Plasma Membrane Calcium-Transporting ATPases

质膜钙转运 ATP 酶
  • 文章类型: Journal Article
    我们的研究旨在阐明金羧酸(ATA)抑制质膜Ca2-ATPase(PMCA)的机制,负责钙运输的关键酶。鉴于PMCA在细胞钙稳态中的关键作用,了解它是如何被ATA抑制的,对于潜在的调节该泵参与的生理病理细胞过程具有重要意义。我们的实验发现表明,ATA采用多种作用方式来抑制PMCA活性,受ATP的影响,也受钙和镁离子的影响。具体来说,镁似乎增强了这种抑制作用。我们的实验和计算机模拟结果表明,与其他蛋白质中报道的不同,与镁复合的ATA(ATA·Mg)是抑制PMCA的分子。总之,我们的研究提出了一个新的观点,并为未来旨在开发PMCA和其他蛋白质的新药理分子的研究工作奠定了坚实的基础。
    Our research aimed to elucidate the mechanism by which aurintricarboxylic acid (ATA) inhibits plasma membrane Ca2+-ATPase (PMCA), a crucial enzyme responsible for calcium transport. Given the pivotal role of PMCA in cellular calcium homeostasis, understanding how it is inhibited by ATA holds significant implications for potentially regulating physiopathological cellular processes in which this pump is involved. Our experimental findings revealed that ATA employs multiple modes of action to inhibit PMCA activity, which are influenced by ATP but also by the presence of calcium and magnesium ions. Specifically, magnesium appears to enhance this inhibitory effect. Our experimental and in-silico results suggest that, unlike those reported in other proteins, ATA complexed with magnesium (ATA·Mg) is the molecule that inhibits PMCA. In summary, our study presents a novel perspective and establishes a solid foundation for future research efforts aimed at the development of new pharmacological molecules both for PMCA and other proteins.
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  • 文章类型: Journal Article
    高血清雌激素浓度与哮喘的发展和严重程度有关。提示雌二醇与气道高反应性(AHR)之间存在联系。17β-雌二醇(E2)通过Ca2调节机制具有非基因组效应;然而,其对质膜Ca2ATPases(PMCA-1和-4)和肌浆网Ca2ATPase(SERCA)的影响尚不清楚。因此,在本研究中,我们的目的是通过涉及Ca2ATPases的机制,通过增加豚鼠气道平滑肌(ASM)中的细胞内Ca2浓度来证明E2是否有利于AHR。在豚鼠ASM中,Ca2+微量荧光法,肌肉收缩,和Westernblot进行评价。然后,我们在雌激素和Ca2+ATP酶之间进行了分子对接分析。在气管环中,E2对卡巴胆碱产生AHR。在豚鼠肌细胞中,急性暴露于生理水平的E2将咖啡因诱导的短暂Ca2峰值改变为Ca2平台。与PMCA抑制剂(镧和羧花素,CE)部分逆转了E2诱导的咖啡因反应持续平台。相比之下,环吡嗪酸(SERCA抑制剂),U-0126(ERK1/2抑制剂),氯化胆碱没有改变E2产生的Ca2平台。E2不影响线粒体单转运蛋白的活性和电容性Ca2进入。在豚鼠ASM中,Western印迹分析显示PMCA1和PMCA4表达。对接建模的结果表明E2与两种质膜ATP酶结合。在豚鼠气管平滑肌中,用CE抑制PMCA,诱导对卡巴胆碱的高反应性。17β-雌二醇通过抑制ASM中的PMCA产生高反应性,可能是导致女性哮喘危象增加的机制之一。
    High serum estrogen concentrations are associated with asthma development and severity, suggesting a link between estradiol and airway hyperresponsiveness (AHR). 17β-estradiol (E2) has non-genomic effects via Ca2+ regulatory mechanisms; however, its effect on the plasma membrane Ca2+-ATPases (PMCA1 and 4) and sarcoplasmic reticulum Ca2+-ATPase (SERCA) is unknown. Hence, in the present study, we aim to demonstrate if E2 favors AHR by increasing intracellular Ca2+ concentrations in guinea pig airway smooth muscle (ASM) through a mechanism involving Ca2+-ATPases. In guinea pig ASM, Ca2+ microfluorometry, muscle contraction, and Western blot were evaluated. Then, we performed molecular docking analysis between the estrogens and Ca2+ ATPases. In tracheal rings, E2 produced AHR to carbachol. In guinea pig myocytes, acute exposure to physiological levels of E2 modified the transient Ca2+ peak induced by caffeine to a Ca2+ plateau. The incubation with PMCA inhibitors (lanthanum and carboxyeosin, CE) partially reversed the E2-induced sustained plateau in the caffeine response. In contrast, cyclopiazonic acid (SERCA inhibitor), U-0126 (an inhibitor of ERK 1/2), and choline chloride did not modify the Ca2+ plateau produced by E2. The mitochondrial uniporter activity and the capacitative Ca2+ entry were unaffected by E2. In guinea pig ASM, Western blot analysis demonstrated PMCA1 and PMCA4 expression. The results from the docking modeling demonstrate that E2 binds to both plasma membrane ATPases. In guinea pig tracheal smooth muscle, inhibiting the PMCA with CE, induced hyperresponsiveness to carbachol. 17β-estradiol produces hyperresponsiveness by inhibiting the PMCA in the ASM and could be one of the mechanisms responsible for the increase in asthmatic crisis in women.
