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Insight into the potential of algorithms using AI technology as in vitro diagnostics utilizing microbial extracellular vesicles. 洞察利用人工智能技术作为体外诊断算法的潜力,利用微生物细胞外囊泡。
IF 2.3 3区 生物学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-21 DOI: 10.1016/j.mcp.2024.101992
Jinho Yang

Recently, the microbiome has been gaining significant attention in the healthcare sector as a next-generation factor. However, there remains a substantial gap in our understanding of the fundamental mechanisms of microbes, particularly regarding the effector microbial products exchanged between the microbiota and the host. Consequently, research on microbial extracellular vesicles (MEVs) has increased. MEVs, which are nano-sized, can circulate throughout the body and penetrate the bloodstream, carrying diverse information. Consequently, they are increasingly being utilized in medical applications. Additionally, AI technologies are being utilized in medicine. The combination of MEVs and AI technology is being explored for the development of algorithm-based in vitro diagnostics (IVD). Therefore, this study aims to review the integration of MEVs and AI technology as diagnostic tools for personalized medicine. This paper reviewed the MEV-based algorithms developed by a variety of human samples and AI technology. Additionally, most of MEV-based diagnostic models showed higher clinical performance. Several important factors are crucial for accurate diagnosis. First, optimizing sample types according to specific diseases is essential. Second, AI technology with higher diagnostic power yields more accurate results. Finally, incorporating additional markers can enhance diagnostic power. However, applying this tool in situ faces several limitations, including method standardization, sample size, and analysis techniques. In the future, we anticipate that research on MEVs will advance our understanding of their role in disease and establish the foundation for precision medicine strategies.

最近,微生物组作为下一代因素在医疗保健领域受到极大关注。然而,我们对微生物基本机制的了解仍有很大差距,尤其是对微生物群与宿主之间交换的效应微生物产物的了解。因此,对微生物胞外囊泡(MEVs)的研究日益增多。微生物胞外囊泡只有纳米大小,可在体内循环并渗透到血液中,携带多种信息。因此,它们越来越多地被应用于医疗领域。此外,人工智能技术也被应用于医疗领域。人们正在探索将 MEV 与人工智能技术相结合,开发基于算法的体外诊断(IVD)。因此,本研究旨在回顾 MEV 与人工智能技术的结合,将其作为个性化医疗的诊断工具。本文回顾了由各种人类样本和人工智能技术开发的基于 MEV 的算法。此外,大多数基于 MEV 的诊断模型都显示出较高的临床性能。有几个重要因素对准确诊断至关重要。首先,根据特定疾病优化样本类型至关重要。其次,诊断能力更强的人工智能技术能产生更准确的结果。最后,加入额外的标记物可以提高诊断能力。然而,原位应用这一工具面临着一些限制,包括方法标准化、样本量和分析技术。未来,我们预计对 MEV 的研究将推进我们对其在疾病中作用的理解,并为精准医疗战略奠定基础。
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引用次数: 0
Caspase-1 knockout disrupts pyroptosis and protects photoreceptor cells from photochemical damage 敲除 Caspase-1 可破坏裂解过程并保护感光细胞免受光化学损伤
IF 2.3 3区 生物学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-17 DOI: 10.1016/j.mcp.2024.101991
Xiaoping Yu , Jiayuan Peng , Qian Zhong , Ailin Wu , Xiaoming Deng , Yanfeng Zhu

Aim

Retinal photochemical damage (RPD) plays a significant role in the development of various ocular diseases, with Caspase-1 being a key contributor. This study investigates the protective effects of Caspase-1 gene-mediated pyroptosis against RPD.

Methods

Differentially expressed genes (DEGs) associated with RPD were identified through the analysis of two expression profiles from the GEO database. Correlation analysis was used to pinpoint pyroptosis-related genes (PRGs) linked to RPD. A Caspase-1 knockout 661 W cell line was generated via CRISPR-Cas9 gene editing, and single-cell colonies were screened and purified. Validation of knockout cells was performed through RT-qPCR, gene sequencing, and Western blot analysis. Comparative assays on cell proliferation, intracellular reactive oxygen species (ROS), and cytotoxicity were conducted between wild-type and Caspase-1 knockout cells under light exposure. Further RT-qPCR and Western blot experiments examined changes in the mRNA and protein levels of key pyroptosis pathway components.

Results

Significant alterations in Caspase-1 expression were observed among PRGs. Homozygous Caspase-1 knockout cell lines were confirmed through RT-qPCR, genomic PCR product sequencing, and Western blot analysis. Compared to wild-type 661 W cells, Caspase-1 knockout cells exhibited higher viability and proliferation rates after 24 h of light exposure, alongside reduced LDH release. The expression of downstream pyroptosis factors at both the mRNA and protein levels was markedly decreased in the knockout group.

