Proteome Science最新文献

英文中文

Identification of different proteins binding to Na, K-ATPase α1 in LPS-induced ARDS cell model by proteomic analysis 通过蛋白质组学分析鉴定lps诱导的ARDS细胞模型中Na, k - atp酶α1的不同结合蛋白

IF 2 3区生物学 Q3 BIOCHEMICAL RESEARCH METHODS

Proteome Science

Pub Date : 2022-06-09 DOI: 10.1186/s12953-022-00193-3

Xu-peng Wen, Guo Long, Yue-Zhong Zhang, He Huang, Tao Liu, Qi-quan Wan

引用次数: 2

A novel nanobody as therapeutics target for EGFR-positive colorectal cancer therapy: exploring the effects of the nanobody on SW480 cells using proteomics approach 一种新型纳米体作为egfr阳性结直肠癌治疗的治疗靶点:利用蛋白质组学方法探索纳米体对SW480细胞的影响

IF 2 3区生物学 Q3 BIOCHEMICAL RESEARCH METHODS

Proteome Science

Pub Date : 2022-05-16 DOI: 10.1186/s12953-022-00190-6

Thomanai Lamtha, Sucheewin Krobthong, Y. Yingchutrakul, Pawitrabhorn Samutrtai, C. Gerner, Lueacha Tabtimmai, K. Choowongkomon

引用次数: 1

Quantitative proteomic analysis of cerebrospinal fluid reveals CD163, A2M and full-length APP as potential diagnostic biomarkers of paediatric bacterial meningitis 脑脊液定量蛋白质组学分析显示CD163、A2M和全长APP可作为儿科细菌性脑膜炎的潜在诊断生物标志物

IF 2 3区生物学 Q3 BIOCHEMICAL RESEARCH METHODS

Proteome Science

Pub Date : 2022-05-06 DOI: 10.1186/s12953-022-00191-5

Ting Luo, Sai Yang, Yan Chen, Shulei Liu, Li-ming Yang, Nan-Zhi Hu, Ye Ma, Jun Qiu, Kewei Wang, Liping Li, Lihong Tan

引用次数: 0

Long noncoding RNA Ftx regulates the protein expression profile in HCT116 human colon cancer cells 长链非编码RNA Ftx调控HCT116人结肠癌细胞的蛋白表达谱

IF 2 3区生物学 Q3 BIOCHEMICAL RESEARCH METHODS

Proteome Science

Pub Date : 2022-04-30 DOI: 10.1186/s12953-022-00187-1

R. Jia, Lulu Song, Zhiqiang Fei, C. Qin, Qi Zhao

引用次数: 3

TMT-based proteomics analysis of the cerebral cortex of TauT knockout rats 基于tmt的TauT基因敲除大鼠大脑皮层蛋白质组学分析

IF 2 3区生物学 Q3 BIOCHEMICAL RESEARCH METHODS

Proteome Science

Pub Date : 2022-04-25 DOI: 10.1186/s12953-022-00189-z

Xia, Yiming, Huang, Xiaoling, Mo, Lidong, Wang, Chen, Fan, Weijia, Huang, Huiling

Taurine serves a variety of nutritional and physiological roles, and it is mostly transported in cells via taurine transporter (TauT). The effect of taurine transporter in cerebral cortex is still unknown. We employed TMT label-based proteomics to find differences in proteins in the cerebral cortex of TauT knockout rats in this investigation. The goal of this research was to see how TauT deletion affected protein alterations in brain tissue and to see if there was a new research area for TauT. The cerebral cortex of TauT knockout rats and wild-type control rats were analyzed using TMT-based proteomics, and differentially expressed proteins were analyzed by bioinformatics analysis means such as GO and KEGG, the association between the proteins was found by PPI, and biologically significant and interesting proteins were selected for verification by WB and immunohistochemistry. There were total of 8275 proteins found, but only 35 differentially expressed proteins were identified (27 up-regulated and 8 down-regulated), and gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to predict the biological pathways and functional classification of the proteins. The results show that these differentially expressed proteins are mainly enriched in lysine degradation, cell cycle, chronic myeloid leukemia, and longevity regulating pathways-multiple species, renal cell carcinoma, pathways in cancer, etc. To verify the proteomic data, we analyzed the expression of Annexin6 and Pik3r2 by western blotting and immunofluorescence. The results are consistent with proteomics, which proves the reliability of our proteomics data. Through TMT-based proteomics, we have a comprehensive understanding of the effect of TauT knockout on the changes of other proteins in the cerebral cortex, providing new evidence for further understanding the function of TauT.