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  • 文章类型: Journal Article
    在电化学疗法中,通过电脉冲使细胞膜透化增加了化学疗法的抗肿瘤作用。在钙电穿孔中,用氯化钙代替化疗,有明显的好处。本研究探讨了使用高频或低频电穿孔的钙电穿孔对基底细胞癌的影响和潜在机制。低风险的原发性基底细胞癌在局部麻醉中用瘤内氯化钙治疗,然后以高(167kHz)或低(5kHz)频率进行电穿孔。非完全缓解者在3个月后再次治疗。主要终点是最后一次钙电穿孔后3个月的肿瘤反应。在各种细胞系中检查了质膜钙ATP酶,因为质膜钙ATP酶水平与钙电穿孔功效相关。25名患者中有22名完成了研究,其中7名(32%)在3个月时达到了完全缓解,高频脉冲和低频脉冲之间的功效没有差异。高频钙电穿孔的疼痛明显减轻(p=0.03)。与其他4种癌细胞系相比,基底细胞癌细胞系的质膜钙ATP酶增加了16-32倍。低风险基底细胞癌的钙电穿孔不能满足新的皮肤病学基底细胞癌治疗的要求,但可用作更晚期基底细胞癌手术的辅助治疗。基底细胞癌中PMCA水平升高可能导致疗效低下。
    In electrochemotherapy, permeabilization of the cell membrane by electric pulses increases the anti-tumour effect of chemotherapeutics. In calcium electroporation, chemotherapy is replaced by calcium chloride with obvious benefits. This study explores the effect and underlying mechanisms of calcium electroporation on basal cell carcinomas using either high- or low-frequency electroporation. Low-risk primary basal cell carcinomas were treated in local anaesthesia with intratumoral calcium chloride followed by electroporation with high (167 kHz) or low (5 kHz) frequencies. Non-complete responders were retreated after 3 months. The primary endpoint was tumour response 3 months after last calcium electroporation. Plasma membrane calcium ATPase was examined in various cell lines as plasma membrane calcium ATPase levels have been associated with calcium electroporation efficacy. Twenty-two out of 25 included patients complete the study and 7 of these (32%) achieved complete response at 3 months with no difference in efficacy between high- and low-frequency pulses. High-frequency calcium electroporation was significantly less painful (p=0.03). Plasma membrane calcium ATPase was increased 16-32-fold in basal cell carcinoma cell lines compared with 4 other cancer cell lines. Calcium electroporation for low-risk basal cell carcinomas does not fulfil the requirements of a new dermatological basal cell carcinoma treatment but may be useful as adjuvant treatment to surgery in more advanced basal cell carcinomas. The elevated PMCA levels in basal cell carcinomas may contribute to low efficacy.
