Biochimica et biophysica acta. General subjects最新文献_第5页

Extracellular vesicles from hypoxia-preconditioned mesenchymal stem cells preserve mitochondrial functions and redox homeostasis in ischemia–reperfusion-induced acute kidney injury 缺氧预处理间充质干细胞的细胞外囊泡在缺血-再灌注诱导的急性肾损伤中保护线粒体功能和氧化还原稳态。

IF 2.2 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. General subjects

Pub Date : 2025-10-29 DOI: 10.1016/j.bbagen.2025.130874

Marcela Andrade-Soares , Mayra Alves , Clara Rodrigues-Ferreira , Jarlene A. Lopes , Thuany Crisóstomo , Gloria Costa-Sarmento , Christina M. Takiya , Amaury Pereira-Acácio , Adalberto Vieyra

Acute kidney injury (AKI) induced by ischemia-reperfusion (I/R) remains a significant clinical challenge due to its rapid progression, limited therapeutic options, and high morbidity. Mitochondrial dysfunction is a critical component of AKI pathogenesis, contributing to oxidative stress, impaired bioenergetics, and tissue injury. Extracellular vesicles (EV) derived from mesenchymal stem cells (MSC) have emerged as potential candidates for organ protection through the modulation of inflammatory and oxidative pathways. This study evaluated the effects of EV secreted by hypoxia-preconditioned adipose-derived MSC on mitochondrial function in a rat model of I/R-induced AKI. Wistar rats were assigned to four groups: SHAM, I/R, SHAM + EV, and I/R + EV. Hypoxia-preconditioned EV (2 × 10⁹) or vehicle were administered subcapsularly 1 h prior to bilateral renal artery clamping (45 min ischemia, 1 h reperfusion). Histological analyses demonstrated that EV treatment effectively prevented tubular injury, inflammatory infiltration, and preserved renal architecture. EV enhanced Nrf2 nuclear translocation, upregulated HO-1 expression, and stabilized antioxidant defenses. Furthermore, EV preserved mitochondrial membrane potential, respiratory control ratio, ATP synthesis, and the abundance of electron transport chain complexes I, III, and IV, although complex II remained vulnerable. Proton leak responses were unaffected. These results demonstrate that hypoxia-preconditioned MSC-derived EV exert rapid protective effects on renal mitochondria and redox homeostasis during early reperfusion, offering a promising therapeutic strategy for AKI prevention in clinical scenarios such as transplantation and major cardiovascular surgeries. Further studies are needed to characterize the cargo of EV and their long-term outcomes.

缺血再灌注（I/R）引起的急性肾损伤（AKI）由于其进展迅速、治疗选择有限和发病率高，仍然是一个重大的临床挑战。线粒体功能障碍是AKI发病机制的关键组成部分，有助于氧化应激，生物能量受损和组织损伤。来自间充质干细胞（MSC）的细胞外囊泡（EV）已成为通过调节炎症和氧化途径来保护器官的潜在候选者。本研究评估了缺氧预处理脂肪源性间充质干细胞分泌的EV对I/ r诱导AKI大鼠模型线粒体功能的影响。Wistar大鼠分为SHAM、I/R、SHAM+EV和I/R + EV四组。在双侧肾动脉夹闭（45 min缺血，1 h再灌注）前1 h给予低氧预处理EV（2 × 109）或载药。组织学分析表明，EV治疗可有效预防肾小管损伤、炎症浸润和保留肾脏结构。EV增强Nrf2核易位，上调HO-1表达，稳定抗氧化防御。此外，EV保留了线粒体膜电位、呼吸控制率、ATP合成和电子传递链复合物I、III和IV的丰度，尽管复合物II仍然脆弱。质子泄漏反应未受影响。这些结果表明，缺氧预处理的间充质干细胞来源的EV在早期再灌注时对肾脏线粒体和氧化还原稳态具有快速的保护作用，为移植和重大心血管手术等临床情况下预防AKI提供了有希望的治疗策略。需要进一步的研究来描述电动汽车的货物及其长期结果。

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引用次数: 0

Exosome-derived mtDNA disrupts endothelial barrier integrity and accelerates sepsis progression by inducing mitochondrial dysfunction through the PKCδ gene 外泌体衍生的mtDNA通过PKCδ基因诱导线粒体功能障碍，破坏内皮屏障的完整性，加速败血症的进展

