signature 基因表达-回复基因表达(Gene Expression Signature)基因表达是指基因在细胞中转录成mRNA,并进一步转化为蛋白质的过程。
基因表达的变化可以直接影响个体的生理特征和疾病的发展。
在基因组学研究中,人们常常使用基因表达的模式或模式集合来描述特定疾病状态或生物学过程,这被称为基因表达签名(Gene Expression Signature)。
基因表达签名是通过高通量技术(如基因芯片或RNA测序)获得的基因表达数据,并使用统计学方法对这些数据进行分析得到的结果。
这些数据可以被用于识别特定疾病或生物学过程的生物标记物。
基因表达签名的发现可以帮助我们更好地理解疾病的发生机制,预测疾病的进展和预后,以及指导治疗策略的制定。
首先,为了获得基因表达签名,我们需要采集样本并进行基因表达测定。
常见的方法是通过基因芯片或RNA测序技术,获取样本中上千个基因的表达水平。
这些数据中包含了大量的信息,但直接分析这些数据是困难且复杂的。
因此,我们需要将数据进行预处理和归一化,以去除噪声并使不同样本之间的比较更加准确。
经过预处理后,我们可以进行差异表达分析,以发现在不同条件下表达差异显著的基因。
这些差异表达的基因可能是与特定疾病或生物学过程相关的候选基因。
接下来,我们可以使用一系列的统计学方法,如聚类分析、主成分分析或机器学习算法,对这些差异表达的基因进行分组和分类。
通过比较不同组别或类别之间的基因表达模式,我们可以鉴定出与特定疾病或生物学过程相关的基因表达签名。
这些基因表达签名可以包含一组上调或下调的基因,它们共同参与了某个特定的生物学过程或疾病发生的关键途径。
通过研究这些基因表达签名,我们可以更深入地了解疾病的发展机制,找到新的治疗靶点,并开发出更精确的诊断和预测工具。
除了在疾病研究中的应用,基因表达签名也可以帮助个体化医疗的实现。
通过分析个体的基因表达数据,我们可以预测他们对特定药物的反应,为患者提供更准确的个体化治疗方案。
gene expression signature 基因表达-回复什么是基因表达(gene expression)?基因表达指的是基因通过转录和翻译过程,将基因序列中的信息转化为蛋白质的过程。
在细胞中,基因是DNA分子的一部分,DNA分子则包含了编码蛋白质所需的遗传信息。
基因表达是生物体内复杂而精确的调控过程,对个体发育、生理功能和适应环境起着重要作用。
什么是基因表达签名(gene expression signature)?基因表达签名是指与特定生物学过程、疾病状态或临床表型相关联的一组基因的表达模式。
通过对大量样本的基因表达数据进行分析,可以识别出与特定生物学状态相关的不同基因组合。
基因表达签名的发现可以揭示基因与疾病之间的潜在关系,为研究疾病发生机制、预测个体疾病风险以及疾病分类和治疗提供重要依据。
如何得到基因表达签名?获得基因表达签名的常用方法是通过进行高通量基因表达分析。
常见的基因表达分析技术包括芯片芯片技术和RNA测序技术。
芯片技术利用具有数万个已知基因的DNA探针,通过与样本中的RNA分子的互补配对反应来检测和量化特定基因的表达水平。
而RNA测序则通过将RNA分子转换为DNA序列,再进行高通量的DNA测序,以获得基因表达的全面信息。
基因表达签名在生物学研究中的应用基因表达签名在许多生物学研究领域中都有广泛的应用。
首先,在疾病研究中,基因表达签名可以用来识别特定疾病的生物标记物,帮助研究人员进行早期诊断和疾病分类。
例如,在癌症研究中,通过分析肿瘤组织中的基因表达数据,可以发现与肿瘤发生和进展密切相关的基因表达签名,从而为癌症的早期检测和个体化治疗提供依据。
其次,基因表达签名也可以用来预测个体对药物的反应和治疗效果。
通过对大量患者样本进行基因表达分析,可以寻找与特定药物治疗效果相关的基因表达模式,进而为个体化药物治疗提供指导。
这种个体化治疗策略可以减少不必要的药物治疗,提高治疗效果,并降低药物不良反应的风险。
Gene expression signatures in neutrophils exposed to glucocorticoids:A new paradigm to help explain ‘‘neutrophil dysfunction’’in parturient dairy cowsJeanne L.Burton a ,b ,*,Sally A.Madsen a ,Ling-Chu Chang a ,Patty S.D.Weber a ,Kelly R.Buckham a ,Renate van Dorp b ,Mary-Clare Hickey c ,Bernadette Earley caImmunogenetics Laboratory,Department of Animal Science,Michigan State University,1205E Anthony Hall,East Lansing,MI 48824,USAbCenter for Animal Functional Genomics,Department of Animal Science,East Lansing,MI 48824,USA cAnimal Health and Welfare Department,Teagasc,Grange Research Center,Co Meath,IrelandAbstractNeutrophils are the first line of immunity against most pathogens that infect cattle.These normally short-lived white blood cells develop from myeloid-lineage cells in bone marrow.Upon maturation,bone marrow neutrophils are released into the circulation where they marginate on inflamed blood vessel endothelial cells and migrate through them into the area of infection.Once migrated,neutrophils do not reenter the circulation,but rather,perform their bactericidal functions and die by apoptosis in the tissue.The cytokine and hormonal milieu of the blood and extracellular tissue fluid can influence neutrophil development and immunity-related activities,but the molecular basis of these phenotypic changes and physiological benefits or drawbacks of them are poorly understood.In the current paper,we review new gene expression information that resulted from two of our functional genomics studies designed to evaluate effects of glucocorticoid hormones on bovine neutrophils.This work provides one model to describe complex changes that occur in neutrophils as the cells respond to glucocorticoids,which might act to alter the cells’functional priorities and tip the delicate balance between health and disease during stress,including at parturition.A bovine immunobiology microarray and real time RT-PCR were used to study blood neutrophils collected during the natural surge of endogenous glucocorticoid (cortisol)in parturient dairy cows and bone marrow neutrophils collected from glucocorticoid (dexamethasone)-treated dairy steers.The gene expression signatures we observed led us to perform additional phenotyping of the neutrophils and correlation analyses,which together painted a picture suggesting that glucocorticoids have key roles in modulating neutrophil development,life span,and