牛磺酸具有多种营养和生理作用，主要通过牛磺酸转运蛋白(Taurine transporter, TauT)在细胞内转运。牛磺酸转运蛋白在大脑皮层中的作用尚不清楚。在这项研究中，我们采用基于TMT标记的蛋白质组学方法来发现TauT基因敲除大鼠大脑皮层中蛋白质的差异。这项研究的目的是了解TauT缺失如何影响脑组织中蛋白质的改变，并看看是否有一个新的研究领域。采用基于tmt的蛋白质组学分析TauT基因敲除大鼠和野生型对照大鼠的大脑皮层，采用GO、KEGG等生物信息学分析手段分析差异表达蛋白，通过PPI发现蛋白之间的相关性，并通过WB和免疫组织化学选择具有生物学意义和感兴趣的蛋白进行验证。共发现8275个蛋白，但仅鉴定出35个差异表达蛋白(27个上调，8个下调)，并通过基因本体(GO)和京都基因与基因组百科全书(KEGG)分析预测了这些蛋白的生物学途径和功能分类。结果表明，这些差异表达蛋白主要富集于赖氨酸降解、细胞周期、慢性髓系白血病、多物种长寿调节通路、肾细胞癌、肿瘤通路等。为了验证蛋白质组学数据，我们用western blotting和免疫荧光分析了Annexin6和Pik3r2的表达。结果与蛋白质组学一致，证明了我们的蛋白质组学数据的可靠性。通过基于tmt的蛋白质组学，我们全面了解了TauT敲除对大脑皮层其他蛋白变化的影响，为进一步了解TauT的功能提供了新的证据。

{"title":"TMT-based proteomics analysis of the cerebral cortex of TauT knockout rats","authors":"Xia, Yiming, Huang, Xiaoling, Mo, Lidong, Wang, Chen, Fan, Weijia, Huang, Huiling","doi":"10.1186/s12953-022-00189-z","DOIUrl":"https://doi.org/10.1186/s12953-022-00189-z","url":null,"abstract":"Taurine serves a variety of nutritional and physiological roles, and it is mostly transported in cells via taurine transporter (TauT). The effect of taurine transporter in cerebral cortex is still unknown. We employed TMT label-based proteomics to find differences in proteins in the cerebral cortex of TauT knockout rats in this investigation. The goal of this research was to see how TauT deletion affected protein alterations in brain tissue and to see if there was a new research area for TauT. The cerebral cortex of TauT knockout rats and wild-type control rats were analyzed using TMT-based proteomics, and differentially expressed proteins were analyzed by bioinformatics analysis means such as GO and KEGG, the association between the proteins was found by PPI, and biologically significant and interesting proteins were selected for verification by WB and immunohistochemistry. There were total of 8275 proteins found, but only 35 differentially expressed proteins were identified (27 up-regulated and 8 down-regulated), and gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to predict the biological pathways and functional classification of the proteins. The results show that these differentially expressed proteins are mainly enriched in lysine degradation, cell cycle, chronic myeloid leukemia, and longevity regulating pathways-multiple species, renal cell carcinoma, pathways in cancer, etc. To verify the proteomic data, we analyzed the expression of Annexin6 and Pik3r2 by western blotting and immunofluorescence. The results are consistent with proteomics, which proves the reliability of our proteomics data. Through TMT-based proteomics, we have a comprehensive understanding of the effect of TauT knockout on the changes of other proteins in the cerebral cortex, providing new evidence for further understanding the function of TauT.","PeriodicalId":20857,"journal":{"name":"Proteome Science","volume":"114 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2022-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138540454","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Integrative proteomic characterization of trace FFPE samples in early-stage gastrointestinal cancer 早期胃肠道肿瘤中微量FFPE样品的综合蛋白质组学特征