IF 2.2 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. General subjects

Pub Date : 2025-10-25 DOI: 10.1016/j.bbagen.2025.130871

Zhiyong Peng , Xiaojuan Cao , Hejun Gao , Cuiling Li , Jinhan Zhang , Youtan Liu

Sepsis, a severe inflammatory response to infection, is characterized by complex and rapidly evolving pathophysiology with high mortality. Mitochondrial DNA (mtDNA) in exosomes is a key damage-associated molecular pattern implicated in sepsis; however, its exact role and mechanisms are unclear. This study investigates how exosome-derived mtDNA induces mitochondrial dysfunction via protein kinase C delta (PKCδ), leading to endothelial barrier disruption and the progression of sepsis. Our analysis revealed significantly elevated levels of the mtDNA markers ND2 and D-loop in serum exosomes from sepsis patients compared to healthy controls. These elevated exosomal mtDNA levels correlated with disease severity and showed a positive association with lung injury markers, including SRAGE, SP-D, and CC16. In vitro experiments demonstrated that both isolated mtDNA and exosomes significantly impaired mitochondrial membrane potential, increased reactive oxygen species (ROS) levels, and reduced the oxygen consumption rate (OCR), suggesting the induction of mitochondrial dysfunction. Moreover, mtDNA promoted endothelial cell damage and increased permeability via PKCδ. Crucially, PKCδ knockdown markedly restored mtDNA-induced mitochondrial dysfunction and cellular permeability damage. In conclusion, Exosome-derived mtDNA triggers mitochondrial dysfunction and endothelial barrier disruption via PKCδ, promoting sepsis progression, suggesting potential therapeutic targets.

脓毒症是一种对感染的严重炎症反应，其特点是病理生理复杂且发展迅速，死亡率高。外泌体中的线粒体DNA （mtDNA）是涉及败血症的关键损伤相关分子模式；然而，它的确切作用和机制尚不清楚。本研究探讨了外泌体衍生的mtDNA如何通过蛋白激酶Cδ (PKCδ)诱导线粒体功能障碍，导致内皮屏障破坏和败血症的进展。我们的分析显示，与健康对照组相比，败血症患者血清外泌体中mtDNA标记ND2和D-loop水平显著升高。外泌体mtDNA水平升高与疾病严重程度相关，并与肺损伤标志物（包括SRAGE、SP-D和CC16）呈正相关。体外实验表明，分离的mtDNA和外泌体均显著损害线粒体膜电位，增加活性氧（ROS）水平，降低耗氧率（OCR），提示诱导线粒体功能障碍。此外，mtDNA通过PKCδ促进内皮细胞损伤和通透性增加。关键是，PKCδ敲低可显著恢复mtdna诱导的线粒体功能障碍和细胞通透性损伤。总之，外泌体衍生的mtDNA通过PKCδ触发线粒体功能障碍和内皮屏障破坏，促进脓毒症的进展，提示潜在的治疗靶点。

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引用次数: 0

Selection and evaluation of new sites for splitting beta-lactamase to modulate auto-complementation enzyme activity β -内酰胺酶分裂调节自互补酶活性新位点的选择与评价

IF 2.2 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. General subjects

Pub Date : 2025-10-24 DOI: 10.1016/j.bbagen.2025.130867

Morgan C. Marsh , Shawn C. Owen

Split protein systems, including split fluorescent proteins and split enzymes, have predominantly been applied to monitor protein-protein interactions but have recently gained popularity as components in induced complementation diagnostic platforms. Many of these systems are limited by self-affinity which limits the dynamics or causes a false-positive high background signal. To overcome these challenges, it is necessary to either modify the interacting residues of established split fragments or by exploring new split-sites. Using the computational modeling tool SPELL to identify stable candidates, we developed five unique split sites for TEM-1 β-lactamase to compare structure and activity versus the original split site. We monitored structural changes through MMS IR spectroscopy as well as functional activity of each split enzyme. Expected structural changes of each fragment and changes in self-affinity driven complementation were observed. By utilizing specific binding proteins attached to the split enzyme, we monitored enzyme activity with forced complementation when bound to the target compared to auto-complementation when the enzymes were auto-complexed in solution. Of the five new split sites, one maintained high binding-mediated complementation activity with significant reduction in background auto-complementation. Changing the split site is a relatively simple approach to reduce background activity while maintaining on-target activity. The ability to tune split-systems has the potential to enable more sensitive and complex studies that previously were limited by the high background from self-affinity.

