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Genetic analysis of albinism caused by compound heterozygous mutations of the OCA2 gene in a Chinese family. 一个中国家庭中 OCA2 基因复合杂合突变所致白化病的遗传学分析。
IF 2.7 3区 生物学 Pub Date : 2024-02-06 DOI: 10.1186/s41065-024-00312-4
Yanan Wang, Yujie Chang, Mingya Gao, Weiwei Zang, Xiaofei Liu

Background: Oculocutaneous albinism (OCA) is a group of rare genetic disorders characterized by a reduced or complete lack of melanin in the skin, hair, and eyes. Patients present with colorless retina, pale pink iris, and pupil, and fear of light. The skin, eyebrows, hair, and other body hair are white or yellowish-white. These conditions are caused by mutations in specific genes necessary for the production of melanin. OCA is divided into eight clinical types (OCA1-8), each with different clinical phenotypes and potential genetic factors. This study aimed to identify the genetic causes of non-syndromic OCA in a Chinese Han family.

Methods: We performed a comprehensive clinical examination of family members, screened for mutation loci using whole exome sequencing (WES) technology, and predicted mutations using In silico tools.

Results: The patient's clinical manifestations were white skin, yellow hair, a few freckles on the cheeks and bridge of the nose, decreased vision, blue iris, poorly defined optic disk borders, pigmentation of the fundus being insufficient, and significant vascular exposure. The WES test results indicate that the patient has compound heterozygous mutations in the OCA2 gene (c.1258G > A (p.G420R), c.1441G > A (p.A481T), and c.2267-2 A > C), respectively, originating from her parents. Among them, c.1258G > A (p.G420R) is a de novo mutation with pathogenic. Our analysis suggests that compound heterozygous mutations in the OCA2 gene are the primary cause of the disease in this patient.

Conclusions: The widespread application of next-generation sequencing technologies such as WES in clinical practice can effectively replace conventional detection methods and assist in the diagnosis of clinical diseases more quickly and accurately. The newly discovered c.1258G > A (p.G420R) mutation can update and expand the gene mutation spectrum of OCA2-type albinism.