IF 2 3区生物学 Q3 BIOCHEMICAL RESEARCH METHODS

Proteome Science

Pub Date : 2022-04-09 DOI: 10.1186/s12953-022-00188-0

Lingling Li, Hui Liu, Yan Li, Chun-feng Guo, Bin Wang, Dan Shen, Qiao Zhang, C. Ding

引用次数: 1

Predicting protein–protein interactions between banana and Fusarium oxysporum f. sp. cubense race 4 integrating sequence and domain homologous alignment and neural network verification 基于序列、结构域同源比对和神经网络验证的香蕉与cubense Fusarium oxysporum f. sp. cubense小种4蛋白相互作用预测

IF 2 3区生物学 Q3 BIOCHEMICAL RESEARCH METHODS

Proteome Science

Pub Date : 2022-03-29 DOI: 10.1186/s12953-022-00186-2

Fang, Hui, Zhong, Cheng, Tang, Chunyan

The pathogen of banana Fusarium oxysporum f. sp. cubense race 4(Foc4) infects almost all banana species, and it is the most destructive. The molecular mechanism of the interactions between Fusarium oxysporum and banana still needs to be further investigated. We use both the interolog and domain-domain method to predict the protein–protein interactions (PPIs) between banana and Foc4. The predicted protein interaction sequences are encoded by the conjoint triad and autocovariance method respectively to obtain continuous and discontinuous information of protein sequences. This information is used as the input data of the neural network model. The Long Short-Term Memory (LSTM) neural network five-fold cross-validation and independent test methods are used to verify the predicted protein interaction sequences. To further confirm the PPIs between banana and Foc4, the GO (Gene Ontology) and KEGG (Kyoto Encylopedia of Genes and Genomics) functional annotation and interaction network analysis are carried out. The experimental results show that the PPIs for banana and foc4 predicted by our proposed method may interact with each other in terms of sequence structure, GO and KEGG functional annotation, and Foc4 protein plays a more active role in the process of Foc4 infecting banana. This study obtained the PPIs between banana and Foc4 by using computing means for the first time, which will provide data support for molecular biology experiments.

香蕉尖孢镰刀菌(Fusarium oxysporum f. sp. cubense race 4, Foc4)几乎侵染所有香蕉品种，是最具破坏性的病原菌。尖孢镰刀菌与香蕉相互作用的分子机制有待进一步研究。我们使用interolog和domain-domain方法来预测香蕉与Foc4之间的蛋白-蛋白相互作用(PPIs)。预测的蛋白质相互作用序列分别采用联合三联体和自协方差方法进行编码，获得蛋白质序列的连续和不连续信息。这些信息被用作神经网络模型的输入数据。采用长短期记忆(LSTM)神经网络五重交叉验证和独立测试方法对预测的蛋白相互作用序列进行验证。为了进一步确认香蕉与Foc4之间的PPIs，我们进行了GO (Gene Ontology)和KEGG (Kyoto encyclopedia of Genes and Genomics)的功能注释和交互网络分析。实验结果表明，本文方法预测的香蕉与foc4的PPIs在序列结构、GO和KEGG功能注释等方面存在相互作用，foc4蛋白在foc4侵染香蕉的过程中发挥了更为积极的作用。本研究首次利用计算手段获得香蕉与Foc4之间的PPIs，为分子生物学实验提供数据支持。