Conclusion

CRISPR/Cas9-mediated Caspase-1 knockout enhanced the resistance of 661 W cells to photochemical damage, suggesting that Caspase-1 may serve as a potential therapeutic target for RPD-related diseases.
目的:视网膜光化学损伤(RPD)在各种眼部疾病的发生发展中起着重要作用,而Caspase-1是其中的关键因素。本研究探讨了 Caspase-1 基因介导的热蛋白沉积对 RPD 的保护作用:方法:通过分析 GEO 数据库中的两个表达谱,确定了与 RPD 相关的差异表达基因(DEGs)。方法:通过分析 GEO 数据库中的两个表达谱,确定了与 RPD 相关的差异表达基因(DEGs),并利用相关性分析确定了与 RPD 相关的热蛋白沉积相关基因(PRGs)。通过 CRISPR-Cas9 基因编辑生成了 Caspase-1 基因敲除的 661W 细胞系,并筛选和纯化了单细胞菌落。通过 RT-qPCR、基因测序和 Western 印迹分析对基因敲除细胞进行了验证。在光照条件下,对野生型细胞和 Caspase-1 基因敲除细胞的细胞增殖、细胞内活性氧(ROS)和细胞毒性进行了比较分析。进一步的 RT-qPCR 和 Western 印迹实验检测了主要热蛋白沉积途径成分的 mRNA 和蛋白质水平的变化:结果:在 PRGs 中观察到 Caspase-1 表达的显著变化。通过 RT-qPCR、基因组 PCR 产物测序和 Western 印迹分析确认了同基因 Caspase-1 基因敲除细胞系。与野生型 661W 细胞相比,Caspase-1 基因敲除细胞在光照 24 小时后表现出更高的存活率和增殖率,同时 LDH 释放量减少。Caspase-1基因敲除组的下游热休克因子在mRNA和蛋白质水平上的表达都明显下降:结论:CRISPR/Cas9介导的Caspase-1基因敲除增强了661W细胞对光化学损伤的抵抗力,这表明Caspase-1可作为RPD相关疾病的潜在治疗靶点。
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引用次数: 0
Honokiol inhibits human osteosarcoma MG63 cell migration by upregulating FTO and Smad6 to promote autophagy Honokiol通过上调FTO和Smad6来促进自噬,从而抑制人骨肉瘤MG63细胞的迁移。
IF 2.3 3区 生物学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-07 DOI: 10.1016/j.mcp.2024.101988
Jian Wu , Wenqiang Xu , Jingchi Li , Cheng Luo , Bo Chen , Luo Lin , Tianyu Huang , Tao Luo , Lin Yang , Jiexiang Yang

Background

Osteosarcoma (OS) is a common primary malignant tumor of bone, most commonly seen in children and adolescents, which has a low survival rate and is a serious threat to patients' lives. Honokiol (HKL) is the main active components of Magnolia officinalis, which have significant anti-tumor properties. The aim of this study was to observe the autophagic and migratory effects of HKL on MG63 cells and to investigate whether the mechanism of action was related to FTO and Smad6.

Methods

Firstly, we cultured MG63 cells in vitro and intervened with different concentrations of HKL to detect cell activity by CCK8, apoptosis by flow cytometry, cell migration ability by scratch assay, cell invasion ability by transwell assay and MMP2, P62, LC3 I/II, FTO and Smad6 protein expression by Western blot.

Results

HKL inhibited MG63 cells activity and that this effect was dose and time dependent. Although there was no significant effect on apoptosis and invasive ability, HKL could act through effects such as promoting cell autophagy and inhibiting migration. HKL increased the protein expression levels of FTO, Smad6, MMP2, LC3 I/II and P62, and this effect was reduced after silencing of Smad6.

