Proteome Science最新文献

{"title":"Isolation and proteomic profiling of urinary exosomes from patients with colorectal cancer.","authors":"Ling Ma,&nbsp;Haijiao Yu,&nbsp;Yubing Zhu,&nbsp;Kaiyu Xu,&nbsp;Aimin Zhao,&nbsp;Lei Ding,&nbsp;Hong Gao,&nbsp;Man Zhang","doi":"10.1186/s12953-023-00203-y","DOIUrl":"https://doi.org/10.1186/s12953-023-00203-y","url":null,"abstract":"<p><p>Exosomes in the body fluid are effective cell-derived membranous structures transferring various molecules to mediate intercellular communication. The expression of protein in the urinary exosomes from the colorectal cancer (CRC) patients could reflect the characteristics of tumorigenesis. The urinary exosomes with globular membrane structure, the size of 30 ~ 100 nm and positive expression of CD9, CD63 and CD81 were successfully isolated from 9 CRC patients and 3 heathy adults using the density gradient ultracentrifugation. Proteome profiles revealed by label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS) indicated that several proteins were differentially expressed among different stages of CRC. Compared with normal controls, 67 proteins in CRC urinary exosomes were upregulated and 74 proteins were downregulated. The bioinformatics analysis revealed the decreased proteins were related to ESCRT III complex disassembly. The CHMP family was further determined to be the hub of interaction network of proteins enriched in ESCRT signaling. The significant decrease of CHMP4A, CHMP4B, CHMP2A, CHMP2B and CHMP1B were respectively found in the total CRC group and distant metastasis group compared with NC group. Moreover, the CEACAM family also showed significant aberrant changes in the urinary exosomes of CRC patients. The CEACAM7 and CEACAM1 were increased in the CRC patients compared with healthy individuals (P < 0.05). Significant changes of proteomic profile could be found in the urinary exosomes in the CRC patients. The differential expressed urinary exosomes derived proteins showed potential usage in diagnosis and prognosis of CRC.</p>","PeriodicalId":20857,"journal":{"name":"Proteome Science","volume":"21 1","pages":"3"},"PeriodicalIF":2.0,"publicationDate":"2023-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9909931/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9242950","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}

{"title":"Quantitative proteomics analysis revealed the potential role of lncRNA Ftx in cardiomyocytes.","authors":"Xiangfei Sun,&nbsp;Ying Jiang,&nbsp;Qingbao Li,&nbsp;Qi Tan,&nbsp;Mingliang Dong,&nbsp;Bi'e Cai,&nbsp;Di Zhang,&nbsp;Qi Zhao","doi":"10.1186/s12953-022-00201-6","DOIUrl":"https://doi.org/10.1186/s12953-022-00201-6","url":null,"abstract":"<p><strong>Objective: </strong>This study aims to decode the proteomic signature of cardiomyocytes in response to lncRNA Ftx knockdown and overexpression via proteomic analysis, and to study the biological role of lncRNA Ftx in cardiomyocytes.  METHODS: The expression level of the lncRNA Ftx in cardiomyocytes cultured in vitro was intervened, and the changes in protein levels in cardiomyocytes were quantitatively detected by liquid chromatography-mass spectrometry. The key molecules and pathways of the lncRNA-Ftx response were further examined by GO, KEGG, and protein interaction analysis.</p><p><strong>Results: </strong>A total of 2828 proteins are quantified. With a 1.5-fold change threshold, 32 upregulated proteins and 49 downregulated proteins are identified in the lncRNA Ftx overexpression group, while 67 up-regulated proteins and 54 down-regulated proteins are identified in the lncRNA Ftx knockdown group. Functional clustering analysis of differential genes revealed that the lncRNA Ftx is involved in regulating cardiomyocyte apoptosis and ferroptosis and improving cellular energy metabolism. In addition, Hub genes such as ITGB1, HMGA2, STAT3, GSS, and LPCAT3 are regulated downstream by lncRNA Ftx.</p><p><strong>Conclusion: </strong>This study demonstrates that lncRNA Ftx plays a vital role in cardiomyocytes and may be involved in the occurrence and development of various myocardial diseases. It provides a potential target for clinical protection of the myocardium and reversal of myocardial fibrosis.</p>","PeriodicalId":20857,"journal":{"name":"Proteome Science","volume":"21 1","pages":"2"},"PeriodicalIF":2.0,"publicationDate":"2023-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9814437/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10559642","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}

