Journal of Proteome Research最新文献_第3页

Development and Validation of a Predictive Model for Resistance to Platinum-Based Chemotherapy in Patients with Ovarian Cancer through Proteomic Analysis 通过蛋白质组分析建立并验证卵巢癌患者对铂类化疗耐药性的预测模型

IF 4.4 2区生物学

Journal of Proteome Research Pub Date : 2024-09-10 DOI: 10.1021/acs.jproteome.4c00558

Yanqun Mo, Junliang Liu, Yi Hu, Xiaotong Peng, Huining Liu

{"title":"Development and Validation of a Predictive Model for Resistance to Platinum-Based Chemotherapy in Patients with Ovarian Cancer through Proteomic Analysis","authors":"Yanqun Mo, Junliang Liu, Yi Hu, Xiaotong Peng, Huining Liu","doi":"10.1021/acs.jproteome.4c00558","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00558","url":null,"abstract":"Platinum resistance in ovarian cancer poses a significant challenge, substantially impacting patient outcomes. Developing an accurate predictive model is crucial for improving clinical decision-making and guiding treatment strategies. Proteomic data from 217 high-grade serous ovarian cancer (HGSOC) biospecimens obtained from JHU, PNNL, and PTRC were used to construct a prediction model for identifying individuals who are resistant to platinum-based chemotherapy. A total of 6437 common proteins were detected across all data sets, with 26 proteins overlapping between the development cohorts JHU and PNNL. Using LASSO and logistic regression analysis, a six-protein model (P31323_PRKAR2B, Q13309_SKP2, Q14997_PSME4, Q6ZRP7_QSOX2, Q7LGA3_HS2ST1, and Q7Z2Z2_EFL1) was developed, which accurately predicted platinum resistance, with an AUC of 0.964 (95% CI, 0.929–0.999). Internal validation by resampling resulted in a C-index of 0.972 (95% CI 0.894–0.988). External validation performed on the PTRC cohort achieved an AUC of 0.855 (95% CI 0.748–0.963). Calibration curves showed good consistency, and DCA indicated superior clinical utility. The model also performed well in predicting PFS and OS at various time points. Based on these proteins, our predictive model can precisely predict platinum response and survival outcomes in HGSOC patients, which can assist clinicians in promptly identifying potentially platinum-resistant individuals.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142179217","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

Proteomic Characterization of Transfusable Blood Components: Fresh Frozen Plasma, Cryoprecipitate, and Derived Extracellular Vesicles via Data-Independent Mass Spectrometry 可输血成分的蛋白质组特征：通过数据独立质谱法鉴定新鲜冷冻血浆、冷沉淀和衍生细胞外小泡

IF 4.4 2区生物学

Journal of Proteome Research Pub Date : 2024-09-10 DOI: 10.1021/acs.jproteome.4c00417

Ji Hui Hwang, Andrew Lai, John-Paul Tung, Damien G Harkin, Robert L Flower, Natalie M Pecheniuk

{"title":"Proteomic Characterization of Transfusable Blood Components: Fresh Frozen Plasma, Cryoprecipitate, and Derived Extracellular Vesicles via Data-Independent Mass Spectrometry","authors":"Ji Hui Hwang, Andrew Lai, John-Paul Tung, Damien G Harkin, Robert L Flower, Natalie M Pecheniuk","doi":"10.1021/acs.jproteome.4c00417","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00417","url":null,"abstract":"Extracellular vesicles (EVs) are a heterogeneous collection of particles that play a crucial role in cell-to-cell communication, primarily due to their ability to transport molecules, such as proteins. Thus, profiling EV-associated proteins offers insight into their biological effects. EVs can be isolated from various biological fluids, including donor blood components such as cryoprecipitate and fresh frozen plasma (FFP). In this study, we conducted a proteomic analysis of five single donor units of cryoprecipitate, FFP, and EVs derived from these blood components using a quantitative mass spectrometry approach. EVs were successfully isolated from both cryoprecipitate and FFP based on community guidelines. We identified and quantified approximately 360 proteins across all sample groups. Principal component analysis and heatmaps revealed that both cryoprecipitate and FFP are similar. Similarly, EVs derived from cryoprecipitate and FFP are comparable. However, they differ between the originating fluids and their derived EVs. Using the R-package MS-DAP, differentially expressed proteins (DEPs) were identified. The DEPs for all comparisons, when submitted for gene enrichment analysis, are involved in the complement and coagulation pathways. The protein profile generated from this study will have important clinical implications in increasing our knowledge of the proteins that are associated with EVs derived from blood components.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142179216","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

Analysis and Visualization of Quantitative Proteomics Data Using FragPipe-Analyst 使用 FragPipe-Analyst 对定量蛋白质组学数据进行分析和可视化

IF 4.4 2区生物学

Journal of Proteome Research Pub Date : 2024-09-10 DOI: 10.1021/acs.jproteome.4c00294

Yi Hsiao, Haijian Zhang, Ginny Xiaohe Li, Yamei Deng, Fengchao Yu, Hossein Valipour Kahrood, Joel R. Steele, Ralf B. Schittenhelm, Alexey I. Nesvizhskii