分裂蛋白系统，包括分裂荧光蛋白和分裂酶，主要用于监测蛋白质-蛋白质相互作用，但最近作为诱导互补诊断平台的组成部分越来越受欢迎。这些系统中的许多都受到自亲和性的限制，这限制了动态或导致假阳性高背景信号。为了克服这些挑战，有必要修改已建立的分裂片段的相互作用残基或通过探索新的分裂位点。使用计算建模工具SPELL来确定稳定的候选者，我们为TEM-1 β-内酰胺酶开发了五个独特的分裂位点，以比较其结构和活性与原始分裂位点的差异。我们通过MMS - IR光谱检测了各分裂酶的结构变化和功能活性。观察了每个片段的预期结构变化和自亲和互补的变化。通过利用附着在分裂酶上的特异性结合蛋白，我们监测了酶与靶标结合时的强制互补与酶在溶液中自动络合时的自动互补的活性。在五个新的分裂位点中，一个位点保持高结合介导的互补活性，背景自动互补显著降低。更改拆分站点是一种相对简单的方法，可以在保持目标活动的同时减少后台活动。调整分裂系统的能力有可能使更敏感和复杂的研究成为可能，而这些研究以前受到自亲和性高背景的限制。

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引用次数: 0

The CEBPA/FDX1 axis elevates sensitivity to cuproptosis in lung adenocarcinoma cells CEBPA/FDX1轴提高肺腺癌细胞对铜增生的敏感性。

IF 2.2 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. General subjects

Pub Date : 2025-10-22 DOI: 10.1016/j.bbagen.2025.130872

Yongsheng Zhao , Renyan Zheng , Kexin Luo , Haiyang Zhao , Wanping Xiang

Background

The recent introduction of “cuproptosis” into the oncological lexicon has opened up new horizons for cancer therapy, yet our understanding of how this process operates in lung adenocarcinoma (LUAD) is still limited. In this work we have investigated the core genetic factors and provided theoretical support for the application of cuproptosis in the treatment of LUAD. Through bioinformatics analysis, we found that FDX1 was significantly downregulated in LUAD and highly correlated with cuproptosis markers. Therefore, we chose FDX1 as the research object.

Methods

Biochemical and bioinformatic analyses were assessed FDX1 and CEBPA expression in LUAD. The binding relationship between CEBPA and FDX1 was validated via CHIP and dual-luciferase assays. FDX1 expression in LUAD cells was evaluated by qRT-PCR and Western blot. The impact of FDX1 overexpression on LUAD progression was examined using CCK-8 and Transwell assays. Experiments involving CCK-8, copper ion measurement, cuproptosis-related protein detection, and DLAT immunofluorescence confirmed the successful LUAD cuproptosis model.

Results

FDX1 was downregulated in LUAD tissues and cells, and its overexpression inhibited LUAD cell migration, invasion, and proliferation. Cuproptosis significantly reduced LUAD cell viability and the protein levels of Lipoy-DLAT, DLAT, and FDX1, while increasing HSP70 expression, DLAT aggregation, and intracellular copper ion levels. CEBPA, a transcriptional activator of FDX1, positively correlated with and bound to it. Overexpressed FDX1 enhanced cuproptosis in LUAD cells, an effect partially reversible by CEBPA suppression.

Conclusion

These analyses were performed to construct a proposed cellular model of cuproptosis in LUAD.

背景：近年来，“铜增生”一词被引入肿瘤学词典，为癌症治疗开辟了新的视野，但我们对肺腺癌（LUAD）中这一过程如何运作的理解仍然有限。本研究探讨了其核心遗传因素，为其在LUAD治疗中的应用提供了理论支持。通过生物信息学分析，我们发现FDX1在LUAD中显著下调，并与cuprotosis标志物高度相关。因此，我们选择FDX1作为研究对象。方法：采用生化和生物信息学方法检测LUAD中FDX1和CEBPA的表达。通过CHIP和双荧光素酶实验验证了CEBPA与FDX1的结合关系。采用qRT-PCR和Western blot检测FDX1在LUAD细胞中的表达。使用CCK-8和Transwell检测FDX1过表达对LUAD进展的影响。通过CCK-8、铜离子测定、铜裂相关蛋白检测和DLAT免疫荧光等实验证实了LUAD铜裂模型的成功建立。结果：FDX1在LUAD组织和细胞中表达下调，其过表达抑制LUAD细胞迁移、侵袭和增殖。cuprotosis显著降低LUAD细胞活力和Lipoy-DLAT、DLAT和FDX1蛋白水平，同时增加HSP70表达、DLAT聚集和细胞内铜离子水平。CEBPA是FDX1的转录激活因子，与FDX1正相关并结合。过表达的FDX1增强LUAD细胞中的铜突起，这一作用通过抑制CEBPA部分可逆。结论：通过这些分析，我们建立了LUAD铜体畸形的细胞模型。