{"title":"Proteomic Analysis of Protective Effects of Dl-3-n-Butylphthalide against mpp + -Induced Toxicity via downregulating P53 pathway in N2A Cells.","authors":"Yuan Zhao,&nbsp;Jian Zhang,&nbsp;Yidan Zhang,&nbsp;Shuyue Li,&nbsp;Ya Gao,&nbsp;Cui Chang,&nbsp;Xiang Liu,&nbsp;Lei Xu,&nbsp;Guofeng Yang","doi":"10.1186/s12953-022-00199-x","DOIUrl":"https://doi.org/10.1186/s12953-022-00199-x","url":null,"abstract":"<p><strong>Background: </strong>Dl-3-n-butylphthalide (NBP) is an important medial therapy for acute ischemic stroke in China. Recent studied have revealed that NBP not only rescued the loss of dopaminergic neurons in cellular and animal models of Parkinson's disease (PD), but also could improve motor symptoms in PD patients. However, the protective mechanism is not fully understood. P53 is a multifunctional protein implicated in numerous cellular processes, including apoptosis, DNA repair, mitochondrial functions, redox homeostasis, autophagy and protein aggregations. In PD, p53 integrated with various neurodegeneration-related signals inducing neuronal loss, indicating the suppression of P53 might be a promising target for PD treatment. Therefore, the purpose of the current study was to systemically screen new therapeutic targets of NBP in PD.</p><p><strong>Method: </strong>In our study, we constructed mpp + induced N2A cells to investigate the benefit effect of NBP in PD. MTT assay was performed to evaluate the cell viability; TMT-based LC-MS/MS was applied to determine the different expressed proteins (DEPs) of NBP pretreatment; online bioinformatics databases such as DAVID, STRING, and KEGG was used to construe the proteomic data. After further analyzed and visualized the protein-protein interactions (PPI) by Cytoscape, DEPs were verified by western blot.</p><p><strong>Result: </strong>A total of 5828 proteins were quantified in the comparative proteomics experiments and 417 proteins were considered as DEPs (fold change > 1.5 and p < 0.05). Among the 417 DEPs, 140 were upregulated and 277 were downregulated in mpp + -induced N2A cells with NBP pretreatment. KEGG pathway analysis indicated that lysosome, phagosome, apoptosis, endocytosis and ferroptosis are the mainly enriched pathways. By using MCL clustering in PPI analysis, 48 clusters were generated and the subsequent KEGG analysis of the top 3 clusters revealed that P53 signaling pathway was recognized as the dominant pathway for NBP treatment.</p><p><strong>Conclusion: </strong>NBP significantly relived mpp + -induced cell toxicity. The neuroprotective role of NBP was implicated with P53 signaling pathway in some extent. These findings will reinforce the understanding of the mechanism of NBP in PD and identify novel therapeutic targets.</p>","PeriodicalId":20857,"journal":{"name":"Proteome Science","volume":"21 1","pages":"1"},"PeriodicalIF":2.0,"publicationDate":"2023-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9809048/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10855487","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}