Conclusions

HKL induced autophagy and inhibited cell migration in MG63 cells by increasing the expression of FTP and Smad6. It can be seen that HKL may be a promising drug for the treatment of OS.
背景:骨肉瘤(Osteosarcoma,OS)是一种常见的原发性骨恶性肿瘤,多见于儿童和青少年,存活率低,严重威胁患者生命。厚朴酚(HKL)是厚朴的主要活性成分,具有显著的抗肿瘤作用。本研究旨在观察HKL对MG63细胞的自噬和迁移作用,并探讨其作用机制是否与FTO和Smad6有关:方法:首先体外培养MG63细胞,用不同浓度的HKL干预,用CCK8检测细胞活性,用流式细胞仪检测细胞凋亡,用划痕试验检测细胞迁移能力,用Transwell试验检测细胞侵袭能力,用Western blot检测MMP2、P62、LC3 I/II、FTO和Smad6蛋白表达:结果:香港六合彩资料大全抑制了 MG63 细胞的活性,而且这种作用与剂量和时间有关。虽然 HKL 对细胞凋亡和侵袭能力没有明显影响,但它可以通过促进细胞自噬和抑制迁移等作用发挥作用。香港六合彩资料大全增加了FTO、Smad6、MMP2、LC3 I/II和P62的蛋白表达水平,而沉默Smad6后这一效应降低:结论:HKL通过增加FTP和Smad6的表达诱导MG63细胞自噬并抑制细胞迁移。由此可见,HKL可能是一种治疗OS的有效药物。
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引用次数: 0
The activation of SYNJ2/GRB2 axis accelerates the malignant metastasis and angiogenesis of gastric cancer cells. SYNJ2/GRB2轴的激活加速了胃癌细胞的恶性转移和血管生成。
IF 2.3 3区 生物学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-07 DOI: 10.1016/j.mcp.2024.101990
Weiwei Ning, Qingxu Yang, Zhengbiao Li, Ming Xie

In gastric cancer (GC), tumor cell metastasis to lymph node may occur, and can be impacted by synaptojanin 2 (SYNJ2). Herein, we explored the mechanism of SYNJ2 in the progress of GC. SYNJ2 level in GC tissues was predicted by GEPIA database. After GC cells were transfected with short hairpin RNA against SYNJ2 (shSYNJ2), shGRB2, SYNJ2 overexpression plasmid and GRB2 overexpression plasmid, the mRNA levels of SYNJ2 and growth factor receptor-bound protein 2 (GRB2) in GC cells were quantified by qRT-PCR. CCK-8, flow cytometry, wound healing, transwell and tube formation assays were performed for detecting viability, apoptosis, migration, invasion and angiogenesis of GC cells. Protein levels of GRB2, vascular endothelial growth factor (VEGF), E-Cadherin, N-Cadherin and Vimentin in GC cells were measured by Western blot. The relationship between SYNJ2 and GRB2 was assessed by Co-immunoprecipitation (CO-IP) assay. SYNJ2 was highly expressed in GC tissues and cells. SYNJ2 overexpression promoted viability, migration, invasion, angiogenesis and GRB2 level, and inhibited apoptosis of GC cells, while shSYNJ2 exhibited opposite effects. GRB2 overexpression boosted yet shGRB2 suppressed cell migration, invasion and angiogenesis. Notably, SYNJ2 could interact with GRB2. GRB2 overexpression and shGRB2 reversed the effects of shSYNJ2 and overexpressed SYNJ2 on cell migration, invasion and angiogenesis and levels of metastasis-related proteins, respectively. In conclusion, SYNJ2 promotes GC cell metastasis and angiogenesis by up-regulating GRB2.