背景:眼皮肤白化病(OCA)是一组罕见的遗传性疾病,其特征是皮肤、头发和眼睛中黑色素减少或完全缺乏。患者表现为视网膜无色、虹膜和瞳孔呈淡粉色、怕光。皮肤、眉毛、头发和其他体毛呈白色或黄白色。这些病症是由产生黑色素所需的特定基因突变引起的。OCA分为八种临床类型(OCA1-8),每种类型都有不同的临床表型和潜在的遗传因素。本研究旨在确定一个中国汉族家庭中非综合征 OCA 的遗传原因:我们对家族成员进行了全面的临床检查,利用全外显子组测序(WES)技术筛选突变位点,并利用 In silico 工具预测突变:患者的临床表现为皮肤白、头发黄、脸颊和鼻梁上有少量雀斑、视力下降、虹膜呈蓝色、视盘边界不清、眼底色素沉着不足以及明显的血管暴露。WES 检测结果显示,患者的 OCA2 基因存在复合杂合突变(c.1258G > A (p.G420R)、c.1441G > A (p.A481T)和 c.2267-2 A > C),分别源自其父母。其中,c.1258G > A (p.G420R)是一个具有致病性的新突变。我们的分析表明,OCA2基因的复合杂合突变是该患者患病的主要原因:WES等新一代测序技术在临床上的广泛应用,可有效替代传统检测方法,更快、更准确地辅助临床疾病的诊断。新发现的c.1258G > A (p.G420R)突变可以更新和扩展OCA2型白化病的基因突变谱。
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引用次数: 0
Integrative single-cell analysis: dissecting CD8 + memory cell roles in LUAD and COVID-19 via eQTLs and Mendelian Randomization 整合单细胞分析:通过 eQTL 和孟德尔随机化分析 CD8 + 记忆细胞在 LUAD 和 COVID-19 中的作用
IF 2.7 3区 生物学 Pub Date : 2024-01-31 DOI: 10.1186/s41065-023-00307-7
Jintao Wu, Xiaocheng Mao, Xiaohua Liu, Junying Mao, Xianxin Yang, Xiangwu zhou, Lu Tianzhu, Yulong Ji, Zhao Li, Huijuan Xu
Lung adenocarcinoma exhibits high incidence and mortality rates, presenting a significant health concern. Concurrently, the COVID-19 pandemic has emerged as a grave global public health challenge. Existing literature suggests that T cells, pivotal components of cellular immunity, are integral to both antiviral and antitumor responses. Yet, the nuanced alterations and consequent functions of T cells across diverse disease states have not been comprehensively elucidated. We gathered transcriptomic data of peripheral blood mononuclear cells from lung adenocarcinoma patients, COVID-19 patients, and healthy controls. We followed a standardized analytical approach for quality assurance, batch effect adjustments, and preliminary data processing. We discerned distinct T cell subsets and conducted differential gene expression analysis. Potential key genes and pathways were inferred from GO and Pathway enrichment analyses. Additionally, we implemented Mendelian randomization to probe the potential links between pivotal genes and lung adenocarcinoma susceptibility. Our findings underscored a notable reduction in mature CD8 + central memory T cells in both lung adenocarcinoma and COVID-19 cohorts relative to the control group. Notably, the downregulation of specific genes, such as TRGV9, could impede the immunological efficacy of CD8 + T cells. Comprehensive multi-omics assessment highlighted genetic aberrations in genes, including TRGV9, correlating with heightened lung adenocarcinoma risk. Through rigorous single-cell transcriptomic analyses, this investigation meticulously delineated variations in T cell subsets across different pathological states and extrapolated key regulatory genes via an integrated multi-omics approach, establishing a robust groundwork for future functional inquiries. This study furnishes valuable perspectives into the etiology of multifaceted diseases and augments the progression of precision medicine.
肺腺癌的发病率和死亡率都很高,是一个重大的健康问题。与此同时,COVID-19 大流行已成为全球公共卫生面临的严峻挑战。现有文献表明,T 细胞是细胞免疫的关键组成部分,在抗病毒和抗肿瘤反应中都不可或缺。然而,T 细胞在不同疾病状态下的细微变化及其功能尚未得到全面阐明。我们收集了肺腺癌患者、COVID-19 患者和健康对照者外周血单核细胞的转录组数据。我们采用标准化分析方法进行质量保证、批次效应调整和初步数据处理。我们发现了不同的 T 细胞亚群,并进行了差异基因表达分析。通过 GO 和通路富集分析推断出潜在的关键基因和通路。此外,我们还采用了孟德尔随机化方法来探究关键基因与肺腺癌易感性之间的潜在联系。我们的研究结果表明,与对照组相比,肺腺癌组和 COVID-19 组中成熟的 CD8 + 中心记忆 T 细胞明显减少。值得注意的是,特定基因(如 TRGV9)的下调可能会阻碍 CD8 + T 细胞的免疫功效。全面的多组学评估突显了与肺腺癌风险增加相关的基因畸变,包括TRGV9。通过严格的单细胞转录组分析,这项研究细致地描述了不同病理状态下T细胞亚群的变化,并通过综合多组学方法推断出关键的调控基因,为未来的功能研究奠定了坚实的基础。这项研究为研究多种疾病的病因提供了宝贵的视角,并推动了精准医学的发展。
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引用次数: 0
Comprehensive analysis revealed the immunoinflammatory targets of rheumatoid arthritis based on intestinal flora, miRNA, transcription factors, and RNA-binding proteins databases, GSEA and GSVA pathway observations, and immunoinfiltration typing 基于肠道菌群、miRNA、转录因子和 RNA 结合蛋白数据库、GSEA 和 GSVA 通路观察以及免疫渗透分型的综合分析揭示了类风湿性关节炎的免疫炎症靶点
IF 2.7 3区 生物学 Pub Date : 2024-01-25 DOI: 10.1186/s41065-024-00310-6
Yin Guan, Yue Zhang, Xiaoqian Zhao, Yue Wang
Rheumatoid arthritis (RA) is a chronic inflammatory arthritis. This study aimed to identify potential biomarkers and possible pathogenesis of RA using various bioinformatics analysis tools. The GMrepo database provided a visual representation of the analysis of intestinal flora. We selected the GSE55235 and GSE55457 datasets from the Gene Expression Omnibus database to identify differentially expressed genes (DEGs) separately. With the intersection of these DEGs with the target genes associated with RA found in the GeneCards database, we obtained the DEGs targeted by RA (DERATGs). Subsequently, Disease Ontology, Gene Ontology, and the Kyoto Encyclopedia of Genes and Genomes were used to analyze DERATGs functionally. Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA) were performed on the data from the gene expression matrix. Additionally, the protein-protein interaction network, transcription factor (TF)-targets, target-drug, microRNA (miRNA)-mRNA networks, and RNA-binding proteins (RBPs)-DERATGs correlation analyses were built. The CIBERSORT was used to evaluate the inflammatory immune state. The single-sample GSEA (ssGSEA) algorithm and differential analysis of DERATGs were used among the infiltration degree subtypes. There were some correlations between the abundance of gut flora and the prevalence of RA. A total of 54 DERATGs were identified, mainly related to immune and inflammatory responses and immunodeficiency diseases. Through GSEA and GSVA analysis, we found pathway alterations related to metabolic regulations, autoimmune diseases, and immunodeficiency-related disorders. We obtained 20 hub genes and 2 subnetworks. Additionally, we found that 39 TFs, 174 drugs, 2310 miRNAs, and several RBPs were related to DERATGs. Mast, plasma, and naive B cells differed during immune infiltration. We discovered DERATGs’ differences among subtypes using the ssGSEA algorithm and subtype grouping. The findings of this study could help with RA diagnosis, prognosis, and targeted molecular treatment.
类风湿性关节炎(RA)是一种慢性炎症性关节炎。本研究旨在利用各种生物信息学分析工具确定类风湿性关节炎的潜在生物标志物和可能的发病机制。GMrepo 数据库提供了肠道菌群分析的直观表示。我们从基因表达总库(Gene Expression Omnibus)数据库中选择了GSE55235和GSE55457数据集,分别鉴定差异表达基因(DEGs)。将这些 DEGs 与 GeneCards 数据库中与 RA 相关的靶基因相交,我们得到了 RA 靶向的 DEGs(DERATGs)。随后,我们利用疾病本体(Disease Ontology)、基因本体(Gene Ontology)和京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes)对DERATGs进行了功能分析。对基因表达矩阵的数据进行了基因组富集分析(GSEA)和基因组变异分析(GSVA)。此外,还建立了蛋白质-蛋白质相互作用网络、转录因子(TF)-靶点、靶点-药物、microRNA(miRNA)-mRNA 网络和 RNA 结合蛋白(RBPs)-DERATGs 相关性分析。CIBERSORT用于评估炎症免疫状态。在浸润程度亚型中使用了单样本 GSEA(ssGSEA)算法和 DERATGs 差异分析。肠道菌群的丰度与RA发病率之间存在一定的相关性。共鉴定出54个DERATGs,主要与免疫和炎症反应以及免疫缺陷疾病有关。通过GSEA和GSVA分析,我们发现了与代谢调节、自身免疫性疾病和免疫缺陷相关疾病有关的通路改变。我们获得了 20 个枢纽基因和 2 个子网络。此外,我们还发现 39 个 TFs、174 种药物、2310 个 miRNAs 和几个 RBPs 与 DERATGs 有关。肥大细胞、浆细胞和幼稚B细胞在免疫浸润过程中存在差异。我们利用ssGSEA算法和亚型分组发现了DERATGs在亚型间的差异。本研究的发现有助于RA的诊断、预后和分子靶向治疗。
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引用次数: 0
Correction: Identification of five hub genes as monitoring biomarkers for breast cancer metastasis in silico 更正:确定五个枢纽基因作为乳腺癌转移的监测生物标志物
IF 2.7 3区 生物学 Pub Date : 2024-01-19 DOI: 10.1186/s41065-023-00300-0
Yun Cai, Jie Mei, Zhuang Xiao, Bujie Xu, Xiaozheng Jiang, Yongjie Zhang, Yichao Zhu

Correction: Hereditas 156, 20 (2019).

https://doi.org/10.1186/s41065-019-0096-6.