tissue defense functions during parturition and hormone therapy.Based on these observations,we postulate that glucocorticoids orchestrate adaptive changes in the entire neutrophil system that support increased cell numbers and longevity in blood and heightened remodeling activity in tissues,while at the same time decreasing some important antimicrobial defense activities of the cells.Thus,our functional genomics studies have enabled us to elucidate multiple consequences of neutrophil exposure to glucocorticoids,highlighting a probable role for this interaction in the/locate/vetimmVeterinary Immunology and Immunopathology 105(2005)197–219*Corresponding author.Tel.:+15173539702/9815(Laboratory);fax:+15173531699.E-mail address:burtonj@ (J.L.Burton).0165-2427/$–see front matter #2005Elsevier B.V .All rights reserved.doi:10.1016/j.vetimm.2005.02.012induction of parturition and partly explaining why some parturient dairy cows may experience heightened incidence and severity of in flammatory diseases like mastitis.#2005Elsevier B.V .All rights reserved.Keywords:cDNA microarray;Neutrophils;Bone marrow cells;Cortisol;Dexamethasone1.BackgroundElevated blood levels of glucocorticoid hormone during stress and exogenous administration of the steroid have been associated with increased suscept-ibility to infectious diseases in cattle that affect production,including mastitis in parturient dairy cows and shipping fever in transportation stressed feedlot animals (Roth and Kaeberle,1982;Burton and Erskine,2003).Our groups are interested in the effects of glucocorticoids on bovine neutrophils because of the critical role these leukocytes play in innate immune defense against such diseases.We have studied bovine neutrophils following administration of the potent glucocorticoid,dexamethasone (Burton et al.,1995;Burton and Kehrli,1995;Weber et al.,2001,2004;Chang et al.,2004)and during parturition when there is a surge in blood concentrations of the endogenous glucocorticoid,cortisol (Preisler et al.,2000;Weber et al.,2001;Madsen et al.,2002,2004;Chang et al.,2004).Pronounced neutrophilia occurs in both cases,showing that glucocorticoids profoundly alter neutrophil homeostasis.The vast majority of circulating cells in the early phase of glucocorticoid-induced neutrophilia are segmented neutrophils that have de-marginated from blood vessels due to down-regulated expression of surface adhesion molecules (Burton et al.,1995;Weber et al.,2004)and,possibly,up regulation of anti-adhesion molecules (Goulding et al.,1998;La et al.,2001).However,signi ficant release of mature (segmented and band)neutrophils from bone marrow is clearly detectable in cattle !24h following glucocorticoid challenge and may contri-bute to additional waves of neutrophilia later in the steroid response (Burton and Kehrli,1995;Weber et al.,2004).Thus,when studying in vivo effects of glucocorticoids on bovine neutrophils,it is relevant to do so in both blood and bone marrow pools of the cells.In cattle,circulating neutrophils are sensitive to glucocorticoids because they possess high expressionof glucocorticoid receptors (GR).In most mammalian cells,including bovine neutrophils (Chang et al.,2004),GR exists in two main isoforms,GR a and GR b (Hollenberg et al.,1985).However,only GR a has glucocorticoid binding capacity (Bamberger et al.,1996;Kino et al.,2001).We have shown that bovine blood neutrophils have $8-fold higher GR a mRNA abundance compared with the cells ’more immature counterparts developing in bone marrow (Fig.1).Thus,bovine blood neutrophils are predicted to beJ.L.Burton et al./Veterinary Immunology and Immunopathology 105(2005)197–219198Fig.1.Bovine blood neutrophils express $8-fold higher abundance of mRNA for the hormone-binding alpha isoform of the glucocor-ticoid receptor (GR a )than immature neutrophil-lineage cells devel-oping in bone marrow.Data were generated by quantitative slot blot analysis with b -actin as the control gene (Madsen et al.,2002),GR a and b -actin cDNA probes described in Weber et al.