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  • 文章类型: Journal Article
    巨细胞胞吞作用(MPC)是一种大规模的内吞作用途径,涉及肌动蛋白依赖性膜皱褶的形成和随后的皱褶闭合,以产生用于摄取液相货物的巨细胞胞体。MPC分为两种类型:组成型和刺激诱导型。巨噬细胞中的组成型MPC依赖于钙感应受体的细胞外Ca2感应。然而,刺激诱导的MPC与Ca2+之间的联系尚不清楚。这里,我们发现A431人表皮样癌细胞中表皮生长因子(EGF)诱导的MPC需要细胞内和细胞外Ca2。通过研究腔体细胞摄取缺陷(CUP)基因的哺乳动物同源物,我们鉴定了ATP2B4,编码称为质膜钙ATP酶4(PMCA4)的Ca2+泵,作为EGF诱导的MPC的Ca2相关调节因子。ATP2B4的敲除(KO),以及细胞外/细胞内Ca2+的消耗,抑制荷叶边闭合和macropinosome形成,不影响荷叶边的形成。我们证明了PMCA4活性本身的重要性,独立于通过其C末端与其他蛋白质的相互作用,称为PDZ结构域结合基序。此外,我们表明ATP2B4-KO降低了MPC过程中EGF刺激的Ca2振荡。我们的发现表明EGF诱导的MPC需要ATP2B4依赖性Ca2动力学。
    Macropinocytosis (MPC) is a large-scale endocytosis pathway that involves actin-dependent membrane ruffle formation and subsequent ruffle closure to generate macropinosomes for the uptake of fluid-phase cargos. MPC is categorized into two types: constitutive and stimuli-induced. Constitutive MPC in macrophages relies on extracellular Ca2+ sensing by a calcium-sensing receptor. However, the link between stimuli-induced MPC and Ca2+ remains unclear. Here, we find that both intracellular and extracellular Ca2+ are required for epidermal growth factor (EGF)-induced MPC in A431 human epidermoid carcinoma cells. Through investigation of mammalian homologs of coelomocyte uptake defective (CUP) genes, we identify ATP2B4, encoding for a Ca2+ pump called the plasma membrane calcium ATPase 4 (PMCA4), as a Ca2+-related regulator of EGF-induced MPC. Knockout (KO) of ATP2B4, as well as depletion of extracellular/intracellular Ca2+, inhibited ruffle closure and macropinosome formation, without affecting ruffle formation. We demonstrate the importance of PMCA4 activity itself, independent of interactions with other proteins via its C-terminus known as a PDZ domain-binding motif. Additionally, we show that ATP2B4-KO reduces EGF-stimulated Ca2+ oscillation during MPC. Our findings suggest that EGF-induced MPC requires ATP2B4-dependent Ca2+ dynamics.
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  • 文章类型: Journal Article
    目的:本研究旨在阐明参与清除神经元胞质Ca2+的主要ATP依赖性机制,并确定与海马锥体神经元这些机制相关的主要ATP生成途径-糖酵解或三羧酸循环/氧化磷酸化(TCA/OxPhos)。
    方法:我们的研究涉及评估基础Ca2+水平,并分析选择性结合抑制/阻断关键ATP依赖性机制和抑制TCA/OxPhos或糖酵解ATP来源后诱发神经元Ca2+瞬变的动力学特征。
    结果:我们的发现揭示了质膜Ca2ATPase(PMCA)是清除海马锥体神经元中胞质Ca2的主要ATP依赖性机制,在休息和神经元活动期间。值得注意的是,在细胞活动期间,PMCA依赖于糖酵解的ATP,挑战神经元依赖TCA/OxPhos获取ATP的传统观念。锥体神经元中Ca2+清除的其他机制,如SERCA和NCX,似乎依赖于TCA/OxPhos。有趣的是,在休息时,为PMCA和SERCA提供燃料所需的ATP,保持静息Ca2+的两种主要机制,似乎起源于糖酵解或TCA/OxPhos以外的来源。
    结论:这些发现强调了糖酵解在支持PMCA神经元功能以维持Ca2+稳态方面的重要作用。此外,他们阐明了细胞质Ca2清除机制对不同能量来源的不同依赖性。
    OBJECTIVE: This study sought to elucidate the primary ATP-dependent mechanisms involved in clearing cytosolic Ca2+ in neurons and determine the predominant ATP-generating pathway-glycolysis or tricarboxylic acid cycle/oxidative phosphorylation (TCA/OxPhos)-associated with these mechanisms in hippocampal pyramidal neurons.
    METHODS: Our investigation involved evaluating basal Ca2+ levels and analyzing the kinetic characteristics of evoked neuronal Ca2+ transients after selectively combined the inhibition/blockade of key ATP-dependent mechanisms with the suppression of either TCA/OxPhos or glycolytic ATP sources.
