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TcellInflamedDetector: an R package to distinguish T cell inflamed tumor types from non–T cell inflamed tumor types TcellInflamedDetector:一个R包,用于区分T细胞炎症肿瘤类型和非T细胞炎症肿瘤类型
Pub Date : 2022-03-01 DOI: 10.5808/gi.22005
San-Duk Yang, Hyun-Seok Park
A major issue in the use of immune checkpoint inhibitors is their lack of efficacy in many patients. Previous studies have reported that the T cell inflamed signature can help predict the response to immunotherapy. Thus, many studies have investigated mechanisms of immunotherapy resistance by defining the tumor microenvironment based on T cell inflamed and non–T cell inflamed subsets. Although methods of calculating T cell inflamed subsets have been developed, valid screening tools for distinguishing T cell inflamed from non–T cell inflamed subsets using gene expression data are still needed, since general researchers who are unfamiliar with the details of the equations can experience difficulties using extant scoring formulas to conduct analyses. Thus, we introduce TcellInflamedDetector, an R package for distinguishing T cell inflamed from non–T cell inflamed samples using cancer gene expression data via bulk RNA sequencing.
使用免疫检查点抑制剂的一个主要问题是它们对许多患者缺乏疗效。先前的研究报道,T细胞发炎的特征可以帮助预测免疫疗法的反应。因此,许多研究通过定义基于T细胞炎症和非T细胞炎症亚群的肿瘤微环境来研究免疫疗法耐药性的机制。尽管已经开发出计算T细胞炎症亚群的方法,但仍然需要使用基因表达数据来区分炎症T细胞和非炎症T细胞亚群的有效筛选工具,因为不熟悉方程细节的普通研究人员在使用现有的评分公式进行分析时可能会遇到困难。因此,我们引入了TcellInflamedDetector,这是一种R包,用于通过批量RNA测序,使用癌症基因表达数据区分发炎的T细胞和非发炎的T淋巴细胞样本。
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引用次数: 0
Hypothetical protein predicted to be tumor suppressor: a protein functional analysis 预测为肿瘤抑制因子的假设蛋白质:蛋白质功能分析
Pub Date : 2021-06-18 DOI: 10.21203/rs.3.rs-602073/v1
M. Kader, Akash Ahammed, Md. Sharif Khan, Sheikh Abdullah Al Ashik, M. Islam, Mohammad Uzzal Hossain
Litorilituus sediminis is a Gram-negative, aerobic, novel bacterium under the family of Colwelliaceae, has a stunning hypothetical protein containing domain called von Hippel-Lindau that has significant tumor suppressor activity. Therefore, this study was designed to elucidate the structure and function of the biologically important hypothetical protein EMK97_00595 (QBG34344.1) using several bioinformatics tools. The functional annotation exposed that the hypothetical protein is an extracellular secretory soluble signal peptide and contains the von Hippel-Lindau (VHL; VHL beta) domain that has a significant role in tumor suppression. This domain is conserved throughout evolution, as its homologs are available in various types of the organism like mammals, insects, and nematode. The gene product of VHL has a critical regulatory activity in the ubiquitous oxygen-sensing pathway. This domain has a significant role in inhibiting cell proliferation, angiogenesis progression, kidney cancer, breast cancer, and colon cancer. At last, the current study depicts that the annotated hypothetical protein is linked with tumor suppressor activity which might be of great interest to future research in the higher organism.
