首页 > 最新文献

Biology Direct最新文献

英文 中文
Integrative genomics unveils basement membrane-related diagnostic markers and therapeutic targets in esophageal squamous cell carcinoma 整合基因组学揭示了食管鳞状细胞癌中与基底膜相关的诊断标记物和治疗靶点
IF 5.5 2区 生物学 Q1 BIOLOGY Pub Date : 2024-09-11 DOI: 10.1186/s13062-024-00529-3
Han Zhang, Xia Zhang, Zhenyu Huang, Hao Zhang
Esophageal squamous cell carcinoma (ESCC) is often diagnosed at advanced stages due to the inherent limitations of current screening methodologies. Central to evaluating tumor invasion and prognostic assessment in ESCC is the integrity of the basement membrane (BM). However, current research on the implications of BM-related genes (BMRGs) in diagnosing ESCC remains sparse. We performed a comprehensive analysis using single-cell RNA-sequencing (scRNA-seq) data from the Gene Expression Omnibus (GEO) database, alongside gene expression profiles acquired from GEO and The Cancer Genome Atlas (TCGA) databases. This identified differentially expressed BMRGs in ESCC. Employing LASSO, RF, and SVM-RFE, we selected potential BM biomarkers and crafted a diagnostic nomogram for ESCC, validated by ROC curves and AUC values. We also explored immune infiltration and biological mechanisms through consensus clustering and GSVA, and utilized single cell trajectory analysis and GSCALite to study gene distributions and pathways. In vitro experiments further elucidated the role of these genes in ESCC carcinogenesis. Here, we discovered that ESCC cell types exhibited markedly elevated BM-related scores. Our analysis pinpointed seven BM genes upregulated and linked to immune infiltration, showcasing unique gene expression profiles and varying immune cell densities across the BM-related subtypes. Furthermore, a robust positive correlation was observed between these genes expression and EMT activity. The knockdown of BGN significantly suppressed cell proliferation, migration, invasion, while also augmenting cell viability following chemotherapy drug treatment. Our study identified seven key BMRGs (BGN, LAMB3, SPARC, MMP1, LUM, COL4A1, and NELL2) and established a diagnostic nomogram for ESCC. Of noteworthy significance is the discovery of BGN as a promising drug target, indicating a novel strategy for future clinical combination therapies in ESCC.
由于目前筛查方法的固有局限性,食管鳞状细胞癌(ESCC)往往在晚期才被诊断出来。基底膜(BM)的完整性是评估 ESCC 肿瘤侵袭和预后的核心。然而,目前关于基底膜相关基因(BMRGs)在诊断 ESCC 中的意义的研究仍然很少。我们利用基因表达总库(GEO)数据库中的单细胞RNA测序(scRNA-seq)数据以及GEO和癌症基因组图谱(TCGA)数据库中的基因表达谱进行了综合分析。这确定了 ESCC 中差异表达的 BMRGs。利用 LASSO、RF 和 SVM-RFE,我们筛选出了潜在的 BM 生物标记物,并制作了 ESCC 诊断提名图,通过 ROC 曲线和 AUC 值进行了验证。我们还通过共识聚类和GSVA探讨了免疫浸润和生物机制,并利用单细胞轨迹分析和GSCALite研究了基因分布和通路。体外实验进一步阐明了这些基因在 ESCC 癌变中的作用。在这里,我们发现 ESCC 细胞类型表现出明显升高的 BM 相关评分。我们的分析确定了 7 个上调并与免疫浸润相关的 BM 基因,这些基因在 BM 相关亚型中显示出独特的基因表达谱和不同的免疫细胞密度。此外,还观察到这些基因的表达与 EMT 活性之间存在很强的正相关性。敲除 BGN 能显著抑制细胞增殖、迁移和侵袭,同时还能提高化疗药物治疗后的细胞存活率。我们的研究发现了七个关键的 BMRGs(BGN、LAMB3、SPARC、MMP1、LUM、COL4A1 和 NELL2),并建立了 ESCC 的诊断提名图。值得注意的是,发现 BGN 是一个很有前景的药物靶点,这为 ESCC 未来的临床联合疗法提供了一种新策略。
{"title":"Integrative genomics unveils basement membrane-related diagnostic markers and therapeutic targets in esophageal squamous cell carcinoma","authors":"Han Zhang, Xia Zhang, Zhenyu Huang, Hao Zhang","doi":"10.1186/s13062-024-00529-3","DOIUrl":"https://doi.org/10.1186/s13062-024-00529-3","url":null,"abstract":"Esophageal squamous cell carcinoma (ESCC) is often diagnosed at advanced stages due to the inherent limitations of current screening methodologies. Central to evaluating tumor invasion and prognostic assessment in ESCC is the integrity of the basement membrane (BM). However, current research on the implications of BM-related genes (BMRGs) in diagnosing ESCC remains sparse. We performed a comprehensive analysis using single-cell RNA-sequencing (scRNA-seq) data from the Gene Expression Omnibus (GEO) database, alongside gene expression profiles acquired from GEO and The Cancer Genome Atlas (TCGA) databases. This identified differentially expressed BMRGs in ESCC. Employing LASSO, RF, and SVM-RFE, we selected potential BM biomarkers and crafted a diagnostic nomogram for ESCC, validated by ROC curves and AUC values. We also explored immune infiltration and biological mechanisms through consensus clustering and GSVA, and utilized single cell trajectory analysis and GSCALite to study gene distributions and pathways. In vitro experiments further elucidated the role of these genes in ESCC carcinogenesis. Here, we discovered that ESCC cell types exhibited markedly elevated BM-related scores. Our analysis pinpointed seven BM genes upregulated and linked to immune infiltration, showcasing unique gene expression profiles and varying immune cell densities across the BM-related subtypes. Furthermore, a robust positive correlation was observed between these genes expression and EMT activity. The knockdown of BGN significantly suppressed cell proliferation, migration, invasion, while also augmenting cell viability following chemotherapy drug treatment. Our study identified seven key BMRGs (BGN, LAMB3, SPARC, MMP1, LUM, COL4A1, and NELL2) and established a diagnostic nomogram for ESCC. Of noteworthy significance is the discovery of BGN as a promising drug target, indicating a novel strategy for future clinical combination therapies in ESCC.","PeriodicalId":9164,"journal":{"name":"Biology Direct","volume":"29 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142189257","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Equol exerts anti-tumor effects on choriocarcinoma cells by promoting TRIM21-mediated ubiquitination of ANXA2. Equol通过促进TRIM21介导的ANXA2泛素化,对绒毛膜癌细胞产生抗肿瘤作用。
IF 5.7 2区 生物学 Q1 BIOLOGY Pub Date : 2024-09-06 DOI: 10.1186/s13062-024-00519-5
Xiao-Mei Liu, Zi-Hao Wang, Qian-Xue Wei, Yang Song, Xiao-Xin Ma

Choriocarcinoma is a malignant cancer that belongs to gestational trophoblastic neoplasia (GTN). Herein, serum metabolomic analysis was performed on 29 GTN patients and 30 healthy individuals to characterize the metabolic variations during GTN progression. Ultimately 24 differential metabolites (DMs) were identified, of which, Equol was down-regulated in GTN patients, whose VIP score is the 3rd highest among the 24 DMs. As an intestinal metabolite of daidzein, the anticancer potential of Equol has been demonstrated in multiple cancers, but not choriocarcinoma. Hence, human choriocarcinoma cell lines JEG-3 and Bewo were used and JEG-3-derived subcutaneous xenograft models were developed to assess the effect of Equol on choriocarcinoma. The results suggested that Equol treatment effectively suppressed choriocarcinoma cell proliferation, induced cell apoptosis, and reduced tumorigenesis. Label-free quantitative proteomics showed that 136 proteins were significantly affected by Equol and 20 proteins were enriched in Gene Ontology terms linked to protein degradation. Tripartite motif containing 21 (TRIM21), a E3 ubiquitin ligase, was up-regulated by Equol. Equol-induced effects on choriocarcinoma cells could be reversed by TRIM21 inhibition. Annexin A2 (ANXA2) interacted with TRIM21 and its ubiquitination was modulated by TRIM21. We found that TRIM21 was responsible for proteasome-mediated degradation of ANXA2 induced by Equol, and the inhibitory effects of Equol on the malignant behaviors of choriocarcinoma cells were realized by TRIM21-mediated down-regulation of ANXA2. Moreover, β-catenin activation was inhibited by Equol, which also depended on TRIM21-mediated down-regulation of ANXA2. Taken together, Equol may be a novel candidate for the treatment for choriocarcinoma.

