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Prioritization of therapeutic targets for cancers using integrative multi-omics analysis 利用多组学综合分析确定癌症治疗目标的优先次序
IF 4.5 3区 医学 Q1 Pharmacology, Toxicology and Pharmaceutics Pub Date : 2024-04-24 DOI: 10.1186/s40246-024-00571-2
Xin Jin, Yunyun Mei, Puyu Yang, Runze Huang, Haifeng Zhang, Yibin Wu, Miao Wang, Xigan He, Ziting Jiang, Weiping Zhu, Lu Wang
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引用次数: 0
Meta-analysis of the global distribution of clinically relevant CYP2C8 alleles and their inferred functional consequences 临床相关 CYP2C8 等位基因全球分布及其推断功能后果的元分析
IF 4.5 3区 医学 Q1 Pharmacology, Toxicology and Pharmaceutics Pub Date : 2024-04-22 DOI: 10.1186/s40246-024-00610-y
Mahamadou D. Camara, Yitian Zhou, Taís Nóbrega De Sousa, José P. Gil, Abdoulaye A. Djimde, Volker M. Lauschke
CYP2C8 is responsible for the metabolism of 5% of clinically prescribed drugs, including antimalarials, anti-cancer and anti-inflammatory drugs. Genetic variability is an important factor that influences CYP2C8 activity and modulates the pharmacokinetics, efficacy and safety of its substrates. We profiled the genetic landscape of CYP2C8 variability using data from 96 original studies and data repositories that included a total of 33,185 unrelated participants across 44 countries and 43 ethnic groups. The reduced function allele CYP2C8*2 was most common in West and Central Africa with frequencies of 16–36.9%, whereas it was rare in Europe and Asia (< 2%). In contrast, CYP2C8*3 and CYP2C8*4 were common throughout Europe and the Americas (6.9–19.8% for *3 and 2.3–7.5% for *4), but rare in African and East Asian populations. Importantly, we observe pronounced differences (> 2.3-fold) between neighboring countries and even between geographically overlapping populations. Overall, we found that 20–60% of individuals in Africa and Europe carry at least one CYP2C8 allele associated with reduced metabolism and increased adverse event risk of the anti-malarial amodiaquine. Furthermore, up to 60% of individuals of West African ancestry harbored variants that reduced the clearance of pioglitazone, repaglinide, paclitaxel and ibuprofen. In contrast, reduced function alleles are only found in < 2% of East Asian and 8.3–12.8% of South and West Asian individuals. Combined, the presented analyses mapped the genetic and inferred functional variability of CYP2C8 with high ethnogeographic resolution. These results can serve as a valuable resource for CYP2C8 allele frequencies and distribution estimates of CYP2C8 phenotypes that could help identify populations at risk upon treatment with CYP2C8 substrates. The high variability between ethnic groups incentivizes high-resolution pharmacogenetic profiling to guide precision medicine and maximize its socioeconomic benefits, particularly for understudied populations with distinct genetic profiles.