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引用次数: 0

P2X7 receptor contributes to DNA damage repair and acquisition of malignant phenotypes in irradiated human glioblastoma cells P2X7受体参与辐照人胶质母细胞瘤细胞DNA损伤修复和恶性表型获得。

IF 2.2 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. General subjects

Pub Date : 2025-10-22 DOI: 10.1016/j.bbagen.2025.130873

Hiromu Seki , Kazuki Kitabatake , Fumiaki Uchiumi , Sei-ichi Tanuma , Mitsutoshi Tsukimoto

Radiation therapy for cancer takes advantage of the higher sensitivity of tumor cells to radiation compared to normal tissue, but some cancers, such as glioblastoma (GBM) and malignant melanoma, acquire radiation resistance (radioresistance), rendering treatment ineffective. Radioresistance is characterized by strong activation of DNA repair mechanisms in response DNA damage induced by radiation, together with possession of malignant property such as enhanced invasiveness and metastasis, though the molecular mechanisms involved remain to be fully established. Here, we show that P2X7 receptor-specific inhibitors suppress the γ-irradiation-induced DNA damage response (DDR) and enhance cell death of A172 GBM cells. In contrast, ATP, a P2X7 receptor ligand, promotes the DDR and suppresses cell death. Irradiation immediately induced ATP release from cells, and P2X7 receptor inhibitor suppressed the release of ATP. Furthermore, P2X7 receptor inhibitors suppress the release of high mobility group box 1 (HMGB1), which is known to promote cancer cell migration. Inhibitors of the receptor for advanced glycation end products (RAGE) also suppress ATP-induced cell motility, indicating that the P2X7-HMGB1-RAGE pathway contributes to radiation-induced malignant transformation. These data indicate firstly that the P2X7 receptor promotes the γ-irradiation-induced DDR, leading to increased resistance of GBM cells to γ-radiation-induced death, and secondly that the P2X7 receptor and extracellular ATP may be involved in the γ-irradiation-induced acquisition of malignant property such as cytoskeletal changes and enhanced motility in GBM cells.

癌症的放射治疗利用了肿瘤细胞比正常组织对辐射更高的敏感性，但一些癌症，如胶质母细胞瘤（GBM）和恶性黑色素瘤，获得了辐射抗性（radiresistant），使治疗无效。辐射抗性的特征是DNA修复机制在响应辐射引起的DNA损伤时被强烈激活，同时具有恶性性质，如增强侵袭性和转移性，尽管涉及的分子机制尚未完全确定。在这里，我们发现P2X7受体特异性抑制剂抑制γ辐照诱导的DNA损伤反应（DDR），并增强A172 GBM细胞的细胞死亡。相反，P2X7受体配体ATP可促进DDR并抑制细胞死亡。辐照立即诱导ATP从细胞中释放，而P2X7受体抑制剂抑制ATP的释放。此外，P2X7受体抑制剂抑制高迁移率组框1 （HMGB1）的释放，而HMGB1是促进癌细胞迁移的已知物质。晚期糖基化终产物受体（RAGE）的抑制剂也抑制atp诱导的细胞运动，表明P2X7-HMGB1-RAGE通路参与辐射诱导的恶性转化。这些数据表明，首先，P2X7受体促进γ辐射诱导的DDR，导致GBM细胞对γ辐射诱导的死亡的抵抗力增强；其次，P2X7受体和细胞外ATP可能参与γ辐射诱导的GBM细胞获得恶性特性，如细胞骨架变化和运动增强。