    RESULTS: Our findings unveiled that the plasma membrane Ca2+ ATPase (PMCA) serves as the principal ATP-dependent mechanism for clearance cytosolic Ca2+ in hippocampal pyramidal neurons, both during rest and neuronal activity. Remarkably, during cellular activity, PMCA relies on ATP derived from glycolysis, challenging the traditional notion of neuronal reliance on TCA/OxPhos for ATP. Other mechanisms for Ca2+ clearance in pyramidal neurons, such as SERCA and NCX, appear to be dependent on TCA/OxPhos. Interestingly, at rest, the ATP required to fuel PMCA and SERCA, the two main mechanisms to keep resting Ca2+, seems to originate from a source other than glycolysis or the TCA/OxPhos.
    CONCLUSIONS: These findings underscore the vital role of glycolysis in bolstering PMCA neuronal function to uphold Ca2+ homeostasis. Moreover, they elucidate the varying dependencies of cytoplasmic Ca2+ clearance mechanisms on distinct energy sources for their operation.
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  • 文章类型: Journal Article
    质膜Ca2-ATP酶(PMCA)对于真核细胞中细胞内钙水平的微调至关重要。在这项研究中,我们显示了所有人类和大鼠PMCA亚型中CARC序列的存在,我们通过分子动力学模拟进行了进一步分析.此分析侧重于PMCA1,包含三个CARC基序,和PMCA4,具有四个CARC结构域。在PMCA1中,两个CARC基序位于跨膜结构域内,而第三个位于细胞内界面。模拟描述了在胆固醇存在下更稳定的RMSD值和更低的RMSF波动,强调其潜在的稳定作用。在PMCA4中,发现了不同的动态。值得注意的是,与PMCA1相比,PMCA4中胆固醇和磷脂模拟之间的总能量差异明显。PMCA4的RMSD值表明在存在胆固醇的情况下具有更积极的构象,表明CARC和膜中的这种脂质之间存在强烈的相互作用。此外,与单独的POPC相比,两种PMCA同种型中的CARC的RMSF分析在胆固醇存在下表现出较低的值。对H键占有率和总能量值的分析强烈表明了CARC与胆固醇的潜在相互作用。鉴于PMCA在生理钙调节中的关键作用及其参与多种病理过程,这项研究强调了CARC基序及其与胆固醇的相互作用在阐明PMCA功能中的意义.这些对与CARC-胆固醇相互作用相关的能量偏好的见解为理解PMCA在维持钙稳态和解决潜在的相关病理方面的功能提供了有价值的启示。
    The plasma membrane Ca2+-ATPase (PMCA) is crucial for the fine tuning of intracellular calcium levels in eukaryotic cells. In this study, we show the presence of CARC sequences in all human and rat PMCA isoforms and we performed further analysis by molecular dynamics simulations. This analysis focuses on PMCA1, containing three CARC motifs, and PMCA4, with four CARC domains. In PMCA1, two CARC motifs reside within transmembrane domains, while the third is situated at the intracellular interface. The simulations depict more stable RMSD values and lower RMSF fluctuations in the presence of cholesterol, emphasizing its potential stabilizing effect. In PMCA4, a distinct dynamic was found. Notably, the total energy differences between simulations with cholesterol and phospholipids are pronounced in PMCA4 compared to PMCA1. RMSD values for PMCA4 indicate a more energetically favorable conformation in the presence of cholesterol, suggesting a robust interaction between CARCs and this lipid in the membranes. Furthermore, RMSF analysis for CARCs in both PMCA isoforms exhibit lower values in the presence of cholesterol compared to POPC alone. The analysis of H-bond occupancy and total energy values strongly suggests the potential interaction of CARCs with cholesterol. Given the crucial role of PMCAs in physiological calcium regulation and their involvement in diverse pathological processes, this study underscores the significance of CARC motifs and their interaction with cholesterol in elucidating PMCA function. These insights into the energetic preferences associated with CARC-cholesterol interactions offer valuable implications for understanding PMCA function in maintaining calcium homeostasis and addressing potential associated pathologies.