Following publication of the original article [1], the author reported that Fig. 6B and 6C were repeated. The correct Figure is included here and the original article has been updated.

Fig. 6
figure 6

Diagnostic value of the five hub genes in identifying normal and breast cancer tissues. The ROC curve revealed that the mRNA levels of these five genes exhibited excellent diagnostic efficiency for breast cancer and adjacent tissues. (a) TPX2, (b) KIF2C, (c) CDCA8, (d) BUB1B, (E) CCNA2

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  1. Cai Y, Mei J, Xiao Z, et al. Identification of five hub genes as monitoring biomarkers for Breast cancer Metastasis in silico. Hereditas. 2019;156:20. https://doi.org/10.1186/s41065-019-0096-6.

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Author notes
  1. Yun Cai, Jie Mei and Zhuang Xiao contributed equally to this work and should be considered co-first authors.

Authors and Affiliations

  1. Department of Physiology, Nanjing Medical University, Nanjing, 211166, China

    Yun Cai, Jie Mei, Zhuang Xiao, Bujie Xu, Xiaozheng Jiang & Yichao Zhu

  2. Department of Bioinformatics, Nanjing Medical University, Nanjing, 211166, China

    Yun Cai

  3. Department of Human Anatomy, Nanjing Medical University, Nanjing, 211166, China

    Yongjie Zhang

  4. Key Laboratory for Aging & Diseases of Nanjing Medical University, Nanjing Medical University, Nanjing, 211166, China

    Yongjie Zhang

  5. State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China

    Yichao Zhu

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更正:Hereditas 156, 20 (2019).https://doi.org/10.1186/s41065-019-0096-6.Following 原文[1]发表时,作者报告图6B和6C重复。图 6Diagnostic value of the five hub genes in identification normal and breast cancer tissues.ROC 曲线显示,这五个基因的 mRNA 水平对乳腺癌和邻近组织具有极佳的诊断效率。(a) TPX2, (b) KIF2C, (c) CDCA8, (d) BUB1B, (E) CCNA2Full size imageCai Y, Mei J, Xiao Z, et al.Hereditas.2019;156:20. https://doi.org/10.1186/s41065-019-0096-6.Article PubMed PubMed Central Google Scholar Download references作者注释蔡云、梅杰和肖庄对本工作做出了同等贡献,应视为共同第一作者。作者和通讯单位南京医科大学生理学系(南京,211166)蔡云、梅洁、肖壮、徐步杰、蒋晓政、朱一超南京医科大学生物信息学系(南京,211166)蔡云南京医科大学人体解剖学系(南京,211166)张永杰南京医科大学衰老与疾病重点实验室(南京,211166中国南京,211166 南京医科大学生殖医学国家重点实验室,南京,211166、朱义超作者简介蔡云查看作者发表的论文您也可以在PubMed谷歌学术中搜索该作者梅洁查看作者发表的论文您也可以在PubMed谷歌学术中搜索该作者肖庄查看作者发表的论文您也可以在PubMed谷歌学术中搜索该作者徐步杰查看作者发表的论文您也可以在PubMed谷歌学术中搜索该作者Google Scholar蒋孝正查看作者发表的论文您也可以在 PubMed Google Scholar中搜索该作者张永杰查看作者发表的论文您也可以在 PubMed Google Scholar中搜索该作者朱义超查看作者发表的论文您也可以在 PubMed Google Scholar中搜索该作者通讯作者:张永杰或朱义超。出版者注释Springer Nature对出版地图中的管辖权主张和机构隶属关系保持中立。原文的在线版本可在以下网址找到:https://doi.org/10.1186/s41065-019-0096-6.Open Access 本文采用知识共享署名 4.0 国际许可协议进行许可,该协议允许以任何媒介或格式使用、共享、改编、分发和复制,只要您适当注明原作者和来源,提供知识共享许可协议的链接,并说明是否进行了修改。本文中的图片或其他第三方材料均包含在文章的知识共享许可协议中,除非在材料的署名栏中另有说明。如果材料未包含在文章的知识共享许可协议中,且您打算使用的材料不符合法律规定或超出许可使用范围,您需要直接从版权所有者处获得许可。要查看该许可的副本,请访问 http://creativecommons.org/licenses/by/4.0/。除非在数据的信用行中另有说明,否则创作共用公共领域专用免责声明(http://creativecommons.org/publicdomain/zero/1.0/)适用于本文提供的数据。转载与许可引用本文Cai, Y., Mei, J., Xiao, Z. et al. Correction:五种枢纽基因作为乳腺癌转移监测生物标志物的硅学鉴定。Hereditas 161, 5 (2024). https://doi.org/10.1186/s41065-023-00300-0Download citationPublished: 19 January 2024DOI: https://doi.org/10.1186/s41065-023-00300-0Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy to clipboard Provided by the Springer Nature SharedIt content-sharing initiative.
{"title":"Correction: Identification of five hub genes as monitoring biomarkers for breast cancer metastasis in silico","authors":"Yun Cai, Jie Mei, Zhuang Xiao, Bujie Xu, Xiaozheng Jiang, Yongjie Zhang, Yichao Zhu","doi":"10.1186/s41065-023-00300-0","DOIUrl":"https://doi.org/10.1186/s41065-023-00300-0","url":null,"abstract":"<p><b>Correction: Hereditas 156, 20 (2019).</b></p><p><b>https://doi.org/10.1186/s41065-019-0096-6</b>.</p><p>Following publication of the original article [1], the author reported that Fig. 6B and 6C were repeated. The correct Figure is included here and the original article has been updated.