CYP2C8 负责 5%的临床处方药的代谢,包括抗疟药、抗癌药和抗炎药。遗传变异是影响 CYP2C8 活性的一个重要因素,并可调节其底物的药代动力学、疗效和安全性。我们利用来自 96 项原始研究和数据储存库的数据分析了 CYP2C8 变异的遗传情况,这些数据包括 44 个国家和 43 个民族的 33,185 名无亲属关系的参与者。功能降低的等位基因 CYP2C8*2 在西非和中非最为常见,频率为 16-36.9%,而在欧洲和亚洲,相邻国家之间,甚至地理重叠人群之间都很少见(2.3 倍)。总体而言,我们发现非洲和欧洲至少有 20-60% 的人携带一个与抗疟药物阿莫地喹代谢降低和不良事件风险增加有关的 CYP2C8 等位基因。此外,多达 60% 的西非血统个体携带的变体会降低匹格列酮、瑞格列奈、紫杉醇和布洛芬的清除率。相比之下,功能降低的等位基因只出现在< 2%的东亚人和8.3-12.8%的南亚和西亚人身上。综合上述分析,我们绘制了CYP2C8的遗传和推断功能变异图,具有很高的人种地理分辨率。这些结果可作为 CYP2C8 等位基因频率和 CYP2C8 表型分布估计的宝贵资源,有助于确定使用 CYP2C8 底物治疗时的高危人群。种族群体之间的高变异性促使人们进行高分辨率的药物基因分析,以指导精准医疗并最大限度地提高其社会经济效益,尤其是对那些未被充分研究的、具有独特遗传特征的人群。
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引用次数: 0
Epidemiologic association and shared genetic architecture between cataract and hearing difficulties among middle-aged and older adults 中老年人白内障与听力障碍之间的流行病学关联和共同遗传结构
IF 4.5 3区 医学 Q1 Pharmacology, Toxicology and Pharmaceutics Pub Date : 2024-04-17 DOI: 10.1186/s40246-024-00601-z
Xiayin Zhang, Shan Wang, Shunming Liu, Zijing Du, Guanrong Wu, Yingying Liang, Yu Huang, Xianwen Shang, Yijun Hu, Zhuoting Zhu, Wei Sun, Xueli Zhang, Honghua Yu
Age-related cataract and hearing difficulties are major sensory disorders that often co-exist in the global-wide elderly and have a tangible influence on the quality of life. However, the epidemiologic association between cataract and hearing difficulties remains unexplored, while little is known about whether the two share their genetic etiology. We first investigated the clinical association between cataract and hearing difficulties using the UK Biobank covering 502,543 individuals. Both unmatched analysis (adjusted for confounders) and a matched analysis (one control matched for each patient with cataract according to confounding factors) were undertaken and confirmed that cataract was associated with hearing difficulties (OR, 2.12; 95% CI, 1.98–2.27; OR, 2.03; 95% CI, 1.86–2.23, respectively). Furthermore, we explored and quantified the shared genetic architecture of these two complex sensory disorders at the common variant level using the bivariate causal mixture model (MiXeR) and conditional/conjunctional false discovery rate method based on the largest available genome-wide association studies of cataract (N = 585,243) and hearing difficulties (N = 323,978). Despite detecting only a negligible genetic correlation, we observe polygenic overlap between cataract and hearing difficulties and identify 6 shared loci with mixed directions of effects. Follow-up analysis of the shared loci implicates candidate genes QKI, STK17A, TYR, NSF, and TCF4 likely contribute to the pathophysiology of cataracts and hearing difficulties. In conclusion, this study demonstrates the presence of epidemiologic association between cataract and hearing difficulties and provides new insights into the shared genetic architecture of these two disorders at the common variant level.
老年性白内障和听力障碍是全球老年人经常并存的主要感官障碍,对生活质量有着切实的影响。然而,白内障和听力障碍之间的流行病学关联仍未得到探讨,而两者是否具有共同的遗传病因也鲜为人知。我们首先利用英国生物数据库(UK Biobank)对白内障和听力障碍之间的临床联系进行了调查,该数据库涵盖 502543 人。我们进行了非匹配分析(根据混杂因素进行调整)和匹配分析(根据混杂因素为每名白内障患者匹配一名对照),结果证实白内障与听力障碍有关(OR,2.12;95% CI,1.98-2.27;OR,2.03;95% CI,1.86-2.23)。此外,我们基于现有最大的白内障(N = 585,243 例)和听力障碍(N = 323,978 例)全基因组关联研究,使用双变量因果混合模型(MiXeR)和条件/联合错误发现率方法,在共同变异水平上探索和量化了这两种复杂感官疾病的共同遗传结构。尽管检测到的遗传相关性微乎其微,但我们观察到白内障和听力障碍之间存在多基因重叠,并确定了 6 个具有混合效应方向的共享基因位点。对共享基因位点的后续分析表明,候选基因 QKI、STK17A、TYR、NSF 和 TCF4 有可能对白内障和听力障碍的病理生理学起作用。总之,这项研究证明了白内障和听力障碍之间存在流行病学关联,并在共同变异水平上为这两种疾病的共同遗传结构提供了新的见解。
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引用次数: 0