{"title":"Responses of the tree peony (Paeonia suffruticosa, Paeoniaceae) cultivar 'Yu Hong' to heat stress revealed by iTRAQ-based quantitative proteomics.","authors":"Jin Ma, Qun Wang, Ling-Ling Wei, Yu Zhao, Guo-Zhe Zhang, Jie Wang, Cui-Hua Gu","doi":"10.1186/s12953-022-00202-5","DOIUrl":"10.1186/s12953-022-00202-5","url":null,"abstract":"<p><p>Horticulture productivity has been increasingly restricted by heat stress from growing global warming, making it far below the optimum production capacity. As a popular ornamental cultivar of tree peony, Paeonia suffruticosa 'Yu Hong' has also been suffering from heat stress not suitable for its optimal growth. To better understand the response mechanisms against heat stress of tree peony, investigations of phenotypic changes, physiological responses, and quantitative proteomics were conducted. Phenotypic and physiological changes indicated that 24 h of exposure to heat stress (40 °C) was the critical duration of heat stress in tree peony. The proteomic analyses revealed a total of 100 heat-responsive proteins (HRPs). According to bioinformatic analysis of HRPs, the heat tolerance of tree peony might be related to signal transduction, synthesis/degradation, heat kinetic proteins, antioxidants, photosynthesis, energy conversion, and metabolism. Our research will provide some new insights into the molecular mechanism under the response against the heat stress of tree peony, which will benefit the future breeding of heat-resistant ornamental plants.</p>","PeriodicalId":20857,"journal":{"name":"Proteome Science","volume":"20 1","pages":"18"},"PeriodicalIF":2.1,"publicationDate":"2022-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9798725/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10453244","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}

{"title":"TMT-based quantitative proteomics analysis of the effects of Jiawei Danshen decoction myocardial ischemia-reperfusion injury.","authors":"Xiang-Mei Zhu,&nbsp;Yang Tan,&nbsp;Yu-He Shi,&nbsp;Qing Li,&nbsp;Jue Zhu,&nbsp;Xiang-Dan Liu,&nbsp;Qiao-Zhen Tong","doi":"10.1186/s12953-022-00200-7","DOIUrl":"https://doi.org/10.1186/s12953-022-00200-7","url":null,"abstract":"<p><strong>Background: </strong>Every year, approximately 17 million people worldwide die due to coronary heart disease, with China ranking second in terms of the death toll. Myocardial ischemia-reperfusion injury (MIRI) significantly influences cardiac function and prognosis in cardiac surgery patients. Jiawei Danshen Decoction (JWDSD) is a traditional Chinese herbal prescription that has been used clinically for many years in China to treat MIRI. The underlying molecular mechanisms, however, remain unknown. To investigate the proteomic changes in myocardial tissue of rats given JWDSD for MIRI therapy-based proteomics.</p><p><strong>Methods: </strong>MIRI rat model was created by ligating/releasing the left anterior descending coronary artery. For seven days, the drugs were administered twice daily. The model was created following the last drug administration. JWDSD's efficacy in improving MIRI was evaluated using biochemical markers and cardiac histology. Tandem mass tag-based quantitative proteomics (TMT) technology was also used to detect proteins in the extracted heart tissue. To analyze differentially expressed proteins (DEPs), bioinformatics analysis, including gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathways, were employed. Furthermore, western blotting confirmed the potential targets regulated by JWDSD.</p><p><strong>Results: </strong>The histopathologic characteristics and biochemical data showed JWDSD's protective effects on MIRI rats. A total of 4549 proteins were identified with FDR (false discovery rate) ≤1%. Twenty overlapping were identified (162 DEPs and 45 DEPs in Model/Control or JWDSD/Model group, respectively). Of these DEPs, 16 were regulated by JWDSD. GO analysis provided a summary of the deregulated protein expression in the categories of biological process (BP), cell component (CC), and molecular function (MF). KEGG enrichment analysis revealed that the signaling pathways of neutrophil extracellular trap formation, RNA polymerase, serotonergic synapse, and linoleic acid metabolism are all closely related to JWDSD effects in MIRI rats. Furthermore, T-cell lymphoma invasion and metastasis 1 (TIAM1) was validated using western blotting, and the results were consistent with proteomics data.</p><p><strong>Conclusions: </strong>Our study suggests that JWDSD may exert therapeutic effects through multi-pathways regulation in MIRI treatment. This work may provide proteomics clues for continuing research on JWDSD in treating MIRI.</p>","PeriodicalId":20857,"journal":{"name":"Proteome Science","volume":"20 1","pages":"17"},"PeriodicalIF":2.0,"publicationDate":"2022-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9749149/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10712246","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}