</p><figure><figcaption><b data-test=\"figure-caption-text\">Fig. 6</b></figcaption><picture><source srcset=\"//media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs41065-023-00300-0/MediaObjects/41065_2023_300_Figa_HTML.png?as=webp\" type=\"image/webp\"/><img alt=\"figure 6\" aria-describedby=\"Fig6\" height=\"446\" loading=\"lazy\" src=\"//media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs41065-023-00300-0/MediaObjects/41065_2023_300_Figa_HTML.png\" width=\"685\"/></picture><p>Diagnostic value of the five hub genes in identifying normal and breast cancer tissues. The ROC curve revealed that the mRNA levels of these five genes exhibited excellent diagnostic efficiency for breast cancer and adjacent tissues. <b>(a)</b> TPX2, <b>(b)</b> KIF2C, <b>(c)</b> CDCA8, <b>(d)</b> BUB1B, <b>(E)</b> CCNA2</p><span>Full size image</span><svg aria-hidden=\"true\" focusable=\"false\" height=\"16\" role=\"img\" width=\"16\"><use xlink:href=\"#icon-eds-i-chevron-right-small\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"></use></svg></figure><ol data-track-component=\"outbound reference\"><li data-counter=\"1.\"><p>Cai Y, Mei J, Xiao Z, et al. Identification of five hub genes as monitoring biomarkers for Breast cancer Metastasis in silico. Hereditas. 2019;156:20. https://doi.org/10.1186/s41065-019-0096-6.</p><p>Article PubMed PubMed Central Google Scholar </p></li></ol><p>Download references<svg aria-hidden=\"true\" focusable=\"false\" height=\"16\" role=\"img\" width=\"16\"><use xlink:href=\"#icon-eds-i-download-medium\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"></use></svg></p><span>Author notes</span><ol><li><p>Yun Cai, Jie Mei and Zhuang Xiao contributed equally to this work and should be considered co-first authors.</p></li></ol><h3>Authors and Affiliations</h3><ol><li><p>Department of Physiology, Nanjing Medical University, Nanjing, 211166, China</p><p>Yun Cai, Jie Mei, Zhuang Xiao, Bujie Xu, Xiaozheng Jiang &amp; Yichao Zhu</p></li><li><p>Department of Bioinformatics, Nanjing Medical University, Nanjing, 211166, China</p><p>Yun Cai</p></li><li><p>Department of Human Anatomy, Nanjing Medical University, Nanjing, 211166, China</p><p>Yongjie Zhang</p></li><li><p>Key Laboratory for Aging &amp; Diseases of Nanjing Medical University, Nanjing Medical University, Nanjing, 211166, China</p><p>Yongjie Zhang</p></li><li><p>State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China</p><p>Yichao Zhu</p></li></ol><span>Authors</span><ol><li><span>Yun Cai</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Jie Mei</span>View author publications<p>You can also search fo","PeriodicalId":12862,"journal":{"name":"Hereditas","volume":"26 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139498940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A novel missense mutation (FGG c.1168G > T) in the gamma chain of fibrinogen causing congenital hypodysfibrinogenemia with bleeding phenotype. 纤维蛋白原 gamma 链中的一个新型错义突变(FGG c.1168G > T)导致先天性低纤维蛋白原血症伴出血表型。
IF 2.7 3区 生物学 Pub Date : 2024-01-18 DOI: 10.1186/s41065-024-00308-0
Nuo Xu, Liping Zheng, Zhehao Dai, Jun Zhu, Peng Xie, Shun Yang, Fei Chen

Background: Fibrinogen plays pivotal roles in multiple biological processes. Genetic mutation of the fibrinogen coding genes can result in congenital fibrinogen disorders (CFDs). We identified a novel heterozygous missense mutation, FGG c.1168G > T (NCBI NM_000509.6), and conducted expression studies and functional analyses to explore the influence on fibrinogen synthesis, secretion, and polymerization.

Methods: Coagulation tests were performed on the patients to detect the fibrinogen concentration. Whole-exome sequencing (WES) and Sanger sequencing were employed to detect the novel mutation. Recombinant fibrinogen-producing Chinese hamster ovary (CHO) cell lines were built to examine the recombinant fibrinogen synthesis and secretion by western blotting and enzyme-linked immunosorbent assay (ELISA). The functional analysis of fibrinogen was performed by thrombin-catalyzed fibrin polymerization assay. In silico molecular analyses were carried out to elucidate the potential molecular mechanisms.

Results: The clinical manifestations, medical history, and laboratory tests indicated the diagnosis of hypodysfibrinogenemia with bleeding phenotype in two patients. The WES and Sanger sequencing revealed that they shared the same heterozygous missense mutation, FGG c.1168G > T. In the expression studies and functional analysis, the missense mutation impaired the recombinant fibrinogen's synthesis, secretion, and polymerization. Furthermore, the in silico analyses indicated novel mutation led to the hydrogen bond substitution.

Conclusion: The study highlighted that the novel heterozygous missense mutation, FGG c.1168G > T, would change the protein secondary structure, impair the "A: a" interaction, and consequently deteriorate the fibrinogen synthesis, secretion, and polymerization.

