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Downregulation of KHSRP enhances carboplatin sensitivity in non-small cell lung cancer. KHSRP下调可增强非小细胞肺癌患者对卡铂的敏感性。
IF 2.5 3区 生物学 Pub Date : 2025-11-05 DOI: 10.1186/s41065-025-00584-4
Bao Wen, Shuguang Bao, Yanqing Gao, Haoyuan Li, Pengjie Yang, Luri Bao, Chuanhui Teng, Bateer Han

Background: Carboplatin resistance represents a critical therapeutic challenge in non-small cell lung cancer (NSCLC) treatment. Although KHSRP has been implicated in lung cancer progression, its molecular mechanisms and impacts on chemotherapy sensitivity remain elusive. Notably, KHSRP has the capacity to activate the transcription of HMGB1, an oncogene known to influence chemotherapy sensitivity. However, it remains to be determined whether KHSRP affects chemotherapy response in NSCLC via HMGB1.

Methods: KHSRP expression in NSCLC cells was analyzed using qRT-PCR. Cell proliferation, apoptosis, and migration were evaluated using colony formation, flow cytometry and wound healing assays. A luciferase reporter assay was conducted to assess whether KHSRP transcriptionally regulates HMGB1. Additionally, A549 cell xenografts were established in nude mice to investigate the tumor growth-promoting effects of KHSRP in vivo.

Results: KHSRP expression was notably elevated in NSCLC cells. Overexpression of KHSRP remarkably promoted A549 cell proliferation, migration, and epithelial-mesenchymal transition (EMT); while KHSRP knockdown exhibited the opposite effects. Mechanically, KHSRP notably promoted the transcription of HMGB1 and upregulated its expression in A549 cells. Importantly, deficiency of KHSRP remarkably enhanced the suppressive effects of carboplatin on A549 cell proliferation, migration, EMT and HMGB1 expression. Meanwhile, in vivo experiments demonstrated that downregulation of KHSRP potentiated the inhibitory effect of carboplatin on tumor growth in tumor-bearing nude mice.

Conclusion: These findings demonstrate that silencing of KHSRP enhances the drug sensitivity of carboplatin in NSCLC, potentially mediated through the inhibition of HMGB1. Targeting KHSRP may represent a promising therapeutic strategy to improve chemotherapy efficacy in NSCLC.

背景:卡铂耐药是非小细胞肺癌(NSCLC)治疗的关键挑战。虽然KHSRP与肺癌进展有关,但其分子机制及其对化疗敏感性的影响尚不清楚。值得注意的是,KHSRP具有激活HMGB1转录的能力,HMGB1是一种已知影响化疗敏感性的致癌基因。然而,KHSRP是否通过HMGB1影响NSCLC的化疗反应仍有待确定。方法:采用qRT-PCR方法分析KHSRP在NSCLC细胞中的表达。利用菌落形成、流式细胞术和伤口愈合试验评估细胞增殖、凋亡和迁移。荧光素酶报告基因试验评估KHSRP是否转录调控HMGB1。另外,在裸鼠体内建立A549细胞异种移植,研究KHSRP对肿瘤生长的促进作用。结果:KHSRP在NSCLC细胞中的表达明显升高。过表达KHSRP显著促进A549细胞增殖、迁移和上皮-间质转化(EMT);而KHSRP敲低则表现出相反的效果。机械上,KHSRP显著促进HMGB1的转录,上调其在A549细胞中的表达。重要的是,KHSRP缺失显著增强了卡铂对A549细胞增殖、迁移、EMT和HMGB1表达的抑制作用。同时,体内实验表明,下调KHSRP可增强卡铂对荷瘤裸鼠肿瘤生长的抑制作用。结论:这些发现表明,沉默KHSRP可增强卡铂在非小细胞肺癌中的药物敏感性,可能是通过抑制HMGB1介导的。靶向KHSRP可能是提高非小细胞肺癌化疗疗效的一种有前景的治疗策略。
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引用次数: 0
The synergistic antitumor effects of psoralidin and cisplatin in gastric cancer by inducing ACSL4-mediated ferroptosis. 补骨脂素和顺铂通过诱导acsl4介导的胃癌铁下垂的协同抗肿瘤作用。
IF 2.5 3区 生物学 Pub Date : 2025-11-04 DOI: 10.1186/s41065-025-00591-5
Ling Yao, Jinhua Yan, Lihong Gan, Li Zheng, Peng Liu, Ling Lei, Yaqin Huang

Objective: Cisplatin (DDP) is the major chemotherapeutic drug used to treat gastric cancer (GC). However, DDP-associated side effects and resistance chemoresistance have limited its clinical application. Psoralidin (PSO) is the main extract of Psoralea corylifolia and has antitumor effects. The present study is designed to investigate the antitumor functions and mechanisms of PSO and DDP in GC.