{"title":"Predicting protein–protein interactions between banana and Fusarium oxysporum f. sp. cubense race 4 integrating sequence and domain homologous alignment and neural network verification","authors":"Fang, Hui, Zhong, Cheng, Tang, Chunyan","doi":"10.1186/s12953-022-00186-2","DOIUrl":"https://doi.org/10.1186/s12953-022-00186-2","url":null,"abstract":"The pathogen of banana Fusarium oxysporum f. sp. cubense race 4(Foc4) infects almost all banana species, and it is the most destructive. The molecular mechanism of the interactions between Fusarium oxysporum and banana still needs to be further investigated. We use both the interolog and domain-domain method to predict the protein–protein interactions (PPIs) between banana and Foc4. The predicted protein interaction sequences are encoded by the conjoint triad and autocovariance method respectively to obtain continuous and discontinuous information of protein sequences. This information is used as the input data of the neural network model. The Long Short-Term Memory (LSTM) neural network five-fold cross-validation and independent test methods are used to verify the predicted protein interaction sequences. To further confirm the PPIs between banana and Foc4, the GO (Gene Ontology) and KEGG (Kyoto Encylopedia of Genes and Genomics) functional annotation and interaction network analysis are carried out. The experimental results show that the PPIs for banana and foc4 predicted by our proposed method may interact with each other in terms of sequence structure, GO and KEGG functional annotation, and Foc4 protein plays a more active role in the process of Foc4 infecting banana. This study obtained the PPIs between banana and Foc4 by using computing means for the first time, which will provide data support for molecular biology experiments.","PeriodicalId":20857,"journal":{"name":"Proteome Science","volume":"8 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2022-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138540460","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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: 6

Identification and validation of serum autoantibodies in children with B-cell acute lymphoblastic leukemia by serological proteome analysis. b细胞急性淋巴细胞白血病儿童血清自身抗体的血清学蛋白质组学分析鉴定和验证。

IF 2 3区生物学 Q3 BIOCHEMICAL RESEARCH METHODS

Proteome Science

Pub Date : 2022-02-02 DOI: 10.1186/s12953-021-00184-w

Runhong Yu, Shiwei Yang, Yufeng Liu, Zunmin Zhu

Background: B-cell acute lymphoblastic leukemia (B-ALL) is the most common malignancy of childhood. Even though significant progresses have been made in the treatment of B-ALL, some pediatric B-ALL have still poor prognosis. The identification of tumor autoantibodies may have utility in early cancer diagnosis and immunotherapy. In this study, we used serological proteome analysis (SERPA) to screen serum autoantibodies of pediatric B-ALL, aiming to contribute to the early detection of B-ALL in children.

Methods: The total proteins from three pooled B-ALL cell lines (NALM-6, REH and BALL-1 cells) were separated using two-dimensional gel electrophoresis (2-DE), which was followed by Western blot by mixed serum samples from children with B-ALL (n=20) or healthy controls (n=20). We analyzed the images of 2-D gel and Western blot by PDQuest software, and then identified the spots of immune responses in B-ALL samples compared with those in control samples. The proteins from spots were identified using mass spectrometry (MS). The autoantibodies against alpha-enolase (α-enolase) and voltage-dependent anion-selective channel protein 1 (VDAC1) were further validated in sera from another 30 children with B-ALL and 25 normal individuals by the use of enzyme-linked immunosorbent assay (ELISA). The protein expression levels of the candidate antigens α-enolase and VDAC1 in B-ALL were thoroughly studied by immunohistochemical analysis.

Results: Utilizing the SERPA approach, α-enolase and VDAC1 were identified as candidate autoantigens in children with B-ALL. The frequencies of autoantibodies against α-enolase and VDAC1 in children with B-ALL were 27% and 23% by using ELISA analysis, respectively, which were significantly higher than those in normal controls (4% and 0, p<0.05). Immunohistochemical analysis showed the expression of α-enolase and VDAC1 was positive in 95% and 85% of B-ALL patients, respectively, but negative expression levels were showed in the control group.

Conclusions: This study incidated that α-enolase and VDAC1 may be the autoantigens associated with B-ALL. Therefore, α-enolase and VDAC1 autoantibodies may be the potential serological markers for children with B-ALL.