The causal associations of circulating lipids with Barrett’s Esophagus and Esophageal Cancer: a bi-directional, two sample mendelian randomization analysis 循环血脂与巴雷特食管和食管癌的因果关系:双向、双样本泯灭随机分析
IF 4.5 3区 医学 Q1 Pharmacology, Toxicology and Pharmaceutics Pub Date : 2024-04-16 DOI: 10.1186/s40246-024-00608-6
Baofeng Li, Meng Li, Xiao Qi, Ti Tong, Guangxin zhang
The causal associations of circulating lipids with Barrett’s Esophagus (BE) and Esophageal Cancer (EC) has been a topic of debate. This study sought to elucidate the causality between circulating lipids and the risk of BE and EC. We conducted two-sample Mendelian randomization (MR) analyses using single nucleotide polymorphisms (SNPs) of circulating lipids (n = 94,595 − 431,167 individuals), BE (218,792 individuals), and EC (190,190 individuals) obtained from the publicly available IEU OpenGWAS database. The robustness and reliability of the results were ensured by employing inverse-variance weighted (IVW), weighted median, MR-Egger, and MR-PRESSO methods. The presence of horizontal pleiotropy, heterogeneities, and stability of instrumental variables were assessed through MR-Egger intercept test, Cochran’s Q test, and leave-one-out sensitivity analysis. Additionally, bidirectional MR and multivariable MR (MVMR) were performed to explore reverse causality and adjust for known confounders, respectively. None of the testing methods revealed statistically significant horizontal pleiotropy, directional pleiotropy, or heterogeneity. Univariate MR analyses using IVW indicated a robust causal relationship between increased triglycerides and BE (odds ratio [OR] = 1.79, p-value = 0.009), while no significant association with EC was observed. Inverse MR analysis indicated no evidence of reverse causality in the aforementioned outcomes. In MVMR analyses, elevated triglycerides (TRG) were significantly and positively associated with BE risk (OR = 1.79, p-value = 0.041). This MR study suggested that genetically increased triglycerides were closely related to an elevated risk of BE, potentially serving as a biomarker for the diagnosis of BE in the future.
循环血脂与巴雷特食管(BE)和食管癌(EC)的因果关系一直是一个争论不休的话题。本研究旨在阐明循环血脂与巴雷特食管癌和食管癌风险之间的因果关系。我们使用从公开的 IEU OpenGWAS 数据库中获得的循环血脂(n = 94,595 - 431,167 人)、BE(218,792 人)和 EC(190,190 人)的单核苷酸多态性(SNPs)进行了双样本孟德尔随机化(MR)分析。采用反方差加权法(IVW)、加权中值法、MR-Egger 法和 MR-PRESSO 法确保了结果的稳健性和可靠性。通过MR-Egger截距检验、Cochran's Q检验和leave-one-out敏感性分析,评估了工具变量的水平多向性、异质性和稳定性。此外,还进行了双向磁共振和多变量磁共振(MVMR),以分别探索反向因果关系和调整已知混杂因素。所有测试方法均未发现具有统计学意义的水平多效性、方向多效性或异质性。使用 IVW 进行的单变量 MR 分析表明,甘油三酯增加与 BE 之间存在稳健的因果关系(几率比 [OR] = 1.79,P 值 = 0.009),而与 EC 之间则无明显关联。反向 MR 分析表明,没有证据表明上述结果存在反向因果关系。在 MVMR 分析中,甘油三酯(TRG)升高与 BE 风险显著正相关(OR = 1.79,p 值 = 0.041)。这项磁共振研究表明,遗传性甘油三酯升高与 BE 风险升高密切相关,将来有可能成为诊断 BE 的生物标志物。
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引用次数: 0
Altered skin microbiome, inflammation, and JAK/STAT signaling in Southeast Asian ichthyosis patients 东南亚鱼鳞病患者皮肤微生物群、炎症和 JAK/STAT 信号转导的改变
IF 4.5 3区 医学 Q1 Pharmacology, Toxicology and Pharmaceutics Pub Date : 2024-04-16 DOI: 10.1186/s40246-024-00603-x
Minh Ho, Huynh-Nga Nguyen, Minh Van Hoang, Tien Thuy Thi Bui, Bao-Quoc Vu, Truc Huong Thi Dinh, Hoa Thi My Vo, Diana C. Blaydon, Sherif A. Eldirany, Christopher G. Bunick, Chi-Bao Bui