{"title":"A combined protein toxin screening based on the transcriptome and proteome of Solenopsis invicta.","authors":"Liuyang Cai,&nbsp;Fengling Yang,&nbsp;Yongfang Wang,&nbsp;Jishun Yang,&nbsp;Yina Zhu,&nbsp;Xueqi Ma,&nbsp;Juan Höfer,&nbsp;Yichao Wang,&nbsp;Yajun Ma,&nbsp;Liang Xiao","doi":"10.1186/s12953-022-00197-z","DOIUrl":"https://doi.org/10.1186/s12953-022-00197-z","url":null,"abstract":"<p><strong>Background: </strong>Multi-omics technology provides a good tool to analyze the protein toxin composition and search for the potential pathogenic factors of Solenopsis invicta, under the great harm of the accelerated invasion in southern China.</p><p><strong>Methods: </strong>Species collection, functional annotation, toxin screening, and 3D modeling construction of three interested toxins were performed based on the successfully constructed transcriptome and proteome of S. invicta.</p><p><strong>Results: </strong>A total of 33,231 unigenes and 721 proteins were obtained from the constructed transcriptome and proteome, of which 9,842 (29.62%) and 4,844 (14.58%) unigenes, as well as 469 (65.05%) and 71 (99.45%) proteins were annotated against the databases of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes, respectively. After comparing with the uniprot toxin database, a total of 316 unigenes and 47 proteins (calglandulin, venom allergen 3, and venom prothrombin activator hopsarin-D, etc.) were successfully screened.</p><p><strong>Conclusions: </strong>The update of annotations at the transcriptome and proteome levels presents a progression in the comprehension of S. invicta in China. We also provide a protein toxin list that could be used for further exploration of toxicity as well as its antagonistic strategy by S. invicta.</p>","PeriodicalId":20857,"journal":{"name":"Proteome Science","volume":" ","pages":"15"},"PeriodicalIF":2.0,"publicationDate":"2022-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9494847/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40372640","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}

{"title":"Effect of downregulated citrate synthase on oxidative phosphorylation signaling pathway in HEI-OC1 cells.","authors":"Xiaowen Xu,&nbsp;Yue Liu,&nbsp;Jun Luan,&nbsp;Rongrong Liu,&nbsp;Yan Wang,&nbsp;Yingying Liu,&nbsp;Ang Xu,&nbsp;Bingxin Zhou,&nbsp;Fengchan Han,&nbsp;Wenjing Shang","doi":"10.1186/s12953-022-00196-0","DOIUrl":"https://doi.org/10.1186/s12953-022-00196-0","url":null,"abstract":"<p><strong>Background: </strong>Citrate Synthase (Cs) gene mutation (locus ahL4) has been found to play an important role in progressive hearing loss of A/J mice. HEI-OC1 cells have been widely used as an in vitro system to study cellular and molecular mechanisms related to hearing lose. We previously reported the increased apoptosis and the accumulation of reactive oxygen species in shRNACs-1429 cells, a Cs low-expressed cell model from HEI-OCI. The details of the mechanism of ROS production and apoptosis mediated by the abnormal expression of Cs needed to research furtherly.</p><p><strong>Methods: </strong>iTRAQ proteomics was utilized to detect the differentially expressed proteins (DEPs) caused by low expression of Cs. The GO and KEGG pathways analysis were performed for annotation of the differentially expressed proteins. Protein-protein interaction network was constructed by STRING online database. Immunoblotting was utilized to confirm the protein levels of the the differentially expressed proteins.