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引用次数: 0

Development of a polyclonal antibody against the protein encoded by the metabolic syndrome-associated gene for dissecting its function and underlying mechanism 针对代谢综合征相关基因编码蛋白的多克隆抗体的研制，以解剖其功能和潜在机制。

IF 2.2 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. General subjects

Pub Date : 2025-10-16 DOI: 10.1016/j.bbagen.2025.130870

Jia Jing Cai , Yi Lin Shen , Jia Lin , Jun Tao Ren , Yan Zhi Yi , Xue Cheng Li , Ke Xin Jia , Jun Yi Liu , Guo Ming Su , Yong Yan Song , Qi Wei Guo , Ding Zhi Fang

The metabolic syndrome-associated gene (MSAG) encodes a polypeptide of MSAG composed of 110 amino acids and was observed to responds to high glucose conditions. However, scant studies have been documented since it was first reported in 2009. The function of MSAG and its underlying mechanisms remain unclear. To explore them, antibodies against MSAG are needed. Therefore, the current study aimed to generate a polyclonal antibody against MSAG and assess its applications. The pET-28a-mMSAG vector was constructed for prokaryotic expression. The recombinant MSAG was obtained and identified with a coverage of 100 %. Subsequently, a polyclonal antibody against MSAG was prepared by rabbit immunization with an antibody titer exceeding 1:128,000 as determined by ELISA. The prepared antibody was validated using MSAG knockdown mouse and HepG2 cells. The mRNA and protein levels of MSAG were lower in MSAG knockdown mouse livers and HepG2 cells. Additionally, MSAG mRNA and protein levels in mouse hepatic tissues were significantly increased following the intervention with a high carbohydrate diet as evaluated by RT-qPCR and western blotting using the prepared antibody. This reproducibly demonstrated that MSAG was involved in the regulation of glucose metabolism. Taken together, the rabbit anti-MSAG polyclonal antibody has been successfully generated in the current study, which lays the foundation for future studies to explore the functions of MSAG and its underlying mechanisms.

代谢综合征相关基因（MSAG）编码由110个氨基酸组成的MSAG多肽，并被观察到对高糖条件作出反应。然而，自2009年首次报道以来，很少有研究记录在案。MSAG的功能及其潜在机制尚不清楚。为了探索它们，需要针对MSAG的抗体。因此，本研究旨在制备一种抗MSAG的多克隆抗体，并对其应用前景进行评价。构建pET-28a-mMSAG载体进行原核表达。重组MSAG得到并鉴定，覆盖率为100% %。经兔免疫制备抗MSAG的多克隆抗体，ELISA测定抗体效价超过1:12万8千。用MSAG敲除小鼠和HepG2细胞对制备的抗体进行验证。MSAG敲除小鼠肝脏和HepG2细胞中MSAG mRNA和蛋白水平均降低。此外，利用制备的抗体进行RT-qPCR和western blotting检测，高碳水化合物饮食干预后，小鼠肝组织中MSAG mRNA和蛋白水平显著升高。这可重复地证明MSAG参与糖代谢的调节。综上所述，本研究成功制备了兔抗MSAG多克隆抗体，为进一步研究MSAG的功能及其机制奠定了基础。

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引用次数: 0

Calcium oxalate alters lipid profiles and annexin A2 enrichment in membrane fractions of murine inner medullary collecting duct cells 草酸钙改变小鼠髓内集管细胞膜组分的脂质谱和膜联蛋白A2的富集。

IF 2.2 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. General subjects

Pub Date : 2025-10-11 DOI: 10.1016/j.bbagen.2025.130868

Zenab Shahzad , Ramish Rafay , Saeed Khan , Amir Kazory , Nancy D. Denslow , Abdel A. Alli