背景:b细胞急性淋巴细胞白血病(B-ALL)是儿童最常见的恶性肿瘤。尽管B-ALL的治疗已取得重大进展，但仍有部分儿童B-ALL预后较差。肿瘤自身抗体的鉴定对早期肿瘤诊断和免疫治疗具有重要意义。本研究采用血清蛋白质组学分析(SERPA)筛选儿童B-ALL的血清自身抗体，旨在为儿童B-ALL的早期发现做出贡献。方法:采用二维凝胶电泳(2-DE)分离3株合并的B-ALL细胞系(NALM-6、REH和BALL-1细胞)的总蛋白，然后用B-ALL患儿(n=20)和健康对照(n=20)的混合血清样本进行Western blot检测。通过PDQuest软件对二维凝胶和Western blot图像进行分析，鉴定出B-ALL样品与对照样品的免疫应答点。用质谱法对斑点中的蛋白质进行鉴定。采用酶联免疫吸附试验(ELISA)在另外30例B-ALL患儿和25例正常人的血清中进一步验证了抗α-烯醇化酶(α-烯醇化酶)和电压依赖性阴离子选择通道蛋白1 (VDAC1)的自身抗体。采用免疫组化方法研究候选抗原α-烯醇化酶和VDAC1在B-ALL中的蛋白表达水平。结果:利用SERPA方法，α-烯醇化酶和VDAC1被确定为B-ALL患儿的候选自身抗原。ELISA检测B-ALL患儿α-烯醇化酶和VDAC1自身抗体阳性率分别为27%和23%，显著高于正常对照组(4%和0%)。结论:α-烯醇化酶和VDAC1可能是B-ALL相关的自身抗原。因此，α-烯醇化酶和VDAC1自身抗体可能是B-ALL患儿的潜在血清学标志物。

{"title":"Identification and validation of serum autoantibodies in children with B-cell acute lymphoblastic leukemia by serological proteome analysis.","authors":"Runhong Yu, Shiwei Yang, Yufeng Liu, Zunmin Zhu","doi":"10.1186/s12953-021-00184-w","DOIUrl":"https://doi.org/10.1186/s12953-021-00184-w","url":null,"abstract":"Background: B-cell acute lymphoblastic leukemia (B-ALL) is the most common malignancy of childhood. Even though significant progresses have been made in the treatment of B-ALL, some pediatric B-ALL have still poor prognosis. The identification of tumor autoantibodies may have utility in early cancer diagnosis and immunotherapy. In this study, we used serological proteome analysis (SERPA) to screen serum autoantibodies of pediatric B-ALL, aiming to contribute to the early detection of B-ALL in children.Methods: The total proteins from three pooled B-ALL cell lines (NALM-6, REH and BALL-1 cells) were separated using two-dimensional gel electrophoresis (2-DE), which was followed by Western blot by mixed serum samples from children with B-ALL (n=20) or healthy controls (n=20). We analyzed the images of 2-D gel and Western blot by PDQuest software, and then identified the spots of immune responses in B-ALL samples compared with those in control samples. The proteins from spots were identified using mass spectrometry (MS). The autoantibodies against alpha-enolase (α-enolase) and voltage-dependent anion-selective channel protein 1 (VDAC1) were further validated in sera from another 30 children with B-ALL and 25 normal individuals by the use of enzyme-linked immunosorbent assay (ELISA). The protein expression levels of the candidate antigens α-enolase and VDAC1 in B-ALL were thoroughly studied by immunohistochemical analysis.Results: Utilizing the SERPA approach, α-enolase and VDAC1 were identified as candidate autoantigens in children with B-ALL. The frequencies of autoantibodies against α-enolase and VDAC1 in children with B-ALL were 27% and 23% by using ELISA analysis, respectively, which were significantly higher than those in normal controls (4% and 0, p<0.05). Immunohistochemical analysis showed the expression of α-enolase and VDAC1 was positive in 95% and 85% of B-ALL patients, respectively, but negative expression levels were showed in the control group.Conclusions: This study incidated that α-enolase and VDAC1 may be the autoantigens associated with B-ALL. Therefore, α-enolase and VDAC1 autoantibodies may be the potential serological markers for children with B-ALL.","PeriodicalId":20857,"journal":{"name":"Proteome Science","volume":" ","pages":"3"},"PeriodicalIF":2.0,"publicationDate":"2022-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8808998/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39881080","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: 4