背景:纤维蛋白原在多种生物过程中发挥着关键作用。纤维蛋白原编码基因的基因突变可导致先天性纤维蛋白原紊乱(CFDs)。我们发现了一个新的杂合子错义突变 FGG c.1168G > T(NCBI NM_000509.6),并进行了表达研究和功能分析,以探讨其对纤维蛋白原合成、分泌和聚合的影响:方法:对患者进行凝血试验,检测纤维蛋白原浓度。采用全外显子组测序(WES)和桑格测序检测新型突变。建立了可产生重组纤维蛋白原的中国仓鼠卵巢(CHO)细胞系,通过免疫印迹法和酶联免疫吸附法(ELISA)检测重组纤维蛋白原的合成和分泌。凝血酶催化纤维蛋白聚合试验对纤维蛋白原进行了功能分析。为阐明潜在的分子机制,还进行了硅分子分析:结果:根据临床表现、病史和实验室检查,两名患者被诊断为出血表型低纤维蛋白原血症。WES和Sanger测序显示,他们具有相同的杂合错义突变FGG c.1168G > T。在表达研究和功能分析中,该错义突变损害了重组纤维蛋白原的合成、分泌和聚合。此外,硅学分析表明,新型突变导致了氢键置换:研究结果表明,FGG c.1168G > T 这一新型杂合错义突变会改变蛋白质的二级结构,损害 "A:a "相互作用,从而影响纤维蛋白原的合成、分泌和聚合。
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引用次数: 0
Network pharmacology to unveil the mechanism of suanzaoren decoction in the treatment of alzheimer’s with diabetes 网络药理学揭示山楂煎剂治疗老年痴呆症合并糖尿病的机制
IF 2.7 3区 生物学 Pub Date : 2024-01-03 DOI: 10.1186/s41065-023-00301-z
Tao Chen, Yining Lei, Manqin Li, Xinran Liu, Lu Zhang, Fei Cai, Xiaoming Gong, Ruyi Zhang
Suanzaoren Decoction (SZRD), a well-known formula from traditional Chinese medicine, has been shown to have reasonable cognitive effects while relaxing and alleviating insomnia. Several studies have demonstrated significant therapeutic effects of SZRD on diabetes and Alzheimer’s disease (AD). However, the active ingredients and probable processes of SZRD in treating Alzheimer’s with diabetes are unknown. This study aims to preliminarily elucidate the potential mechanisms and potential active ingredients of SZRD in the treatment of Alzheimer’s with diabetes. The main components and corresponding protein targets of SZRD were searched on the TCMSP database. Differential gene expression analysis for diabetes and Alzheimer’s disease was conducted using the Gene Expression Omnibus database, with supplementation from OMIM and genecards databases for differentially expressed genes. The drug-compound-target-disease network was constructed using Cytoscape 3.8.0. Disease and SZRD targets were imported into the STRING database to construct a protein-protein interaction network. Further, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed on the intersection of genes. Molecular docking and molecular dynamics simulations were conducted on the Hub gene and active compounds. Gene Set Enrichment Analysis was performed to further analyze key genes. Through the Gene Expression Omnibus database, we obtained 1977 diabetes related genes and 622 AD related genes. Among drugs, diabetes and AD, 97 genes were identified. The drug-compound-target-disease network revealed that quercetin, kaempferol, licochalcone a, isorhamnetin, formononetin, and naringenin may be the core components exerting effects. PPI network analysis identified hub genes such as IL6, TNF, IL1B, CXCL8, IL10, CCL2, ICAM1, STAT3, and IL4. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that SZRD in the treatment of Alzheimer’s with diabetes is mainly involved in biological processes such as response to drug, aging, response to xenobiotic, and enzyme binding; as well as signaling pathways such as Pathways in cancer, Chemical carcinogenesis - receptor activation, and Fluid shear stress and atherosclerosis. Molecular docking results showed that licochalcone a, isorhamnetin, kaempferol, quercetin, and formononetin have high affinity with CXCL8, IL1B, and CCL2. Molecular dynamics simulations also confirmed a strong interaction between CXCL8 and licochalcone a, isorhamnetin, and kaempferol. Gene Set Enrichment Analysis revealed that CXCL8, IL1B, and CCL2 have significant potential in diabetes. This study provides, for the first time, insights into the active ingredients and potential molecular mechanisms of SZRD in the treatment of Alzheimer’s with diabetes, laying a theoretical foundation for future basic research. • SZRD may improve Alzheimer’s with diabetes through potential active ingredients and hub genes. • licochalcone a, isorhamnetin, kaempferol, q