Methods: GC cells (HGC-27 and MKN-45 cells) were treated with PSO (2.5 to 120 µM) and/or DDP. A CCK-8 assay, colony formation assay, and EdU staining were used to test cell proliferation. Cell migration and invasion were tested via a transwell assay. An in vivo assay in nude mice was carried out to analyze the influence of PSO and DDP on tumor growth. H&E staining was conducted to test the histopathological changes of organs and tumor tissues. Ferroptosis-associated indicators, including GSH, MDA, Fe2+ levels, were examined. Western blotting was conducted to determine the profiles of ACSL4, GPX4, AIFM2, and SLC7A11.

Results: PSO impeded GC cell proliferation, migration, invasion, and growth in vivo. PSO exhibited no significant toxic effects on organs and mitigated DDP-mediated liver and kidney injuries. The combination of PSO and DDP exhibited enhanced inhibitory functions. PSO and DDP can significantly promote GC cell ferroptosis. Moreover, PSO promoted ACSL4 expression and suppressed GPX4, AIFM2, and SLC7A11.

Conclusion: The combination of PSO and DDP has synergistic antitumor effects on GC cells by inducing ACSL4-mediated ferroptosis. PSO may serve as a nontoxic adjuvant to enhance DDP's efficacy and reduce side effects in GC.

目的:顺铂(DDP)是目前治疗胃癌的主要化疗药物。然而,ddp相关的副作用和耐药化疗限制了其临床应用。补骨脂素(PSO)是补骨脂的主要提取物,具有抗肿瘤作用。本研究旨在探讨PSO和DDP在胃癌中的抗肿瘤作用及其机制。方法:用PSO(2.5 ~ 120µM)和/或DDP处理GC细胞(HGC-27和MKN-45细胞)。CCK-8法、菌落形成法、EdU染色法检测细胞增殖情况。通过transwell实验检测细胞迁移和侵袭。通过裸鼠体内实验,分析PSO和DDP对肿瘤生长的影响。H&E染色检测各脏器及肿瘤组织的组织病理变化。检测凋亡相关指标,包括GSH、MDA、Fe2+水平。Western blotting检测ACSL4、GPX4、AIFM2和SLC7A11的表达谱。结果:PSO抑制GC细胞在体内的增殖、迁移、侵袭和生长。PSO对器官没有明显的毒性作用,并减轻了ddp介导的肝和肾损伤。PSO与DDP结合后,抑制作用增强。PSO和DDP均能显著促进GC细胞铁下垂。此外,PSO促进ACSL4的表达,抑制GPX4、AIFM2和SLC7A11的表达。结论:PSO联合DDP通过诱导acsl4介导的铁下垂对胃癌细胞具有协同抗肿瘤作用。PSO可以作为一种无毒的佐剂,提高DDP的疗效,减少GC的副作用。
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引用次数: 0
Downregulation of PDIA4 inhibits proliferation and migration in human oral squamous cell carcinoma. 下调PDIA4抑制口腔鳞状细胞癌的增殖和迁移。
IF 2.5 3区 生物学 Pub Date : 2025-11-03 DOI: 10.1186/s41065-025-00594-2
Yue Hu, Wei Zhang, Fuyu Zhang, Qiaoyun Liu, Hao Yang

Background: Protein disulfide isomerase family A member 4 (PDIA4), a member of the protein disulfide isomerase family, has been associated with the progression of cancer. Nevertheless, its specific function in oral squamous cell carcinoma (OSCC) is not yet well understood.

Methods: To assess the prognostic significance and functional profile of the PDIA4, survival analysis and GSEA were conducted. Additionally, we examined the differences in immune infiltration and immunotherapy response between groups with low and high expression levels of PDIA4. Subsequently, RT-qPCR and western blot assays were employed to verify PDIA4 expression in OSCC tissues. The functional implications of PDIA4 in OSCC cells were also investigated.

Results: Analysis of the TCGA-OSCC dataset revealed a notable increase in PDIA4 expression in OSCC tissues, as verified by RT-qPCR and western blot analyses. Additionally, elevated PDIA4 levels were associated with poor prognosis in OSCC patients. GSEA results showed that the cellular senescence, FoxO and Hippo signaling pathways were remarkably inactivated in the high PDIA4 expression group. Moreover, a negative correlation was observed between PDIA4 levels and the infiltration of CD4, CD8 and natural killer T cells. Conversely, a positive correlation was observed between PDIA4 levels and M0 macrophage and regulatory T cell infiltration. Meanwhile, OSCC patients exhibiting elevated PDIA4 expression demonstrated elevated TIDE scores, implying a reduced responsiveness to immunotherapy in these individuals. Functionally, the suppression of PDIA4 significantly suppressed both proliferation and migration of OSCC cells, potentially through activating the FoxO1/p21CIP1 pathway.

Conclusion: These findings suggest that PDIA4 may potentially serve as both a prognostic biomarker and a therapeutic target for OSCC patients.