(2001),and RNA samples assayed in duplicate.The RNA samples were obtained from bone marrow neutrophil-lineage cells and blood neutrophils of healthy steers (n =12)using Percoll density gradients (Weber et al.,2004).Bone marrow F1cells contained $70%early-immature myeloblasts and promyelocytes,F2cells $55%late-immature myelocytes and metamyelocytes,and F3cells $70%band and segmented neutrophils.The P -value indicates the level of signi fi-cance for the main effect of granulocyte maturation fraction,obtained by general linear models analysis of the data,and a and b above individual bars indicate signi ficant (P 0.05)differences in mean (ÆS.E.M.)GR a mRNA abundance by maturation fraction.highly sensitive to changes in circulating glucocorti-coid concentrations.In cells not exposed to stress or therapeutic levels of glucocorticoids,most GR a are located in the cytoplasm as complexes with accessory proteins that maintain the receptors in a high af finity hormone-binding state (Bamberger et al.,1996).When glucocorticoid concentrations rise inside the cell due to elevated extracellular concentrations,hormone binding to GR a activates the receptor causing it to dissociate from its protein complex.This allows GR a to translocate into the cell ’s nucleus (Eicher and Burton,2004).In the nucleus,hormone-bound GR a employs multiple mechanisms to change expression of hormone sensitive genes,including binding to DNA and other transcription factors to in fluence rates of gene transcription and to mRNAs already existing in the cytoplasm to affect their stability (Bamberger et al.,1996;Newton,2000;Beato and Klug,2000;Almawi and Melemedjian,2002).In previous studies,we demonstrated that blood neutrophils of dairy cows express functional GR a proteins,staining brightly with fluorescently labeled hormone when collected during mid and late lactation and exiting the cells ’cytosol in response to the cortisol surge at parturition (Preisler et al.,2000;Fig.2a).We also showed that glucocorticoid-induced loss of GR a from the cytosol is time-and dose-dependent when cultured neutrophils are treated with the steroid in vitro (Chang et al.,2004and our unpublished data).In both scenarios of endogenous and exogenous gluco-corticoid challenge,GR a loss from the neutrophils ’cytosol is associated with acute and pronounced changes in expression of two genes that regulate neutrophil behavior,including margination (CD62L;Weber et al.,2001,2004)and programmed cell death (Fas;Chang et al.,2004).Thus,GR a activation by glucocorticoids in circulating neutrophils causes distinctive phenotypic changes in the cells via altered expression of hormone-sensitive genes.However,these changes are relatively short-lived ($48h),possibly due to the fact that GR a activation rapidly decreases abundance of its own mRNA (Fig.2b)byJ.L.Burton et al./Veterinary Immunology and Immunopathology 105(2005)197–219199Fig.2.The surge in blood cortisol during bovine parturition (a)is correlated (r =À0.71;P =0.06)with rapid down regulation of glucocorticoid receptor-alpha (GR a )mRNA abundance in blood neutrophils (b),possibly due to the ability of glucocorticoid to reduce the rate of transcription of its own receptor gene (c).Blood for serum cortisol assays and neutrophil GR a mRNA abundance assessment (a and b)was collected from three primiparous Holstein cows on days À7,0,0.25,and 1relative to parturition (on day 0).Serum cortisol was measured in duplicate by EIA (Assay Designs,Inc.,Ann Arbor,MI)and GR a mRNA by quantitative real time RT-PCR (Madsen et al.,2004).GR a mRNA abundance on days 0,0.25,and 1were relative to expression on day À7(b)and calculated using the 2ÀDD Ct method (Livak and Schmittgen,2001).Nuclear run on assay was used to generate data in panel (c).Brie fly,Percoll-isolated blood neutrophils of four healthy Holstein steers (3–4months of age)were left untreated (Control)or treated with 10À7M of dexamethasone (Dex)for 4h prior to isolation of the cells ’nuclei,which were snap frozen before being used to transcribe new radi-olabeled mRNA in vitro.GR a and b -actin (control)cDNA probes (Weber et al.,2001)were spotted in excess on nylon membrane