冠心病全基因组关联研究进展

近年来全基因组关联研究在世界范围内发展迅猛,研究者应用全基因组关联研究策略发现了一系列疾病的相关基因或变异,将疾病的基因组研究推向一个新的阶段。冠心病是一种由环境因素和遗传因素共同作用导致的复杂疾病,且是世界范围内死亡和致残的首要原因之一,世界各地的研究者应用此策略发现了候选基因关联研究未曾发现的多个冠心病相关易感区域。文章对近年来世界范围内针对冠心病的全基因组关联研究取得的重要进展进行简要总结,然后就现阶段全基因组关联研究所面临的挑战以及对未来研究的发展趋势进行分析阐述,为进一步探究冠心病的遗传机制提供指导。     

复杂疾病全基因组关联研究进展——遗传统计分析

2005年, Science杂志首次报道了有关人类年龄相关性黄斑变性的全基因组关联研究, 此后有关肥胖、2型糖尿病、冠心病、阿尔茨海默病等一系列复杂疾病的全基因组关联研究被陆续报道, 这一阶段被称为人类全基因组关联研究的第一次浪潮。文章分别介绍了全基因组关联研究统计分析的方法、软件和应用实例; 比较了关联分析中多重检验的P值调整方法, 包括Bonferroni、递减的Bonferroni校正法、模拟运算法和控制错误发现率的方法; 还讨论了人群混杂对关联分析结果可能产生的影响及原理, 以及全基因组关联研究中控制人群混杂的方法的研究进展和应用实例。在全基因组关联研究的第一次浪潮中, 应用经典的遗传统计方法发现了许多基因-表型之间的关联并且能够对这些关联做出解释, 其中包括许多基因组中的未知基因和染色体区域。然而, 全基因组关联研究的继续发展需要进一步阐述基因组内基因之间相互作用、基因-基因之间的复杂作用网络与环境因素的相互作用在复杂疾病发生中的作用, 现有的统计分析方法肯定不能满足需要, 开发更为高级的统计分析方法势在必行。最后, 文章还给出了全基因组关联研究统计分析软件的相关网站信息。     

随机SNP在全基因组关联研究人群分层分析中的应用

在复杂疾病的全基因组关联研究中,人群分层现象会增加结果的假阳性率,因此考虑人群遗传结构、控制人群分层是很有必要的。而在人群分层研究中,使用随机选择的SNP的效果还有待进一步探讨。文章利用HapMap Phase2人群中无关个体的Affymetrix SNP 6.0芯片分型数据,在全基因组上随机均匀选择不同数量的SNP,同时利用f值和Fisher精确检验方法筛选祖先信息标记（Ancestry Informative Markers,AIMs）。然后利用HapMap Phase3中的无关个体的数据,以F-statistics和STRUCTURE分析两种方法评估所选出的不同SNP组合对人群的区分效果。研究发现,随机均匀分布于全基因组的SNP可用于识别人群内部存在的遗传结构。文章进一步提示,在全基因组关联研究中,当没有针对特定人群的AIMs时,可在全基因组上随机选择3000以上均匀分布的SNP来控制人群分层。     

复杂疾病全基因组关联研究进展—— 研究设计和遗传标记

实现全基因组关联研究(Genome-wide association study, GWA)在数年前还是遗传学家们的梦想, 如今它已经变成了现实。自2005年Science杂志报道了第一项有关年龄相关性(视网膜)黄斑变性全基因组关联研究研究以来, 有关与复杂疾病的全基因组关联研究如雨后春笋般层出不穷。文中介绍了近两年来全基因组关联研究在复杂疾病研究领域内的主要发现、全基因组关联研究设计原理、遗传标记的选择、比较及相关商品信息。最后介绍了人类基因组拷贝数变异的研究进展, 总结了人类全基因组关联研究所取得成就和存在的问题, 并对全基因组关联研究未来的研究重点和要解决的问题进行了展望。     