川芎煎剂(SZRD)是一种传统中药名方,已被证明具有合理的认知效果,同时还能放松和缓解失眠。多项研究表明,川芎嗪对糖尿病和阿尔茨海默病(AD)有明显的治疗效果。然而,SZRD 治疗糖尿病阿尔茨海默病的有效成分和可能过程尚不清楚。本研究旨在初步阐明 SZRD 治疗糖尿病阿尔茨海默病的潜在机制和潜在活性成分。研究人员在TCMSP数据库中检索了SZRD的主要成分和相应的蛋白靶点。利用基因表达总库数据库对糖尿病和阿尔茨海默病的差异基因表达进行了分析,并从 OMIM 和 genecards 数据库中对差异表达基因进行了补充。药物-化合物-靶点-疾病网络使用 Cytoscape 3.8.0 构建。疾病和深部靶标被导入 STRING 数据库,以构建蛋白质-蛋白质相互作用网络。此外,还对基因交叉点进行了基因本体和京都基因与基因组百科全书分析。对中枢基因和活性化合物进行了分子对接和分子动力学模拟。为进一步分析关键基因,还进行了基因组富集分析(Gene Set Enrichment Analysis)。通过基因表达总库(Gene Expression Omnibus)数据库,我们获得了1977个糖尿病相关基因和622个AD相关基因。在药物、糖尿病和AD中,我们发现了97个基因。药物-化合物-靶标-疾病网络显示,槲皮素、山柰醇、甘草查耳酮 a、异鼠李素、甲萘素和柚皮素可能是发挥效应的核心成分。PPI 网络分析确定了 IL6、TNF、IL1B、CXCL8、IL10、CCL2、ICAM1、STAT3 和 IL4 等枢纽基因。基因本体和京都基因和基因组百科全书分析表明,SZRD在治疗阿尔茨海默氏症合并糖尿病中主要参与药物反应、衰老、异生物反应和酶结合等生物过程,以及癌症通路、化学致癌-受体激活、流体剪切应力和动脉粥样硬化等信号通路。分子对接结果表明,甘草查耳酮 a、异鼠李素、山柰醇、槲皮素和福莫西汀与 CXCL8、IL1B 和 CCL2 具有很高的亲和力。分子动力学模拟也证实了 CXCL8 与甘草查耳酮 a、异鼠李素和山奈果醇之间存在很强的相互作用。基因组富集分析(Gene Set Enrichment Analysis)显示,CXCL8、IL1B 和 CCL2 在糖尿病中具有重要的潜在作用。这项研究首次揭示了SZRD治疗阿尔茨海默氏症合并糖尿病的有效成分和潜在分子机制,为今后的基础研究奠定了理论基础。- SZRD可能通过潜在的活性成分和枢纽基因改善糖尿病阿尔茨海默氏症。- 甘草查耳酮 a、异鼠李素、山柰醇、槲皮素和福莫西汀是 SZRD 治疗糖尿病阿尔茨海默氏症的潜在活性成分。- IL6、TNF、IL1B、CXCL8、IL10、CCL2、ICAM1、STAT3 和 IL4 是枢纽基因,与潜在的活性成分有很强的结合能力。
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引用次数: 0
Extracellular vesicle-derived TP53BP1, CD34, and PBX1 from human peripheral blood serve as potential biomarkers for the assessment and prediction of vascular aging 来自人体外周血的细胞外囊泡衍生 TP53BP1、CD34 和 PBX1 是评估和预测血管老化的潜在生物标记物
IF 2.7 3区 生物学 Pub Date : 2024-01-03 DOI: 10.1186/s41065-023-00306-8
Yichao Wen, Haiyang Chen, Yu Wang, Yiqing Sun, Fangfang Dou, Xiling Du, Te Liu, Chuan Chen
Vascular aging is an important pathophysiological basis for the senescence of various organs and systems in the human body, and it is a common pathogenetic trigger for many chronic diseases in the elderly. The extracellular vesicles (EVs) from young and aged umbilical vein endothelial cells were isolated and identified by qPCR the differential expression levels of 47 mRNAs of genes closely related to aging in the two groups. There were significant differences in the expression levels of 18 genes (we noted upregulation in PLA2G12A, TP53BP1, CD144, PDE11A, FPGT, SERPINB4, POLD1, and PPFIBP2 and downregulation in ATP2C2, ROBO2, RRM2, GUCY1B1, NAT1-14, VEGFR2, WTAPP1, CD146, DMC1, and GRIK2). Subsequent qPCR identification of the above-mentioned genes in PBMCs and plasma-EVs from the various age groups revealed that the trend in expression levels in peripheral blood plasma-EVs of the different age groups was approximately the same as that in PBMCs. Of these mRNAs, the expression of four genes–PLA2G12A, TP53BP1, OPRL1, and KIAA0895–was commensurate with increasing age. In contradistinction, the expression trend of four genes (CREG1, PBX1, CD34, and SLIT2) was inversely proportional to the increase in age. Finally, by taking their intersection, we determined that the expression of TP53BP1 was upregulated with increasing human age and that CD34 and PBX1 were downregulated with increasing age. Our study indicates that human peripheral blood plasma-EV-derived TP53BP1, CD34, and PBX1 potentially comprise a noninvasive biomarker for assessing and predicting vascular aging.
血管衰老是人体各器官和系统衰老的重要病理生理基础,也是老年人多种慢性疾病的常见致病诱因。本研究分离了年轻脐静脉内皮细胞和老年脐静脉内皮细胞的胞外囊泡(EVs),并通过 qPCR 方法鉴定了两组细胞中与衰老密切相关的 47 个基因 mRNAs 的不同表达水平。其中 18 个基因的表达水平存在明显差异(我们注意到 PLA2G12A、TP53BP1、CD144、PDE11A、FPGT、SERPINB4、POLD1 和 PPFIBP2 上调,ATP2C2、ROBO2、RRM2、GUCY1B1、NAT1-14、VEGFR2、WTAPP1、CD146、DMC1 和 GRIK2 下调)。随后对不同年龄组的 PBMC 和血浆-EV 中的上述基因进行 qPCR 鉴定,发现不同年龄组的外周血血浆-EV 的表达水平趋势与 PBMC 大致相同。在这些 mRNA 中,PLA2G12A、TP53BP1、OPRL1 和 KIAA0895 这四个基因的表达量与年龄的增长相一致。与此相反,四个基因(CREG1、PBX1、CD34 和 SLIT2)的表达趋势与年龄的增长成反比。最后,通过它们之间的交集,我们确定 TP53BP1 的表达随着人体年龄的增加而上调,CD34 和 PBX1 则随着年龄的增加而下调。我们的研究表明,人体外周血血浆-EV 衍生的 TP53BP1、CD34 和 PBX1 有可能成为评估和预测血管老化的无创生物标志物。
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引用次数: 0
Revisiting bicoid function: complete inactivation reveals an additional fundamental role in Drosophila egg geometry specification 重新审视双核功能:完全失活揭示了果蝇卵几何规格化中的另一个基本作用
IF 2.7 3区 生物学 Pub Date : 2024-01-02 DOI: 10.1186/s41065-023-00305-9
Stefan Baumgartner