Congenital ichthyosis (CI) is a collective group of rare hereditary skin disorders. Patients present with epidermal scaling, fissuring, chronic inflammation, and increased susceptibility to infections. Recently, there is increased interest in the skin microbiome; therefore, we hypothesized that CI patients likely exhibit an abnormal profile of epidermal microbes because of their various underlying skin barrier defects. Among recruited individuals of Southeast Asian ethnicity, we performed skin meta-genomics (i.e., whole-exome sequencing to capture the entire multi-kingdom profile, including fungi, protists, archaea, bacteria, and viruses), comparing 36 CI patients (representing seven subtypes) with that of 15 CI age-and gender-matched controls who had no family history of CI. This case–control study revealed 20 novel and 31 recurrent pathogenic variants. Microbiome meta-analysis showed distinct microbial populations, decreases in commensal microbiota, and higher colonization by pathogenic species associated with CI; these were correlated with increased production of inflammatory cytokines and Th17- and JAK/STAT-signaling pathways in peripheral blood mononuclear cells. In the wounds of CI patients, we identified specific changes in microbiota and alterations in inflammatory pathways, which are likely responsible for impaired wound healing. Together, this research enhances our understanding of the microbiological, immunological, and molecular properties of CI and should provide critical information for improving therapeutic management of CI patients.
先天性鱼鳞病(CI)是一组罕见的遗传性皮肤病。患者表现为表皮脱屑、裂开、慢性炎症和更易感染。近来,人们对皮肤微生物组的兴趣日益浓厚;因此,我们推测,CI 患者很可能因为各种潜在的皮肤屏障缺陷而表现出表皮微生物异常。在招募的东南亚人种中,我们进行了皮肤元基因组学研究(即全外显子组测序,以捕捉包括真菌、原生生物、古生菌、细菌和病毒在内的整个多基因组图谱),将 36 名 CI 患者(代表 7 个亚型)与 15 名无 CI 家族史的年龄和性别匹配的对照者进行了比较。这项病例对照研究发现了 20 种新型致病变异和 31 种复发性致病变异。微生物组元分析表明,与 CI 相关的微生物种群不同、共生微生物群减少、病原体定植率升高;这些与外周血单核细胞中炎症细胞因子和 Th17- 及 JAK/STAT 信号通路的产生增加有关。在 CI 患者的伤口中,我们发现了微生物群的特定变化和炎症通路的改变,这可能是导致伤口愈合受损的原因。总之,这项研究加深了我们对 CI 微生物、免疫学和分子特性的了解,并为改善 CI 患者的治疗管理提供了重要信息。
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引用次数: 0
FiTMuSiC: leveraging structural and (co)evolutionary data for protein fitness prediction FiTMuSiC:利用结构和(共)进化数据进行蛋白质适宜性预测
IF 4.5 3区 医学 Q1 Pharmacology, Toxicology and Pharmaceutics Pub Date : 2024-04-16 DOI: 10.1186/s40246-024-00605-9
Matsvei Tsishyn, Gabriel Cia, Pauline Hermans, Jean Kwasigroch, Marianne Rooman, Fabrizio Pucci
Systematically predicting the effects of mutations on protein fitness is essential for the understanding of genetic diseases. Indeed, predictions complement experimental efforts in analyzing how variants lead to dysfunctional proteins that in turn can cause diseases. Here we present our new fitness predictor, FiTMuSiC, which leverages structural, evolutionary and coevolutionary information. We show that FiTMuSiC predicts fitness with high accuracy despite the simplicity of its underlying model: it was among the top predictors on the hydroxymethylbilane synthase (HMBS) target of the sixth round of the Critical Assessment of Genome Interpretation challenge (CAGI6) and performs as well as much more complex deep learning models such as AlphaMissense. To further demonstrate FiTMuSiC’s robustness, we compared its predictions with in vitro activity data on HMBS, variant fitness data on human glucokinase (GCK), and variant deleteriousness data on HMBS and GCK. These analyses further confirm FiTMuSiC’s qualities and accuracy, which compare favorably with those of other predictors. Additionally, FiTMuSiC returns two scores that separately describe the functional and structural effects of the variant, thus providing mechanistic insight into why the variant leads to fitness loss or gain. We also provide an easy-to-use webserver at https://babylone.ulb.ac.be/FiTMuSiC , which is freely available for academic use and does not require any bioinformatics expertise, which simplifies the accessibility of our tool for the entire scientific community.