</p><p><strong>Results: </strong>The differentially expressed proteins were significantly enriched in various signaling pathways mainly related to mitochondrial dysfunction diseases including Parkinson's disease, Alzheimer's disease, Huntington's disease, et al. Most noteworthy, the oxidative phosphorylation pathway was most significantly suppressed in the shRNACs-1429 cells,, in which a total of 10 differentially expressed proteins were enriched and were all downregulated by the abnormal expression of Cs. The downregulations of Ndufb5, Ndufv1 and Uqcrb were confirmed by immunoblotting. Meanwhile, the ATP levels of shRNACs-1429 cells were also reduced.</p><p><strong>Conclusions: </strong>These results suggest that low level expression of Cs induces the inhibition of oxidative phosphorylation pathway, which is responsible for the high level production of reactive oxygen species and low level of ATP, leading to the apoptosis of cochlear cells. This study may provide new theories for understanding and therapy of progressive hearing loss.</p>","PeriodicalId":20857,"journal":{"name":"Proteome Science","volume":" ","pages":"14"},"PeriodicalIF":2.0,"publicationDate":"2022-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9450364/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33449671","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}

{"title":"Tear proteomics analysis of patient suffered from delayed mustard gas keratopathy.","authors":"Shahram Parvin,&nbsp;Alireza Shahriary,&nbsp;Hossein Aghamollaei,&nbsp;B Fatemeh Nobakht M Gh,&nbsp;Hasan Bagheri,&nbsp;Mostafa Ghanei,&nbsp;Seyed-Hashem Daryabari,&nbsp;Khosrow Jadidi,&nbsp;Masoud Arabfard","doi":"10.1186/s12953-022-00195-1","DOIUrl":"https://doi.org/10.1186/s12953-022-00195-1","url":null,"abstract":"<p><p>Understanding the molecular and cellular mechanisms involved in the pathogenesis of ocular injured induced by mustard gas can help better identify complications and discover appropriate therapies. This study aimed to analyze the proteomics of tears of chemical warfare victims with mustard gas ocular injuries and compare it with healthy individuals. In this case-control research, 10 mustard gas victims with long-term ocular difficulties (Chronic) were included in the patient group, while 10 healthy persons who were age and sex matched to the patients were included in the control group. Schirmer strips were used to collect the tears of the participants. Proteomics experiments were performed using the high-efficiency TMT10X method to evaluate the tear protein profile, and statistical bioinformatics methods were used to identify the differently expressed proteins. 24 proteins had different expressions between the two groups. Among these 24 proteins, 8 proteins had increased expression in veterans' tears, while the remaining 16 proteins had decreased expression. Reactome pathways were used to look at proteins with various expressions, and 13 proteins were found to be engaged in the immune system, 9 of which were effective in the innate immune system, and 5 proteins were effective in the complement cascade. Ocular mustard gas exposure may cause a compromised immune system on the eye's surface, exposing the cornea to external and endogenous infections, and eventually causing corneal opacity and reduced vision.</p>","PeriodicalId":20857,"journal":{"name":"Proteome Science","volume":" ","pages":"13"},"PeriodicalIF":2.0,"publicationDate":"2022-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9364592/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40696955","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}

{"title":"Phosphoproteome profiling of mouse liver during normal aging.","authors":"Jiang-Feng Liu,&nbsp;Yue Wu,&nbsp;Ye-Hong Yang,&nbsp;Song-Feng Wu,&nbsp;Shu Liu,&nbsp;Ping Xu,&nbsp;Jun-Tao Yang","doi":"10.1186/s12953-022-00194-2","DOIUrl":"https://doi.org/10.1186/s12953-022-00194-2","url":null,"abstract":"<p><strong>Background: </strong>Aging is a complex biological process accompanied by a time-dependent functional decline that affects most living organisms. Omics studies help to comprehensively understand the mechanism of aging and discover potential intervention methods. Old mice are frequently obese with a fatty liver.