Litorilitus sediminis是一种革兰氏阴性、需氧、新细菌,隶属于冬青科,有一个令人惊叹的假设蛋白质含有结构域,称为von Hippel-Lindau,具有显著的肿瘤抑制活性。因此,本研究旨在使用几种生物信息学工具阐明具有生物学意义的假设蛋白EMK97_00595(QBG34344.1)的结构和功能。功能注释表明,假设的蛋白质是一种细胞外分泌可溶性信号肽,含有在肿瘤抑制中发挥重要作用的von Hippel-Lindau(VHL;VHLβ)结构域。这个结构域在整个进化过程中都是保守的,因为它的同源物存在于各种类型的生物体中,如哺乳动物、昆虫和线虫。VHL的基因产物在普遍存在的氧感应途径中具有关键的调节活性。该结构域在抑制细胞增殖、血管生成进展、肾脏癌症、癌症乳腺癌和癌症中具有重要作用。最后,目前的研究表明,注释的假设蛋白与肿瘤抑制活性有关,这可能对未来高等生物的研究具有重要意义。
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引用次数: 0
Correlation-based and feature-driven mutation signature analyses to identify genetic features associated with DNA mutagenic processes in cancer genomes 基于相关性和特征驱动的突变特征分析,以确定与癌症基因组中DNA诱变过程相关的遗传特征
Pub Date : 2020-01-06 DOI: 10.1101/2020.01.06.895698
H. Jeong, Jinseon Yoo, Hyunwoo J. Kim, Tae-Min Kim
Mutation signatures represent unique sequence footprints of somatic mutations resulting from specific DNA mutagenic and repair processes; however, their causal associations and potential utility for genome research remain largely unknown. In this study, we performed PanCancer-scale correlative analyses to identify the genomic features associated with tumor mutation burdens (TMB) and individual mutation signatures. We observed that TMB was correlated with tumor purity, ploidy, and the level of aneuploidy, as well as with the expression of cell proliferation-related genes representing genomic covariates in evaluating TMB. Correlative analyses of mutation signature levels with genes belonging to DNA damage-repair processes revealed that deficiencies of NHEJ1 and ALKBH3 may elevate TMB levels in cancer genomes accompanying APOBEC overactivity and DNA mismatch repair deficiency, respectively. We further employed a strategy to identify feature-driven, de novo mutation signatures and demonstrated they can be reconstructed using known causal features such as APOBEC overexpression, MLH1 underexpression, POLE mutations, and the level of homologous recombination deficiency. We further demonstrated, that tumor hypoxia-related mutation signatures are similar to those associated with APOBEC suggesting that APOBEC-related mutagenic activity mediates hypoxia-related mutational consequences in cancer genomes, and also, that mutation signatures can be further used to predict hypoxic tumors. Taken together, our study advances mutation signature-level mechanistic insights in cancer genomes, extending categories of cancer-relevant mutation signatures and their potential biological implications. Author summary Mutation signature analysis is powerful in deciphering the causative mutagenic events and their contributions in individual cancer genomes, but the causal relationship of individual mutation signatures are still largely unknown. PanCancer-scaled correlative analysis revealed mutation resource candidates in cancer genomes such as NHEJ1 and ALKBH3 deficiencies that may facilitate the accumulation of mutations in the setting of APOBEC overactivity and DNA mismatch repair deficiency, respectively. A feature-driven mutation discovery approach was employed to identify the mutation signatures representing homologous recombination deficiency and tumor hypoxia, the extent of which may serve as mutation-based phenotypic measures, previously estimated by DNA copy number alterations and mRNA expression signatures, respectively. Our study advances our understanding into the mechanistic insights of mutation signatures and proposes a method to utilize somatic mutations as a molecular proxy in terms of mutation signatures.