系统预测变异对蛋白质适应性的影响对于了解遗传疾病至关重要。事实上,在分析变异如何导致蛋白质功能失调进而引发疾病时,预测是对实验工作的补充。在这里,我们介绍了新的适应性预测器 FiTMuSiC,它充分利用了结构、进化和协同进化信息。我们的研究表明,尽管 FiTMuSiC 的底层模型非常简单,但它却能高精度地预测适应性:在第六轮基因组解读关键评估挑战赛(CAGI6)中,它是羟甲基硅烷合成酶(HMBS)靶标的顶级预测器之一,其表现不亚于 AlphaMissense 等更复杂的深度学习模型。为了进一步证明 FiTMuSiC 的稳健性,我们将其预测结果与 HMBS 的体外活性数据、人类葡萄糖激酶(GCK)的变异适配性数据以及 HMBS 和 GCK 的变异缺失性数据进行了比较。这些分析进一步证实了 FiTMuSiC 的质量和准确性,与其他预测工具相比,FiTMuSiC 的质量和准确性更胜一筹。此外,FiTMuSiC 还能返回两个分数,分别描述变异体的功能和结构效应,从而从机理上揭示变异体导致适性损失或增益的原因。我们还提供了一个简单易用的网络服务器 https://babylone.ulb.ac.be/FiTMuSiC,供学术界免费使用,不需要任何生物信息学专业知识,从而简化了整个科学界对我们工具的使用。
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引用次数: 0
The genetic basis of early-onset hereditary ataxia in Iran: results of a national registry of a heterogeneous population 伊朗早发遗传性共济失调的遗传基础:全国异质人群登记结果
IF 4.5 3区 医学 Q1 Pharmacology, Toxicology and Pharmaceutics Pub Date : 2024-04-03 DOI: 10.1186/s40246-024-00598-5
Nejat Mahdieh, Morteza Heidari, Zahra Rezaei, Ali Reza Tavasoli, Sareh Hosseinpour, Maryam Rasulinejad, Ali Zare Dehnavi, Masoud Ghahvechi Akbari, Reza Shervin Badv, Elahe Vafaei, Ali Mohebbi, Pouria Mohammadi, Seyyed Mohammad Mahdi Hosseiny, Reza Azizimalamiri, Ali Nikkhah, Elham Pourbakhtyaran, Mohammad Rohani, Narges Khanbanha, Sedigheh Nikbakht, Mojtaba Movahedinia, Parviz Karimi, Homa Ghabeli, Seyed Ahmad Hosseini, Fatemeh Sadat Rashidi, Masoud Garshasbi, Morteza Rezvani Kashani, Noor M. Ghiasvand, Stephan Zuchner, Matthis Synofzik, Mahmoud Reza Ashrafi
To investigate the genetics of early-onset progressive cerebellar ataxia in Iran, we conducted a study at the Children’s Medical Center (CMC), the primary referral center for pediatric disorders in the country, over a three-year period from 2019 to 2022. In this report, we provide the initial findings from the national registry. We selected all early-onset patients with an autosomal recessive mode of inheritance to assess their phenotype, paraclinical tests, and genotypes. The clinical data encompassed clinical features, the Scale for the Assessment and Rating of Ataxia (SARA) scores, Magnetic Resonance Imaging (MRI) results, Electrodiagnostic exams (EDX), and biomarker features. Our genetic investigations included single-gene testing, Whole Exome Sequencing (WES), and Whole Genome Sequencing (WGS). Our study enrolled 162 patients from various geographic regions of our country. Among our subpopulations, we identified known and novel pathogenic variants in 42 genes in 97 families. The overall genetic diagnostic rate was 59.9%. Notably, we observed PLA2G6, ATM, SACS, and SCA variants in 19, 14, 12, and 10 families, respectively. Remarkably, more than 59% of the cases were attributed to pathogenic variants in these genes. Iran, being at the crossroad of the Middle East, exhibits a highly diverse genetic etiology for autosomal recessive hereditary ataxia. In light of this heterogeneity, the development of preventive strategies and targeted molecular therapeutics becomes crucial. A national guideline for the diagnosis and management of patients with these conditions could significantly aid in advancing healthcare approaches and improving patient outcomes.