绒毛膜癌是一种恶性肿瘤,属于妊娠滋养细胞肿瘤(GTN)。本文对29名GTN患者和30名健康人进行了血清代谢组学分析,以确定GTN进展过程中的代谢变化特征。最终确定了 24 种差异代谢物(DMs),其中 Equol 在 GTN 患者中下调,其 VIP 评分在 24 种 DMs 中排名第三。Equol是代泽因的一种肠道代谢物,其抗癌潜力已在多种癌症中得到证实,但未在绒毛膜癌中得到证实。因此,研究人员使用了人类绒毛膜癌细胞系 JEG-3 和 Bewo,并建立了源自 JEG-3 的皮下异种移植模型,以评估 Equol 对绒毛膜癌的影响。结果表明,Equol 能有效抑制绒毛膜癌细胞增殖,诱导细胞凋亡,减少肿瘤发生。无标记定量蛋白质组学显示,136 个蛋白质受到 Equol 的显著影响,20 个蛋白质富集在与蛋白质降解相关的基因本体术语中。Equol 上调了含有三方基序 21 (TRIM21) 的 E3 泛素连接酶。抑制 TRIM21 可逆转 Equol 诱导的对绒毛膜癌细胞的影响。Annexin A2(ANXA2)与 TRIM21 相互作用,其泛素化受 TRIM21 的调节。我们发现,TRIM21 负责 Equol 诱导的蛋白酶体介导的 ANXA2 降解,而 Equol 对绒毛膜癌细胞恶性行为的抑制作用是通过 TRIM21 介导的 ANXA2 下调实现的。此外,Equol 还能抑制 β-catenin 的活化,这也取决于 TRIM21 介导的 ANXA2 下调。综上所述,Equol 可能是一种治疗绒毛膜癌的新型候选药物。
{"title":"Equol exerts anti-tumor effects on choriocarcinoma cells by promoting TRIM21-mediated ubiquitination of ANXA2.","authors":"Xiao-Mei Liu, Zi-Hao Wang, Qian-Xue Wei, Yang Song, Xiao-Xin Ma","doi":"10.1186/s13062-024-00519-5","DOIUrl":"10.1186/s13062-024-00519-5","url":null,"abstract":"<p><p>Choriocarcinoma is a malignant cancer that belongs to gestational trophoblastic neoplasia (GTN). Herein, serum metabolomic analysis was performed on 29 GTN patients and 30 healthy individuals to characterize the metabolic variations during GTN progression. Ultimately 24 differential metabolites (DMs) were identified, of which, Equol was down-regulated in GTN patients, whose VIP score is the 3rd highest among the 24 DMs. As an intestinal metabolite of daidzein, the anticancer potential of Equol has been demonstrated in multiple cancers, but not choriocarcinoma. Hence, human choriocarcinoma cell lines JEG-3 and Bewo were used and JEG-3-derived subcutaneous xenograft models were developed to assess the effect of Equol on choriocarcinoma. The results suggested that Equol treatment effectively suppressed choriocarcinoma cell proliferation, induced cell apoptosis, and reduced tumorigenesis. Label-free quantitative proteomics showed that 136 proteins were significantly affected by Equol and 20 proteins were enriched in Gene Ontology terms linked to protein degradation. Tripartite motif containing 21 (TRIM21), a E3 ubiquitin ligase, was up-regulated by Equol. Equol-induced effects on choriocarcinoma cells could be reversed by TRIM21 inhibition. Annexin A2 (ANXA2) interacted with TRIM21 and its ubiquitination was modulated by TRIM21. We found that TRIM21 was responsible for proteasome-mediated degradation of ANXA2 induced by Equol, and the inhibitory effects of Equol on the malignant behaviors of choriocarcinoma cells were realized by TRIM21-mediated down-regulation of ANXA2. Moreover, β-catenin activation was inhibited by Equol, which also depended on TRIM21-mediated down-regulation of ANXA2. Taken together, Equol may be a novel candidate for the treatment for choriocarcinoma.</p>","PeriodicalId":9164,"journal":{"name":"Biology Direct","volume":"19 1","pages":"78"},"PeriodicalIF":5.7,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11378480/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142145136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
GALNT9 enrichment attenuates MPP+-induced cytotoxicity by ameliorating protein aggregations containing α-synuclein and mitochondrial dysfunction. GALNT9 富集可通过改善含有α-突触核蛋白的蛋白质聚集和线粒体功能障碍,减轻 MPP+ 诱导的细胞毒性。
IF 5.7 2区 生物学 Q1 BIOLOGY Pub Date : 2024-09-05 DOI: 10.1186/s13062-024-00524-8
Yuanwen Peng, Jun Liu, Lili Sun, Qiuying Zheng, Can Cao, Wenyong Ding, Shufeng Yang, Li Ma, Wenli Zhang

Background: GALNTs (UDP-GalNAc; polypeptide N-acetylgalactosaminyltransferases) initiate mucin-type O-GalNAc glycosylation by adding N-GalNAc to protein serine/threonine residues. Abnormalities in O-GalNAc glycosylation are involved in various disorders such as Parkinson's disease (PD), a neurodegenerative disorder. GALNT9 is potentially downregulated in PD patients.

Methods: To determine whether GALNT9 enrichment ameliorates cytotoxicity related to PD-like variations, a pcDNA3.1-GALNT9 plasmid was constructed and transfected into SH-SY5Y cells to establish a GALNT9-overexpressing cell model.

Results: Downregulation of GALNT9 and O-GalNAc glycosylation was confirmed in our animal and cellular models of PD-like variations. GALNT9 supplementation greatly attenuated cytotoxicity induced by MPP+ (1-Methyl-4-phenylpyridinium iodide) since it led to increased levels of tyrosine hydroxylase and dopamine, reduced rates of apoptosis, and significantly ameliorated MPP+-induced mitochondrial dysfunction by alleviating abnormal levels of mitochondrial membrane potential and reactive oxygen species. A long-lasting mPTP (mitochondrial permeability transition pores) opening and calcium efflux resulted in significantly lower activity in the cytochrome C-associated apoptotic pathway and mitophagy process, signifying that GALNT9 supplementation maintained neuronal cell health under MPP+ exposure. Additionally, it was found that glycans linked to proteins influenced the formation of protein aggregates containing α-synuclein, and GALNT9 supplement dramatically reduced such insoluble protein aggregations under MPP+ treatment. Glial GALNT9 predominantly appears under pathological conditions like PD-like variations.