胃癌(GC)可能会发生肿瘤细胞向淋巴结的转移,而淋巴结转移可能会受到突触素2(SYNJ2)的影响。在此,我们探讨了SYNJ2在胃癌进展过程中的作用机制。我们通过 GEPIA 数据库预测了 GC 组织中 SYNJ2 的水平。用针对SYNJ2的短发夹RNA(shSYNJ2)、shGRB2、SYNJ2过表达质粒和GRB2过表达质粒转染GC细胞后,通过qRT-PCR定量检测GC细胞中SYNJ2和生长因子受体结合蛋白2(GRB2)的mRNA水平。通过 CCK-8、流式细胞术、伤口愈合、transwell 和试管形成试验检测 GC 细胞的活力、凋亡、迁移、侵袭和血管生成。通过 Western 印迹法测定了 GC 细胞中 GRB2、血管内皮生长因子(VEGF)、E-Cadherin、N-Cadherin 和 Vimentin 的蛋白水平。SYNJ2和GRB2之间的关系通过共免疫沉淀(CO-IP)法进行了评估。SYNJ2在GC组织和细胞中高表达。SYNJ2过表达可促进GC细胞的活力、迁移、侵袭、血管生成和GRB2水平,并抑制细胞凋亡,而shSYNJ2则表现出相反的作用。过表达 GRB2 会促进细胞迁移、侵袭和血管生成,而 shSYNJ2 则会抑制细胞迁移、侵袭和血管生成。值得注意的是,SYNJ2 可以与 GRB2 相互作用。过表达 GRB2 和 shGRB2 分别逆转了 shSYNJ2 和过表达 SYNJ2 对细胞迁移、侵袭和血管生成以及转移相关蛋白水平的影响。总之,SYNJ2通过上调GRB2促进GC细胞转移和血管生成。
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引用次数: 0
TNFRSF11B promotes the progression of bladder cancer through PI3K/AKT signaling pathway TNFRSF11B 通过 PI3K/AKT 信号通路促进膀胱癌的进展。
IF 2.3 3区 生物学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-31 DOI: 10.1016/j.mcp.2024.101989
Hao Deng , Jinzhuo Ning , Yuan Ruan , Weimin Yu , Fan Cheng
TNFRSF11B contributes to tumorigenesis in many malignancies. Nevertheless, its function and underlying tumorigenic mechanism in bladder cancer (BC) has been rare.
The clinical significance and relevant signaling pathway of TNFRSF11B in BC were assessed using bioinformatic analysis. The determination of TNFRSF11B expression was conducted in bladder tissues and BC cells. BC cells were subjected to functional experiments to evaluate their ability to proliferate, migrate, and invade. Cell apoptosis experiments were conducted. The protein levels of markers associated with epithelial-mesenchymal transition (EMT) and molecules linked to the PI3K/AKT pathway were assessed. To evaluate the effect of the PI3K/AKT pathway on TNFRSF11B, LY294002, a PI3K/AKT pathway inhibitor, was utilized. TNFRSF11B exhibited significant upregulation in both BC tissues and various cell lines. Inhibited TNFRSF11B expression impeded the growth, movement, infiltration of BC cells. Conversely, the ultimate outcome varied when TNFRSF11B was overexpressed. In vivo assay further confirmed the above results. Furthermore, TNFRSF11B promoted malignant traits by controlling the PI3K/AKT pathway. In BC, TNFRSF11B exhibits elevated expression levels and has a substantial tumor-promoting role in BC via the PI3K/AKT pathway. Importantly, TNFRSF11B may represent a valuable prognostic tumor marker for BC treatment.
TNFRSF11B 在许多恶性肿瘤中都有助于肿瘤的发生。然而,它在膀胱癌(BC)中的功能及其潜在的致瘤机制却很少见。本研究利用生物信息学分析评估了TNFRSF11B在膀胱癌中的临床意义和相关信号通路。在膀胱组织和BC细胞中测定了TNFRSF11B的表达。对 BC 细胞进行功能实验,评估其增殖、迁移和侵袭能力。还进行了细胞凋亡实验。评估了与上皮-间质转化(EMT)相关的标记物和与 PI3K/AKT 通路相关的分子的蛋白水平。为了评估 PI3K/AKT 通路对 TNFRSF11B 的影响,使用了 PI3K/AKT 通路抑制剂 LY294002。TNFRSF11B在BC组织和各种细胞系中均表现出明显的上调。抑制 TNFRSF11B 的表达会阻碍 BC 细胞的生长、移动和浸润。相反,当TNFRSF11B表达过高时,最终的结果也不尽相同。体内试验进一步证实了上述结果。此外,TNFRSF11B通过控制PI3K/AKT通路促进恶性特征。在BC中,TNFRSF11B的表达水平升高,并通过PI3K/AKT通路对BC的肿瘤有实质性的促进作用。重要的是,TNFRSF11B可能是一种有价值的预后肿瘤标志物,可用于BC的治疗。
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引用次数: 0
METTL14-mediated m6A modification upregulated SOCS3 expression alleviates thyroid cancer progression by regulating the JAK2/STAT3 pathway METTL14 介导的 m6A 修饰上调了 SOCS3 的表达,通过调节 JAK2/STAT3 通路缓解了甲状腺癌的进展。
IF 2.3 3区 生物学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-30 DOI: 10.1016/j.mcp.2024.101987
Ming Zhou , Yaqi Zhang , Qiong Zhang , Yanchu Tong
Thyroid cancer (TC) is the most common malignant tumor of the head and neck. As a common epigenetic modification in mRNAs, N6-methyladenosine (m6A) modification plays critical roles in biological process of cancers. However, m6A methyltransferase methyltransferase-like 14 (METTL14)-mediated m6A modification and its potential regulatory mechanisms in TC are not fully elucidated. In our study, we observed that METTL14 was decreased in TC tissues and cells. And upregulation of METTL14 induced apoptotic cell death and hampered cell proliferation, epithelial mesenchymal transition (EMT) and tumor growth in vitro and in vivo. Mechanistically, METTL14 increased the expression of suppressor of cytokine signaling 3 (SOCS3) through m6A methylation modification, and knockdown of SOCS3 reversed the inhibitory effect of overexpressing METTL14 on TC tumorigenesis. In addition, METTL14-mediated m6A modification of SOCS3 inactivated the janus kinase 2 (JAK2)-signal transducer and activator of transcription 3 (STAT3) pathway, and in the METTL14-overexpressing TC cells, silencing SOCS3-induced upregulation of cell proliferation, EMT and suppression of apoptosis was reversed by JAK2/STAT3 inhibitor AG490 and WP1066. Together, we indicated that METTL14/m6A/SOCS3/JAK2/STAT3 axis play an important role in the progression of TC.
甲状腺癌(TC)是头颈部最常见的恶性肿瘤。作为mRNA中常见的表观遗传修饰,N6-甲基腺苷(m6A)修饰在癌症的生物学过程中发挥着关键作用。然而,m6A甲基转移酶甲基转移酶样14(METTL14)介导的m6A修饰及其在TC中的潜在调控机制尚未完全阐明。在我们的研究中,我们观察到 METTL14 在 TC 组织和细胞中减少。METTL14的上调可诱导细胞凋亡,阻碍细胞增殖、上皮间质转化(EMT)以及体外和体内的肿瘤生长。从机制上讲,METTL14通过m6A甲基化修饰增加了细胞因子信号转导抑制因子3(SOCS3)的表达,而敲除SOCS3逆转了过表达METTL14对TC肿瘤发生的抑制作用。此外,METTL14介导的SOCS3的m6A修饰使janus激酶2(JAK2)-信号转导和激活剂转录3(STAT3)通路失活,在METTL14过表达的TC细胞中,沉默SOCS3诱导的细胞增殖、EMT上调和细胞凋亡抑制被JAK2/STAT3抑制剂AG490和WP1066逆转。综上所述,METTL14/m6A/SOCS3/ JAK2/STAT3轴在TC的进展中起着重要作用。
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引用次数: 0
Role of microRNAs in neutrophil extracellular trap formation and prevention: Systematic narrative review. 微RNA在中性粒细胞胞外捕获器的形成和预防中的作用:系统叙述性综述。
IF 2.3 3区 生物学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-13 DOI: 10.1016/j.mcp.2024.101986
Bashdar Mahmud Hussen, Mohammed Fatih Rasul, Goran Sedeeq Hama Faraj, Snur Rasool Abdullah, Seerwan Hamadameen Sulaiman, Hasan Pourmoshtagh, Mohammad Taheri