The bicoid (bcd) gene in Drosophila has served as a paradigm for a morphogen in textbooks for decades. Discovered in 1986 as a mutation affecting anterior development in the embryo, its expression pattern as a protein gradient later confirmed the prediction from transplantation experiments. These experiments suggested that the protein fulfills the criteria of a true morphogen, with the existence of a homeodomain crucial for activation of genes along the anterior-posterior axis, based on the concentration of the morphogen. The bcd gene undergoes alternative splicing, resulting in, among other isoforms, a small and often neglected isoform with low abundance, which lacks the homeodomain, termed small bicoid (smbcd). Most importantly, all known classical strong bcd alleles used in the past to determine bcd function apparently do not affect the function of this isoform. To overcome the uncertainty regarding which isoform regulates what, I removed the bcd locus entirely using CRISPR technology. bcdCRISPR eggs exhibited a short and round appearance. The phenotype could be ascribed to smbcd because all bcd alleles affecting the function of the major transcript, termed large bicoid (lgbcd) showed normally sized eggs. Several patterning genes for the embryo showed expression in the oocyte, and their expression patterns were altered in bcdCRISPR oocytes. In bcdCRISPR embryos, all downstream segmentation genes showed altered expression patterns, consistent with the expression patterns in “classical” alleles; however, due to the altered egg geometry resulting in fewer blastoderm nuclei, additional constraints came into play, further affecting their expression patterns. This study unveils a novel and fundamental role of bcd in shaping the egg’s geometry. This discovery demands a comprehensive revision of our understanding of this important patterning gene and prompts a reevaluation of past experiments conducted under the assumption that bcd mutants were bcdnull-mutants.
几十年来,果蝇的 bicoid(bcd)基因一直是教科书中形态发生器的范例。该基因于 1986 年作为影响胚胎前部发育的突变基因被发现,其蛋白梯度表达模式后来证实了移植实验的预测。这些实验表明,该蛋白符合真正的形态发生蛋白的标准,它存在一个同源结构域,对于根据形态发生蛋白的浓度沿前后轴激活基因至关重要。bcd 基因会发生替代剪接,除其他异构体外,还会产生一种小的、经常被忽视的低丰度异构体,这种异构体缺乏同源结构域,被称为小 bicoid(smbcd)。最重要的是,过去用于确定 bcd 功能的所有已知经典强 bcd 等位基因显然都不影响该异构体的功能。为了克服哪种同工酶调控哪种功能的不确定性,我利用 CRISPR 技术完全移除了 bcd 基因座。这种表型可以归因于 smbcd,因为所有影响主要转录本功能的 bcd 等位基因(称为大双核(lgbcd))都表现出正常大小的卵子。胚胎的几个模式基因在卵母细胞中都有表达,而它们在 bcdCRISPR 卵母细胞中的表达模式发生了改变。在 bcdCRISPR 胚胎中,所有下游分割基因的表达模式都发生了改变,这与 "经典 "等位基因的表达模式一致;然而,由于卵子几何形状的改变导致胚泡核减少,额外的限制因素开始发挥作用,进一步影响了它们的表达模式。这项研究揭示了 bcd 在塑造卵子几何形状中的新的基本作用。这一发现要求我们全面修正对这一重要模式基因的认识,并促使我们重新评估过去假设 bcd 突变体为 bcdnull 突变体所进行的实验。
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引用次数: 0
Mechanisms of Actinidia chinensis Planch in treating colon cancer based on the integration of network pharmacology, molecular docking, and experimental verification 基于网络药理学、分子对接和实验验证整合的放线菌治疗结肠癌的机制
IF 2.7 3区 生物学 Pub Date : 2023-12-15 DOI: 10.1186/s41065-023-00303-x
Jin-Fang Chen, Shi-Wei Wu, Zi-Man Shi, Yan-Jie Qu, Min-Rui Ding, Bing Hu
As an anticancer Chinese herbal medicine, the effective components and mechanism of Actinidia chinensis Planch (ACP, Tengligen) in the treatment of colon cancer are still unclear. In the present study, the integration of network pharmacology, molecular docking, and cell experiments was employed to study the effective mechanism of ACP against colon cancer. The Venn diagram and STRING database were used to construct the protein–protein interaction network (PPI) of ACP-colon cancer, and further topological analysis was used to obtain the key target genes of ACP in colon cancer. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to visualize the related functions and pathways. Molecular docking between key targets and compounds was determined using software such as AutoDockTools. Finally, the effect of ACP on CT26 cells was observed in vitro. The study identified 40 ACP-colon key targets, including CASP3, CDK2, GSK3B, and PIK3R1. GO and KEGG enrichment analyses found that these genes were involved in 211 biological processes and 92 pathways, among which pathways in cancer, PI3K-Akt, p53, and cell cycle might be the main pathways of ACP against colon cancer. Molecular docking verified that the key components of ACP could stably bind to the corresponding targets. The experimental results showed that ACP could inhibit proliferation, induce apoptosis, and downregulate the phosphorylation of PIK3R1, Akt, and GSK3B in CT26 cells. ACP is an anti-colon cancer herb with multiple components, and involvement of multiple target genes and signaling pathways. ACP can significantly inhibit proliferation and induce apoptosis of colon cancer cells, which may be closely related to the regulation of PI3K/AKT/GSK3B signal transduction.