Integrative proteomic characterization of trace FFPE samples in early-stage gastrointestinal cancer 早期胃肠道肿瘤中微量FFPE样品的综合蛋白质组学特征

IF 2 3区生物学 Q3 BIOCHEMICAL RESEARCH METHODS

Proteome Science

Pub Date : 2021-12-03 DOI: 10.21203/rs.3.rs-1084524/v1

Lingling Li, Hui Liu, Yan Li, Chun-feng Guo, Bing Wang, D. Shen, Qiao‐an Zhang, Chen Ding

Background The surveillance and therapy of early-stage cancer would be better for patients’ prognosis. However, the extreme trace amount of tissue samples in different stages have limited in portraying the characterization of early-stage cancer. Therefore, we focused on and presented comprehensive proteomic and phosphoproproteomic profiling of the trace FFPE samples from early-stage gastrointestinal cancer, and then explored the potential biomarkers of early-stage gastrointestinal cancer. Methods In this study, a quantitative proteomic method with chromatography with mass spectrometry (LC-MS/MS) was used to analyse the proteomic difference between the trace early-stage esophageal squamous cell carcinoma (EESCC) and early-stage duodenum adenocarcinoma cancer (EDAC). Results We identified ~ 6000 proteins and > 10,000 phosphosites in single trace FFPE samples. Comparative analysis disclosed the diverse proteomic features of tumor tissues compared with paired normal tissue of EESCC and EDAC, and revealed the difference of EESCC and EDAC was derived from their origin normal tissue. The distinct separation of EESCC and EDAC illustrated the functions of cell cycle (RB1 T373, EGFR T693) in EESCC, and the positive impacts of apoptosis, metabolic processes (MTOR and MTOR S1261) in EDAC. Furthermore, we deconvoluted the immune infiltration of early-stage gastrointestinal cancer, in which higher immune cell signatures were detected in EDAC, and showed the specific cytokines in EESCC and EDAC. We performed kinases-substates relationship analysis and elucidated the specific proteomic kinase characterization of EESCC and EDAC, and proposed the medicative effects and corresponding drugs for EESCC and EDAC at the clinic. Conclusion We disclosed the specific immune characterization of the early-stage gastrointestinal cancer, and presented potential makers of EESCC (EGFR, PDGFRB, CDK4, WEE1) and EDAC (MTOR, MAP2K1, MAPK3). This study represents a major stepping stone towards investigating the carcinogenesis mechanism of gastrointestinal cancer, and providing a rich resource for medicative strategy in the clinic. Graphical Abstract

背景早期肿瘤的监测和治疗有利于患者预后。然而，不同阶段的极微量组织样本在描绘早期癌症的特征方面受到限制。因此，我们关注并提出了早期胃肠道癌微量FFPE样本的综合蛋白质组学和磷酸化原蛋白质组学分析，进而探索早期胃肠道癌的潜在生物标志物。方法采用色谱-质谱联用定量蛋白质组学方法(LC-MS/MS)分析微量早期食管鳞状细胞癌(EESCC)和早期十二指肠腺癌(EDAC)的蛋白质组学差异。结果在单痕量FFPE样品中鉴定出约6000个蛋白和约10000个磷酸基。对比分析揭示了EESCC和EDAC的肿瘤组织与配对正常组织的不同蛋白质组学特征，并揭示了EESCC和EDAC的差异来源于其原正常组织。EESCC和EDAC的明显分离说明了细胞周期(RB1 T373、EGFR T693)在EESCC中的作用，以及EDAC中凋亡、代谢过程(MTOR和MTOR S1261)的积极影响。此外，我们对早期胃肠道肿瘤的免疫浸润进行了反卷积，发现在EDAC中检测到更高的免疫细胞特征，并显示了EESCC和EDAC中的特异性细胞因子。我们进行了激酶-底物关系分析，明确了EESCC和EDAC的特异性蛋白组激酶特征，并提出了EESCC和EDAC的临床疗效及相应药物。我们揭示了早期胃肠道肿瘤的特异性免疫特征，并提出了EESCC (EGFR、PDGFRB、CDK4、WEE1)和EDAC (MTOR、MAP2K1、MAPK3)的潜在致癌物。本研究为探索胃肠道肿瘤的癌变机制提供了重要的基础，并为临床用药策略提供了丰富的资源。图形抽象