strips and the blots probed with the newly synthesized,radiolabeled mRNA.Densitometry was used to quantify abundance of tran-scribed GR a and b -actin mRNA,and the GR a transcription ratewas expressed as the mRNA abundance ratio of GR a :b -actin.P -values associated with each graph show the level of signi ficance for the main effect of parturition (a and b)or treatment (c),and a –c above individual bars indicate signi ficant (P 0.05)differences in means (ÆS.E.M.)shown in each plot.repressing the transcription rate of its gene(Fig.2c). Thus,choices of blood sampling times relative to glucocorticoid challenges in vivo and in vitro are critical in experiments designed to study neutrophil gene expression changes in response to the hormone.Results of our studies cited above led us to ask several questions about possible additional impacts of glucocorticoids on the bovine neutrophil system.In particular,we wanted to know what other genes might be affected in blood neutrophils during the cortisol surge at parturition.This is important because such knowledge may elucidate why blood neutrophils have depressed bactericidal activities that correspond with increased susceptibility to opportunistic infectious diseases,such as coliform mastitis,during parturition (reviewed in Kehrli and Harp,2001;Burton and Erskine,2003;Burvenich et al.,2003).Also,though neutrophil-lineage cells developing in bone marrow express low levels of GR a(Fig.1),we sought to understand if glucocorticoid challenge could never-theless impact gene expression in this only renewable source of blood neutrophils.To begin to address these questions we collected blood neutrophils from dairy cows around the parturient cortisol surge,and bone marrow cells from dairy steers treated with a high dose of dexamethasone.Total RNA isolated from these cells was used to obtain preliminary gene expression profiles by cDNA microarray and quantitative real time RT-PCR(Q-RT-PCR)analyses.2.Gene expression profiling of blood neutrophils during the surge in cortisol at parturition In ourfirst cDNA microarray experiment,blood from four primiparous Holstein cows was collected close to the surge in parturient cortisol.These animals were healthy and did not experience retained placenta, metritis,or mastitis at or following parturition. Neutrophils were enriched from the blood samples to94–98%purity using Percoll density gradients(as in Weber et al.,2001)and their gene expression patterns profiled using our group’s third generation BOTL(for bovine total leukocyte)cDNA microarrays(clones searchable at ).As we reported in Madsen et al.(2004),expression changes (P<0.05)for302genes were detected over the time the cows transitioned from the dry period(dayÀ7relative to parturition)through parturition(day0)and into thefirst day of lactation(days0.25and1). Pronounced changes occurred for most affected genes at parturition and6h postpartum(day0.25),when blood cortisol concentrations and neutrophilia were highest(Fig.2a and Madsen et al.,2004).2.1.Apoptosis gene expression profiles during the cortisol surge at parturitionThe largest ontological cluster of affected known genes(42genes)in our microarray study encoded apoptosis regulatory proteins.Quantitative real time RT-PCR was used to substantiate expression changes for some of the best known of these apoptosis genes (Fig.3).Percoll enriched blood neutrophils from three additional primiparous parturient cows were used for RNA isolations and cDNA synthesis in this work,as per our described methods(Madsen et al.,2004;Weber et al.,2004).Beta-actin was selected as the control gene for Q-RT-PCR because its amplification efficiency was the same as that for all test genes and abundance of its mRNA in bovine blood neutrophils does not change through the peripartum period(Weber et al.,2001; Madsen et al.,2002).Using this approach,we verified that expression of genes encoding4death inducing signaling complex(DISC)proteins(i.e.,FADD,Daxx, FLASH,and RIP),which are associated with Fas activation by its ligand(FasL;Fig.3),were profoundly down regulated during