The mechanism underlying calcium oxalate (CaOx) stone formation remains unclear, although recurrent kidney stone formation has been linked to injury of kidney tubular cells in response to their exposure to higher oxalate and CaOx crystals. We hypothesized that CaOx induces the externalization and membrane enrichment of the negatively charged phospholipid phosphatidylserine (PS), while simultaneously enhancing the expression of calcium-binding proteins as a protective mechanism against cell death in inner medullary collecting duct (IMCD) cells. Annexin A2, a calcium-dependent phospholipid-binding protein, may play a protective role in CaOx stone formation. Mouse IMCD (mIMCD3) cells were treated with CaOx before performing a targeted lipidomic analysis of membrane fractions. Additionally, mIMCD3 cells were challenged with methyl-beta-cyclodextrin (MBCD) PS liposomes, Annexin A2 was evaluated by Western blotting and densitometric analysis. Lipidomic analysis revealed an enrichment of multiple PS lipid species in membrane fractions of mIMCD3 cells treated with CaOx. Western blotting and densitometric analysis further demonstrated a significant increase in Annexin A2 protein expression in the membrane fractions of mIMCD3 cells treated with MBCD PS liposomes. CaOx and MBCD PS liposomes were found to differentially affect membrane fluidity in mIMCD3 cells. Importantly, CaOx treatment caused an increase in ACSL4 and caspase 9 protein expression, indicating initiation of ferroptosis and apoptosis, respectively. The siRNA mediated knockdown of annexin A2 further augmented the upregulation of caspase 9 after CaOx treatment. Collectively, these findings suggest that Annexin A2, a calcium-binding and plasma membrane repair protein, is upregulated in response to CaOx-induced PS enrichment in mIMCD3 cells.

草酸钙（CaOx）结石形成的机制尚不清楚，尽管复发性肾结石的形成与肾小管细胞暴露于较高的草酸钙和CaOx晶体后的损伤有关。我们假设CaOx诱导带负电荷的磷脂酰丝氨酸（PS）的外化和膜富集，同时增强钙结合蛋白的表达，这是一种防止髓内集管（IMCD）细胞死亡的保护机制。膜联蛋白A2是一种钙依赖性磷脂结合蛋白，可能在CaOx结石形成中起保护作用。小鼠IMCD （mIMCD3）细胞用CaOx处理，然后对膜组分进行靶向脂质组学分析。此外，用甲基- β -环糊精（MBCD） PS脂质体刺激mIMCD3细胞，用Western blotting和密度分析评估Annexin A2。脂质组学分析显示，CaOx处理的mIMCD3细胞的膜组分中富集了多种PS脂质。Western blotting和密度分析进一步表明，MBCD PS脂质体处理的mIMCD3细胞膜组分中Annexin A2蛋白表达显著增加。发现CaOx和MBCD PS脂质体对mIMCD3细胞膜流动性有不同的影响。重要的是，CaOx处理引起ACSL4和caspase 9蛋白表达的增加，分别表明铁下垂和细胞凋亡的开始。siRNA介导的膜联蛋白A2的下调进一步增强了CaOx处理后caspase 9的上调。综上所述，这些发现表明，钙结合和质膜修复蛋白Annexin A2在caox诱导的mIMCD3细胞PS富集反应中上调。

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引用次数: 0

Alterations in the transcriptome of human primary bronchial epithelial cells exposed to emissions from a heated tobacco product 暴露于加热烟草制品排放物的人原代支气管上皮细胞转录组的改变。

IF 2.2 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. General subjects

Pub Date : 2025-10-10 DOI: 10.1016/j.bbagen.2025.130869

M. Davigo , F. Caiment , M. Verheijen , F.J. van Schooten , M. van Herwijnen , A. Mommers , A. Opperhuizen , R. Talhout , A.H.V. Remels

Introduction

IQOS is a Heated Tobacco Product marketed as reduced-risk alternative to cigarettes. This is based on limited industry-independent toxicological evidence.

Methods

Cigarette Smoke Extract (CSE) and IQOS extract (IQOSE) were generated by puffing mainstream emissions in PBS. Nicotine levels were quantified via liquid chromatography-mass spectrometry (LC-MS). Subsequently, undifferentiated Primary human Bronchial Epithelial Cells (PBECs) from three donors were exposed (24 h) to 1 %CSE, 1 %IQOSE, 3 %IQOSE (v/v), or nicotine concentrations (1.5, 6 or 18 μg/mL), representative of the levels present in the extracts. Transcriptomic alterations were assessed via RNA sequencing, and specific mRNA alterations were validated at the protein level by Western blot.

Results

IQOSE contained about 4-fold more nicotine than CSE. Nicotine did not significantly affect PBECs transcriptome. Substantial differences in the amount of differentially expressed genes (DEGs) were observed in response to CSE and IQOSE between donors. However, in all donors, 3 %IQOSE exposure downregulated pathways involved in cell cycle progress. In addition, both mRNA and protein levels of molecules controlling autophagy and mitophagy increased in response to IQOSE in one donor, and the disease Chronic Obstructive Pulmonary Disease (COPD) was enriched in cells from two donors upon exposure to CSE or IQOSE. In the most responsive donor, pathways associated with ER-stress and DNA replication were deregulated.