背景:蛋白二硫异构酶家族A成员4 (PDIA4)是蛋白二硫异构酶家族的一员,与癌症的进展有关。然而,其在口腔鳞状细胞癌(OSCC)中的具体功能尚不清楚。方法:通过生存分析和GSEA评估PDIA4的预后意义和功能特征。此外,我们还检测了PDIA4低表达组和高表达组之间免疫浸润和免疫治疗反应的差异。随后,采用RT-qPCR和western blot方法验证PDIA4在OSCC组织中的表达。我们还研究了PDIA4在OSCC细胞中的功能意义。结果:TCGA-OSCC数据集分析显示,PDIA4在OSCC组织中的表达显著增加,RT-qPCR和western blot分析证实了这一点。此外,PDIA4水平升高与OSCC患者预后不良相关。GSEA结果显示PDIA4高表达组细胞衰老、FoxO和Hippo信号通路明显失活。此外,PDIA4水平与CD4、CD8和自然杀伤T细胞浸润呈负相关。相反,PDIA4水平与M0巨噬细胞和调节性T细胞浸润呈正相关。同时,PDIA4表达升高的OSCC患者表现出较高的TIDE评分,这意味着这些个体对免疫治疗的反应性降低。功能上,PDIA4的抑制可能通过激活FoxO1/p21CIP1通路,显著抑制了OSCC细胞的增殖和迁移。结论:这些发现提示PDIA4可能作为OSCC患者的预后生物标志物和治疗靶点。
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引用次数: 0
Identification of metabolic reprogramming-associated biomarkers in endometriosis through integrated bioinformatics analysis. 通过综合生物信息学分析鉴定子宫内膜异位症中代谢重编程相关生物标志物。
IF 2.5 3区 生物学 Pub Date : 2025-10-30 DOI: 10.1186/s41065-025-00590-6
Jia Zhen, Ziyuan Zhao, Qi Wu, Xinqian Dong, Zilu Wang, Xiaoxue Han, Wei Shi, Li Xu

Background: Endometriosis (EMs), a common gynecological disorder, involves complex molecular mechanisms. Metabolic reprogramming (MR) has been recognized as a hallmark of EMs, contributing to lesion survival and immune microenvironment remodeling. This study aimed to identify MR-associated hub genes and pathways associated with EMs through integrated multi-omics analyses.

Methods: EMs-related datasets were downloaded from the Gene Expression Omnibus database, including training sets (GSE51981 and GSE7305) and validation sets (GSE25628 and GSE141549). MR related genes were retrieved from the Genecards database. EMs-related differentially expressed genes (DEGs) were identified, and WGCNA was performed to identify module genes. Protein-protein interaction (PPI) networks were constructed. The expression of key genes was validated in an external dataset and clinical samples (immunohi0stochemistry). The CIBERSORT and ssGSEA tools were utilized to explore immune cell infiltration. In vitro experiments involving overexpression and RT-qPCR in Z12 cells were conducted to explore gene function on MR.

Results: A total 107 MR-associated candidate genes were identified. PPI network analysis identified top 10 hub genes. External validation confirmed significant downregulation of key genes in ectopic endometrium, with HNRNPR, SYNCRIP, HSP90B1, HSPA4, HSPA8, CCT2 and CCT5 demonstrating high diagnostic value (AUC > 0.8). Immune infiltration analysis revealed associations between key genes and CD8 + T cells, regulatory T cells, and mast cells. Immunohistochemistry confirmed reduced expression of CCT2, HSP90B1, and SYNCRIP in EMs lesions. In vitro validation confirmed that HSP90B1 overexpression upregulated GLUT1, LDH, and COX-2 expression in Z12 cells.

Conclusion: This study identified several MR-related genes, as potential diagnostic biomarkers and mechanistic contributors to EMs.

背景:子宫内膜异位症(EMs)是一种常见的妇科疾病,涉及复杂的分子机制。代谢重编程(MR)已被认为是EMs的一个标志,有助于病变存活和免疫微环境重塑。本研究旨在通过综合多组学分析确定与核磁共振相关的中枢基因和与em相关的途径。方法:从Gene Expression Omnibus数据库下载ems相关数据集,包括训练集(GSE51981和GSE7305)和验证集(GSE25628和GSE141549)。从Genecards数据库中检索MR相关基因。鉴定ems相关差异表达基因(DEGs),并采用WGCNA方法鉴定模块基因。构建蛋白-蛋白相互作用(PPI)网络。在外部数据集和临床样本(免疫组织化学)中验证了关键基因的表达。利用CIBERSORT和ssGSEA工具探查免疫细胞浸润。通过在Z12细胞中进行过表达和RT-qPCR的体外实验,探讨基因在mr中的功能。结果:共鉴定出107个mr相关候选基因。PPI网络分析鉴定出前10个枢纽基因。外部验证证实异位子宫内膜关键基因显著下调,HNRNPR、SYNCRIP、HSP90B1、HSPA4、HSPA8、CCT2和CCT5具有较高的诊断价值(AUC > 0.8)。免疫浸润分析显示关键基因与CD8 + T细胞、调节性T细胞和肥大细胞之间存在关联。免疫组织化学证实,CCT2、HSP90B1和SYNCRIP在EMs病变中表达降低。体外验证证实,HSP90B1过表达上调Z12细胞中GLUT1、LDH和COX-2的表达。结论:本研究确定了几个核磁共振相关基因,作为潜在的诊断生物标志物和机制因素。
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引用次数: 0
Therapeutic effects of Bushen Chushi formula on knee osteoarthritis via modulation of MAPK/SLC7A11/GPX4 signaling in rats. 补肾祛湿方通过调节MAPK/SLC7A11/GPX4信号通路对大鼠膝关节骨关节炎的治疗作用
IF 2.5 3区 生物学 Pub Date : 2025-10-29 DOI: 10.1186/s41065-025-00587-1
Yuanyuan Li, Hai Tang, Mingjiang He, Xinyue Wang, Yanbai Chen, Siye Liu, Hongmei Zhang