突变特征代表由特定DNA诱变和修复过程引起的体细胞突变的独特序列足迹;然而,它们的因果关系和对基因组研究的潜在效用在很大程度上仍然未知。在这项研究中,我们进行了泛癌规模的相关分析,以确定与肿瘤突变负荷(TMB)和个体突变特征相关的基因组特征。我们观察到TMB与肿瘤纯度、倍性、非整倍性水平以及代表TMB评估中基因组协变量的细胞增殖相关基因的表达相关。突变特征水平与属于DNA损伤修复过程的基因的相关性分析表明,NHEJ1和ALKBH3的缺失可能分别升高癌症基因组中的TMB水平,同时伴有APOBEC过度活性和DNA错配修复缺陷。我们进一步采用了一种策略来识别特征驱动的从头突变特征,并证明它们可以使用已知的因果特征来重建,如APOBEC过表达、MLH1低表达、POLE突变和同源重组缺乏水平。我们进一步证明,肿瘤低氧相关突变信号与APOBEC相关突变信号相似,表明APOBEC相关性突变活性介导癌症基因组中低氧相关突变结果,并且突变信号可进一步用于预测低氧肿瘤。总之,我们的研究在癌症基因组中推进了突变信号水平的机制见解,扩展了癌症相关突变信号的类别及其潜在的生物学意义。作者总结突变特征分析在破译癌症个体基因组中的致突变事件及其贡献方面很强大,但个体突变特征的因果关系在很大程度上仍然未知。PanCancer-scale相关分析揭示了癌症基因组中的候选突变资源,如NHEJ1和ALKBH3缺陷,它们可能分别在APOBEC过度活性和DNA错配修复缺陷的情况下促进突变的积累。采用特征驱动的突变发现方法来识别代表同源重组缺陷和肿瘤缺氧的突变特征,其程度可以作为基于突变的表型测量,先前分别通过DNA拷贝数变化和mRNA表达特征来估计。我们的研究推进了我们对突变特征的机制见解的理解,并提出了一种利用体细胞突变作为突变特征的分子代理的方法。
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引用次数: 1
The interaction between gut microbiome and nutrients on development of human disease through epigenetic mechanisms 肠道微生物群和营养物质通过表观遗传机制在人类疾病发展中的相互作用
Pub Date : 2019-09-01 DOI: 10.5808/GI.2019.17.3.e24
Ho-Sun Lee
Early environmental exposure is recognized as a key factor for long-term health based on the Developmental Origins of Health and Disease hypothesis. It considers that early-life nutrition is now being recognized as a major contributor that may permanently program change of organ structure and function toward the development of diseases, in which epigenetic mechanisms are involved. Recent researches indicate early-life environmental factors modulate the microbiome development and the microbiome might be mediate diet-epigenetic interaction. This review aims to define which nutrients involve microbiome development during the critical window of susceptibility to disease, and how microbiome modulation regulates epigenetic changes and influences human health and future prevention strategies.
基于健康和疾病的发展起源假说,早期环境暴露被认为是长期健康的关键因素。它认为,生命早期的营养现在被认为是一个主要的贡献者,可能永久性地规划器官结构和功能的变化,导致疾病的发展,其中涉及表观遗传机制。近年来的研究表明,早期环境因素调节微生物组的发育,微生物组可能介导饮食与表观遗传的相互作用。本综述旨在确定哪些营养物质在疾病易感性的关键窗口期参与微生物组的发育,以及微生物组调节如何调节表观遗传变化并影响人类健康和未来的预防策略。
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引用次数: 12
Editor’s introduction to this issue (G&I 17:3, 2019) 编者对本期的介绍(G&I 17:3, 2019)
Pub Date : 2019-09-01 DOI: 10.5808/GI.2019.17.3.e22
T. Park
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引用次数: 0
Direct-to-consumer genetic testing: advantages and pitfalls. 直接面向消费者的基因检测:优点和缺点。
Pub Date : 2019-09-01 Epub Date: 2019-09-26 DOI: 10.5808/GI.2019.17.3.e33
Bermseok Oh

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引用次数: 10
De novo transcriptome sequencing and gene expression profiling with/without B-chromosome plants of Lilium amabile 带/不带B染色体植物的无芒百合从头转录组测序和基因表达谱
Pub Date : 2019-09-01 DOI: 10.5808/gi.2019.17.3.e27
Doori Park, Jong-Hwa Kim, Nam-Soo Kim
Supernumerary B chromosomes were found in Lilium amabile (2n = 2x = 24), an endemic Korean lily that grows in the wild throughout the Korean Peninsula. The extra B chromosomes do not affect the host-plant morphology; therefore, whole transcriptome analysis was performed in 0B and 1B plants to identify differentially expressed genes. A total of 154,810 transcripts were obtained from over 10 Gbp data by de novo assembly. By mapping the raw reads to the de novo transcripts, we identified 7,852 differentially expressed genes (log2FC > |10|), in which 4,059 and 3,794 were up-and down-regulated, respectively, in 1B plants compared to 0B plants. Functional enrichment analysis revealed that various differentially expressed genes were involved in cellular processes including the cell cycle, chromosome breakage and repair, and microtubule formation; all of which may be related to the occurrence and maintenance of B chromosomes. Our data provide insight into transcriptomic changes and evolution of plant B chromosomes and deliver an informative database for future study of B chromosome transcriptomes in the Korean lily.