parturition(Madsen et al., 2004).In addition,parturition down-regulated gene expression for the pro-apoptotic Bcl-2family member, Bak,while simultaneously up regulating expression of genes encoding the anti-apoptotic Bcl-2homologue, A1,and the potent pro-survival chemokine,IL-8 (Fig.3;Madsen et al.,2004).These preliminary gene expression data supported a hypothesis that parturition reprograms neutrophils for extended survival in blood. In addition,IL-8is known to enhance cell survival by signaling the down regulation of Bak gene expression (Grutkoski et al.,2002).Therefore,parturition may also induce an autocrine short-loop in neutrophils whereby induction of IL-8suppresses Bak expression to support continued survival of the cells.In turn, survival induction in neutrophils could partly explain the neutrophilia that occurs in conjunction with the cortisol surge at parturition(Fig.2a;Preisler et al., 2000;Weber et al.,2001).J.L.Burton et al./Veterinary Immunology and Immunopathology105(2005)197–219 200Since publishing those original data we have Q-RT-PCR profiled expression patterns for an additional six apoptosis regulatory genes,including pro-apoptotic Fas,FasL,and DAP5,and anti-apoptotic TRAF6, TANK,and BAFF(Fig.3).Thefirstfive genes listed were significantly down regulated between parturition and thefirst day of lactation,while BAFF was up regulated at parturition(Fig.4).BAFF is a relatively newly identified member of the growing family of TNF ligands and is best known for its critical role in development of long-lived mature peripheral B cells (Chin et al.,1999;Mak and Yeh,2002;Mackay and Ambrose,2003).Its pronounced up regulation in blood neutrophils at parturition argues in favor of cell survival.Down regulation of the TRAF-6and TANK genes is not necessarily congruent with a survival gene expression signature during parturition because protein products of these genes act to desensitize cells to pro-apoptotic signals from activated TNF-a receptors(Fig.3;Bradley and Pober,2001;Wu and Arron,2003).However,TRAF-6and TANK act downstream of other key death inducing molecules, including Fas and FasL,which are highly potent in their ability to induce apoptosis in bovine neutrophils and were dramatically down regulated in the cells during parturition(Fig.4).Presence of DAP5proteins in cells ensures that continued translation of death effector proteins occurs even as cells undergo apoptosis (Fig.3;Henis-Korenblit et al.,2000,2002).Thus,the down regulation of DAP5gene expression that we observed during parturition(Fig.4)would be expected to have a positive impact on neutrophil survival.So,J.L.Burton et al./Veterinary Immunology and Immunopathology105(2005)197–219201Fig.3.Blood neutrophils are normally programmed to undergo rapid apoptosis through a combination of death receptor signaling initiated at the plasma membrane and spontaneous death initiated through mitochondrial signaling.For example,ligation of membrane bound Fas by its ligand (FasL)recruits a variety of adaptor proteins[the death initiating signaling complex(DISC)molecules FADD,FLASH,RIP,and Daxx]to Fas’cytoplasmic tails,which then recruit and sequentially activate caspases8and3to effect cell death.At the mitochondrial membrane,reactive oxygen species(ROS)generated during oxidative metabolism(not shown)and pro-apoptotic Bcl-2family members Bak and Bax induce release of cytochrome c(cyt c)and Smac/DIABLO(not shown),which activate caspase9to directly and indirectly activate caspase3and cell death.This spontaneous form of apoptosis is normally uninhibited in circulating neutrophils because electron transport chain activity is high and expression of key anti-apoptotic molecules like A1(Bcl-2homologue)and IL-8(chemokine)is low or absent.Furthermore,expression of DAP-5ensures that the cells continue translating death effector proteins even as they undergo apoptotic cell death.In both pathways,cell death is mediated by caspase-induced cleavage of proteins that are critical for DNA repair,cytoskeletal stability,and plasma membrane integrity.Thus,apoptotic neutrophils are distinguished from