Conclusions: GALNT9 enrichment improved cell survival, and glial GALNT9 potentially represents a pathogenic index for PD patients. This study provides insights into the development of therapeutic strategies for the treatment of PD.

背景:GALNTs(UDP-GalNAc;多肽N-乙酰半乳糖氨酰转移酶)通过在蛋白质丝氨酸/苏氨酸残基上添加N-GalNAc来启动粘蛋白型O-GalNAc糖基化。O-GalNAc 糖基化异常与多种疾病有关,如神经退行性疾病帕金森病(PD)。GALNT9在帕金森病患者中可能被下调:为了确定 GALNT9 的富集是否能改善与帕金森病样变异相关的细胞毒性,我们构建了 pcDNA3.1-GALNT9 质粒并将其转染到 SH-SY5Y 细胞中,以建立 GALNT9 基因缺失的细胞模型:结果:GALNT9和O-GalNAc糖基化的下调在我们的PD样变异动物模型和细胞模型中得到了证实。补充 GALNT9 大大减轻了 MPP+(1-甲基-4-苯基吡啶碘化物)诱导的细胞毒性,因为它导致酪氨酸羟化酶和多巴胺水平升高,降低了细胞凋亡率,并通过减轻线粒体膜电位和活性氧的异常水平,显著改善了 MPP+诱导的线粒体功能障碍。持久的 mPTP(线粒体通透性转换孔)开放和钙外流导致细胞色素 C 相关凋亡途径和有丝分裂过程的活性明显降低,这表明补充 GALNT9 能在 MPP+ 暴露下维持神经细胞的健康。此外,研究还发现,与蛋白质相连的聚糖会影响含有α-突触核蛋白的蛋白质聚集体的形成,而补充 GALNT9 能显著减少 MPP+ 处理下的这种不溶性蛋白质聚集体。神经胶质 GALNT9 主要出现在 PD 样变等病理条件下:结论:GALNT9的富集提高了细胞的存活率,胶质GALNT9可能代表了PD患者的致病指标。这项研究为制定治疗帕金森病的策略提供了启示。
{"title":"GALNT9 enrichment attenuates MPP<sup>+</sup>-induced cytotoxicity by ameliorating protein aggregations containing α-synuclein and mitochondrial dysfunction.","authors":"Yuanwen Peng, Jun Liu, Lili Sun, Qiuying Zheng, Can Cao, Wenyong Ding, Shufeng Yang, Li Ma, Wenli Zhang","doi":"10.1186/s13062-024-00524-8","DOIUrl":"10.1186/s13062-024-00524-8","url":null,"abstract":"<p><strong>Background: </strong>GALNTs (UDP-GalNAc; polypeptide N-acetylgalactosaminyltransferases) initiate mucin-type O-GalNAc glycosylation by adding N-GalNAc to protein serine/threonine residues. Abnormalities in O-GalNAc glycosylation are involved in various disorders such as Parkinson's disease (PD), a neurodegenerative disorder. GALNT9 is potentially downregulated in PD patients.</p><p><strong>Methods: </strong>To determine whether GALNT9 enrichment ameliorates cytotoxicity related to PD-like variations, a pcDNA3.1-GALNT9 plasmid was constructed and transfected into SH-SY5Y cells to establish a GALNT9-overexpressing cell model.</p><p><strong>Results: </strong>Downregulation of GALNT9 and O-GalNAc glycosylation was confirmed in our animal and cellular models of PD-like variations. GALNT9 supplementation greatly attenuated cytotoxicity induced by MPP<sup>+</sup> (1-Methyl-4-phenylpyridinium iodide) since it led to increased levels of tyrosine hydroxylase and dopamine, reduced rates of apoptosis, and significantly ameliorated MPP<sup>+</sup>-induced mitochondrial dysfunction by alleviating abnormal levels of mitochondrial membrane potential and reactive oxygen species. A long-lasting mPTP (mitochondrial permeability transition pores) opening and calcium efflux resulted in significantly lower activity in the cytochrome C-associated apoptotic pathway and mitophagy process, signifying that GALNT9 supplementation maintained neuronal cell health under MPP<sup>+</sup> exposure. Additionally, it was found that glycans linked to proteins influenced the formation of protein aggregates containing α-synuclein, and GALNT9 supplement dramatically reduced such insoluble protein aggregations under MPP<sup>+</sup> treatment. Glial GALNT9 predominantly appears under pathological conditions like PD-like variations.</p><p><strong>Conclusions: </strong>GALNT9 enrichment improved cell survival, and glial GALNT9 potentially represents a pathogenic index for PD patients. This study provides insights into the development of therapeutic strategies for the treatment of PD.</p>","PeriodicalId":9164,"journal":{"name":"Biology Direct","volume":"19 1","pages":"77"},"PeriodicalIF":5.7,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11378468/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142139269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Proteomics and digital subtraction angiography approaches reveal CDH18 as a potential target for therapy of moyamoya disease. 蛋白质组学和数字减影血管造影方法揭示了 CDH18 是治疗 moyamoya 病的潜在靶点。
IF 5.7 2区 生物学 Q1 BIOLOGY Pub Date : 2024-09-05 DOI: 10.1186/s13062-024-00522-w
Dong Guo, Yang Dong, Hongbin Li, Hongwei Li, Bo Yang

Moyamoya disease, characterized by basal cerebral artery obstruction, was studied for differential protein expression to elucidate its pathogenesis. Proteomic analysis of cerebrospinal fluid from 10 patients, categorized by postoperative angiography into good and poor prognosis groups, revealed 46 differentially expressed proteins. Notably, cadherin 18 (CDH18) was the most significantly upregulated in the good prognosis group. In addition, the expression of cadherin 18 (CDH18) and phenotypic transformation-related proteins were measured by qRT-PCR and western blot. The effects of CDH18 in vascular smooth muscle cells were detected by CCK-8, EdU, transwell and wound healing assays. The overexpression of CDH18 in vascular smooth muscle cells (VSMCs) was found to inhibit proliferation, migration, and phenotypic transformation. These findings suggest CDH18 as a potential therapeutic target in moyamoya disease.

研究人员对以大脑基底动脉阻塞为特征的莫亚莫亚病进行了蛋白质差异表达研究,以阐明其发病机制。根据术后血管造影术将 10 名患者分为预后良好组和预后不良组,对这些患者的脑脊液进行的蛋白质组学分析发现了 46 种不同表达的蛋白质。值得注意的是,在预后良好组中,粘连蛋白 18(CDH18)的上调最为显著。此外,还通过 qRT-PCR 和 Western blot 检测了粘连蛋白 18(CDH18)和表型转化相关蛋白的表达。CDH18对血管平滑肌细胞的影响通过CCK-8、EdU、transwell和伤口愈合实验进行了检测。在血管平滑肌细胞(VSMCs)中过表达 CDH18 可抑制其增殖、迁移和表型转化。这些发现表明 CDH18 是治疗 moyamoya 病的潜在靶点。
{"title":"Proteomics and digital subtraction angiography approaches reveal CDH18 as a potential target for therapy of moyamoya disease.","authors":"Dong Guo, Yang Dong, Hongbin Li, Hongwei Li, Bo Yang","doi":"10.1186/s13062-024-00522-w","DOIUrl":"10.1186/s13062-024-00522-w","url":null,"abstract":"<p><p>Moyamoya disease, characterized by basal cerebral artery obstruction, was studied for differential protein expression to elucidate its pathogenesis. Proteomic analysis of cerebrospinal fluid from 10 patients, categorized by postoperative angiography into good and poor prognosis groups, revealed 46 differentially expressed proteins. Notably, cadherin 18 (CDH18) was the most significantly upregulated in the good prognosis group. In addition, the expression of cadherin 18 (CDH18) and phenotypic transformation-related proteins were measured by qRT-PCR and western blot. The effects of CDH18 in vascular smooth muscle cells were detected by CCK-8, EdU, transwell and wound healing assays. The overexpression of CDH18 in vascular smooth muscle cells (VSMCs) was found to inhibit proliferation, migration, and phenotypic transformation. These findings suggest CDH18 as a potential therapeutic target in moyamoya disease.</p>","PeriodicalId":9164,"journal":{"name":"Biology Direct","volume":"19 1","pages":"76"},"PeriodicalIF":5.7,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11378584/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142139270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Gastrin-related circRNA_0017065 promotes the proliferation and metastasis of colorectal cancer through the miR-3174/RBFOX2 axis. 胃泌素相关circRNA_0017065通过miR-3174/RBFOX2轴促进结直肠癌的增殖和转移
IF 5.7 2区 生物学 Q1 BIOLOGY Pub Date : 2024-08-29 DOI: 10.1186/s13062-024-00509-7
Xu Wang, Tianjiao Sun, Jiapeng Fan, Xueliang Zuo, Jiading Mao