Objective: The aim of this study is to evaluate the therapeutic efficacy of Bushen Chushi Formula (BSCSF) in a rat model of knee osteoarthritis (KOA), with a focus on the modulation of ferroptosis-related signaling pathways and inflammatory responses, and to assess its effects on cartilage integrity and subchondral bone microstructure.

Methods: A total of 66 male Sprague-Dawley rats were randomly assigned to six groups: control, model, diclofenac sodium (DCF), and BSCSF high-dose (BSCSF-H), medium-dose (BSCSF-M), and low-dose (BSCSF-L) groups. KOA was induced via intra-articular injection of monosodium iodoacetate. Following induction, BSCSF or DCF was administered orally for 4 weeks. Therapeutic outcomes were assessed through Lequesne MG scores, body weight measurements, histopathological evaluation (hematoxylin and eosin, Safranin O-Fast Green staining), and micro-computed tomography of the subchondral bone. Expression levels of ferroptosis-associated proteins (SLC7A11, GPX4, p38 MAPK, MMP-13), glutathione (GSH), and iron accumulation (Fe²⁺), as well as inflammatory cytokines (IL-1β, TNF-α), were also measured.

Results: When compared to the model group, rats in the BSCSF-H and BSCSF-M groups exhibited significantly lower Lequesne MG scores, improved cartilage morphology, and enhanced subchondral bone microstructure, as indicated by increased bone volume fraction, trabecular thickness, trabecular number, and connectivity density along with decreased bone surface-to-volume ratio and trabecular separation. These groups also demonstrated increased expression of SLC7A11 and GPX4, elevated GSH levels, and reduced Fe²⁺ accumulation in cartilage, suggesting attenuation of ferroptosis. Inflammatory mediators, including IL-1β, TNF-α, MMP-13, and p38 MAPK, were significantly downregulated, indicating reduced inflammation and extracellular matrix degradation. The BSCSF-L group indicated modest improvements, primarily in inflammatory parameters and joint function.

Conclusion: BSCSF attenuated KOA progression in rats by inhibiting ferroptosis through the MAPK/SLC7A11/GPX4 signaling axis and suppressing inflammatory responses. The observed preservation of cartilage structure and enhancement of subchondral bone quality highlight its therapeutic potential in the management of KOA.