基于全基因组关联的中国常见肿瘤遗传病因学研究

肿瘤是基因-环境交互作用引起的复杂性疾病.在同样的环境暴露下,不同遗传背景的个体发生肿瘤的风险有很大差异.研究肿瘤相关遗传因素对理解肿瘤发生发展乃至诊断治疗都有重要意义.近年来发展的全基因组关联研究(genome-wide association study,GWAS)可在全基因组范围内发现与复杂疾病或表型关联的遗传因素,为复杂疾病遗传学研究提供了强有力的手段.欧美研究者运用全基因组关联研究的方法,对各种常见肿瘤进行了研究,获得了重要成果.2010年以来,中国科学家在国际核心期刊发表了一系列高水平的肿瘤全基因组关联研究成果,在中国常见肿瘤的遗传病因学研究方面取得了重要进展.     

人类复杂疾病关联研究中群体分层的检出和校正

病例对照研究是鉴定多基因疾病易感位点重要的遗传流行病学方法, 而群体分层是导致病例对照研究关联研究结果出现偏倚甚至是假关联的重要原因之一。文章对人群分层的检出及校正的方法和原理进行了阐述, 包括基于核心家系的传递/不平衡检验(TDT)以及基于不相关基因组遗传标记的基因组对照(GC)和结构化关联(SA)等, 并且对这几种方法进行了比较。     

重大生殖疾病的分子机制研究

重大生殖疾病是一组严重影响生殖健康,病因和临床表现高度异质的疾病群,其中女性常见的有多囊卵巢综合征(PCOS)、卵巢早衰(POF)等,遗传因素在疾病的发生发展中起到重要作用。近年来,依靠高通量技术,如全基因组关联分析、全外显子组测序等,我国在重大生殖疾病的遗传学研究中取得了重要进展,主要包括对PCOS和POF大样本散发病例及其对照进行全基因组关联研究、家系患者的全外显子组或全基因组测序研究等,鉴定出多个遗传易感位点,获得大量候选基因的信息。虽然这些研究结果为解析疾病提供了大量线索,但是也提出了更多挑战。如何深入研究这些易感位点在疾病中的致病机制,及其在复杂疾病诊治中的转化应用成为日后的工作重点,现就相关分子机制研究进展做一简要论述。     

原发性高血压全基因组关联研究进展

原发性高血压是一种由遗传与环境因素共同导致的复杂疾病,具有高度的遗传异质性。自2007年首个高血压全基因组关联研究(Genome-wide association studies,GWAS)报道以来,许多GWAS相继开展。文章首先对2007年1月至2011年9月期间报道的24篇血压/高血压易感基因的GWAS按人种与染色体位置对其结果进行汇总,经统计位点rs17249754、rs1378942和rs11191548报道频数最多。其次介绍了GWAS方法学的研究进展,包括选择高质量的数量表型和选择多阶段研究设计来增加研究发现阳性关联的机会。统计分析方面,除强调了已经报道过的多重比较和重复(验证)研究等问题外,文章还介绍了通过Meta分析对GWAS数据进行深度发掘,并应用基因型填补法对缺失数据进行填补可以提高全基因组遗传标记的覆盖率的方法。尽管GWAS发现了许多我们未知的基因与疾病表型的关联,为了解高血压的发病机制提供了更多线索,但是目前GWAS发现的血压/高血压相关变异多为对人群血压的影响极其微弱的常见变异。因此今后的研究中可加强深度功能学研究对易感基因精细定位和外显子组测序技术的应用,结合GWAS的成果进行生物信息学通路分析和表观遗传学机制研究等,逐步揭示高血压的遗传机制。     