viable cells by their reduced size,flipping of inner leaflet phosphatidylserine(PS)residues to the outer leaflet of the plasma membrane,and irreversible fragmentation of genomic DNA(hypodiploidy).Factors that reduce mitochondrial ROS production or induce expression of genes encoding the potent anti-apoptotic proteins A1,IL-8,BAFF,TRAF-6,and TANK temporarily prevent these cellular events and extend neutrophil life span by quenching mitochondrial membrane destabilizing activities of ROS,Bak,and Bax and blocking signaling pathways derived from death receptors such as Fas and TNF-a(TNF-R).while the down regulation we observed in TRAF6and TANK gene expression may lead to neutrophil apoptosis in some circumstances,it is possible that parturient physiology overrides such effects by simultaneously down regulating gene expression for pro-apoptotic Fas,FasL,DAP5,FADD,Daxx,FLASH,RIP,and Bak and up regulating gene expression for anti-apoptotic A1,BAFF,and IL-8.2.2.Apoptosis gene expression pro files correlate with blood cortisol pro files during parturition Because blood neutrophils express abundant GR a mRNA (Fig.1)and protein (Chang et al.,2004),we postulated that cortisol may have been one blood factor responsible for inducing apoptosis gene expression changes in circulating neutrophils of the parturient cows that,by in large,appeared to favor cell survival.To test this possibility,we performed correlation analyses on these data sets using the PROC CORR procedure of SAS.Results in Table 1show that blood cortisol pro files were signi ficantly (P 0.05)associated with gene expression pro files for A1,BAFF,Bak,DAP5,Fas,FLASH,IL-8,and TRAF6,and tended (P =0.06)to be associated with expression pro files for FasL and Daxx.However,other unidenti fied factors also must have participated in the regulationJ.L.Burton et al./Veterinary Immunology and Immunopathology 105(2005)197–219202Fig.4.Expression changes in six neutrophil genes (Fas,FasL,TRAF6,TANK,DAP5,and BAFF)whose protein products regulate apoptosis.Data were generated using quantitative real time RT-PCR (Madsen et al.,2004),with all samples run in duplicate and b -actin used as the control gene (Weber et al.,2001;Madsen et al.,2002).Test RNA for these assays was obtained from Percoll-isolated blood neutrophils of three primiparous Holstein cows on days À7,0,0.25,and 1relative to parturition (on day 0).Gene expression changes for days 0,0.25,and 1were relative to expression on day À7and calculated using the 2ÀDD Ct method (Livak and Schmittgen,2001).P -values above each graph are the level of signi ficance for the main effect of day relative to parturition obtained through repeated measures analysis of the data,and a –c above individual bars indicate signi ficant (P 0.05)differences in mean (ÆS.E.M.)gene expression by day relative to parturition.The PCR primers and conditions used to generate these data are listed under the Links icon on our Center for Animal Functional Genomics web site (/).of specific components of the apoptosis program in bovine neutrophils at parturition because correla-tions between cortisol and gene expression profiles for FADD,RIP,and TANK were not detected (Table1).It is unlikely that estradiol was one of these factors because we(unpublished data)and others(Winters et al.,2003)could not detect estrogen receptor proteins in bovine blood neutro-phils.Also,correlations between the cows’serum estradiol profiles and neutrophil apoptosis gene expression profiles were not significant(P>0.10; not shown).While bovine neutrophils also do not express progesterone receptor mRNA or protein(our unpublished data;Winters et al.,2003),it is possible thatfluctuations in serum progesterone around parturition contributed to the apoptosis gene expression profiles we observed because progester-one can act as a GR a antagonist(Preisler et al., 2000).Thus,it is possible that the parturient drop in blood progesterone as cortisol levels soar may have facilitated glucocorticoid activity on the expression of some apoptosis genes.In support of this possibility,we observed significant(P<0.05) correlations