为了研究伊朗早发进行性小脑共济失调症的遗传学,我们在该国儿科疾病的主要转诊中心--儿童医学中心(CMC)开展了一项研究,研究时间为 2019 年至 2022 年,为期三年。在本报告中,我们提供了国家登记处的初步调查结果。我们选择了所有具有常染色体隐性遗传模式的早发性患者,对他们的表型、辅助临床检查和基因型进行评估。临床数据包括临床特征、共济失调评估和评级量表(SARA)评分、磁共振成像(MRI)结果、电诊断检查(EDX)和生物标记特征。我们的基因检测包括单基因检测、全外显子组测序(WES)和全基因组测序(WGS)。我们的研究招募了来自我国不同地区的 162 名患者。在我们的亚群中,我们在 97 个家庭的 42 个基因中发现了已知和新的致病变体。总体基因诊断率为 59.9%。值得注意的是,我们分别在 19、14、12 和 10 个家庭中观察到了 PLA2G6、ATM、SACS 和 SCA 变异。值得注意的是,超过 59% 的病例归因于这些基因的致病变异。伊朗地处中东地区的十字路口,常染色体隐性遗传性共济失调的遗传病因极为多样。鉴于这种异质性,制定预防策略和有针对性的分子疗法变得至关重要。为这些疾病患者的诊断和管理制定国家指南,将大大有助于推进医疗保健方法和改善患者预后。
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引用次数: 0
Prioritizing susceptibility genes for the prognosis of male-pattern baldness with transcriptome-wide association study 通过全转录组关联研究确定男性型秃发预后的易感基因优先顺序
IF 4.5 3区 医学 Q1 Pharmacology, Toxicology and Pharmaceutics Pub Date : 2024-04-02 DOI: 10.1186/s40246-024-00591-y
Eunyoung Choi, Jaeseung Song, Yubin Lee, Yeonbin Jeong, Wonhee Jang
Male-pattern baldness (MPB) is the most common cause of hair loss in men. It can be categorized into three types: type 2 (T2), type 3 (T3), and type 4 (T4), with type 1 (T1) being considered normal. Although various MPB-associated genetic variants have been suggested, a comprehensive study for linking these variants to gene expression regulation has not been performed to the best of our knowledge. In this study, we prioritized MPB-related tissue panels using tissue-specific enrichment analysis and utilized single-tissue panels from genotype-tissue expression version 8, as well as cross-tissue panels from context-specific genetics. Through a transcriptome-wide association study and colocalization analysis, we identified 52, 75, and 144 MPB associations for T2, T3, and T4, respectively. To assess the causality of MPB genes, we performed a conditional and joint analysis, which revealed 10, 11, and 54 putative causality genes for T2, T3, and T4, respectively. Finally, we conducted drug repositioning and identified potential drug candidates that are connected to MPB-associated genes. Overall, through an integrative analysis of gene expression and genotype data, we have identified robust MPB susceptibility genes that may help uncover the underlying molecular mechanisms and the novel drug candidates that may alleviate MPB.