Conclusions

Despite significant inter-donor variability, IQOSE induced specific gene signatures associated with pathways known to be involved in (smoking-related) lung diseases in all donors. Collectively, these findings provide novel insights into the molecular toxicity of IQOS mainstream emissions in human bronchial epithelial cells.

IQOS是一种加热烟草产品，作为香烟的低风险替代品销售。这是基于有限的独立于行业的毒理学证据。方法：在PBS中雾化主流排放物生成香烟烟雾提取物（CSE）和IQOS提取物（IQOSE）。通过液相色谱-质谱（LC-MS）测定尼古丁水平。随后，将来自三个供体的未分化的原代人支气管上皮细胞（PBECs）暴露于1 %CSE、1 %IQOSE、3 %IQOSE （v/v）或尼古丁浓度（1.5、6或18 μg/mL）中（代表提取物中存在的水平）（24 h）。通过RNA测序评估转录组学改变，并通过Western blot在蛋白质水平验证特异性mRNA改变。结果：IQOSE的尼古丁含量约为CSE的4倍。尼古丁对PBECs转录组无显著影响。不同供者对CSE和IQOSE的反应中，差异表达基因（DEGs）的数量存在显著差异。然而，在所有供体中，3 %IQOSE暴露下调了参与细胞周期进程的途径。此外，在一个供体中，控制自噬和有丝自噬的分子的mRNA和蛋白水平在IQOSE的作用下升高，并且在暴露于CSE或IQOSE的两个供体细胞中，慢性阻塞性肺疾病（COPD）富集。在最敏感的供体中，与内质网应激和DNA复制相关的途径被解除了管制。结论：尽管供体间存在显著差异，IQOSE诱导的特异性基因特征与已知参与所有供体（吸烟相关）肺部疾病的途径相关。总的来说，这些发现为IQOS主流排放物在人支气管上皮细胞中的分子毒性提供了新的见解。

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引用次数: 0

Size of aquaporin-4 orthogonal arrays of particles are affected by the palmitoylation state of the M1 isoform 水通道蛋白-4正交阵列粒子的大小受M1亚型棕榈酰化状态的影响。

IF 2.2 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. General subjects

Pub Date : 2025-10-10 DOI: 10.1016/j.bbagen.2025.130866

Jessica D. Carder , Barbara Barile , Alessia Memeo , Eric P. Jacobo , Grazia Paola Nicchia , James A. Brozik

Human aquaporin-4 (AQP4) is a water-channel protein crucial for water-ion homeostasis in the central nervous system. Dysregulation of AQP4 function is linked to neurological conditions like brain edema, neuromyelitis optica, and epilepsy. AQP4 has two isoforms, M1 and M23. The M23 isoform forms large structures known as Orthogonal Arrays of Particles (OAPs), while M1 coats the outer surface of OAPs. The dynamics of OAP aggregation may modulate water permeability and ion homeostasis in the brain. This study shows that the palmitoylation state of M1 influences OAP self-assembly, with depalmitoylated M1 producing OAPs 20 % larger than those formed by palmitoylated M1 at the same concentration. This, along with prior research on M1 aggregation, suggests palmitoylated M1 forms a single outer layer arounf OPAs, whereas depalmitoylated M1 creates a double layer. Single-particle tracking was used to study M23 OAP formation in lipid bilayers under equilibrium conditions. Our data support the idea that M1 regulates M23 OAP size, showing that average OAP size decreases as M1 concentration increases. This study explores the inhibitory effects of M1 on AQP4 M23 assembly and how M1's palmitoylation state affects OAP size regulation. These insights could lead to new therapeutic approaches for managing AQP4 assembly and function in related conditions.