Active neutrophils play a variety of roles in both innate and adaptive immune responses, and one of the most vital roles is the formation and release of neutrophil extracellular traps (NETs). NETs are created when neutrophils release their chromatin contents to get and eradicate pathogenic organisms essentially. While NET helps fight bacteria, viruses, parasites, and infections, it is also linked to asthma, atherosclerosis, and cancer metastasis. Thus, understanding the molecular mechanisms behind NETosis formation and its inhibition is crucial for developing safe and effective therapies. This systematic review aims to identify the list of miRNAs that are associated with the formation of NETosis and illustrate the mechanism of action by classifying them based on their expression site. Moreover, it summarizes the list of miRNAs that can be targeted therapeutically to reduce NETosis in various disorders. The current study entailed the searching of PubMed and Google Scholar for articles related to the research topic role of miRNAs in NETosis in all types of disorders. The search terms and phrases included "NETs," "neutrophil extracellular traps," "NETosis," "miRNA," "miR," and "micro-RNA." The search was limited to articles published in English since October 2024 in both databases. Following a review of 23 papers, 19 of them met the inclusion and exclusion criteria of this study. Four papers have been removed as they are duplicated or do not meet our criteria. According to the published articles till October 2024, there are 14 miRNAs involved in the molecular pathway of NETosis which are miR-155, miR-1696, miR-7, miR-223, miR-146a, miR-142a-3p, miR-3146, miR-505, miR-4512, miR-15b-5p, miR-16-5p, miR-26b-5p, miR-125a-3p and miR-378a-3p. Moreover, eight miRNAs have been identified as possible therapeutic targets for the suppression of NETosis based on in-vivo studies carried out in various organisms, which are miR-155, miR-146a, miR-1696, miR-223, miR-142a-3p, miR-3146, miR-4512, miR-16-5p. Different miRNAs that are expressed inside or outside of neutrophils can regulate and influence NETosis. Eight miRNAs have also been identified as potential therapeutic targets, which can be utilized to inhibit the molecular pathways associated with NETosis and prevent its negative effects, such as asthma, atherosclerosis, cancer metastasis, and cancer recurrence. However, further human-based research is necessary to completely understand the role of miRNAs in the development of NETosis in humans.