Gastrin is a gastrointestinal peptide hormone that plays an important role in the progression of colorectal cancer (CRC). However, the molecular mechanism remains unclear. In this study, we identified gastrin-related circRNAs via high-throughput sequencing and selected circRNA_0017065 as the research focus. We further studied its specific role and molecular mechanism in the progression of CRC. Knockdown and overexpression of circRNA_0017065 were performed, and the biological function of circRNA_0017065 in CRC progression was studied via in vitro and in vivo functional experiments. The potential downstream target genes were subsequently identified via screening of databases and gene chip data. The expression of circRNA_0017065 in tumour tissues was significantly upregulated compared with that in adjacent normal tissues. In vitro and in vivo functional experiments revealed that the proliferation and migration of CRC cells were significantly suppressed after circRNA_0017065 knockdown, while apoptosis was promoted. After overexpression of circRNA_0017065, the proliferation and migration of CRC cells were significantly promoted, while apoptosis was inhibited. Mechanistic studies revealed that circRNA_0017065 can act as a sponge for miR-3174 and promote CRC progression via the miR-3174/RBFOX2 axis. In general, gastrin-related circRNA_0017065 plays a key role in the occurrence and development of CRC and is expected to be a potential molecular target for the treatment of CRC metastasis.

胃泌素是一种胃肠道肽类激素,在结直肠癌(CRC)的进展过程中发挥着重要作用。然而,其分子机制仍不清楚。在这项研究中,我们通过高通量测序鉴定了胃泌素相关的 circRNA,并选择 circRNA_0017065 作为研究重点。我们进一步研究了它在 CRC 进展中的特殊作用和分子机制。我们对circRNA_0017065进行了敲除和过表达,并通过体外和体内功能实验研究了circRNA_0017065在CRC进展中的生物学功能。随后,通过数据库和基因芯片数据的筛选,确定了潜在的下游靶基因。与邻近正常组织相比,circRNA_0017065在肿瘤组织中的表达明显上调。体外和体内功能实验显示,circRNA_0017065敲除后,CRC细胞的增殖和迁移明显受到抑制,同时促进了细胞凋亡。过表达circRNA_0017065后,CRC细胞的增殖和迁移被明显促进,而细胞凋亡受到抑制。机理研究发现,circRNA_0017065可作为miR-3174的海绵,通过miR-3174/RBFOX2轴促进CRC的进展。总之,胃泌素相关的circRNA_0017065在CRC的发生和发展中起着关键作用,有望成为治疗CRC转移的潜在分子靶点。
{"title":"Gastrin-related circRNA_0017065 promotes the proliferation and metastasis of colorectal cancer through the miR-3174/RBFOX2 axis.","authors":"Xu Wang, Tianjiao Sun, Jiapeng Fan, Xueliang Zuo, Jiading Mao","doi":"10.1186/s13062-024-00509-7","DOIUrl":"10.1186/s13062-024-00509-7","url":null,"abstract":"<p><p>Gastrin is a gastrointestinal peptide hormone that plays an important role in the progression of colorectal cancer (CRC). However, the molecular mechanism remains unclear. In this study, we identified gastrin-related circRNAs via high-throughput sequencing and selected circRNA_0017065 as the research focus. We further studied its specific role and molecular mechanism in the progression of CRC. Knockdown and overexpression of circRNA_0017065 were performed, and the biological function of circRNA_0017065 in CRC progression was studied via in vitro and in vivo functional experiments. The potential downstream target genes were subsequently identified via screening of databases and gene chip data. The expression of circRNA_0017065 in tumour tissues was significantly upregulated compared with that in adjacent normal tissues. In vitro and in vivo functional experiments revealed that the proliferation and migration of CRC cells were significantly suppressed after circRNA_0017065 knockdown, while apoptosis was promoted. After overexpression of circRNA_0017065, the proliferation and migration of CRC cells were significantly promoted, while apoptosis was inhibited. Mechanistic studies revealed that circRNA_0017065 can act as a sponge for miR-3174 and promote CRC progression via the miR-3174/RBFOX2 axis. In general, gastrin-related circRNA_0017065 plays a key role in the occurrence and development of CRC and is expected to be a potential molecular target for the treatment of CRC metastasis.</p>","PeriodicalId":9164,"journal":{"name":"Biology Direct","volume":"19 1","pages":"75"},"PeriodicalIF":5.7,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11360539/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142092294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
SUMO3 inhibition by butyric acid suppresses cell viability and glycolysis and promotes gemcitabine antitumor activity in pancreatic cancer. 丁酸抑制 SUMO3 可抑制细胞活力和糖酵解,促进吉西他滨对胰腺癌的抗肿瘤活性。
IF 5.7 2区 生物学 Q1 BIOLOGY Pub Date : 2024-08-26 DOI: 10.1186/s13062-024-00513-x
Liming Zhu, Gang Chen, Changjing Huang, Huifeng Gao, Yilin Wang, Yehua Shen

Background: Excavation of key molecules can help identify therapeutic targets and improve the prognosis of pancreatic cancer. This study evaluated the roles of SUMO3 in cell viability, glycolysis, gemcitabine (GEM) sensitivity, and the antitumor activity of butyric acid (BA) in pancreatic cancer.

Methods: The mRNA and protein levels of SUMO3 were detected by qRT-PCR, Western blot, and immunohistochemical assay. SUMO3 was silenced or overexpressed in pancreatic cancer cells with or without Wnt/β-catenin pathway inhibitor, glycolysis inhibitor, GEM, or BA treatment. Cell viability was measured using the Cell Counting Kit-8 assay. Glycolysis was measured by determining the extracellular acidification rate, ATP level, and lactate content. Apoptosis was measured by flow cytometry, and TUNEL staining was used to examine in vitro and in vivo sensitivity to GEM chemotherapy. Luciferase reporter and chromatin immunoprecipitation assays were conducted to detect the binding of the SUMO3 promoter and NF-κB p65.

Results: SUMO3 was increased and associated with poor survival in pancreatic cancer. SUMO3 knockdown decreased cell viability and glycolysis in vitro and inhibited tumor growth in vivo. SUMO3 overexpression increased cell viability and glycolysis in vitro through the β-catenin pathway. SUMO3 knockdown increased GEM sensitivity, whereas SUMO3 overexpression decreased GEM sensitivity and inhibited the antitumor activity of BA. BA promoted histone acetylation and p-IκBα expression to inhibit NF-κB p65-mediated SUMO3 transcription.