目的:研究补肾祛湿方(BSCSF)对膝关节骨性关节炎(KOA)大鼠模型的治疗作用,重点研究其对凋亡相关信号通路和炎症反应的调节作用,并评估其对软骨完整性和软骨下骨微观结构的影响。方法:雄性sd大鼠66只,随机分为对照组、模型组、双氯芬酸钠(DCF)和BSCSF高剂量组(BSCSF- h)、中剂量组(BSCSF- m)、低剂量组(BSCSF- l)。通过关节内注射碘乙酸钠诱导KOA。诱导后,口服BSCSF或DCF 4周。通过Lequesne MG评分、体重测量、组织病理学评估(苏木精和伊红、红红素O-Fast Green染色)和软骨下骨的显微计算机断层扫描来评估治疗效果。还测量了凋亡相关蛋白(SLC7A11、GPX4、p38 MAPK、MMP-13)、谷胱甘肽(GSH)、铁积累(Fe 2 +)以及炎症因子(IL-1β、TNF-α)的表达水平。结果:与模型组比较,BSCSF-H组和BSCSF-M组大鼠Lequesne MG评分明显降低,软骨形态改善,软骨下骨微结构增强,骨体积分数、骨小梁厚度、骨小梁数量、骨连接密度增加,骨面体积比和骨小梁分离减少。这些组也表现出SLC7A11和GPX4的表达增加,GSH水平升高,软骨中Fe +积累减少,表明铁下垂的衰减。炎症介质,包括IL-1β、TNF-α、MMP-13和p38 MAPK,显著下调,表明炎症和细胞外基质降解减少。BSCSF-L组表现出适度的改善,主要是炎症参数和关节功能。结论:BSCSF通过MAPK/SLC7A11/GPX4信号轴抑制铁下垂,抑制炎症反应,从而减轻大鼠KOA的进展。观察到软骨结构的保存和软骨下骨质量的增强突出了其在KOA治疗中的治疗潜力。
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引用次数: 0
The microRNAs landscape of luminal B breast cancer cells in a three-dimensional microenvironment. 乳腺B细胞在三维微环境中的microrna景观。
IF 2.5 3区 生物学 Pub Date : 2025-10-29 DOI: 10.1186/s41065-025-00586-2
Stephanie I Nuñez-Olvera, Lorena Aguilar-Arnal, Jonathan Puente-Rivera, Alfredo Hidalgo-Miranda, Mireya Cisneros-Villanueva, Yarely M Salinas-Vera, Laurence A Marchat, María Elizbeth Álvarez-Sánchez, Karla Rubio, César López-Camarillo
<p><strong>Background: </strong>Three-dimensional (3D) culture captures key features of tumor architecture and microenvironmental signaling. Because microRNAs (miRNAs) are central post-transcriptional regulators, we asked whether 3D growth would reveal disease-relevant lncRNA-miRNA-mRNA programs in BT-474 luminal breast cancer cells.</p><p><strong>Methods: </strong>BT-474 cells were profiled with GeneChip miRNA 4.0 microarrays to compare 3D versus 2D conditions. We then performed an integrative analysis consisting of: (i) extracting miRNA-mRNA interactions from miRNet and ENCORI (predicted and curated) for the differentially expressed miRNAs; (ii) identifying inverse miRNA-mRNA pairs (miRNA downregulated with target mRNA upregulated, or the reverse) using public mRNA data from BT-474 3D versus 2D cultures so that pairs were consistent with regulatory repression; and (iii) retaining only those miRNA-mRNA pairs that also appeared in miRNet/ENCORI. In a separate step, we examined public luminal breast tumor datasets versus BT-474 2D cultures to determine which 3D-identified miRNAs showed a similar direction of expression change in luminal tumors, thereby prioritizing signals with putative in vivo relevance. Finally, to enhance biological plausibility, we incorporated an lncRNA layer by leveraging their miRNA "sponge" (ceRNA) activity, and we assembled an integrated miRNA-mRNA-lncRNA network. Key miRNAs from this network were then evaluated for expression in external TCGA cohorts and for diagnostic potential using area-under-the-curve (AUC) analysis.</p><p><strong>Results: </strong>Our data reveal a reprogramming of miRNA expression between 3D and 2D cultures. Using a threshold of FC > 1.5 and p < 0.05, we found 75 miRNAs upregulated and 82 downregulated in 3D relative to 2D. To strengthen biological interpretation, we integrated our miRNA expression data with public mRNA profiles from BT-474 cells cultured in 3D versus 2D. We then cross-referenced interactions reported in miRNet and ENCORI, retaining only miRNA-mRNA pairs showing inverse regulation. This integrative layer yielded a pathway-level view in which 3D-modulated miRNAs collectively favored proliferative programs, ESR1/estrogen signaling, MAPK/JNK activity, cell-cycle control, and extracellular-matrix remodeling, with relative attenuation of EGFR/TGF-β signaling. Together, the inferred miRNA-mRNA network supports a shift toward a more tumor-like, transcriptionally active state in 3D. To reinforce translational relevance, we cross-referenced public luminal breast tumor datasets with BT-474 2D cultures and identified 14 miRNAs in common, with the same direction of change as observed in 3D cultures. From these, we assembled co-regulatory networks linking miRNAs to their mRNA targets and to lncRNAs. This analysis highlighted four key miRNA nodes: miR-92a-3p, miR-539-5p, miR-18a-5p, and miR-130a-3p, which are connected to 58 mRNAs and modulated by 12 lncRNAs. The hubs converge on pathways for gr
背景:三维(3D)培养捕捉肿瘤结构和微环境信号的关键特征。由于microrna (mirna)是主要的转录后调控因子,我们想知道3D生长是否会揭示BT-474腔内乳腺癌细胞中与疾病相关的lncRNA-miRNA-mRNA程序。方法:使用GeneChip miRNA 4.0微阵列对BT-474细胞进行分析,比较3D和2D条件。然后,我们进行了一项综合分析,包括:(i)从miRNet和ENCORI(预测和策划)中提取差异表达的miRNA-mRNA相互作用;(ii)利用BT-474 3D与2D培养的公开mRNA数据鉴定反向miRNA-mRNA对(miRNA下调,靶mRNA上调,或相反),使其对与调控抑制一致;(iii)只保留那些也出现在miRNet/ENCORI中的miRNA-mRNA对。在另一个单独的步骤中,我们检查了公开的乳腺腔内肿瘤数据集和BT-474 2D培养物,以确定哪些3d鉴定的mirna在腔内肿瘤中表现出相似的表达变化方向,从而优先考虑具有推测的体内相关性的信号。最后,为了增强生物学上的可信性,我们利用miRNA“海绵”(ceRNA)活性将lncRNA层纳入其中,并组装了一个集成的miRNA- mrna -lncRNA网络。然后评估来自该网络的关键mirna在外部TCGA队列中的表达,并使用曲线下面积(AUC)分析评估诊断潜力。结果:我们的数据揭示了3D和2D培养之间miRNA表达的重编程。结论:总的来说,本研究强调了3D培养在研究乳腺癌生物学中的作用,强调了lncrna、mirna和mrna之间的关键相互作用。我们的研究结果为发现新的潜在生物标志物提供了见解,强调了整合体外3D培养和体内表达数据的重要性,以便更准确地识别mirna,并可能在癌症治疗中应用。