男性型脱发(MPB)是男性脱发最常见的原因。它可分为三种类型:2 型(T2)、3 型(T3)和 4 型(T4),其中 1 型(T1)被认为是正常的。虽然已经提出了各种与 MPB 相关的基因变异,但就我们所知,还没有进行过将这些变异与基因表达调控联系起来的全面研究。在本研究中,我们利用组织特异性富集分析确定了 MPB 相关组织面板的优先级,并利用了基因型-组织表达版本 8 中的单个组织面板以及上下文特异性遗传学中的跨组织面板。通过全转录组关联研究和共定位分析,我们分别为 T2、T3 和 T4 确定了 52、75 和 144 个 MPB 关联。为了评估 MPB 基因的因果关系,我们进行了条件分析和联合分析,结果发现 T2、T3 和 T4 的推定因果关系基因分别为 10、11 和 54 个。最后,我们进行了药物重新定位,确定了与 MPB 相关基因有关的潜在候选药物。总之,通过对基因表达和基因型数据的综合分析,我们发现了稳健的 MPB 易感基因,这些基因可能有助于揭示潜在的分子机制和可能缓解 MPB 的新型候选药物。
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引用次数: 0
Profiling the role of m6A effectors in the regulation of pluripotent reprogramming 剖析m6A效应因子在多能性重编程调控中的作用
IF 4.5 3区 医学 Q1 Pharmacology, Toxicology and Pharmaceutics Pub Date : 2024-04-02 DOI: 10.1186/s40246-024-00597-6
Wenjun Wang, Lei Zhou, Hui Li, Tingge Sun, Xue Wen, Wei Li, Miguel A. Esteban, Andrew R. Hoffman, Ji-Fan Hu, Jiuwei Cui
The N6-methyladenosine (m6A) RNA modification plays essential roles in multiple biological processes, including stem cell fate determination. To explore the role of the m6A modification in pluripotent reprogramming, we used RNA-seq to map m6A effectors in human iPSCs, fibroblasts, and H9 ESCs, as well as in mouse ESCs and fibroblasts. By integrating the human and mouse RNA-seq data, we found that 19 m6A effectors were significantly upregulated in reprogramming. Notably, IGF2BPs, particularly IGF2BP1, were among the most upregulated genes in pluripotent cells, while YTHDF3 had high levels of expression in fibroblasts. Using quantitative PCR and Western blot, we validated the pluripotency-associated elevation of IGF2BPs. Knockdown of IGF2BP1 induced the downregulation of stemness genes and exit from pluripotency. Proteome analysis of cells collected at both the beginning and terminal states of the reprogramming process revealed that the IGF2BP1 protein was positively correlated with stemness markers SOX2 and OCT4. The eCLIP-seq target analysis showed that IGF2BP1 interacted with the coding sequence (CDS) and 3’UTR regions of the SOX2 transcripts, in agreement with the location of m6A modifications. This study identifies IGF2BP1 as a vital pluripotency-associated m6A effector, providing new insight into the interplay between m6A epigenetic modifications and pluripotent reprogramming.
N6-甲基腺苷(m6A)RNA修饰在多种生物过程中发挥着重要作用,包括干细胞命运的决定。为了探索m6A修饰在多能性重编程中的作用,我们使用RNA-seq绘制了人类iPSCs、成纤维细胞、H9 ESCs以及小鼠ESCs和成纤维细胞中的m6A效应因子。通过整合人类和小鼠的RNA-seq数据,我们发现19个m6A效应因子在重编程过程中显著上调。值得注意的是,IGF2BPs,尤其是IGF2BP1,是多能细胞中上调最多的基因之一,而YTHDF3在成纤维细胞中有高水平的表达。通过定量 PCR 和 Western 印迹,我们验证了与多能性相关的 IGF2BPs 的升高。敲除 IGF2BP1 会诱导干性基因下调并退出多能性。对重编程过程初期和末期收集的细胞进行的蛋白质组分析表明,IGF2BP1蛋白与干性标志物SOX2和OCT4呈正相关。eCLIP-seq目标分析显示,IGF2BP1与SOX2转录本的编码序列(CDS)和3'UTR区域相互作用,这与m6A修饰的位置一致。这项研究确定了 IGF2BP1 是与多能性相关的重要 m6A 效应因子,为 m6A 表观遗传修饰与多能性重编程之间的相互作用提供了新的视角。
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引用次数: 0
Paternal aging impacts expression and epigenetic markers as early as the first embryonic tissue lineage differentiation. 父亲的衰老早在胚胎组织第一次分化时就会影响表达和表观遗传标记。
IF 3.8 3区 医学 Q2 GENETICS & HEREDITY Pub Date : 2024-03-26 DOI: 10.1186/s40246-024-00599-4
Michelle M Denomme, Blair R McCallie, Mary E Haywood, Jason C Parks, William B Schoolcraft, Mandy G Katz-Jaffe

Background: Advanced paternal age (APA) is associated with adverse outcomes to offspring health, including increased risk for neurodevelopmental disorders. The aim of this study was to investigate the methylome and transcriptome of the first two early embryonic tissue lineages, the inner cell mass (ICM) and the trophectoderm (TE), from human blastocysts in association with paternal age and disease risk. High quality human blastocysts were donated with patient consent from donor oocyte IVF cycles from either APA (≥ 50 years) or young fathers. Blastocysts were mechanically separated into ICM and TE lineage samples for both methylome and transcriptome analyses.