Conclusion: SUMO3 acted as an active molecule in cell survival and growth by enhancing glycolysis in response to either GEM or BA. The mechanism was related to the constitutive IκBα/NF-κB/SUMO3/β-catenin signaling pathway.

背景:挖掘关键分子有助于确定治疗靶点并改善胰腺癌的预后。本研究评估了 SUMO3 在胰腺癌细胞活力、糖酵解、吉西他滨(GEM)敏感性和丁酸(BA)抗肿瘤活性中的作用:方法:通过 qRT-PCR、Western 印迹和免疫组化检测 SUMO3 的 mRNA 和蛋白水平。在胰腺癌细胞中沉默或过表达 SUMO3,并使用或不使用 Wnt/β-catenin 通路抑制剂、糖酵解抑制剂、GEM 或 BA 处理。细胞活力用细胞计数试剂盒-8测定。糖酵解是通过测定细胞外酸化率、ATP水平和乳酸含量来测量的。通过流式细胞仪测量细胞凋亡,并使用 TUNEL 染色法检测体外和体内对 GEM 化疗的敏感性。通过荧光素酶报告和染色质免疫沉淀实验检测 SUMO3 启动子与 NF-κB p65 的结合情况:结果:SUMO3的增加与胰腺癌患者的生存率低有关。体外敲除 SUMO3 会降低细胞活力和糖酵解,并抑制体内肿瘤生长。SUMO3过表达可通过β-catenin通路增加体外细胞活力和糖酵解。SUMO3敲除增加了GEM的敏感性,而SUMO3过表达则降低了GEM的敏感性并抑制了BA的抗肿瘤活性。BA促进组蛋白乙酰化和p-IκBα的表达,从而抑制NF-κB p65介导的SUMO3转录:结论:SUMO3 是细胞存活和生长的活性分子,在 GEM 或 BA 作用下可促进糖酵解。其机制与组成型 IκBα/NF-κB/SUMO3/β-catenin 信号通路有关。
{"title":"SUMO3 inhibition by butyric acid suppresses cell viability and glycolysis and promotes gemcitabine antitumor activity in pancreatic cancer.","authors":"Liming Zhu, Gang Chen, Changjing Huang, Huifeng Gao, Yilin Wang, Yehua Shen","doi":"10.1186/s13062-024-00513-x","DOIUrl":"10.1186/s13062-024-00513-x","url":null,"abstract":"<p><strong>Background: </strong>Excavation of key molecules can help identify therapeutic targets and improve the prognosis of pancreatic cancer. This study evaluated the roles of SUMO3 in cell viability, glycolysis, gemcitabine (GEM) sensitivity, and the antitumor activity of butyric acid (BA) in pancreatic cancer.</p><p><strong>Methods: </strong>The mRNA and protein levels of SUMO3 were detected by qRT-PCR, Western blot, and immunohistochemical assay. SUMO3 was silenced or overexpressed in pancreatic cancer cells with or without Wnt/β-catenin pathway inhibitor, glycolysis inhibitor, GEM, or BA treatment. Cell viability was measured using the Cell Counting Kit-8 assay. Glycolysis was measured by determining the extracellular acidification rate, ATP level, and lactate content. Apoptosis was measured by flow cytometry, and TUNEL staining was used to examine in vitro and in vivo sensitivity to GEM chemotherapy. Luciferase reporter and chromatin immunoprecipitation assays were conducted to detect the binding of the SUMO3 promoter and NF-κB p65.</p><p><strong>Results: </strong>SUMO3 was increased and associated with poor survival in pancreatic cancer. SUMO3 knockdown decreased cell viability and glycolysis in vitro and inhibited tumor growth in vivo. SUMO3 overexpression increased cell viability and glycolysis in vitro through the β-catenin pathway. SUMO3 knockdown increased GEM sensitivity, whereas SUMO3 overexpression decreased GEM sensitivity and inhibited the antitumor activity of BA. BA promoted histone acetylation and p-IκBα expression to inhibit NF-κB p65-mediated SUMO3 transcription.</p><p><strong>Conclusion: </strong>SUMO3 acted as an active molecule in cell survival and growth by enhancing glycolysis in response to either GEM or BA. The mechanism was related to the constitutive IκBα/NF-κB/SUMO3/β-catenin signaling pathway.</p>","PeriodicalId":9164,"journal":{"name":"Biology Direct","volume":"19 1","pages":"74"},"PeriodicalIF":5.7,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11345958/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142055002","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Reprogramming hematopoietic stem cell metabolism in lung cancer: glycolysis, oxidative phosphorylation, and the role of 2-DG. 肺癌造血干细胞新陈代谢重编程:糖酵解、氧化磷酸化和 2-DG 的作用。
IF 5.7 2区 生物学 Q1 BIOLOGY Pub Date : 2024-08-24 DOI: 10.1186/s13062-024-00514-w
Ziqi Guo, Yaping Liu, Xin Li, Yuying Huang, Zuping Zhou, Cheng Yang

Hematopoietic stem cells (HSCs) exhibit significant functional and metabolic alterations within the lung cancer microenvironment, contributing to tumor progression and immune evasion by increasing differentiation into myeloid-derived suppressor cells (MDSCs). Our aim is to analyze the metabolic transition of HSCs from glycolysis to oxidative phosphorylation (OXPHOS) in lung cancer and determine its effects on HSC functionality. Using a murine Lewis Lung Carcinoma lung cancer model, we conducted metabolic profiling of long-term and short-term HSCs, as well as multipotent progenitors, comparing their metabolic states in normal and cancer conditions. We measured glucose uptake using 2-[N-(7-Nitrobenz-2-oxa-1,3-diazol-4-yl)Amino]-2-Deoxyglucose (2-NBDG) and assessed levels of lactate, acetyl-coenzyme A, and ATP. Mitochondrial functionality was evaluated through flow cytometry, alongside the impact of the glucose metabolism inhibitor 2-DG on HSC differentiation and mitochondrial activity. HSCs under lung cancer conditions showed increased glucose uptake and lactate production, with an associated rise in OXPHOS activity, marking a metabolic shift. Treatment with 2-DG led to decreased T-HSCs and MDSCs and an increased red blood cell count, highlighting its potential to influence metabolic and differentiation pathways in HSCs. This study provides novel insights into the metabolic reprogramming of HSCs in lung cancer, emphasizing the critical shift from glycolysis to OXPHOS and its implications for the therapeutic targeting of cancer-related metabolic pathways.