{"title":"Integrative proteomic characterization of trace FFPE samples in early-stage gastrointestinal cancer","authors":"Lingling Li, Hui Liu, Yan Li, Chun-feng Guo, Bing Wang, D. Shen, Qiao‐an Zhang, Chen Ding","doi":"10.21203/rs.3.rs-1084524/v1","DOIUrl":"https://doi.org/10.21203/rs.3.rs-1084524/v1","url":null,"abstract":"Background The surveillance and therapy of early-stage cancer would be better for patients’ prognosis. However, the extreme trace amount of tissue samples in different stages have limited in portraying the characterization of early-stage cancer. Therefore, we focused on and presented comprehensive proteomic and phosphoproproteomic profiling of the trace FFPE samples from early-stage gastrointestinal cancer, and then explored the potential biomarkers of early-stage gastrointestinal cancer. Methods In this study, a quantitative proteomic method with chromatography with mass spectrometry (LC-MS/MS) was used to analyse the proteomic difference between the trace early-stage esophageal squamous cell carcinoma (EESCC) and early-stage duodenum adenocarcinoma cancer (EDAC). Results We identified ~ 6000 proteins and > 10,000 phosphosites in single trace FFPE samples. Comparative analysis disclosed the diverse proteomic features of tumor tissues compared with paired normal tissue of EESCC and EDAC, and revealed the difference of EESCC and EDAC was derived from their origin normal tissue. The distinct separation of EESCC and EDAC illustrated the functions of cell cycle (RB1 T373, EGFR T693) in EESCC, and the positive impacts of apoptosis, metabolic processes (MTOR and MTOR S1261) in EDAC. Furthermore, we deconvoluted the immune infiltration of early-stage gastrointestinal cancer, in which higher immune cell signatures were detected in EDAC, and showed the specific cytokines in EESCC and EDAC. We performed kinases-substates relationship analysis and elucidated the specific proteomic kinase characterization of EESCC and EDAC, and proposed the medicative effects and corresponding drugs for EESCC and EDAC at the clinic. Conclusion We disclosed the specific immune characterization of the early-stage gastrointestinal cancer, and presented potential makers of EESCC (EGFR, PDGFRB, CDK4, WEE1) and EDAC (MTOR, MAP2K1, MAPK3). This study represents a major stepping stone towards investigating the carcinogenesis mechanism of gastrointestinal cancer, and providing a rich resource for medicative strategy in the clinic. Graphical Abstract","PeriodicalId":20857,"journal":{"name":"Proteome Science","volume":"20 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2021-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48755853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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: 1

The proteomics analysis of the effects of Zhishi Rhubarb soup on ischaemic stroke. 枳实大黄汤对缺血性脑卒中影响的蛋白质组学分析。

IF 2 3区生物学 Q3 BIOCHEMICAL RESEARCH METHODS

Proteome Science

Pub Date : 2021-11-10 DOI: 10.1186/s12953-021-00181-z

Jing-Hua Zhang, Yue-Jia Shao, Zhen Hui, Su-Lei Wang, Chi Huang, Yang Zhao

Background: Stroke has always been a major threat worldwide but is most severe in China, with 2.5 million new stroke cases each year and 7.5 million stroke survivors, placing a heavy burden on the social and national health care systems. Zhishi Rhubarb Soup (ZRS) is a traditional Chinese medicine (TCM) that has been used clinically for many years in China. To explore the potential mechanism of ZRS in the treatment of stroke, liquid chromatography with mass spectrometry (LC-MS) was performed.

Methods: In this study, a quantitative proteomic method with LC-MS was used to analyse the proteomic differences between MACO samples treated with ZRS and those without ZRS treatment.