between serum progesterone profiles and neutrophil gene expression profiles for Fas (r=0.703),RIP(r=0.796),BAFF(r=À0.793),IL-8(r=0.724),and TANK(r=0.785).2.3.Cortisol in parturient serum is partly responsible for inducing survival in blood neutrophils To substantiate that the relationships between serum cortisol and apoptosis gene expression profiles we observed translate into changed apoptosis status of the cells,we attempted to phenotype apoptosis of neutrophils in fresh whole blood samples collected from a group of primiparous cows prepartum and at parturition.However,effects of parturition on apop-tosis status were not clear because extremely high animal variation existed in the staining of neutrophils with Annexin-V-FITC,a reagent that binds with phosphatidylserine residues that haveflipped from the inner to the outer leaflet of the plasma membrane during early stages of apoptosis(Fig.3;Vermes et al., 1995).For example,the mean percentage of Annexin-V-FITC+neutrophils in blood from16cows collected $10days prepartum was48.9%(Æ16.20;S.E.M.), with a range of19.1–83.2%.This wide animal variation in Annexin-V-FITC staining in fresh cells is likely related to normal variation in proportions of variously aged neutrophil populations in whole blood (Shidham and Swami,2000).In turn,this is a function of variation in the rates of bone marrow release,cell exit from blood into tissues,and clearance of circulating apoptotic neutrophils by the body’s phagocytic network(Homburg and Roos,1996;Savill, 1997).Thus,it was difficult to conclude whether or not neutrophils in fresh blood samples were less apoptotic overall at parturition versus prepartum.When we instead enriched neutrophils from prepartum blood samples on Percoll density gradients, 4%of the freshly isolated cells stained with Annexin-V-FITC.It thus appears that our neutrophil isolation protocol is relatively selective in its enrichment of blood neutrophils that have no overt signs of this early stage of apoptosis.In fact,the recovery of neutrophils in this procedure averages$75%when neutrophilia is not present(and higher when it is).The majority of neutrophil loss(76%)occurs during removal of the buffy coat and top one-third of the red cell pack prior to addition of the remaining red cell pack to the Percoll gradient for neutrophil isolation.A more minor loss (24%)results from neutrophils that remain on or in the Percoll layer because the cells are not dense enough to penetrate through it.The dense neutrophils that do penetrate the Percoll gradient to form the cell pellet atJ.L.Burton et al./Veterinary Immunology and Immunopathology105(2005)197–219203 Table1Pearson product moment correlations(r-values)between serumcortisol profiles and expression profiles for thirteen apoptosis reg-ulatory genes in Percoll-isolated blood neutrophils from parturientprimiparous Holstein cows(n=3)Gene name Effect on apoptosis r-value P-valueA1Anti-apoptotic0.900.002BAFF Anti-apoptotic0.750.04Bak Pro-apoptoticÀ0.820.01Daxx Pro-apoptoticÀ0.720.06DAP5Pro-apoptoticÀ0.730.05FADD Pro-apoptoticÀ0.330.32Fas Pro-apoptoticÀ0.750.04FasL Pro-apoptoticÀ0.710.06FLASH Pro-apoptoticÀ0.800.02IL-8Anti-apoptotic0.730.01RIP Pro-apoptoticÀ0.550.24TRAF-6Anti-apoptoticÀ0.750.04TANK Anti-apoptoticÀ0.650.11Gene expression changes werefirst detected by cDNA microarrayanalysis(Madsen et al.,2004)and further characterized usingquantitative real time RT-PCR(Fig.4).the bottom of the tube may thus represent the youngest population of neutrophils in blood,presumably those that were recently released from the maturation pool in bone marrow.We suspect that use of Percoll isolated cells standardized the starting population of neutrophils in our apoptosis phenotyping assay because,when allowed to age in culture over48h,these cells had significantly extended viability when collected from cows at parturition versus prepartum(Madsen et al., 2003a).This observation did support those from our microarray and Q-RT-PCR experiments,which sug-gested that the cells gain a predominantly pro-survivalgene expression signature around