造血干细胞(HSCs)在肺癌微环境中表现出显著的功能和代谢改变,通过增加分化成髓源性抑制细胞(MDSCs)来促进肿瘤进展和免疫逃避。我们的目的是分析肺癌中造血干细胞从糖酵解到氧化磷酸化(OXPHOS)的代谢转变,并确定其对造血干细胞功能的影响。我们利用小鼠路易斯肺癌肺癌模型,对长期和短期造血干细胞以及多能祖细胞进行了代谢分析,比较了它们在正常和癌症条件下的代谢状态。我们使用 2-[N-(7-硝基苯并-2-氧杂-1,3-二唑-4-基)氨基]-2-脱氧葡萄糖(2-NBDG)测量葡萄糖摄取量,并评估乳酸、乙酰辅酶 A 和 ATP 的水平。线粒体功能通过流式细胞术进行评估,同时还评估了葡萄糖代谢抑制剂2-DG对造血干细胞分化和线粒体活性的影响。肺癌条件下的造血干细胞显示出葡萄糖摄取和乳酸生成的增加,与之相关的是OXPHOS活性的上升,这标志着新陈代谢的转变。用2-DG处理后,T-造血干细胞和MDSCs减少,红细胞数量增加,这突显了2-DG影响造血干细胞代谢和分化途径的潜力。这项研究为肺癌造血干细胞的代谢重编程提供了新的见解,强调了从糖酵解到OXPHOS的关键转变及其对癌症相关代谢途径靶向治疗的影响。
{"title":"Reprogramming hematopoietic stem cell metabolism in lung cancer: glycolysis, oxidative phosphorylation, and the role of 2-DG.","authors":"Ziqi Guo, Yaping Liu, Xin Li, Yuying Huang, Zuping Zhou, Cheng Yang","doi":"10.1186/s13062-024-00514-w","DOIUrl":"10.1186/s13062-024-00514-w","url":null,"abstract":"<p><p>Hematopoietic stem cells (HSCs) exhibit significant functional and metabolic alterations within the lung cancer microenvironment, contributing to tumor progression and immune evasion by increasing differentiation into myeloid-derived suppressor cells (MDSCs). Our aim is to analyze the metabolic transition of HSCs from glycolysis to oxidative phosphorylation (OXPHOS) in lung cancer and determine its effects on HSC functionality. Using a murine Lewis Lung Carcinoma lung cancer model, we conducted metabolic profiling of long-term and short-term HSCs, as well as multipotent progenitors, comparing their metabolic states in normal and cancer conditions. We measured glucose uptake using 2-[N-(7-Nitrobenz-2-oxa-1,3-diazol-4-yl)Amino]-2-Deoxyglucose (2-NBDG) and assessed levels of lactate, acetyl-coenzyme A, and ATP. Mitochondrial functionality was evaluated through flow cytometry, alongside the impact of the glucose metabolism inhibitor 2-DG on HSC differentiation and mitochondrial activity. HSCs under lung cancer conditions showed increased glucose uptake and lactate production, with an associated rise in OXPHOS activity, marking a metabolic shift. Treatment with 2-DG led to decreased T-HSCs and MDSCs and an increased red blood cell count, highlighting its potential to influence metabolic and differentiation pathways in HSCs. This study provides novel insights into the metabolic reprogramming of HSCs in lung cancer, emphasizing the critical shift from glycolysis to OXPHOS and its implications for the therapeutic targeting of cancer-related metabolic pathways.</p>","PeriodicalId":9164,"journal":{"name":"Biology Direct","volume":"19 1","pages":"73"},"PeriodicalIF":5.7,"publicationDate":"2024-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11344923/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142054926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Disulfidptosis-associated LncRNA signature predicts prognosis and immune response in kidney renal clear cell carcinoma. 二硫化相关LncRNA特征可预测肾透明细胞癌的预后和免疫反应
IF 5.7 2区 生物学 Q1 BIOLOGY Pub Date : 2024-08-22 DOI: 10.1186/s13062-024-00517-7
Kangjie Xu, Dongling Li, Kangkang Ji, Yanhua Zhang, Minglei Zhang, Hai Zhou, Xuefeng Hou, Jian Jiang, Zihang Zhang, Hua Dai, Hang Sun

Background: Kidney renal clear cell carcinoma (KIRC) represents a significant proportion of renal cell carcinomas and is characterized by high aggressiveness and poor prognosis despite advancements in immunotherapy. Disulfidptosis, a novel cell death pathway, has emerged as a critical mechanism in various cellular processes, including cancer. This study leverages machine learning to identify disulfidptosis-related long noncoding RNAs (DRlncRNAs) as potential prognostic biomarkers in KIRC, offering new insights into tumor pathogenesis and treatment avenues.

Results: Our analysis of data from The Cancer Genome Atlas (TCGA) led to the identification of 431 DRlncRNAs correlated with disulfidptosis-related genes. Five key DRlncRNAs (SPINT1-AS1, AL161782.1, OVCH1-AS1, AC131009.3, and AC108673.3) were used to develop a prognostic model that effectively distinguished between low- and high-risk patients with significant differences in overall survival and progression-free survival. The low-risk group had a favorable prognosis associated with a protective immune microenvironment and a better response to targeted drugs. Conversely, the high-risk group displayed aggressive tumor features and poor immunotherapy outcomes. Validation through qRT‒PCR confirmed the differential expression of these DRlncRNAs in KIRC cells compared to normal kidney cells, underscoring their potential functional significance in tumor biology.

Conclusions: This study established a robust link between disulfidptosis-related lncRNAs and patient prognosis in KIRC, underscoring their potential as prognostic biomarkers and therapeutic targets. The differential expression of these lncRNAs in tumor versus normal tissue further highlights their relevance in KIRC pathogenesis. The predictive model not only enhances our understanding of KIRC biology but also provides a novel stratification tool for precision medicine approaches, improving treatment personalization and outcomes in KIRC patients.

背景:肾脏透明细胞癌(KIRC)在肾细胞癌中占很大比例,尽管免疫疗法取得了进展,但其特点是侵袭性强、预后差。二硫化硫是一种新型细胞死亡途径,已成为包括癌症在内的各种细胞过程中的关键机制。本研究利用机器学习技术鉴定出与二硫化相关的长非编码RNA(DRlncRNAs)作为KIRC的潜在预后生物标志物,为肿瘤发病机制和治疗途径提供了新的见解:我们对癌症基因组图谱(The Cancer Genome Atlas,TCGA)中的数据进行了分析,发现了431个与二硫化相关基因相关的DRlncRNAs。我们利用五个关键的DRlncRNA(SPINT1-AS1、AL161782.1、OVCH1-AS1、AC131009.3和AC108673.3)建立了一个预后模型,该模型能有效区分低危和高危患者,并在总生存期和无进展生存期方面存在显著差异。低风险组的预后良好,这与保护性免疫微环境和对靶向药物的较好反应有关。相反,高危组则表现出侵袭性肿瘤特征,免疫治疗效果不佳。通过 qRT-PCR 验证证实,与正常肾细胞相比,这些 DRlncRNAs 在 KIRC 细胞中的表达存在差异,突显了它们在肿瘤生物学中的潜在功能意义:这项研究在二硫化相关lncRNAs与KIRC患者预后之间建立了强有力的联系,强调了它们作为预后生物标志物和治疗靶点的潜力。这些lncRNAs在肿瘤组织与正常组织中的表达差异进一步凸显了它们在KIRC发病机制中的相关性。该预测模型不仅增强了我们对 KIRC 生物学的了解,还为精准医疗方法提供了一种新的分层工具,改善了 KIRC 患者的个性化治疗和预后。
{"title":"Disulfidptosis-associated LncRNA signature predicts prognosis and immune response in kidney renal clear cell carcinoma.","authors":"Kangjie Xu, Dongling Li, Kangkang Ji, Yanhua Zhang, Minglei Zhang, Hai Zhou, Xuefeng Hou, Jian Jiang, Zihang Zhang, Hua Dai, Hang Sun","doi":"10.1186/s13062-024-00517-7","DOIUrl":"10.1186/s13062-024-00517-7","url":null,"abstract":"<p><strong>Background: </strong>Kidney renal clear cell carcinoma (KIRC) represents a significant proportion of renal cell carcinomas and is characterized by high aggressiveness and poor prognosis despite advancements in immunotherapy. Disulfidptosis, a novel cell death pathway, has emerged as a critical mechanism in various cellular processes, including cancer. This study leverages machine learning to identify disulfidptosis-related long noncoding RNAs (DRlncRNAs) as potential prognostic biomarkers in KIRC, offering new insights into tumor pathogenesis and treatment avenues.</p><p><strong>Results: </strong>Our analysis of data from The Cancer Genome Atlas (TCGA) led to the identification of 431 DRlncRNAs correlated with disulfidptosis-related genes. Five key DRlncRNAs (SPINT1-AS1, AL161782.1, OVCH1-AS1, AC131009.3, and AC108673.3) were used to develop a prognostic model that effectively distinguished between low- and high-risk patients with significant differences in overall survival and progression-free survival. The low-risk group had a favorable prognosis associated with a protective immune microenvironment and a better response to targeted drugs. Conversely, the high-risk group displayed aggressive tumor features and poor immunotherapy outcomes. Validation through qRT‒PCR confirmed the differential expression of these DRlncRNAs in KIRC cells compared to normal kidney cells, underscoring their potential functional significance in tumor biology.</p><p><strong>Conclusions: </strong>This study established a robust link between disulfidptosis-related lncRNAs and patient prognosis in KIRC, underscoring their potential as prognostic biomarkers and therapeutic targets. The differential expression of these lncRNAs in tumor versus normal tissue further highlights their relevance in KIRC pathogenesis. The predictive model not only enhances our understanding of KIRC biology but also provides a novel stratification tool for precision medicine approaches, improving treatment personalization and outcomes in KIRC patients.</p>","PeriodicalId":9164,"journal":{"name":"Biology Direct","volume":"19 1","pages":"71"},"PeriodicalIF":5.7,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11340127/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142035291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Unveiling the unique role of TSPAN7 across tumors: a pan-cancer study incorporating retrospective clinical research and bioinformatic analysis. 揭示 TSPAN7 在不同肿瘤中的独特作用:一项结合回顾性临床研究和生物信息学分析的泛癌症研究。
IF 5.7 2区 生物学 Q1 BIOLOGY Pub Date : 2024-08-22 DOI: 10.1186/s13062-024-00516-8
Bingnan Lu, Yifan Liu, Yuntao Yao, Dawei Zhu, Xiangmin Zhang, Keqin Dong, Xiao Xu, Donghao Lv, Zihui Zhao, Haoyu Zhang, Xinyue Yang, Wenjia Fu, Runzhi Huang, Jianwei Cao, Jian Chu, Xiuwu Pan, Xingang Cui