人类水通道蛋白4 （AQP4）是一种对中枢神经系统水离子稳态至关重要的水通道蛋白。AQP4功能失调与脑水肿、视神经脊髓炎和癫痫等神经系统疾病有关。AQP4有两个同工异构体，M1和M23。M23异构体形成称为正交粒子阵列（oap）的大型结构，而M1则覆盖在oap的外表面。OAP聚集的动态可能调节脑内的水渗透性和离子稳态。本研究表明，M1的棕榈酰化状态影响OAP的自组装，在相同浓度下，去棕榈酰化M1产生的OAP比棕榈酰化M1形成的OAP大20 %。这与先前对M1聚集的研究一起表明，棕榈酰化的M1在OPAs周围形成一个单一的外层，而去棕榈酰化的M1则形成一个双层。利用单粒子跟踪技术研究了平衡条件下脂质双分子层中M23 OAP的形成。我们的数据支持M1调节M23 OAP大小的观点，显示平均OAP大小随着M1浓度的增加而减少。本研究探讨M1对AQP4 M23组装的抑制作用，以及M1棕榈酰化状态如何影响OAP大小调节。这些见解可能会导致新的治疗方法来管理AQP4的组装和相关条件下的功能。

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引用次数: 0

RFBGCpred: A Random forest based tool for prediction of biosynthetic gene clusters RFBGCpred：一个基于随机森林的生物合成基因簇预测工具。

IF 2.2 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochimica et biophysica acta. General subjects

Pub Date : 2025-10-08 DOI: 10.1016/j.bbagen.2025.130859

Sharanbasappa D. Madival , Dwijesh Chandra Mishra , Krishna Kumar Chaturvedi , Neeraj Budhlakoti , Mohammad Samir Farooqi , Sudhir Srivastava , Anu Sharma , Shivadarshan S. Jirli , Alka Arora , Girish K. Jha , Shesh N. Rai

Biosynthetic gene clusters (BGCs) encode enzymatic pathways that produce diverse natural products with applications in pharmaceuticals, agriculture, and biotechnology. Broad-spectrum tools such as antiSMASH and DeepBGC cover many BGC classes but may face challenges in detecting atypical or hybrid architectures. Here we present RFBGCPred, an open-source machine learning classifier focused on five clinically and agriculturally important classes—PKS, NRPS, RiPPs, terpenes, and PKS–NRPS hybrids. Rather than replacing existing pipelines, RFBGCPred complements them by improving class-level discrimination within this subset.

Using curated data from the MiBIG database, we applied Word2Vec for feature extraction, supervised UMAP for dimensionality reduction, and SMOTE to address class imbalance. Multiple classifiers were benchmarked, with Random Forest identified as the top performer using the TOPSIS decision-making criterion. The final model achieved an accuracy of 98.0 % (MCC: 0.9752, AUC: 0.9928) on a balanced test set, and maintained strong generalization on an unbalanced validation set (accuracy: 94.8 %, MCC: 0.89, AUC: 0.96). Compared with antiSMASH and DeepBGC, RFBGCPred showed improved recall for hybrid PKS–NRPS clusters while sustaining competitive precision, thereby reducing misclassification of atypical arrangements.

RFBGCPred supports FASTA, GenBank, and CSV inputs, with full source code, curated datasets, and documentation available at: https://github.com/SHARANBASAPPA/RFBGCPred.git.

生物合成基因簇（BGCs）编码产生多种天然产物的酶途径，在制药、农业和生物技术中有广泛的应用。antiSMASH和DeepBGC等广谱工具涵盖了许多BGC类，但在检测非典型或混合架构方面可能面临挑战。在这里，我们提出了RFBGCPred，一个开源的机器学习分类器，专注于五个临床和农业上重要的类别- pks， NRPS, RiPPs，萜烯和PKS-NRPS杂交。RFBGCPred并没有取代现有的管道，而是通过改进这个子集内的类级别区分来补充它们。使用来自MiBIG数据库的精选数据，我们使用Word2Vec进行特征提取，使用监督UMAP进行降维，使用SMOTE来解决类别不平衡问题。对多个分类器进行基准测试，随机森林被确定为使用TOPSIS决策标准的最佳表演者。最终模型在平衡测试集上的准确率为98.0 % (MCC: 0.9752, AUC: 0.9928)，在不平衡验证集上保持了较强的泛化（准确率：94.8 %,MCC: 0.89, AUC: 0.96）。与antiSMASH和DeepBGC相比，RFBGCPred在保持竞争精度的同时，提高了pps - nrps混合簇的召回率，从而减少了非典型排列的错误分类。RFBGCPred支持FASTA， GenBank和CSV输入，完整的源代码，策划的数据集和文档可在：https://github.com/SHARANBASAPPA/RFBGCPred.git。

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引用次数: 0