全基因组关联分析的进展与反思

全基因组关联分析(genomewide association study,GWAS)是应用人类基因组中数以百万计的单核苷酸多态性(single nucleotide polymorphism,SNP)为标记进行病例-对照关联分析,以期发现影响复杂性疾病发生的遗传特征的一种新策略。近年来,随着人类基因组计划和基因组单倍体图谱计划的实施,人们已通过GWAS方法发现并鉴定了大量与人类性状或复杂性疾病关联的遗传变异,为进一步了解控制人类复杂性疾病发生的遗传特征提供了重要的线索。然而,由于造成复杂性疾病/性状的因素较多,而且GWAS研究系统较为复杂,因此目前GWAS本身亦存在诸多的问题。本文将从研究方式、研究对象、遗传标记,以及统计分析等方面,探讨GWAS的研究现状以及存在的潜在问题,并展望GWAS今后的发展方向。     

慢性阻塞性肺疾病全基因组关联研究进展

慢性阻塞性肺疾病(chronic obstructive pulmonary disease, COPD)是一种以不完全可逆的气流受限为主要特征的慢性气道炎症,是一种由遗传因素和环境因素共同作用的复杂疾病,也是世界主要致死疾病之一。近年来,随着全基因组关联研究(genome-wide association study, GWAS)的不断深入,研究者们发现了大量与肺功能或COPD相关的遗传变异或基因位点、药物靶点等。本文综述了2007年以来世界范围内针对肺功能或COPD的GWAS方面的研究工作及其进展综述,分析了可能存在的药物靶点,并探讨了COPD在全基因组关联研究中面临的挑战和困难,为深入研究COPD发病机制提供新思路。     

Prediction of drug resistance in M. tuberculosis: molecular mechanisms,tools, and applications

Management of Tuberculosis is complicated by the emergence of drug resistant strains of Mycobacterium tuberculosis and this poses a threat to the success of Tuberculosis control programmes. Drug susceptibility testing by culture is time-consuming and technically difficult. It is known that resistance to drugs is due to a number of genomic mutations in specific genes of M. tuberculosis. These mutations in combination with molecular techniques can be used as markers for drug resistance, since drug susceptible isolates lack the corresponding gene mutations. This review focuses on molecular mechanisms, methods and applications as a possible new diagnostic tool for the early molecular detection of drug resistance in M. tuberculosis.     

Congenital tuberculosis associated with maternal disseminated miliary tuberculosis

Untreated tuberculosis during pregnancy presents a serious risk for transmission of disease to the newborn and can result in adverse perinatal and obstetrical outcomes. Tuberculosis during pregnancy and congenital tuberculosis are infrequent conditions and are difficult to diagnose due the non-specificity of the symptoms. A case report is presented of a woman who had no children previously with disseminated miliary tuberculosis. Tuberculosis symptoms appeared immediately after birth of the first child, with a clinical diagnosis on the second month after childbirth, whereupon the patient died. The son, a premature infant, showed disease symptoms from the first day, with primary pulmonary complex and persistent atelectasis due to bronchial obstruction. The obstruction was due to thoracic lymphadenitis and coinfection with cytomegalovirus. The infant received standard treatment and his condition improved.     

Genome-wide association studies and susceptibility to infectious diseases

Progress in genomics and the associated technological, statistical and bioinformatics advances have facilitated the successful implementation of genome-wide association studies (GWAS) towards understanding the genetic basis of common diseases. Infectious diseases contribute significantly to the global burden of disease and there is robust epidemiological evidence that host genetic factors are important determinants of the outcome of interactions between host and pathogen. Indeed, infectious diseases have exerted profound selective pressure on human evolution. However, the application of GWAS to infectious diseases has been relatively limited compared with non-communicable diseases. Here we review GWAS findings for important infectious diseases, including malaria, tuberculosis and HIV. We highlight some of the pitfalls recognized more generally for GWAS, as well as issues specific to infection, including the role of the pathogen which also has a genome. We also discuss the challenges encountered when studying African populations which are genetically more ancient and more diverse that other populations and disproportionately bear the main global burden of serious infectious diseases.     