Background: TSPAN7 is an important factor in tumor progression. However, the precise function of TSPAN7 and its role in pan-cancer are not clear.

Methods: Based on Xinhua cohort incorporating 370 patients with kidney neoplasm, we conducted differential expression analysis by immunohistochemistry between tumor and normal tissues, and explored correlations of TSPAN7 with patients' survival. Subsequently, we conducted a pan-cancer study, and successively employed differential expression analysis, competing endogenous RNA (ceRNA) analysis, protein-protein interaction (PPI) analysis, correlation analysis of TSPAN7 with clinical characteristics, tumor purity, tumor genomics, tumor immunity, and drug sensitivity. Last but not least, gene set enrichment analysis was applied to identify enriched pathways of TSPAN7.

Results: In Xinhua cohort, TSPAN7 expression was significantly up-regulated (P-value = 0.0019) in tumor tissues of kidney neoplasm patients. High TSPAN7 expression was associated with decreases in overall survival (OS) (P-value = 0.009) and progression-free survival (P-value = 0.009), and it was further revealed as an independent risk factor for OS (P-value = 0.0326, HR = 5.66, 95%CI = 1.155-27.8). In pan-cancer analysis, TSPAN7 expression was down-regulated in most tumors, and it was associated with patients' survival, tumor purity, tumor genomics, tumor immunity, and drug sensitivity. The ceRNA network and PPI network of TSPAN7 were also constructed. Last but not least, the top five enriched pathways of TSPAN7 in various tumors were identified.

Conclusion: TSPAN7 served as a promising biomarker of various tumors, especially kidney neoplasms, and it was closely associated with tumor purity, tumor genomics, tumor immunology, and drug sensitivity in pan-cancer level.

背景TSPAN7是肿瘤进展的一个重要因素。然而,TSPAN7的确切功能及其在泛癌症中的作用尚不清楚:方法:以新华队列中的 370 例肾脏肿瘤患者为研究对象,采用免疫组化方法对肿瘤组织和正常组织进行差异表达分析,探讨 TSPAN7 与患者生存的相关性。随后,我们进行了一项泛癌症研究,先后采用了差异表达分析、竞争性内源性 RNA(ceRNA)分析、蛋白-蛋白相互作用(PPI)分析,以及 TSPAN7 与临床特征、肿瘤纯度、肿瘤基因组学、肿瘤免疫和药物敏感性的相关性分析。最后,应用基因组富集分析确定了TSPAN7的富集通路:结果:在新华队列中,TSPAN7在肾脏肿瘤患者的肿瘤组织中表达明显上调(P值=0.0019)。TSPAN7的高表达与总生存期(OS)(P值=0.009)和无进展生存期(P值=0.009)的下降有关,并被进一步揭示为OS的独立危险因素(P值=0.0326,HR=5.66,95%CI=1.155-27.8)。在泛癌症分析中,TSPAN7在大多数肿瘤中表达下调,并且与患者生存、肿瘤纯度、肿瘤基因组学、肿瘤免疫和药物敏感性相关。此外,还构建了 TSPAN7 的 ceRNA 网络和 PPI 网络。最后,还确定了TSPAN7在各种肿瘤中的前五大富集通路:结论:TSPAN7是多种肿瘤,尤其是肾脏肿瘤的一种有前景的生物标记物,它与肿瘤纯度、肿瘤基因组学、肿瘤免疫学和泛癌水平的药物敏感性密切相关。
{"title":"Unveiling the unique role of TSPAN7 across tumors: a pan-cancer study incorporating retrospective clinical research and bioinformatic analysis.","authors":"Bingnan Lu, Yifan Liu, Yuntao Yao, Dawei Zhu, Xiangmin Zhang, Keqin Dong, Xiao Xu, Donghao Lv, Zihui Zhao, Haoyu Zhang, Xinyue Yang, Wenjia Fu, Runzhi Huang, Jianwei Cao, Jian Chu, Xiuwu Pan, Xingang Cui","doi":"10.1186/s13062-024-00516-8","DOIUrl":"10.1186/s13062-024-00516-8","url":null,"abstract":"<p><strong>Background: </strong>TSPAN7 is an important factor in tumor progression. However, the precise function of TSPAN7 and its role in pan-cancer are not clear.</p><p><strong>Methods: </strong>Based on Xinhua cohort incorporating 370 patients with kidney neoplasm, we conducted differential expression analysis by immunohistochemistry between tumor and normal tissues, and explored correlations of TSPAN7 with patients' survival. Subsequently, we conducted a pan-cancer study, and successively employed differential expression analysis, competing endogenous RNA (ceRNA) analysis, protein-protein interaction (PPI) analysis, correlation analysis of TSPAN7 with clinical characteristics, tumor purity, tumor genomics, tumor immunity, and drug sensitivity. Last but not least, gene set enrichment analysis was applied to identify enriched pathways of TSPAN7.</p><p><strong>Results: </strong>In Xinhua cohort, TSPAN7 expression was significantly up-regulated (P-value = 0.0019) in tumor tissues of kidney neoplasm patients. High TSPAN7 expression was associated with decreases in overall survival (OS) (P-value = 0.009) and progression-free survival (P-value = 0.009), and it was further revealed as an independent risk factor for OS (P-value = 0.0326, HR = 5.66, 95%CI = 1.155-27.8). In pan-cancer analysis, TSPAN7 expression was down-regulated in most tumors, and it was associated with patients' survival, tumor purity, tumor genomics, tumor immunity, and drug sensitivity. The ceRNA network and PPI network of TSPAN7 were also constructed. Last but not least, the top five enriched pathways of TSPAN7 in various tumors were identified.</p><p><strong>Conclusion: </strong>TSPAN7 served as a promising biomarker of various tumors, especially kidney neoplasms, and it was closely associated with tumor purity, tumor genomics, tumor immunology, and drug sensitivity in pan-cancer level.</p>","PeriodicalId":9164,"journal":{"name":"Biology Direct","volume":"19 1","pages":"72"},"PeriodicalIF":5.7,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11340126/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142035292","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
hsa_circ_0020093 suppresses ovarian cancer progression by modulating LRPPRC activity and miR-107/LATS2 signaling. hsa_circ_0020093 通过调节 LRPPRC 活性和 miR-107/LATS2 信号传导抑制卵巢癌的进展。
IF 5.7 2区 生物学 Q1 BIOLOGY Pub Date : 2024-08-21 DOI: 10.1186/s13062-024-00520-y
Yu Sun, Xiyi Chen, Yaqian Shi, Fang Teng, Chencheng Dai, Lili Ge, Juan Xu, Xuemei Jia