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  • 文章类型: Journal Article
    癫痫发作被视为兴奋性平衡变化的结果,这取决于大脑中突触可塑性的恶化。神经激酶,以及已知在突触可塑性中起作用的相关分子,提供兴奋性平衡的神经递质活动,不同的神经系统疾病,以前没有在癫痫中研究过。在这项研究中,共有34只Sprague-Dawley雄性和雌性大鼠,2个月大,使用重250-300g。用戊四氮(PTZ)制作大鼠癫痫模型。实验程序完成后,取大鼠脑组织,观察海马、皮质部位和脑干的组织病理学改变,以及与免疫组织化学方法相关的蛋白质的免疫反应性。作为组织病理学评估的结果,确定神经元变性和海马中扩张的血管数量,额叶皮质,PTZ癫痫持续状态(SE)组的脑干高于对照组。观察到神经激酶和相关蛋白TNF受体相关因子6(TRAF6),γ-氨基丁酸A型受体[(GABA(A)],和质膜Ca2ATPase(PMCA)蛋白免疫反应性水平增加,尤其是在雄性海马中,只有AMPA受体亚基1型(GluA1)免疫反应性降低,与其他蛋白质不同。我们认为这可能是由调节神经激酶和GluA1相互作用的机制中的问题引起的,并且可能导致实验性癫痫模型中突触可塑性的问题。在确定治疗策略时,阐明这种机制和靶向GluA1可能是有用的。
    Epileptic seizures are seen as a result of changing excitability balance depending on the deterioration in synaptic plasticity in the brain. Neuroplastin, and its related molecules which are known to play a role in synaptic plasticity, neurotransmitter activities that provide balance of excitability and, different neurological diseases, have not been studied before in epilepsy. In this study, a total of 34 Sprague-Dawley male and female rats, 2 months old, weighing 250-300 g were used. The epilepsy model in rats was made via pentylenetetrazole (PTZ). After the completion of the experimental procedure, the brain tissue of the rats were taken and the histopathological changes in the hippocampus and cortex parts and the brain stem were investigated, as well as the immunoreactivity of the proteins related to the immunohistochemical methods. As a result of the histopathological evaluation, it was determined that neuron degeneration and the number of dilated blood vessels in the hippocampus, frontal cortex, and brain stem were higher in the PTZ status epilepticus (SE) groups than in the control groups. It was observed that neuroplastin and related proteins TNF receptor-associated factor 6 (TRAF6), Gamma amino butyric acid type A receptors [(GABA(A)], and plasma membrane Ca2+ ATPase (PMCA) protein immunoreactivity levels increased especially in the male hippocampus, and only AMPA receptor subunit type 1 (GluA1) immunoreactivity decreased, unlike other proteins. We believe this may be caused by a problem in the mechanisms regulating the interaction of neuroplastin and GluA1 and may cause problems in synaptic plasticity in the experimental epilepsy model. It may be useful to elucidate this mechanism and target GluA1 when determining treatment strategies.
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  • 文章类型: Journal Article
    ATP2B1基因的单核苷酸多态性(SNP)与原发性高血压有关,但与顽固性高血压(RHT)的关联尚待研究。作者通过对1124名患有生活方式相关疾病的日本人的ATP2B1基因中的12个SNP进行基因分型,研究了ATP2B1SNP与RHT之间的关系。RHT患者使用三种降压药或使用≥4种降压药的血压(BP)控制不足。控制高血压的患者使用≤3种降压药物控制血压。通过逻辑回归分析每个SNP与RHT之间的关联。最终的队列有888(79.0%)和43(3.8%)患者控制高血压和RHT,分别。与ATP2B1中每个SNP的次要等位基因纯合的患者相比,在10个SNP上携带主要等位基因的患者数量显着增加,表现出RHT(在rs1401982上最显著:5.8%vs.0.8%,p=0.014;rs11105378最不显著:5.7%与0.9%,p=0.035;rs12817819最不显著:5.1%与10%,p=.413)。在对年龄进行多变量调整后,性别,收缩压,和其他混杂因素,rs2681472和rs1401982的相关性仍然显著(分别为OR:7.60,p<.05和OR:7.62,p=.049).此外,rs2681472和rs1401982与rs11105378处于连锁不平衡状态。这项研究在日本人群中确定了两个与RHT相关的ATP2B1SNP。rs1401982与RHT关系最密切,rs1401982的主要等位基因携带者需要更多的抗高血压药物。分析高血压患者的ATP2B1SNP有助于早期预测RHT和识别更可能需要更多降压药物的高危患者。