{"title":"The microRNAs landscape of luminal B breast cancer cells in a three-dimensional microenvironment.","authors":"Stephanie I Nuñez-Olvera, Lorena Aguilar-Arnal, Jonathan Puente-Rivera, Alfredo Hidalgo-Miranda, Mireya Cisneros-Villanueva, Yarely M Salinas-Vera, Laurence A Marchat, María Elizbeth Álvarez-Sánchez, Karla Rubio, César López-Camarillo","doi":"10.1186/s41065-025-00586-2","DOIUrl":"10.1186/s41065-025-00586-2","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Three-dimensional (3D) culture captures key features of tumor architecture and microenvironmental signaling. Because microRNAs (miRNAs) are central post-transcriptional regulators, we asked whether 3D growth would reveal disease-relevant lncRNA-miRNA-mRNA programs in BT-474 luminal breast cancer cells.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;BT-474 cells were profiled with GeneChip miRNA 4.0 microarrays to compare 3D versus 2D conditions. We then performed an integrative analysis consisting of: (i) extracting miRNA-mRNA interactions from miRNet and ENCORI (predicted and curated) for the differentially expressed miRNAs; (ii) identifying inverse miRNA-mRNA pairs (miRNA downregulated with target mRNA upregulated, or the reverse) using public mRNA data from BT-474 3D versus 2D cultures so that pairs were consistent with regulatory repression; and (iii) retaining only those miRNA-mRNA pairs that also appeared in miRNet/ENCORI. In a separate step, we examined public luminal breast tumor datasets versus BT-474 2D cultures to determine which 3D-identified miRNAs showed a similar direction of expression change in luminal tumors, thereby prioritizing signals with putative in vivo relevance. Finally, to enhance biological plausibility, we incorporated an lncRNA layer by leveraging their miRNA \"sponge\" (ceRNA) activity, and we assembled an integrated miRNA-mRNA-lncRNA network. Key miRNAs from this network were then evaluated for expression in external TCGA cohorts and for diagnostic potential using area-under-the-curve (AUC) analysis.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Our data reveal a reprogramming of miRNA expression between 3D and 2D cultures. Using a threshold of FC &gt; 1.5 and p &lt; 0.05, we found 75 miRNAs upregulated and 82 downregulated in 3D relative to 2D. To strengthen biological interpretation, we integrated our miRNA expression data with public mRNA profiles from BT-474 cells cultured in 3D versus 2D. We then cross-referenced interactions reported in miRNet and ENCORI, retaining only miRNA-mRNA pairs showing inverse regulation. This integrative layer yielded a pathway-level view in which 3D-modulated miRNAs collectively favored proliferative programs, ESR1/estrogen signaling, MAPK/JNK activity, cell-cycle control, and extracellular-matrix remodeling, with relative attenuation of EGFR/TGF-β signaling. Together, the inferred miRNA-mRNA network supports a shift toward a more tumor-like, transcriptionally active state in 3D. To reinforce translational relevance, we cross-referenced public luminal breast tumor datasets with BT-474 2D cultures and identified 14 miRNAs in common, with the same direction of change as observed in 3D cultures. From these, we assembled co-regulatory networks linking miRNAs to their mRNA targets and to lncRNAs. This analysis highlighted four key miRNA nodes: miR-92a-3p, miR-539-5p, miR-18a-5p, and miR-130a-3p, which are connected to 58 mRNAs and modulated by 12 lncRNAs. The hubs converge on pathways for gr","PeriodicalId":12862,"journal":{"name":"Hereditas","volume":"162 1","pages":"219"},"PeriodicalIF":2.5,"publicationDate":"2025-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12574175/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145400710","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
DExD-box helicase 39 A, targeted by coumestrol, facilitates the malignant behaviors of osteosarcoma cells. 库美孕酮靶向的DExD-box解旋酶39a促进骨肉瘤细胞的恶性行为。
IF 2.5 3区 生物学 Pub Date : 2025-10-28 DOI: 10.1186/s41065-025-00588-0
Wang Haiqing, Jin Yangli, Zhang Feng
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引用次数: 0
Identification of coagulation-related biomarkers in osteoarthritis and immune infiltration analysis based on bioinformatics. 骨关节炎中凝固相关生物标志物的鉴定及基于生物信息学的免疫浸润分析。
IF 2.5 3区 生物学 Pub Date : 2025-10-27 DOI: 10.1186/s41065-025-00585-3
Linyuwei He, Zhihong Ou, Boyuan Qiu, Siwen Tong, Chu Liu, Pengwei Zhou, Zhixue Ou