parturition.Addi-tionally,we have shown that sera collected from the cows at parturition(day0)supported viability in significantly more Percoll-isolated steer neutrophils over48h in culture than sera collected prepartum(day À7)or postpartum(days0.25and1;Madsen et al., 2004).This suggested,as our correlation analysis did, that parturient blood does indeed contain factors that promote extended neutrophil life span.However,given the differences in Annexin-V-FITC staining character-istics between neutrophils in fresh whole blood samples versus Percoll-isolated cells,it would seem important for investigators to carefully consider which neutrophil isolation method to use for such experiments and to characterize the apoptosis status of neutrophils employed in various assays.We selected the Percoll density gradient method to isolate neutrophils because it was the quickest way to obtain high numbers of very pure neutrophils with enough quantity of high quality RNA needed for our for our microarray and Q-RT-PCR work.We felt that this was critical to our ability to generate gene expression data from which we could draw conclusions about effects of parturition on gene expression changes in neutrophils.However,we acknowledge that our conclusions about the apoptosis gene expression signatures and phenotypes observed around parturition may apply only to younger popula-tions of the cells and not to all circulating neutrophils. With this caveat in mind,we continued with several additional experiments using Percoll-isolated neutro-phils to study potential relationships between gluco-corticoids in serum and neutrophil apoptosis phenotypes.Given our in vitro apoptosis results and the correlations we detected between blood cortisol profiles and neutrophil apoptosis gene expression around parturition(Table1),we sought to determine if the cortisol component of parturient blood is one factor capable of inducing survival in cultured bovine neutrophils.We pooled the parturient(day0)serum samples,split the pool into two aliquots,and used activated charcoal to remove cortisol(Szafarczyk et al.,1995;McCarty and Schwartz,1999)from one aliquot(Table2).Charcoal treatment also removed progesterone and estradiol from this aliquot(Table2) and,perhaps,other unidentified factors.We added these sera at20%of the volume of culture medium to Percoll-isolated steer neutrophils as the cells aged in vitro for12h or24h prior to apoptosis phenotyping. Representative data from one steer in Fig.5show that compared to the steroid extracted serum(panel b), intact parturient serum(panel a)significantly increased the proportion of viable neutrophils in culture at12h(top panels of Fig.5)and reduced DNA fragmentation in the cells at24h(bottom panels of Fig.5).To clarify which extracted steroid may have been responsible for this effect,neutrophils from additional steers were pretreated for10min with steroid receptor antagonists prior to addition of intact parturient serum for12or24h,followed by apoptosis phenotyping.Results in Fig.6a show that RU486(a GR a/progesterone receptor antagonist),but not tamoxifen(an estrogen receptor antagonist),inhibited the ability of the parturient serum to support neutrophil survival,and did so to the same extent as the steroid extracted serum.Thus,cortisol and(or) progesterone were likely factors responsible for neutrophil survival induction by parturient serum.In afinal experiment,we showed that cortisol was the predominant steroid responsible for neutrophil survi-val-induction by parturient serum because only cortisol(not estradiol or progesterone)added backJ.L.Burton et al./Veterinary Immunology and Immunopathology105(2005)197–219204Table2Concentrations(pg/ml)of cortisol,estradiol,and progesterone inpooled parturient serum and charcoal-treated parturient serum withsteroids extractedHormone Parturientserum Steroid extractedparturient serumFetal bovineserumCortisol29,000a150c985b Estradiol1,500a75c869b Progesterone900a110c370b Concentrations in commercial fetal bovine serum are included for comparison.P<0.0001for within hormone differences(a–c)in serum sources.。