来自用户 小年 的文献。
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21.
小年
(2022-10-31 21:19):
#paper doi:10.1016/j.gpb.2022.09.004. ncFO: A Comprehensive Resource of Curated and Predicted ncRNAs Associated with Ferroptosis. Genomics Proteomics Bioinformatics. 2022.
细胞死亡在组织发育和体内平衡中起关键作用,并抑制癌细胞的过度增殖。铁死亡是由脂质过氧化诱导的一种特殊类型的调节性细胞死亡方式,探索铁死亡的潜在调节因子将有助于阐明其分子机制和仔细研究潜在的药物靶点。
目前虽然有铁死亡与疾病关联的调节剂和标志物数据库FerrD,但不便于研究人员对铁死亡相关非编码RNA(ncRNA,包括miRNA、lncRNA、circRNA)进行系统研究,ncRNA已被证实参与铁死亡的调节,文献中的信息不方便研究人员从综合角度表征铁死亡相关的ncRNA。为了填补这一空白,作者开发了ncRNA-铁死亡关联数据库(ncFO, http://www.jianglab.cn/ncFO/),ncFO是第一个收集了实验验证的铁死亡相关ncRNA并预测候选ncRNA-铁死亡关联的平台。用户可以获得经过实验验证的ncRNA-铁死亡关联,包括ncRNA名称、疾病、物种、组织、靶标、调控、发表时间和PMID。此外,ncFO数据库还提供了ncRNA的生存分析和差异表达分析。数据库为查询和分析铁死亡相关的ncRNA提供可靠的分析平台,为癌症治疗靶点的识别提供参考。
Abstract:
Ferroptosis is a form of regulated cell death driven by the accumulation of lipid hydroperoxides. Regulation of ferroptosis might be beneficial to cancer treatment. Non-coding RNAs (ncRNAs) are a class …
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Ferroptosis is a form of regulated cell death driven by the accumulation of lipid hydroperoxides. Regulation of ferroptosis might be beneficial to cancer treatment. Non-coding RNAs (ncRNAs) are a class of RNA transcripts that generally cannot encode proteins and have been demonstrated to play critical roles in regulating ferroptosis. Herein, we developed ncFO, the ncRNA-ferroptosis association database, to document the manually curated and predicted ncRNAs that are associated with ferroptosis. Collectively, ncFO contains 90 experimentally verified entries, including 46 microRNAs (miRNAs), 21 long non-coding RNAs (lncRNAs), and 17 circular RNAs (circRNAs). In addition, ncFO also incorporates two online prediction tools based on the regulation and co-expression of ncRNA and ferroptosis genes. Using default parameters, we obtained 3260 predicted entries, including 598 miRNAs and 178 lncRNAs, by regulation, as well as 2,592,661 predicted entries, including 967 miRNAs and 9632 lncRNAs, by ncRNA-ferroptosis gene co-expression in more than 8000 samples across 20 cancer types. The detailed information of each entry includes ncRNA name, disease, species, tissue, target, regulation, publication time, and PubMed identifier. ncFO also provides survival analysis and differential expression analysis for ncRNAs. In summary, ncFO offers a user-friendly platform to search and predict ferroptosis-associated ncRNAs, which might facilitate research on ferroptosis and discover potential targets for cancer treatment. ncFO can be accessed at http://www.jianglab.cn/ncFO/.
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22.
小年
(2022-09-30 20:36):
#paper doi: 10.3389/fimmu.2021.687975. eCollection 2021. IOBR: Multi-Omics Immuno-Oncology Biological Research to Decode Tumor Microenvironment and Signatures. Front Immunol. 2021. 随着当前免疫疗法和大数据时代的发展,在复杂的多组学数据集中识别新的生物标志物和筛选特征以指导调整治疗策略已成为免疫肿瘤学的焦点。
这篇文章中开发的IOBR包,旨在一站式完成肿瘤多组学数据的免疫学研究,揭示肿瘤微环境和临床特征的关系。包括四个主要的分析模块:特征和TME反卷积模块(the signature and TME deconvolution module)、表型模块(the phenotype module)、突变模块(the mutation module)和模型构建模块(the model construction module),可以有效和系统地分析肿瘤免疫学、临床、基因组学和scRNA-seq数据。集成了8种已发表的用于定量肿瘤微环境(TME)的算法: CIBERSORT, TIMER, xCell, MCPcounter, ESITMATE, EPIC, IPS, quanTIseq,值得注意的是,IOBR收集并使用多种方法进行变量转换、生存分析、特征选择和统计分析,并且支持批量分析和相应结果的可视化。总体而言,基因组和转录组学数据的整合可能会更新和加深我们对肿瘤进展的理解,并通过联合考虑基因组、代谢和TME谱之间的串扰来提供治疗见解。
Abstract:
Recent advances in next-generation sequencing (NGS) technologies have triggered the rapid accumulation of publicly available multi-omics datasets. The application of integrated omics to explore robust signatures for clinical translation is …
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Recent advances in next-generation sequencing (NGS) technologies have triggered the rapid accumulation of publicly available multi-omics datasets. The application of integrated omics to explore robust signatures for clinical translation is increasingly emphasized, and this is attributed to the clinical success of immune checkpoint blockades in diverse malignancies. However, effective tools for comprehensively interpreting multi-omics data are still warranted to provide increased granularity into the intrinsic mechanism of oncogenesis and immunotherapeutic sensitivity. Therefore, we developed a computational tool for effective Immuno-Oncology Biological Research (IOBR), providing a comprehensive investigation of the estimation of reported or user-built signatures, TME deconvolution, and signature construction based on multi-omics data. Notably, IOBR offers batch analyses of these signatures and their correlations with clinical phenotypes, long non-coding RNA (lncRNA) profiling, genomic characteristics, and signatures generated from single-cell RNA sequencing (scRNA-seq) data in different cancer settings. Additionally, IOBR integrates multiple existing microenvironmental deconvolution methodologies and signature construction tools for convenient comparison and selection. Collectively, IOBR is a user-friendly tool for leveraging multi-omics data to facilitate immuno-oncology exploration and to unveil tumor-immune interactions and accelerating precision immunotherapy.