A substantive body of evidence has demonstrated the significant roles of circular RNA (circRNA) in cancer. However, the contribution of dysregulated circRNAs to ovarian cancer (OC) remains elusive. We aim to elucidate the critical roles and mechanisms of hsa_circ_0020093, which was demonstrated to be downregulated in OC tissues in our previous study. In this study, we confirmed the decreased expression of hsa_circ_0020093 in OC tissues and cell lines and demonstrated the negative correlation between its expression and FIGO stage, abdominal implantation and CA125 level of OC patients. Through gain and loss of function studies, we confirmed the inhibitory role of hsa_circ_0020093 in ovarian tumor growth in vitro and in vivo. Mechanistically, based on the peri-nuclear accumulation of hsa_circ_0020093, we discovered the interaction between hsa_circ_0020093 and the mitochondrial protein LRPPRC by RNA pull-down, mass spectrometry, RNA Binding Protein Immunoprecipitation. As a result, qRT-PCR and transmission electron microscopy results showed that the mitochondria mRNA expression and mitochondria abundance were decreased upon hsa_circ_0020093-overexpression. Meanwhile, we also unearthed the hsa_circ_0020093/miR-107/LATS2 axis in OC according to RNA-sequencing, RIP and luciferase reporter assay data. Furthermore, LRPPRC and LATS2 are both reported as the upstream regulators of YAP, our study also studied the crosstalk between hsa_circ_0020093, LRPPRC and miR-107/LATS2, and unearthed the up-regulation of phosphorylated YAP in hsa_circ_0020093-overexpressing OC cells and xenograft tumors. Collectively, our study indicated the novel mechanism of hsa_circ_0020093 in suppressing OC progression through both hsa_circ_0020093/LRPPRC and hsa_circ_0020093/miR-107/LATS2 axes, providing a potential therapeutic target for OC patients.

大量证据表明,环状 RNA(circRNA)在癌症中发挥着重要作用。然而,调控失调的环状 RNA 对卵巢癌(OC)的影响仍然难以捉摸。我们旨在阐明 hsa_circ_0020093 的关键作用和机制。在本研究中,我们证实了 hsa_circ_0020093 在 OC 组织和细胞系中的表达下降,并证明了其表达与 OC 患者的 FIGO 分期、腹腔种植和 CA125 水平呈负相关。通过功能增益和丧失研究,我们证实了 hsa_circ_0020093 在体外和体内对卵巢肿瘤生长的抑制作用。从机理上讲,基于 hsa_circ_0020093 的核周积累,我们通过 RNA 拉取、质谱分析、RNA 结合蛋白免疫沉淀等方法发现了 hsa_circ_0020093 与线粒体蛋白 LRPPRC 之间的相互作用。结果,qRT-PCR 和透射电子显微镜结果表明,线粒体 mRNA 表达量和线粒体丰度在 hsa_circ_0020093 表达后均有所下降。同时,根据RNA测序、RIP和荧光素酶报告实验数据,我们还发现了OC中的hsa_circ_0020093/miR-107/LATS2轴。此外,LRPPRC和LATS2均被报道为YAP的上游调控因子,我们的研究还研究了hsa_circ_0020093、LRPPRC和miR-107/LATS2之间的相互影响,并发现了磷酸化YAP在hsa_circ_0020093过表达的OC细胞和异种移植肿瘤中的上调。总之,我们的研究表明了hsa_circ_0020093通过hsa_circ_0020093/LRPPRC和hsa_circ_0020093/miR-107/LATS2轴抑制OC进展的新机制,为OC患者提供了一个潜在的治疗靶点。
{"title":"hsa_circ_0020093 suppresses ovarian cancer progression by modulating LRPPRC activity and miR-107/LATS2 signaling.","authors":"Yu Sun, Xiyi Chen, Yaqian Shi, Fang Teng, Chencheng Dai, Lili Ge, Juan Xu, Xuemei Jia","doi":"10.1186/s13062-024-00520-y","DOIUrl":"10.1186/s13062-024-00520-y","url":null,"abstract":"<p><p>A substantive body of evidence has demonstrated the significant roles of circular RNA (circRNA) in cancer. However, the contribution of dysregulated circRNAs to ovarian cancer (OC) remains elusive. We aim to elucidate the critical roles and mechanisms of hsa_circ_0020093, which was demonstrated to be downregulated in OC tissues in our previous study. In this study, we confirmed the decreased expression of hsa_circ_0020093 in OC tissues and cell lines and demonstrated the negative correlation between its expression and FIGO stage, abdominal implantation and CA125 level of OC patients. Through gain and loss of function studies, we confirmed the inhibitory role of hsa_circ_0020093 in ovarian tumor growth in vitro and in vivo. Mechanistically, based on the peri-nuclear accumulation of hsa_circ_0020093, we discovered the interaction between hsa_circ_0020093 and the mitochondrial protein LRPPRC by RNA pull-down, mass spectrometry, RNA Binding Protein Immunoprecipitation. As a result, qRT-PCR and transmission electron microscopy results showed that the mitochondria mRNA expression and mitochondria abundance were decreased upon hsa_circ_0020093-overexpression. Meanwhile, we also unearthed the hsa_circ_0020093/miR-107/LATS2 axis in OC according to RNA-sequencing, RIP and luciferase reporter assay data. Furthermore, LRPPRC and LATS2 are both reported as the upstream regulators of YAP, our study also studied the crosstalk between hsa_circ_0020093, LRPPRC and miR-107/LATS2, and unearthed the up-regulation of phosphorylated YAP in hsa_circ_0020093-overexpressing OC cells and xenograft tumors. Collectively, our study indicated the novel mechanism of hsa_circ_0020093 in suppressing OC progression through both hsa_circ_0020093/LRPPRC and hsa_circ_0020093/miR-107/LATS2 axes, providing a potential therapeutic target for OC patients.</p>","PeriodicalId":9164,"journal":{"name":"Biology Direct","volume":"19 1","pages":"69"},"PeriodicalIF":5.7,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11337591/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142008333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
期刊
Biology Direct
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1