在朝鲜半岛野生的朝鲜特有百合Lilium amabile(2n=2x=24)中发现了大量的B染色体。额外的B染色体不影响寄主植物的形态;因此,对0B和1B植物进行了全转录组分析,以鉴定差异表达的基因。通过从头组装从超过10Gbp的数据中总共获得154810个转录本。通过将原始读数映射到从头转录物,我们鉴定了7852个差异表达基因(log2FC>|10|),其中与0B植物相比,1B植物中分别有4059个和3794个基因上调和下调。功能富集分析显示,各种差异表达基因参与细胞过程,包括细胞周期、染色体断裂和修复以及微管的形成;所有这些都可能与B染色体的发生和维持有关。我们的数据深入了解了植物B染色体的转录组变化和进化,并为未来研究韩国百合B染色体转录组提供了信息数据库。
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引用次数: 5
Analysis of differences in human leukocyte antigen between the two Wellcome Trust Case Control Consortium control datasets 两组惠康基金会病例控制联盟对照数据的人白细胞抗原差异分析
Pub Date : 2019-09-01 DOI: 10.5808/gi.2019.17.3.e29
Chloe Soohyun Jang, Wanson Choi, Seungho Cook, B. Han
The Wellcome Trust Case Control Consortium (WTCCC) study was a large genome-wide association study that aimed to identify common variants associated with seven diseases. That study combined two control datasets (58C and UK Blood Services) as shared controls. Prior to using the combined controls, the WTCCC performed analyses to show that the genomic content of the control datasets was not significantly different. Recently, the analysis of human leukocyte antigen (HLA) genes has become prevalent due to the development of HLA imputation technology. In this project, we extended the between-control homogeneity analysis of the WTCCC to HLA. We imputed HLA information in the WTCCC control dataset and showed that the HLA content was not significantly different between the two control datasets, suggesting that the combined controls can be used as controls for HLA fine-mapping analysis based on HLA imputation.
Wellcome Trust病例控制联盟(WTCCC)研究是一项大型全基因组关联研究,旨在确定与七种疾病相关的常见变异。该研究将两个对照数据集(58C和英国血液服务中心)作为共享对照。在使用联合对照之前,WTCCC进行了分析,显示对照数据集的基因组内容没有显着差异。近年来,由于人类白细胞抗原(HLA)基因植入技术的发展,对人类白细胞抗原(HLA)基因的分析已成为一种流行。在本项目中,我们将WTCCC的对照间同质性分析扩展到HLA。我们在WTCCC对照数据集中输入HLA信息,结果显示两个对照数据集的HLA含量没有显著差异,提示合并后的对照可以作为基于HLA输入的HLA精细图谱分析的对照。
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引用次数: 0
In silico approach to calculate the transcript capacity 计算转录能力的计算机方法
Pub Date : 2019-09-01 DOI: 10.5808/GI.2019.17.3.e31
Young-Sup Lee, Kyung-Hye Won, Jae-Don Oh, Donghyun Shin
We sought the novel concept, transcript capacity (TC) and analyzed TC. Our approach to estimate TC was through an in silico method. TC refers to the capacity that a transcript exerts in a cell as enzyme or protein function after translation. We used the genome-wide association study (GWAS) beta effect and transcription level in RNA-sequencing to estimate TC. The trait was body fat percent and the transcript reads were obtained from the human protein atlas. The assumption was that the GWAS beta effect is the gene’s effect and TC was related to the corresponding gene effect and transcript reads. Further, we surveyed gene ontology (GO) in the highest TC and the lowest TC genes. The most frequent GOs with the highest TC were neuronal-related and cell projection organization related. The most frequent GOs with the lowest TC were wound-healing related and embryo development related. We expect that our analysis contributes to estimating TC in the diverse species and playing a benevolent role to the new bioinformatic analysis.