Results: Liquid chromatography with mass spectrometry (LC-MS) analysis led to the identification of 35,006 peptides, with 5160.0 proteins identified and 4094.0 quantified. Significantly differentially expressed proteins were identified through data analysis, and the difference was found to be more than 1.2 times (P < 0.05). The Gene Ontology (GO) analysis provided a summary of the dysregulated protein expression in the biological process (BP), cell component (CC), and molecular function (MF) categories. Proteins related to brain repair, including BDNF, IL-10, IL-6, and TGF-β, were found to change significantly, partially demonstrating the effectiveness of ZRS to attenuate tissue injury.

Conclusion: In this study, LC-MS/MS was performed to assess the effects of ZRS on differentially expressed proteins in rats with cerebral infarction. These promising results could help to improve the understanding of the effects of drugs on stroke.

背景:卒中一直是世界范围内的主要威胁，但在中国最为严重，每年有250万新发卒中病例和750万卒中幸存者，给社会和国家卫生保健系统带来沉重负担。芝士大黄汤(ZRS)是一种在中国临床使用多年的传统中药。为探讨ZRS治疗脑卒中的可能机制，采用液相色谱-质谱联用(LC-MS)方法。方法:采用LC-MS定量蛋白质组学方法分析ZRS处理与未处理MACO样品的蛋白质组学差异。结果:液相色谱-质谱(LC-MS)分析鉴定了35,006个多肽，鉴定了5160.0个蛋白，定量了4094.0个蛋白。通过数据分析，发现有显著差异表达蛋白，差异大于1.2倍(P)。结论:本研究采用LC-MS/MS评价ZRS对脑梗死大鼠差异表达蛋白的影响。这些有希望的结果可能有助于提高对药物对中风的影响的理解。

{"title":"The proteomics analysis of the effects of Zhishi Rhubarb soup on ischaemic stroke.","authors":"Jing-Hua Zhang, Yue-Jia Shao, Zhen Hui, Su-Lei Wang, Chi Huang, Yang Zhao","doi":"10.1186/s12953-021-00181-z","DOIUrl":"https://doi.org/10.1186/s12953-021-00181-z","url":null,"abstract":"Background: Stroke has always been a major threat worldwide but is most severe in China, with 2.5 million new stroke cases each year and 7.5 million stroke survivors, placing a heavy burden on the social and national health care systems. Zhishi Rhubarb Soup (ZRS) is a traditional Chinese medicine (TCM) that has been used clinically for many years in China. To explore the potential mechanism of ZRS in the treatment of stroke, liquid chromatography with mass spectrometry (LC-MS) was performed.Methods: In this study, a quantitative proteomic method with LC-MS was used to analyse the proteomic differences between MACO samples treated with ZRS and those without ZRS treatment.Results: Liquid chromatography with mass spectrometry (LC-MS) analysis led to the identification of 35,006 peptides, with 5160.0 proteins identified and 4094.0 quantified. Significantly differentially expressed proteins were identified through data analysis, and the difference was found to be more than 1.2 times (P < 0.05). The Gene Ontology (GO) analysis provided a summary of the dysregulated protein expression in the biological process (BP), cell component (CC), and molecular function (MF) categories. Proteins related to brain repair, including BDNF, IL-10, IL-6, and TGF-β, were found to change significantly, partially demonstrating the effectiveness of ZRS to attenuate tissue injury.Conclusion: In this study, LC-MS/MS was performed to assess the effects of ZRS on differentially expressed proteins in rats with cerebral infarction. These promising results could help to improve the understanding of the effects of drugs on stroke.","PeriodicalId":20857,"journal":{"name":"Proteome Science","volume":"19 1","pages":"13"},"PeriodicalIF":2.0,"publicationDate":"2021-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8582178/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39607849","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: 1

首页上一页

下一页尾页

类型

全部化学•材料生命科学医学物理工程技术环境•农林材料科学地球科学法学管理学化学环境科学与生态学计算机科学教育学经济学农林科学人文科学生物学数学物理与天体物理心理学综合性期刊其他工业工程理学历史学农学文学信息工程

数据库

全部 ACS Publications Elsevier ieeexplore Springer The Royal Society of Chemistry Wiley

期刊

Proteome Science

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.

﹀