    Single-nucleotide polymorphisms (SNP) of ATP2B1 gene are associated with essential hypertension but their association with resistant hypertension (RHT) remains unexplored. The authors examined the relationship between ATP2B1 SNPs and RHT by genotyping 12 SNPs in ATP2B1 gene of 1124 Japanese individuals with lifestyle-related diseases. Patients with RHT had inadequate blood pressure (BP) control using three antihypertensive drugs or used ≥4 antihypertensive drugs. Patients with controlled hypertension had BP controlled using ≤3 antihypertensive drugs. The association between each SNP and RHT was analyzed by logistic regression. The final cohort had 888 (79.0%) and 43 (3.8%) patients with controlled hypertension and RHT, respectively. Compared with patients homozygous for the minor allele of each SNP in ATP2B1, a significantly higher number of patients carrying the major allele at 10 SNPs exhibited RHT (most significant at rs1401982: 5.8% vs. 0.8%, p = .014; least significant at rs11105378: 5.7% vs. 0.9%, p = .035; most nonsignificant at rs12817819: 5.1% vs. 10%, p = .413). After multivariate adjustment for age, sex, systolic BP, and other confounders, the association remained significant for rs2681472 and rs1401982 (OR: 7.60, p < .05 and OR: 7.62, p = .049, respectively). Additionally, rs2681472 and rs1401982 were in linkage disequilibrium with rs11105378. This study identified two ATP2B1 SNPs associated with RHT in the Japanese population. rs1401982 was most closely associated with RHT, and major allele carriers of rs1401982 required significantly more antihypertensive medications. Analysis of ATP2B1 SNPs in patients with hypertension can help in early prediction of RHT and identification of high-risk patients who are more likely to require more antihypertensive medications.
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  • 文章类型: Journal Article
    背景:LncRNAATP2B1-AS1(ATP2B1-AS1)参与各种疾病的发生和发展,而肺腺癌(LUAD)与ATP2B1-AS1之间的关系尚不清楚。本研究探讨ATP2B1-AS1在LUAD中的表达及其对患者生存和预后的影响。
    方法:收集参加本研究的患者的LUAD组织样本,通过实时定量聚合酶链反应(RT-qPCR)检测LUAD样品中ATP2B1-AS1和miR-141-3p的表达水平。通过细胞计数试剂盒-8(CCK-8)和transwell实验研究ATP2B1-AS1对A549细胞生长的影响。此外,通过Kaplan-Meier曲线和多变量Cox回归评估ATP2B1-AS1在LUAD中的预后价值.
    结果:ATP2B1-AS1在LUAD组织和细胞中下调,而miR-141-3p上调。将pcDNA3.1-ATP2B1-AS1转染入A549细胞后,A549细胞的增殖能力下降,A549细胞的迁移水平和侵袭能力也受到抑制。ATP2B1-AS1海绵miR-141-3p的高表达具有预后价值。
    结论:ATP2B1-AS1海绵miR-141-3p减轻了LUAD的进展,ATP2B1-AS1可作为LUAD的预后标志物。
    BACKGROUND: LncRNA ATP2B1-AS1 (ATP2B1-AS1) is involved in the occurrence and development of various diseases, while the relationship between lung adenocarcinoma (LUAD) and ATP2B1-AS1 is unclear. This study was to investigate the expression of ATP2B1-AS1 in LUAD and its influence on survival and prognosis of patients.
    METHODS: LUAD tissue samples from patients participating in this study were collected, and the expression levels of ATP2B1-AS1 and miR-141-3p in LUAD sampleswere detected by real-time quantitative polymerase chain reaction (RT-qPCR). The effect of ATP2B1-AS1 on the growth of A549 cells was investigated through cell counting kit-8 (CCK-8) and transwell experiments. Besides, the prognostic value of ATP2B1-AS1 in LUAD was assessed via Kaplan-Meier curve and multivariate Cox regression.
    RESULTS: ATP2B1-AS1 was downregulated in LUAD tissues and cells, whereas miR-141-3p was upregulated. After pcDNA3.1-ATP2B1-AS1 was transfected into A549 cells, the proliferation ability of A549 cells was decreased, and the migration level and invasion of A549 cells were also inhibited. High expression of ATP2B1-AS1 sponge miR-141-3p exerted prognostic value.
    CONCLUSIONS: ATP2B1-AS1 sponge miR-141-3p alleviated the progression of LUAD, and ATP2B1-AS1 may be deemed as a prognostic marker for LUAD.