Background: Osteoarthritis (OA) is a common degenerative disorder characterized primarily by articular cartilage degradation and chronic inflammation. Although direct evidence elucidating the specific mechanisms underlying the coagulation-immune axis in OA remains limited, emerging studies have suggested a potential link.

Methods: Four microarray datasets were retrieved from the Gene Expression Omnibus (GEO) database. Then, differentially expressed genes (DEGs) (|log₂FC| ≥ 1, P < 0.05) were identified. Gene Set Enrichment Analysis (GSEA), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed on these DEGs. Molecular Signatures Database (MsigDB) coagulation genes were intersected with DEGs to identify coagulation-related DEGs. Then, hub genes were determined using multiple Machine learning (ML) algorithms, Least Absolute Shrinkage and Selection Operator (LASSO), Support Vector Machine-Recursive Feature Elimination (SVM-RFE), and Random Forest (RF). Diagnostic performance of these genes was evaluated via a nomogram and ROC analysis (AUC). Immune cell infiltration was assessed with CIBERSORT. The expression of hub genes was validated in vitro via real-time qPCR and Western blot (WB).

Results: Based on 103 samples across four datasets, 294 DEGs were identified. Gene set enrichment analyses (GSEA, GO, KEGG) revealed significant enrichment of these genes in immune- and coagulation-related pathways in OA. Intersecting MsigDB coagulation genes with DEGs yielded nine coagulation-associated DEGs. Based on four distinct ML algorithms, six hub genes were selected: Fibroblast activation protein (FAP), Cathepsin H (CTSH), matrix metalloproteinase 1 (MMP1), matrix metalloproteinase 9 (MMP9), Complement component 6 (C6), MAF Basic Leucine Zipper Transcription Factor F (MAFF). These hub genes demonstrated high diagnostic accuracy according to ROC analysis. Immune infiltration analysis showed significant differences between OA and normal samples. M0 macrophages, plasma cells, and γδ T cells were elevated in OA, while activated mast cells and resting memory CD4⁺ T cells were decreased. The qPCR and WB results corroborated the ML findings: in the interleukin-1β (IL-1β)-treated group, FAP, MMP1, MMP9, and CTSH were significantly upregulated, while MAFF and C6 were markedly downregulated.

Conclusions: This study, based on publicly available GEO datasets, identified six potential diagnostic biomarkers for OA: FAP, CTSH, MMP1, MMP9, C6, and MAFF. These findings highlight the potential involvement of coagulation-immune interactions in OA pathogenesis and offer novel insights into the molecular mechanisms and diagnostic strategies for the disease.

背景:骨关节炎(OA)是一种常见的退行性疾病,主要表现为关节软骨退化和慢性炎症。尽管直接证据阐明OA中凝固-免疫轴的具体机制仍然有限,但新兴研究表明存在潜在的联系。方法:从Gene Expression Omnibus (GEO)数据库中检索4个微阵列数据集。然后,差异表达基因(DEGs) (|log 2 FC|≥1,P)。结果:基于4个数据集的103个样本,鉴定出294个DEGs。基因集富集分析(GSEA, GO, KEGG)显示,这些基因在OA的免疫和凝固相关途径中显著富集。将MsigDB凝血基因与DEGs交叉得到9种与凝血相关的DEGs。基于四种不同的ML算法,选择了6个枢纽基因:成纤维细胞活化蛋白(FAP)、组织蛋白酶H (CTSH)、基质金属蛋白酶1 (MMP1)、基质金属蛋白酶9 (MMP9)、补体成分6 (C6)、MAF碱性亮氨酸Zipper转录因子F (MAFF)。根据ROC分析,这些中心基因显示出较高的诊断准确性。免疫浸润分析显示OA与正常样品有显著差异。OA中M0巨噬细胞、浆细胞和γδ T细胞升高,激活肥大细胞和静止记忆CD4 + T细胞减少。qPCR和WB结果证实了ML的发现:在白细胞介素-1β (IL-1β)处理组,FAP、MMP1、MMP9和CTSH显著上调,MAFF和C6显著下调。结论:本研究基于公开的GEO数据集,确定了6种OA的潜在诊断生物标志物:FAP、CTSH、MMP1、MMP9、C6和MAFF。这些发现强调了凝血-免疫相互作用在OA发病机制中的潜在参与,并为该疾病的分子机制和诊断策略提供了新的见解。
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引用次数: 0
MiR-518c-5p/miR-4524a-3p can mediate immune escape and chemotherapy resistance in triple-negative breast cancer and predict its outcome. MiR-518c-5p/miR-4524a-3p可介导三阴性乳腺癌的免疫逃逸和化疗耐药并预测其预后。
IF 2.5 3区 生物学 Pub Date : 2025-10-21 DOI: 10.1186/s41065-025-00572-8
Yuan Sun, Liang An, Linna Kong, Xiaoyan Liu, Huihui Zhang, Jiaqi Liu, Pengfei Qian

Background: Triple-negative breast cancer (TNBC), is characterized by its highly aggressive nature, with chemotherapy resistance and immune evasion contributing to poor outcomes. The role of major histocompatibility complex class I (MHCI) downregulation in TNBC progression remains incompletely understood.

Aim: The present research focused on elucidating the roles of miR-518c-5p/miR-4524a-3p in immune evasion and chemoresistance in TNBC, and evaluating their clinical significance.