作为一种抗癌中药,放线菌(Actinidia chinensis Planch,ACP,Tengligen)治疗结肠癌的有效成分和机制尚不清楚。本研究采用网络药理学、分子对接和细胞实验相结合的方法来研究放线菌素对结肠癌的有效机制。利用维恩图和STRING数据库构建了ACP-结肠癌的蛋白-蛋白相互作用网络(PPI),并进一步通过拓扑分析获得了ACP在结肠癌中的关键靶基因。利用基因本体论(GO)和京都基因组百科全书(KEGG)富集分析可视化相关功能和通路。使用 AutoDockTools 等软件确定了关键靶点与化合物之间的分子对接。最后,在体外观察了 ACP 对 CT26 细胞的影响。研究发现了40个ACP-colon关键靶点,包括CASP3、CDK2、GSK3B和PIK3R1。GO和KEGG富集分析发现,这些基因参与了211个生物学过程和92条通路,其中癌症通路中的PI3K-Akt、p53和细胞周期可能是ACP抗结肠癌的主要通路。分子对接验证了ACP的关键成分能与相应的靶点稳定结合。实验结果表明,ACP能抑制CT26细胞的增殖、诱导凋亡并下调PIK3R1、Akt和GSK3B的磷酸化。ACP是一种具有多种成分的抗结肠癌中草药,涉及多个靶基因和信号通路。ACP 能明显抑制结肠癌细胞的增殖并诱导其凋亡,这可能与 PI3K/AKT/GSK3B 信号转导的调控密切相关。
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引用次数: 0
A pan-cancer analysis of Dyskeratosis congenita 1 (DKC1) as a prognostic biomarker 先天性角化异常 1 (DKC1) 作为预后生物标志物的泛癌症分析
IF 2.7 3区 生物学 Pub Date : 2023-12-11 DOI: 10.1186/s41065-023-00302-y
Xin-ying Liu, Qing Tan, Lin-xiao Li
Dyskeratosis congenita 1 (DKC1), a critical component of telomerase complex, is highly expressed in a variety of human cancers. However, the association of DKC1 with cancer occurrence and development stages is not clear, making a pan-cancer analysis crucial. We conducted a study using various bioinformatic databases such as TIMER, GEPIA, UALCAN, and KM plotter Analysis to examine the different expressions of DKC1 in multiple tissues and its correlation with pathological stages. Through KEGG analysis, GO enrichment analysis and Venn analysis, we were able to reveal DKC1-associated genes and signaling pathways. In addition, we performed several tests including the CCK, wound healing assay, cell cycle arrest assay, transwell assay and Sa-β-gal staining on DKC1-deleted MDA-231 cells. Our study demonstrates that DKC1 has relatively low expression specificity in different tissues. Furthermore, we found that in ACC, KICH, KIRP and LIHC, the expression level of DKC1 is positively correlated with pathological stages. Conversely, in NHSC, KIRP, LGG, LIHC, MESO and SARC, we observed a negative influence of DKC1 expression level on the overall survival rate. We also found a significant positive correlation between DKC1 expression and Tumor Mutational Burden in 14 tumors. Additionally, we observed a significantly negative impact of DKC1 DNA methylation on gene expression at the promoter region in BRCA. We also identified numerous phosphorylation sites concentrated at the C-terminus of the DKC1 protein. Our GO analysis revealed a correlation between DKC1 and ribosomal biosynthesis pathways, and the common element UTP14A was identified. We also observed decreased rates of cell proliferation, migration and invasion abilities in DKC1-knockout MDA-MB-231 cell lines. Furthermore, DKC1-knockout induced cell cycle arrest and caused cell senescence. Our findings suggest that the precise expression of DKC1 is closely associated with the occurrence and developmental stages of cancer in multiple tissues. Depletion of DKC1 can inhibit the abilities of cancer cells to proliferate, migrate, and invade by arresting the cell cycle and inducing cell senescence. Therefore, DKC1 may be a valuable prognostic biomarker for the diagnosis and treatment of cancer in various tissues.
先天性角化异常1(DKC1)是端粒酶复合物的一个重要组成部分,在多种人类癌症中高度表达。然而,DKC1 与癌症发生和发展阶段的关系并不明确,因此泛癌症分析至关重要。我们利用 TIMER、GEPIA、UALCAN 和 KM plotter Analysis 等多个生物信息学数据库进行了一项研究,探讨了 DKC1 在多种组织中的不同表达及其与病理分期的相关性。通过 KEGG 分析、GO 富集分析和 Venn 分析,我们揭示了与 DKC1 相关的基因和信号通路。此外,我们还对删除了DKC1的MDA-231细胞进行了CCK、伤口愈合试验、细胞周期停滞试验、Transwell试验和Sa-β-gal染色等测试。我们的研究表明,DKC1在不同组织中的表达特异性相对较低。此外,我们发现在 ACC、KICH、KIRP 和 LIHC 中,DKC1 的表达水平与病理分期呈正相关。相反,在 NHSC、KIRP、LGG、LIHC、MESO 和 SARC 中,我们观察到 DKC1 表达水平对总生存率有负向影响。在 14 种肿瘤中,我们还发现 DKC1 表达与肿瘤突变负荷之间存在明显的正相关性。此外,我们还观察到 DKC1 DNA 甲基化对 BRCA 启动子区域的基因表达有明显的负面影响。我们还发现许多磷酸化位点集中在 DKC1 蛋白的 C 端。我们的 GO 分析表明,DKC1 与核糖体生物合成途径之间存在相关性,并发现了共同元素 UTP14A。我们还观察到 DKC1 基因敲除的 MDA-MB-231 细胞系的细胞增殖率、迁移率和侵袭能力均有所下降。此外,DKC1-基因敲除诱导细胞周期停滞并导致细胞衰老。我们的研究结果表明,DKC1的精确表达与多种组织中癌症的发生和发展阶段密切相关。通过抑制细胞周期和诱导细胞衰老,DKC1可抑制癌细胞的增殖、迁移和侵袭能力。因此,DKC1 可能是诊断和治疗各种组织癌症的一种有价值的预后生物标志物。
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引用次数: 0
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