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  • 文章类型: Journal Article
    背景:在蛋白质-蛋白质相互作用(PPI)网络的背景下,分析复杂疾病表型的全基因组关联研究(GWAS)数据是有价值的,因为相关的病理生理学是由相互作用的多蛋白途径的功能引起的。分析可能包括设计和管理表型特异性GWAS元数据库,其中包含与PPI和其他生物学数据集相关的基因型和eQTL数据。以及为基于PPI网络的数据集成开发系统的工作流程,以实现蛋白质和途径优先排序。这里,我们对血压(BP)调节进行了这项分析。
    方法:在MicrosoftSQLServerBP-GWAS元数据库中实现的关系方案实现了组合存储:GWAS数据和从GWAS目录和文献中挖掘的属性,Ensembl定义的SNP转录本关联,和GTExeQTL数据。从PICKLEPPImeta数据库重建了BP蛋白相互作用组,扩展GWAS推导的网络,将所有GWAS蛋白连接到一个组件中的最短路径。最短路径中间体被认为是BP相关的。对于蛋白质优先排序,我们将一个新的基于GWAS的综合评分方案与两个基于网络的标准结合起来:一个标准考虑了蛋白质在通过最短路径(RbSP)相互作用的重建组中的作用,另一个新的标准是促进GWAS优先蛋白质的共同邻居.按满足的标准的数量对优先的蛋白质进行排序。
    结果:元数据库包括与1167个BP相关蛋白编码基因相关的6687个变异体。GWAS推导的PPI网络包括1065种蛋白质,672形成一个连接的组件。RbSP相互作用组包含1443个额外的,网络推导的蛋白质,表明基本上所有的BP-GWAS蛋白最多是第二邻居。通过基于GWAS或基于网络的标准中的任一个,从最显著的BP的联合中导出优先的BP-蛋白质组。它包括335种蛋白质,从BPPPI网络扩展中推导出~2/3,至少有两个标准确定了126个优先级。ESR1是唯一满足所有三个标准的蛋白质,排在前十名的是INSR,PTN11,CDK6,CSK,NOS3,SH2B3,ATP2B1,FES和FINC,满足两个RbSP相互作用组的途径分析揭示了许多生物过程,实际上在功能上支持与BP相关的功能,扩展了我们对BP监管的理解。
    结论:实施的工作流程可用于其他多因素疾病。
    BACKGROUND: It is valuable to analyze the genome-wide association studies (GWAS) data for a complex disease phenotype in the context of the protein-protein interaction (PPI) network, as the related pathophysiology results from the function of interacting polyprotein pathways. The analysis may include the design and curation of a phenotype-specific GWAS meta-database incorporating genotypic and eQTL data linking to PPI and other biological datasets, and the development of systematic workflows for PPI network-based data integration toward protein and pathway prioritization. Here, we pursued this analysis for blood pressure (BP) regulation.
    METHODS: The relational scheme of the implemented in Microsoft SQL Server BP-GWAS meta-database enabled the combined storage of: GWAS data and attributes mined from GWAS Catalog and the literature, Ensembl-defined SNP-transcript associations, and GTEx eQTL data. The BP-protein interactome was reconstructed from the PICKLE PPI meta-database, extending the GWAS-deduced network with the shortest paths connecting all GWAS-proteins into one component. The shortest-path intermediates were considered as BP-related. For protein prioritization, we combined a new integrated GWAS-based scoring scheme with two network-based criteria: one considering the protein role in the reconstructed by shortest-path (RbSP) interactome and one novel promoting the common neighbors of GWAS-prioritized proteins. Prioritized proteins were ranked by the number of satisfied criteria.
    RESULTS: The meta-database includes 6687 variants linked with 1167 BP-associated protein-coding genes. The GWAS-deduced PPI network includes 1065 proteins, with 672 forming a connected component. The RbSP interactome contains 1443 additional, network-deduced proteins and indicated that essentially all BP-GWAS proteins are at most second neighbors. The prioritized BP-protein set was derived from the union of the most BP-significant by any of the GWAS-based or the network-based criteria. It included 335 proteins, with ~ 2/3 deduced from the BP PPI network extension and 126 prioritized by at least two criteria. ESR1 was the only protein satisfying all three criteria, followed in the top-10 by INSR, PTN11, CDK6, CSK, NOS3, SH2B3, ATP2B1, FES and FINC, satisfying two. Pathway analysis of the RbSP interactome revealed numerous bioprocesses, which are indeed functionally supported as BP-associated, extending our understanding about BP regulation.
    CONCLUSIONS: The implemented workflow could be used for other multifactorial diseases.
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