Methods: Bioinformatics analysis predicted miRNAs targeting HLA-A/B/C, validated by dual-luciferase assays. Functional studies in TNBC cell lines (MDA-MB-231/468 and ADR-resistant sublines) included chromium release, proliferation, invasion, and apoptosis assays. Clinical relevance was assessed in 88 TNBC patients and 88 controls using RT-PCR and survival analysis.

Results: MiR-518c-5p/miR-4524a-3p directly targeted HLA-A, HLA-B, and HLA-C, downregulating MHCI expression and promoting immune evasion. Overexpression of miR-518c-5p/miR-4524a-3p enhanced TNBC cell proliferation, invasion, and chemoresistance to doxorubicin, while their inhibition reversed these effects. High expression of miR-518c-5p/miR-4524a-3p correlated with adverse clinical outcomes in TNBC patients, including shorter recurrence-free survival.

Conclusions: MiR-518c-5p/miR-4524a-3p contribute to TNBC progression by facilitating immune evasion and chemoresistance. Targeting miR-518c-5p/miR-4524a-3p may represent a promising therapeutic approach for improving TNBC treatment outcomes.

背景:三阴性乳腺癌(TNBC)的特点是具有高度侵袭性,化疗耐药和免疫逃避导致预后不良。主要组织相容性复合体I类(MHCI)下调在TNBC进展中的作用尚不完全清楚。目的:本研究旨在阐明miR-518c-5p/miR-4524a-3p在TNBC免疫逃避和化疗耐药中的作用,并评价其临床意义。方法:生物信息学分析预测靶向HLA-A/B/C的mirna,并通过双荧光素酶检测验证。TNBC细胞系(MDA-MB-231/468和耐药亚系)的功能研究包括铬释放、增殖、侵袭和凋亡测定。采用RT-PCR和生存分析对88例TNBC患者和88例对照组进行临床相关性评估。结果:MiR-518c-5p/miR-4524a-3p直接靶向HLA-A、HLA-B、HLA-C,下调MHCI表达,促进免疫逃避。过表达miR-518c-5p/miR-4524a-3p可增强TNBC细胞的增殖、侵袭和对阿霉素的化疗耐药,而抑制miR-4524a-3p可逆转这些作用。miR-518c-5p/miR-4524a-3p的高表达与TNBC患者的不良临床结果相关,包括更短的无复发生存期。结论:MiR-518c-5p/miR-4524a-3p通过促进免疫逃避和化疗耐药促进TNBC的进展。靶向miR-518c-5p/miR-4524a-3p可能是改善TNBC治疗结果的一种有希望的治疗方法。
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引用次数: 0
Evaluation of cystatin C and microalbuminuria as predictive markers for hypertension-related renal complications. 评价胱抑素C和微量白蛋白尿作为高血压相关肾脏并发症的预测指标。
IF 2.5 3区 生物学 Pub Date : 2025-10-17 DOI: 10.1186/s41065-025-00557-7
Jinyu Li, Shiming Guan, Zhuoqun Zou, Lijuan Yang, Bo Qian, Li Shen, Ye Li

Objective: This study aimed to investigate the correlation between blood pressure and the levels of two renal function markers, cystatin C and microalbuminuria, with the goal of evaluating their correlation across varying blood pressure categories.

Methods: A cohort of 3,000 participants, comprising 1,500 individuals with a diagnosis of hypertension and 1,500 normotensive controls, was analyzed. Data on blood pressure, serum cystatin C, microalbuminuria, and other relevant clinical parameters were collected at admission. Correlations between these markers and blood pressure levels were analyzed using SPSS 26.0 statistical software.

Results: Levels of cystatin C and microalbuminuria were significantly higher in individuals with hypertension compared to the control group (P < 0.05). Furthermore, both biomarkers demonstrated a positive correlation with blood pressure (r = 0.140, P < 0.001). Multiple linear regression analysis revealed that the combined use of cystatin C and microalbuminuria provided a superior predictive value for blood pressure levels (P < 0.001). The combined predictive accuracy (R² = 0.114. R² = 0.112 after rectifying age, body mass index, and blood lipid levels) exceeded that of cystatin C (R² = 0.100) or microalbuminuria (R² = 0.113) when analyzed individually.

Conclusion: The biomarkers cystatin C and microalbuminuria are closely correlated with blood pressure levels. Their combined assessment offers an enhanced diagnostic approach for the early detection of renal complications in individuals with hypertension.

目的:本研究旨在探讨两种肾功能指标胱抑素C和微量蛋白尿水平与血压的相关性,以评估它们在不同血压类别中的相关性。方法:对3000名参与者进行队列分析,其中包括1500名诊断为高血压的个体和1500名血压正常的对照组。入院时收集血压、血清胱抑素C、微量白蛋白尿等相关临床参数。采用SPSS 26.0统计软件分析这些指标与血压水平的相关性。结果:高血压患者血清胱抑素C和微量白蛋白尿水平明显高于对照组(P)。结论:胱抑素C和微量白蛋白尿与血压水平密切相关。他们的综合评估为高血压患者肾脏并发症的早期发现提供了一种增强的诊断方法。
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Hereditas
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