Epidemiological patterns of tuberculosis in Croatia in the period 1996-2005

The last comprehensive publication on tuberculosis in Croatia and the earliest impact of war, besides the yearly routine reports, was done in 1996 in Croatian. We were, therefore, interested to explore incidence trends and to highlight the early post-war tuberculosis epidemiological patterns in the next ten years period (1996-2005). A retrospective analysis of epidemiological data on all registered tuberculosis cases in Croatia searching the databases of 21 Croatian Public Health Institutes and the National Tuberculosis Registry was made. During the study period, the total tuberculosis incidence rates in Croatia dropped from 45 to 25.8/100 000 inhabitants. The average highest age-specific rates were recorded in the age group > or = 65 years being in decrease in all age groups. Paediatric cases (0-14 years) represented 4.5% of all cases. Tuberculosis cases among males were recorded in 64% cases, and 83.6% were indigenous population. Tuberculosis was bacteriologically confirmed in 67.7% cases. A low proportion of drug resistance (3.3%) was recorded. During 1985-2005, 56 tuberculosis cases among 242 AIDS cases were reported. Tuberculosis mortality showed a decreasing trend (p < 0.001). However, tuberculosis has still had the highest mortality rates among infectious diseases in Croatia. Despite the War chain of events and tuberculosis programmatic changes, tuberculosis incidence rates in Croatia have been decreasing but they are still far away from national target, incidence rate of 10/100 000 declared in 1998 and much higher than in European Union and Western Europe. Tuberculosis among children, resistance to tuberculosis drugs and HIV prevalence, significant problems in many European countries, have not caused problems in tuberculosis control in Croatia. This favourable epidemiological situation must be kept and improved through strengthened tuberculosis control measures.     

Recent advances in our understanding of human host responses to tuberculosis

Tuberculosis remains one of the world's greatest public health challenges: 2 billion persons have latent infection, 8 million people develop active tuberculosis annually, and 2–3 million die. Recently, significant advances in our understanding of the human immune response against tuberculosis have occurred. The present review focuses on recent work in macrophage and T-cell biology that sheds light on the human immune response to tuberculosis. The role of key cytokines such as interferon-γ is discussed, as is the role of CD4⁺ and CD8⁺ T cells in immune regulation in tuberculosis, particularly with regard to implications for vaccine development and evaluation.     

A proteomic view of mycobacteria

Tuberculosis, the disease caused by Mycobacterium tuberculosis, remains a relevant public health issue. This is due mostly to the coepidemiology with HIV/AIDS, the appearance of multidrug-resistant strains globally, and failure of BCG (bacillus Calmette-Guerin) vaccination to confer complete protection. This bacterium was one of the first to have its genome sequenced, yet over a decade after the release of the genomic information, the characterization of its phylogenetic tree and of different strain variants inside this species revealed that much is still needed to be done for a full understanding of the M. tuberculosis genome and proteome. Current methods using LC-MS/MS and hybrid high-resolution mass spectrometers can identify 2400-2800 proteins of the 4000 predicted genes in M. tuberculosis. In this article, we review relevant details of this bacterium's pathology and immunology, describing articles where proteomics helped the community to tackle some of the organism biology, from understanding strain diversity, cellular structure composition, immunogenicity, and host-pathogen interactions. Finally, we will discuss the challenges yet to be fulfilled in order to better characterize M. tuberculosis by proteomics.     

抗结核药物及其耐药相关突变位点的研究进展

结核病是结核分枝杆菌复合物引起的传染性疾病,致死率、致残率高,在全球传染病中居第2位。近年来耐药结核病所占比例逐年升高,成为消灭结核病面临的巨大挑战之一。传统的耐药诊断方法基于培养,费时费力,所需技术要求高;而现有分子检测方法仅能检测少量抗结核药物的少数耐药基因。因此,更好地理解抗结核药物的耐药机制有助于全面耐药诊断。本文对临床中使用频率较高的11类一线和二线抗结核药物及其相应耐药相关基因、突变位点的研究进展进行总结,尤其是对环丝氨酸、利奈唑胺、氯法齐明等二线药物的近期研究做了系统描述,为全面耐药诊断、精准治疗指导、新药研发及耐药机制深入研究提供了前期工作基础。     

Incidence of HIV-Associated Tuberculosis among Individuals Taking Combination Antiretroviral Therapy: A Systematic Review and Meta-Analysis

Background

Knowledge of tuberculosis incidence and associated factors is required for the development and evaluation of strategies to reduce the burden of HIV-associated tuberculosis.