活跃的中性粒细胞在先天性和适应性免疫反应中发挥着各种作用,其中最重要的作用之一就是形成和释放中性粒细胞胞外捕获物(NET)。当中性粒细胞释放其染色质内容物以获取和消灭病原体时,就会形成 NET。NET有助于抵抗细菌、病毒、寄生虫和感染,但也与哮喘、动脉粥样硬化和癌症转移有关。因此,了解 NETosis 形成及其抑制背后的分子机制对于开发安全有效的疗法至关重要。本系统综述旨在确定与 NETosis 形成相关的 miRNAs 列表,并根据其表达位点进行分类,从而说明其作用机制。此外,它还总结了可作为治疗靶点的 miRNA 列表,以减少各种疾病的 NETosis。目前的研究需要在 PubMed 和 Google Scholar 上搜索与 miRNA 在各类疾病的 NETosis 中的作用这一研究主题相关的文章。搜索关键词和短语包括 "NETs"、"嗜中性粒细胞胞外陷阱"、"NETosis"、"miRNA"、"miR "和 "micro-RNA"。检索仅限于自 2024 年 10 月以来在这两个数据库中发表的英文文章。在对 23 篇论文进行审查后,其中 19 篇符合本研究的纳入和排除标准。有四篇论文因重复或不符合我们的标准而被删除。根据截至 2024 年 10 月发表的文章,有 14 个 miRNA 参与了 NETosis 的分子通路,它们是 miR-155、miR-1696、miR-7、miR-223、miR-146a、miR-142a-3p、miR-3146、miR-505、miR-4512、miR-15b-5p、miR-16-5p、miR-26b-5p、miR-125a-3p 和 miR-378a-3p。此外,根据在不同生物体内进行的体内研究,有 8 种 miRNA 被确定为抑制 NETosis 的可能治疗靶点,它们是 miR-155、miR-146a、miR-1696、miR-223、miR-142a-3p、miR-3146、miR-4512 和 miR-16-5p。在中性粒细胞内部或外部表达的不同 miRNA 可调节和影响 NETosis。有 8 种 miRNA 被确定为潜在的治疗靶点,可用于抑制与 NETosis 相关的分子通路,防止其负面影响,如哮喘、动脉粥样硬化、癌症转移和癌症复发。然而,要完全了解 miRNA 在人类 NETosis 发展过程中的作用,还需要进一步的人体研究。
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引用次数: 0
Identification of circRNA-mediated competing endogenous RNA network involved in the development of cervical cancer 鉴定参与宫颈癌发展的 circRNA 介导的竞争性内源性 RNA 网络。
IF 2.3 3区 生物学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-10 DOI: 10.1016/j.mcp.2024.101984
Shaosheng Lou , Wang Yang , Qian Zhao , Yunshan Ouyang , Lingling Cao , Chen Lin

Background

The abnormal expression of circRNA may contribute to the progression of cervical cancer by influencing the biological processes.

Aim

This study aimed to identify the differentially expressed circRNAs in cervical cancer and validate the circ_0008193 ceRNA network in cervical cancer cells.

Methods

Using the absolute log2 value of fold change >1 and p-value of <0.05, the differentially expressed circRNAs were obtained from GSE102686 and GSE113696 from cervical cancer tissues and cervical cancer cells with the help of the GEO2R tool. Downstream miRNAs and mRNAs were predicted using relevant informatics databases. The circRNA-miRNA-mRNA interaction network was conducted with the assistance of Cytoscape. Circ_0008193-miR-182-5p-PTEN axis was validated with expression level and cell function using RT-qPCR, a dual-luciferase reporter assay, and cellular experiments.

Results

GSE102686 and GSE113696 databases overlapped 7 differentially expressed circRNAs and five circRNAs have the same expression pattern. Based on the literature and expression pattern, a circRNA-miRNA-mRNA network was conducted. The circ_0008193, miR-182-5p, and PTEN expression patterns were downregulation, upregulation, and downregulation, respectively. Overexpressed circ_0008193 suppressed proliferation, migration, and invasion of cervical cancer cells. MiR-182-5p diminished the inhibitory influence of circ_0008193 on cellular behaviors, while PTEN counteracted the effect of miR-182-5p.