</p><p><strong>Methods: </strong>We applied mass spectrometry-based phosphoproteomics to obtain a global phosphorylation profile of the liver in mice aged 2 or 18 months. MaxQuant was used for quantitative analysis and PCA was used for unsupervised clustering.</p><p><strong>Results: </strong>Through phosphoproteome analysis, a total of 5,685 phosphosites in 2,335 proteins were filtered for quantitative analysis. PCA analysis of both the phosphoproteome and transcriptome data could distinguish young and old mice. However, from kinase prediction, kinase-substrate interaction analysis, and KEGG functional enrichment analysis done with phosphoproteome data, we observed high phosphorylation of fatty acid biosynthesis, β-oxidation, and potential secretory processes, together with low phosphorylation of the Egfr-Sos1-Araf/Braf-Map2k1-Mapk1 pathway and Ctnnb1 during aging. Proteins with differentially expressed phosphosites seemed more directly related to the aging-associated fatty liver phenotype than the differentially expressed transcripts. The phosphoproteome may reveal distinctive biological functions that are lost in the transcriptome.</p><p><strong>Conclusions: </strong>In summary, we constructed a phosphorylation-associated network in the mouse liver during normal aging, which may help to discover novel antiaging strategies.</p>","PeriodicalId":20857,"journal":{"name":"Proteome Science","volume":" ","pages":"12"},"PeriodicalIF":2.0,"publicationDate":"2022-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9354360/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40585222","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}

{"title":"A risk score model based on TGF-β pathway-related genes predicts survival, tumor microenvironment and immunotherapy for liver hepatocellular carcinoma.","authors":"Jingsheng Liao,&nbsp;Qi Liu,&nbsp;Jingtang Chen,&nbsp;Zhibin Lu,&nbsp;Huiting Mo,&nbsp;Jun Jia","doi":"10.1186/s12953-022-00192-4","DOIUrl":"https://doi.org/10.1186/s12953-022-00192-4","url":null,"abstract":"<p><strong>Background: </strong>Transforming growth factor-beta (TGF-β) signal is an important pathway involved in all stages of liver hepatocellular carcinoma (LIHC) initiation and progression. Therefore, targeting TGF- β pathway may be a potential therapeutic strategy for LIHC. Prediction of patients' tumor cells response requires effective biomarkers.</p><p><strong>Methods: </strong>From 54 TGF-β-related genes, this research determined the genes showing the greatest relation to LIHC prognosis, and developed a risk score model with 8 TGF-β-related genes. The model divided LIHC patients from different datasets and platforms into low- and high-risk groups. Multivariate Cox regression analysis confirmed that the model was an independent prognostic factor for LIHC. The differences in genetic mutation, immune cell infiltration, biological pathway, response to immunotherapy or chemotherapy, and tumor microenvironment in LIHC samples showing different risks were analyzed.</p><p><strong>Results: </strong>Compared with low-risk group, in the training set and test set, high-risk group showed shorter survival, lower stromal score and higher M0 macrophages scores, regulatory T cells (Tregs), helper follicular T cells. Moreover, high-risk samples showed higher sensitivity to cisplatin, imatinib, sorafenib and salubrinal and pyrimethamine. High-risk group demonstrated a significantly higher Tumor Immune Dysfunction and Exclusion (TIDE) score, but would significantly benefit less from taking immunotherapy and was less likely to respond to immune checkpoint inhibitors.</p><p><strong>Conclusions: </strong>In general, this work provided a risk scoring model based on 8 TGF-β pathway-related genes, which might be a new potential tool for predicting LIHC.</p>","PeriodicalId":20857,"journal":{"name":"Proteome Science","volume":" ","pages":"11"},"PeriodicalIF":2.0,"publicationDate":"2022-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9215003/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40210774","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}