Methods

Systematic literature review and meta-analysis of tuberculosis incidence rates among HIV-infected individuals taking combination antiretroviral therapy.

Results

From PubMed, EMBASE and Global Index Medicus databases, 42 papers describing 43 cohorts (32 from high/intermediate and 11 from low tuberculosis burden settings) were included in the qualitative review and 33 in the quantitative review. Cohorts from high/intermediate burden settings were smaller in size, had lower median CD4 cell counts at study entry and fewer person-years of follow up. Tuberculosis incidence rates were higher in studies from Sub-Saharan Africa and from World Bank low/middle income countries. Tuberculosis incidence rates decreased with increasing CD4 count at study entry and duration on combination antiretroviral therapy. Summary estimates of tuberculosis incidence among individuals on combination antiretroviral therapy were higher for cohorts from high/intermediate burden settings compared to those from the low tuberculosis burden settings (4.17 per 100 person-years [95% Confidence Interval (CI) 3.39–5.14 per 100 person-years] vs. 0.4 per 100 person-years [95% CI 0.23–0.69 per 100 person-years]) with significant heterogeneity observed between the studies.

Conclusions

Tuberculosis incidence rates were high among individuals on combination antiretroviral therapy in high/intermediate burden settings. Interventions to prevent tuberculosis in this population should address geographical, socioeconomic and individual factors such as low CD4 counts and prior history of tuberculosis.     

Effect of repeat dose of BCG vaccination on humoral response in mice model

BCG is the only vaccine presently available against tuberculosis but it is estimated to prevent only 5% of the all potentially vaccine-preventable deaths due to Tuberculosis. Keeping these in view the present study has been undertaken to evaluate the efficacy of BCG and the effect of repeat dose of BCG on antimycobacterial humoral response in mouse model. To improve BCG immunogenicity, specific anti-mycobacterial immune responses (anti-BCG titre and total IgG level) were evaluated in mouse model using boost immunization protocols with the BCG vaccine. Mice induced with a repeat dose of BCG showed an increased anti mycobacterial humoral response, which gradually declined few weeks after single dose of BCG administration. The results suggest improved efficacy of BCG vaccine by giving repeat dose of BCG that can enhance the level of immunoprotection against tuberculosis as opposed to a single BCG dose.     

Purification and characterization of a functionally active Mycobacterium tuberculosis prephenate dehydrogenase

Tuberculosis (TB) remains to be a global health problem. New drugs are badly needed to drastically reduce treatment time and overcome some of the challenges with tuberculosis treatment, such as multi-drug resistant (MDR) strain infected patients or tuberculosis/HIV co-infected patients. The essentiality of mycobacterial aromatic amino acid biosynthesis pathways and their absence from human host indicate that the member enzymes of these pathways promising drug targets for therapeutic agents against pathogen mycobacteria. Prephenate dehydrogenase (PDH) is a key regulatory enzyme in tyrosine biosynthesis, catalyzing the NAD(+)-dependent conversion of prephenate to p-hydroxyphenylpyruvate, making it a potential drug target for antibiotics discovery. The recombinant PDH with an N-terminal His-tag (His-rMtPDH) was first purified in Escherichia coli, and using enterokinase rMtPDH was obtained by cleaving the N-terminal fusion partner. The effect of pH, temperature and the cation-Na(+) on purified enzyme activity was characterized. The N-terminal fusion partner was found to have little effect on the biochemical properties of PDH. We also provide in vitro evidence that Mycobacterium tuberculosis PDH does not possess any chorismate mutase (CM) activity, which suggests that, unlike many other enteric bacteria (where PDH exists as a fusion protein with CM), M. tuberculosis PDH is a monofunctional protein.