我们寻求了新的概念,转录能力(TC),并分析了TC。我们通过计算机方法估计TC。TC是指转录物在翻译后作为酶或蛋白质功能在细胞中发挥的能力。我们使用全基因组关联研究(GWAS)β效应和RNA测序中的转录水平来估计TC。该特征是体脂百分比,转录物读数来自人类蛋白质图谱。假设GWASβ效应是基因的效应,TC与相应的基因效应和转录物读数有关。此外,我们调查了最高TC和最低TC基因的基因本体论(GO)。TC最高的最常见GOs是神经元相关的和细胞投射组织相关的。TC最低的GOs最常见的是与伤口愈合相关的和与胚胎发育相关的。我们希望我们的分析有助于估计不同物种的TC,并为新的生物信息学分析发挥有益作用。
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引用次数: 0
Comparison of the MGISEQ-2000 and Illumina HiSeq 4000 sequencing platforms for RNA sequencing. 用于RNA测序的MGISEQ-2000和Illumina HiSeq 4000测序平台的比较。
Pub Date : 2019-09-01 Epub Date: 2019-09-27 DOI: 10.5808/GI.2019.17.3.e32
Sol A Jeon, Jong Lyul Park, Jong-Hwan Kim, Jeong Hwan Kim, Yong Sung Kim, Jin Cheon Kim, Seon-Young Kim

Currently, Illumina sequencers are the globally leading sequencing platform in the next-generation sequencing market. Recently, MGI Tech launched a series of new sequencers, including the MGISEQ-2000, which promise to deliver high-quality sequencing data faster and at lower prices than Illumina's sequencers. In this study, we compared the performance of two major sequencers (MGISEQ-2000 and HiSeq 4000) to test whether the MGISEQ-2000 sequencer delivers high-quality sequence data as suggested. We performed RNA sequencing of four human colon cancer samples with the two platforms, and compared the sequencing quality and expression values. The data produced from the MGISEQ-2000 and HiSeq 4000 showed high concordance, with Pearson correlation coefficients ranging from 0.98 to 0.99. Various quality control (QC) analyses showed that the MGISEQ-2000 data fulfilled the required QC measures. Our study suggests that the performance of the MGISEQ-2000 is comparable to that of the HiSeq 4000 and that the MGISEQ-2000 can be a useful platform for sequencing.

目前,Illumina测序仪是下一代测序市场中全球领先的测序平台。最近,MGI Tech推出了一系列新的测序仪,包括MGISEQ-2000,它承诺以比Illumina测序仪更快、更低的价格提供高质量的测序数据。在这项研究中,我们比较了两种主要测序仪(MGISEQ-2000和HiSeq 4000)的性能,以测试MGISEQ-2000测序仪是否能提供所建议的高质量序列数据。我们用两个平台对四个人类癌症样本进行了RNA测序,并比较了测序质量和表达值。MGISEQ-2000和HiSeq 4000产生的数据显示出高度一致性,Pearson相关系数在0.98至0.99之间。各种质量控制(QC)分析表明,MGISEQ-2000数据符合要求的QC措施。我们的研究表明,MGISEQ-2000的性能与HiSeq 4000相当,MGISEQ-2000可以成为一个有用的测序平台。
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引用次数: 28
期刊
Genomics & informatics
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