Conclusion

This investigation revealed the existence of a circRNA-miRNA-mRNA network in cervical cancer, and preliminary verified the function of circ_0008193-miR-182-5p-PTEN axis in cervical cancer cells, which offers additional guidance on investigating the molecular mechanisms of cervical cancer.
背景目的:本研究旨在鉴定宫颈癌中差异表达的circRNA,并验证circ_0008193 ceRNA在宫颈癌细胞中的网络表达:方法:利用 GEO2R 工具从 GSE102686 和 GSE113696 中获取宫颈癌组织和宫颈癌细胞中差异表达的 circRNAs,以折叠变化的绝对对数值大于 1 和 p 值小于 0.05 为标准。利用相关信息学数据库预测了下游 miRNA 和 mRNA。在 Cytoscape 的帮助下,进行了 circRNA-miRNA-mRNA 相互作用网络的研究。利用 RT-qPCR、双荧光素酶报告实验和细胞实验验证了 Circ_0008193-miR-182-5p-PTEN 轴的表达水平和细胞功能:结果:GSE102686和GSE113696数据库重叠了7个差异表达的circRNA,5个circRNA具有相同的表达模式。根据文献和表达模式,建立了 circRNA-miRNA-mRNA 网络。circ_0008193、miR-182-5p和PTEN的表达模式分别为下调、上调和下调。过表达的circ_0008193抑制了宫颈癌细胞的增殖、迁移和侵袭。MiR-182-5p削弱了circ_0008193对细胞行为的抑制作用,而PTEN则抵消了miR-182-5p的作用:结论:这项研究揭示了宫颈癌中存在一个circRNA-miRNA-mRNA网络,并初步验证了circ_0008193-miR-182-5p-PTEN轴在宫颈癌细胞中的功能,为研究宫颈癌的分子机制提供了更多的指导。
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引用次数: 0
The Prospective role of lapatinib as an adjuvant therapy in prevalent cancers: Insights from in silico analysis targeting EGFR and HER2 拉帕替尼作为流行性癌症辅助疗法的前瞻性作用:以表皮生长因子受体(EGFR)和表皮生长因子受体(HER2)为靶点的硅学分析透视。
IF 2.3 3区 生物学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-08 DOI: 10.1016/j.mcp.2024.101985
Behnaz Dolatabadi , Maryam Peymani , Leila Rouhi , Ali Salehzadeh , Kiavash Hushmandi , Mehrdad Hashemi

Introduction

Various pieces of evidence suggest an elevation in the levels of EGFR and HER2 in different cancers leading to the proliferation, invasion, and metastasis of cancer cells. In this study, we conducted a comprehensive investigation into the expression alterations of these two receptors in various cancers using in silico data. In addition, we investigated the therapeutic potential of lapatinib as an inhibitor of these receptors in various cancer types.

Methods

RNAseq data for prevalent cancers were downloaded from The Cancer Genome Atlas (TCGA). After initial preprocessing, expression changes of HER2, EGFR, and candidate genes—identified based on their association with EGFR and HER2 signaling pathways—were examined. Human protein atlas data were utilized to assess the protein expression of HER2 and EGFR. GSE129254 was employed to identify molecular pathways and candidate genes associated with lapatinib. The protein-protein interaction network was used to identify lapatinib-influenced hub genes. Clinical data for common cancers were used to investigate the correlation between the expression of candidate genes and patients' mortality rates by Cox regression test.

Results

The findings clearly indicated a significant increase in the expression levels of HER2 and EGFR in cancers such as kidney, lung, breast, bladder, pancreas, head and neck, stomach, and endometrial, both at the mRNA and protein levels (p-value <0.01). Additionally, more than 30 % of samples in some cancers showed a twofold increase in HER2 or EGFR expression. The analysis of GSE129254 data revealed that lapatinib reduces the expression of numerous genes associated with cell proliferation. METTL1, LYAR, LTV1, CCND1, NOP2, and DDX21 were identified as hub genes related to the effect of lapatinib. Our results demonstrated that many hub genes exhibited elevated expression in candidate cancers, and the upregulation of some of them was correlated with poor prognosis.

Conclusion

Our results indicate an upregulation in the expression levels of HER2 and EGFR in certain common cancers, suggesting that lapatinib, in addition to breast cancer, could be considered for the treatment of these cancers. Furthermore, we demonstrated that some genes with increased expression in prevalent cancers and associated with poor prognosis have the potential to be modulated by lapatinib.
导言:各种证据表明,不同癌症中表皮生长因子受体(EGFR)和表皮生长因子受体(HER2)水平的升高会导致癌细胞的增殖、侵袭和转移。在本研究中,我们利用硅学数据对这两种受体在不同癌症中的表达变化进行了全面调查。此外,我们还研究了拉帕替尼作为这两种受体的抑制剂在各种癌症中的治疗潜力:方法:从癌症基因组图谱(TCGA)下载流行癌症的 RNAseq 数据。经过初步预处理后,对 HER2、表皮生长因子受体和候选基因(根据它们与表皮生长因子受体和 HER2 信号通路的关系确定)的表达变化进行了检测。人类蛋白质图谱数据用于评估 HER2 和表皮生长因子受体的蛋白质表达。利用 GSE129254 确定与拉帕替尼相关的分子通路和候选基因。蛋白-蛋白相互作用网络用于识别受拉帕替尼影响的枢纽基因。利用常见癌症的临床数据,通过 Cox 回归检验研究候选基因的表达与患者死亡率之间的相关性:结果:研究结果表明,在肾癌、肺癌、乳腺癌、膀胱癌、胰腺癌、头颈癌、胃癌和子宫内膜癌等癌症中,HER2和表皮生长因子受体(EGFR)的表达水平在mRNA和蛋白质水平上都有明显增加(p值<0.01)。此外,在某些癌症中,超过 30% 的样本显示 HER2 或表皮生长因子受体表达增加了两倍。对GSE129254数据的分析表明,拉帕替尼降低了许多与细胞增殖相关的基因的表达。METTL1、LYAR、LTV1、CCND1、NOP2和DDX21被确定为与拉帕替尼效应相关的枢纽基因。我们的研究结果表明,许多中枢基因在候选癌症中表达升高,其中一些基因的上调与预后不良相关:结论:我们的研究结果表明,在某些常见癌症中,HER2和表皮生长因子受体(EGFR)的表达水平上调,这表明拉帕替尼除用于治疗乳腺癌外,还可用于治疗这些癌症。此外,我们还证明,一些在常见癌症中表达增加并与预后不良有关的基因有可能受到拉帕替尼的调节。
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引用次数: 0
Prognostic prediction of gastric cancer based on H&E findings and machine learning pathomics 基于 H&E 检查结果和机器学习病理组学的胃癌预后预测。
IF 2.3 3区 生物学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-09-30 DOI: 10.1016/j.mcp.2024.101983
Guoda Han , Xu Liu , Tian Gao , Lei Zhang , Xiaoling Zhang , Xiaonan Wei , Yecheng Lin , Bohong Yin