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23.
小年
(2022-08-31 10:19):
#paper doi.org/10.1038/s41467-021-24213-6 nature communications, 2021, Single-cell transcriptomic analysis reveals disparate effector differentiation pathways in human Treg compartment. 人类调节性 T细胞 (Treg) 是具有高度免疫抑制的一类CD4+ T细胞类群。本文通过对健康人的骨髓及外周血采样分选出Treg细胞,采用单细胞转录组、单细胞TCR技术构建了健康个体两个不同组织的Treg细胞图谱,并通过轨迹分析解析了Treg细胞两条不同功能的主要分化途径,辅以流式细胞仪分选验证。随后采用同样的技术对移植后aGVHD阴性和阳性的患者进行Treg解析,发现这两个分化途径及相应的细胞群体在移植患者中保守,尽管在aGVHD患者中存在一些功能和迁移障碍。这些发现扩大了对 Treg 细胞异质性和分化的理解,并为解剖 Treg 在健康和疾病中的复杂性提供了单细胞图谱参考。
Abstract:
Human FOXP3 regulatory T (T) cells are central to immune tolerance. However, their heterogeneity and differentiation remain incompletely understood. Here we use single-cell RNA and T cell receptor sequencing to …
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Human FOXP3 regulatory T (T) cells are central to immune tolerance. However, their heterogeneity and differentiation remain incompletely understood. Here we use single-cell RNA and T cell receptor sequencing to resolve T cells from healthy individuals and patients with or without acute graft-versus-host disease (aGVHD) who undergo stem cell transplantation. These analyses, combined with functional assays, separate T cells into naïve, activated, and effector stages, and resolve the HLA-DR, LIMS1, highly suppressive FOXP3, and highly proliferative MKI67 effector subsets. Trajectory analysis assembles T subsets into two differentiation paths (I/II) with distinctive phenotypic and functional programs, ending with the FOXP3 and MKI67 subsets, respectively. Transcription factors FOXP3 and SUB1 contribute to some Path I and Path II phenotypes, respectively. These FOXP3 and MKI67 subsets and two differentiation pathways are conserved in transplanted patients, despite having functional and migratory impairments under aGVHD. These findings expand the understanding of T cell heterogeneity and differentiation and provide a single-cell atlas for the dissection of T complexity in health and disease.
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24.
小年
(2022-07-31 16:40):
#paper doi:10.1038/ng.3972
The draft genome of tropical fruit durian (Durio zibethinus)
这是一篇癌症研究所,发表在2017年的Nature Genetics上的关于榴莲(品种是猫山王)基因组组装草图的文章。(不务正业)文章介绍了拼接方法和组装完整性与正确性验证的思路,有一定的参考意义。
文章还用转录组测序,将猫山王、金枕和小猫山王三个品种,与其他水果做了RNA测序,通过富集分析差异比较,发现了榴莲与其他水果气味差异的途径,同时也分析了不同榴莲品种之间味道和气味差异的控制途径,以及连个基因组与转录组分析表明榴莲气味与果实成熟之间存在潜在关联。
看完这个我就在想还有哪些贵的水果还没测基因组的
Abstract:
Durian (Durio zibethinus) is a Southeast Asian tropical plant known for its hefty, spine-covered fruit and sulfury and onion-like odor. Here we present a draft genome assembly of D. zibethinus, …
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Durian (Durio zibethinus) is a Southeast Asian tropical plant known for its hefty, spine-covered fruit and sulfury and onion-like odor. Here we present a draft genome assembly of D. zibethinus, representing the third plant genus in the Malvales order and first in the Helicteroideae subfamily to be sequenced. Single-molecule sequencing and chromosome contact maps enabled assembly of the highly heterozygous durian genome at chromosome-scale resolution. Transcriptomic analysis showed upregulation of sulfur-, ethylene-, and lipid-related pathways in durian fruits. We observed paleopolyploidization events shared by durian and cotton and durian-specific gene expansions in MGL (methionine γ-lyase), associated with production of volatile sulfur compounds (VSCs). MGL and the ethylene-related gene ACS (aminocyclopropane-1-carboxylic acid synthase) were upregulated in fruits concomitantly with their downstream metabolites (VSCs and ethylene), suggesting a potential association between ethylene biosynthesis and methionine regeneration via the Yang cycle. The durian genome provides a resource for tropical fruit biology and agronomy.
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