Results: Significant differential methylation and transcription was observed concurrently in ICM and TE lineages of APA-derived blastocysts compared to those from young fathers. The methylome revealed significant enrichment for neuronal signaling pathways, as well as an association with neurodevelopmental disorders and imprinted genes, largely overlapping within both the ICM and TE lineages. Significant enrichment of neurodevelopmental signaling pathways was also observed for differentially expressed genes, but only in the ICM. In stark contrast, no significant signaling pathways or gene ontology terms were identified in the trophectoderm. Despite normal semen parameters in aged fathers, these significant molecular alterations can adversely contribute to downstream impacts on offspring health, in particular neurodevelopmental disorders like autism spectrum disorder and schizophrenia.

Conclusions: An increased risk for neurodevelopmental disorders is well described in children conceived by aged fathers. Using blastocysts derived from donor oocyte IVF cycles to strategically control for maternal age, our data reveals evidence of methylation dysregulation in both tissue lineages, as well as transcription dysregulation in neurodevelopmental signaling pathways associated with APA fathers. This data also reveals that embryos derived from APA fathers do not appear to be compromised for initial implantation potential with no significant pathway signaling disruption in trophectoderm transcription. Collectively, our work provides insights into the complex molecular mechanisms that occur upon paternal aging during the first lineage differentiation in the preimplantation embryo. Early expression and epigenetic markers of APA-derived preimplantation embryos highlight the susceptibility of the future fetus to adverse health outcomes.

背景:高父系年龄(APA)与后代健康的不良后果有关,包括神经发育障碍风险的增加。本研究旨在调查人类囊胚中前两个早期胚胎组织系(内细胞团(ICM)和滋养层(TE))的甲基组和转录组与父亲年龄和疾病风险的关系。优质人类囊胚是在征得患者同意后从 APA(≥ 50 岁)或年轻父亲的卵母细胞体外受精周期中捐献的。用机械方法将囊胚分离成 ICM 和 TE 系样本,进行甲基组和转录组分析:结果:与来自年轻父亲的囊胚相比,在来自 APA 的囊胚的 ICM 和 TE 系中同时观察到了显著的甲基化和转录差异。甲基组显示神经元信号通路显著富集,并与神经发育障碍和印记基因有关,这在 ICM 和 TE 系中基本重叠。在差异表达基因中也观察到神经发育信号通路的显著富集,但仅存在于 ICM 中。与此形成鲜明对比的是,在滋养层中没有发现重要的信号通路或基因本体术语。尽管高龄父亲的精液参数正常,但这些显著的分子变化会对后代的健康产生不利影响,尤其是自闭症谱系障碍和精神分裂症等神经发育疾病:结论:高龄父亲所怀子女罹患神经发育障碍的风险增加已得到充分证实。我们的数据利用从供体卵母细胞试管婴儿周期中获得的囊胚来策略性地控制母体年龄,发现了与 APA 父亲相关的两个组织系的甲基化失调以及神经发育信号通路的转录失调的证据。这些数据还显示,来自 APA 父亲的胚胎似乎并不影响最初的植入潜力,滋养层外胚层转录信号通路也没有明显的中断。总之,我们的研究工作让我们深入了解了植入前胚胎第一系分化过程中父亲衰老时发生的复杂分子机制。APA衍生的植入前胚胎的早期表达和表观遗传标记突显了未来胎儿对不良健康结果的易感性。
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Human Genomics
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