Aim

In this research, we aimed to develop a model for the accurate prediction of gastric cancer based on H&E findings combined with machine learning pathomics.

Methods

Transcriptome data, pathological images, and clinical data from 443 cases were retrieved from TCGA (The Cancer Genome Atlas Program) for survival analysis. The images were segmented using the Otsu algorithm, and features were extracted using the PyRadiomics package. Subsequently, the cases were randomly divided into a training cohort of 165 cases and a validation cohort of 69 cases. Features selected via minimum Redundancy - Maximum Relevance (mRMR)- recursive feature elimination (RFE) screening were used to train a model using the Gradient Boosting Machine (GBM) algorithm. The model's performance was evaluated using the area under the receiver operating characteristic (ROC) curve (AUC), calibration curves, and decision curves. Additionally, the correlation between the Pathomics score (PS) and immune genes was examined.

Results

In the multivariate analysis, heightened infiltration of activated CD4 memory T cells was strongly associated with improved overall survival (HR = 0.505, 95 % CI = 0.342–0.745, P < 0.001). The pathomic model, exhibiting robust predictive capability, demonstrated impressive AUC values of 0.844 and 0.750 in both study cohorts. The Decision Curve Analysis (DCA) unequivocally underscored the model's exceptional clinical utility. In a subsequent multivariate analysis, heightened infiltration of the PS also emerged as a significant protective factor for overall survival (HR = 0.506, 95 % CI = 0.329–0.777, P = 0.002).

Conclusion

The pathomic model based on H&E slides for predicting the infiltration degree of activated CD4 memory T cells, along with integrated bioinformatics analysis elucidating potential molecular mechanisms, offers novel prognostic indicators for the precise stratification and individualized prognosis of gastric cancer patients.
目的:在这项研究中,我们旨在开发一种基于H&E结果并结合机器学习病理组学的胃癌准确预测模型:方法:我们从 TCGA(癌症基因组图谱计划)中获取了 443 个病例的转录组数据、病理图像和临床数据,用于生存分析。使用Otsu算法对图像进行分割,并使用PyRadiomics软件包提取特征。随后,病例被随机分为 165 例训练队列和 69 例验证队列。通过最小冗余-最大相关性(mRMR)-递归特征剔除(RFE)筛选出的特征被用于使用梯度提升机(GBM)算法训练模型。使用接收者操作特征曲线(ROC)下面积(AUC)、校准曲线和决策曲线对模型的性能进行了评估。此外,还研究了病理组学评分(PS)与免疫基因之间的相关性:在多变量分析中,活化的 CD4 记忆 T 细胞浸润增加与总生存期的改善密切相关(HR = 0.505,95% CI = 0.342-0.745,P <0.001)。病理模型具有强大的预测能力,在两个研究队列中的AUC值分别为0.844和0.750,令人印象深刻。决策曲线分析(DCA)明确强调了该模型卓越的临床实用性。在随后的多变量分析中,PS的高度浸润也成为总生存率的重要保护因素(HR = 0.506,95% CI = 0.329-0.777,P = 0.002):基于H&E切片预测活化CD4记忆T细胞浸润程度的病理模型,以及阐明潜在分子机制的综合生物信息学分析,为胃癌患者的精确分层和个体化预后提供了新的预后指标。
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引用次数: 0
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Molecular and Cellular Probes
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