{"title":"Analysis and Visualization of Quantitative Proteomics Data Using FragPipe-Analyst","authors":"Yi Hsiao, Haijian Zhang, Ginny Xiaohe Li, Yamei Deng, Fengchao Yu, Hossein Valipour Kahrood, Joel R. Steele, Ralf B. Schittenhelm, Alexey I. Nesvizhskii","doi":"10.1021/acs.jproteome.4c00294","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00294","url":null,"abstract":"The FragPipe computational proteomics platform is gaining widespread popularity among the proteomics research community because of its fast processing speed and user-friendly graphical interface. Although FragPipe produces well-formatted output tables that are ready for analysis, there is still a need for an easy-to-use and user-friendly downstream statistical analysis and visualization tool. FragPipe-Analyst addresses this need by providing an R shiny web server to assist FragPipe users in conducting downstream analyses of the resulting quantitative proteomics data. It supports major quantification workflows, including label-free quantification, tandem mass tags, and data-independent acquisition. FragPipe-Analyst offers a range of useful functionalities, such as various missing value imputation options, data quality control, unsupervised clustering, differential expression (DE) analysis using Limma, and gene ontology and pathway enrichment analysis using Enrichr. To support advanced analysis and customized visualizations, we also developed FragPipeAnalystR, an R package encompassing all FragPipe-Analyst functionalities that is extended to support site-specific analysis of post-translational modifications (PTMs). FragPipe-Analyst and FragPipeAnalystR are both open-source and freely available.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142179214","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

Developing Method for Minor Acidic O-Glycan Analysis in Mucin and Cancer Cell Samples 开发粘蛋白和癌细胞样本中微量酸性 O-糖分析方法

IF 4.4 2区生物学

Journal of Proteome Research Pub Date : 2024-09-10 DOI: 10.1021/acs.jproteome.4c00240

Keita Yamada, Kosuke Asada, Ken Hanzawa, Yuma Aoki, Kazuki Nakajima, Mitsuhiro Kinoshita

{"title":"Developing Method for Minor Acidic O-Glycan Analysis in Mucin and Cancer Cell Samples","authors":"Keita Yamada, Kosuke Asada, Ken Hanzawa, Yuma Aoki, Kazuki Nakajima, Mitsuhiro Kinoshita","doi":"10.1021/acs.jproteome.4c00240","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00240","url":null,"abstract":"Minor acidic glycans, such as sulfated and phosphorylated glycans, constitute only a small fraction of biological glycome, making their analysis a considerable challenge. In this study, we developed a technique to analyze minor acidic O-glycans in biological samples. First, efficient reaction conditions for the release of O-glycans from the proteins were determined. Next, a high-throughput method was established for the recovery of minor acidic glycans using NH2 spin columns. The performance of the established method was evaluated using mucin samples, and sulfated O-glycans were successfully detected in bovine submaxillary gland mucin and porcine stomach mucin. We also analyzed the minor acidic O-glycans in cultured cancer cells. In addition to trifucosylated sulfated O-glycans and disulfated O-glycans, sulfated O-glycans with KDN were detected in LS174T cells. The relative amount of sulfated glycans in LS174T cells was almost 10-fold higher than that in the other cells. Moreover, a large polylactosamine-type sulfated O-glycan with a molecular weight >3500 was detected in MKN45 cells. Interestingly, phosphorylated ribose, possibly bound to serine/threonine, was observed in all the cells used in this study. Thus, our established analytical method allows for the analysis of minor acidic O-glycans that cannot be detected using existing glycomics methods.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142179223","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

A Framework for Quality Control in Quantitative Proteomics. 定量蛋白质组学质量控制框架

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-09-09 DOI: 10.1021/acs.jproteome.4c00363

Kristine A Tsantilas, Gennifer E Merrihew, Julia E Robbins, Richard S Johnson, Jea Park, Deanna L Plubell, Jesse D Canterbury, Eric Huang, Michael Riffle, Vagisha Sharma, Brendan X MacLean, Josh Eckels, Christine C Wu, Michael S Bereman, Sandra E Spencer, Andrew N Hoofnagle, Michael J MacCoss

{"title":"A Framework for Quality Control in Quantitative Proteomics.","authors":"Kristine A Tsantilas, Gennifer E Merrihew, Julia E Robbins, Richard S Johnson, Jea Park, Deanna L Plubell, Jesse D Canterbury, Eric Huang, Michael Riffle, Vagisha Sharma, Brendan X MacLean, Josh Eckels, Christine C Wu, Michael S Bereman, Sandra E Spencer, Andrew N Hoofnagle, Michael J MacCoss","doi":"10.1021/acs.jproteome.4c00363","DOIUrl":"10.1021/acs.jproteome.4c00363","url":null,"abstract":"A thorough evaluation of the quality, reproducibility, and variability of bottom-up proteomics data is necessary at every stage of a workflow, from planning to analysis. We share vignettes applying adaptable quality control (QC) measures to assess sample preparation, system function, and quantitative analysis. System suitability samples are repeatedly measured longitudinally with targeted methods, and we share examples where they are used on three instrument platforms to identify severe system failures and track function over months to years. Internal QCs incorporated at the protein and peptide levels allow our team to assess sample preparation issues and to differentiate system failures from sample-specific issues. External QC samples prepared alongside our experimental samples are used to verify the consistency and quantitative potential of our results during batch correction and normalization before assessing biological phenotypes. We combine these controls with rapid analysis (Skyline), longitudinal QC metrics (AutoQC), and server-based data deposition (PanoramaWeb). We propose that this integrated approach to QC is a useful starting point for groups to facilitate rapid quality control assessment to ensure that valuable instrument time is used to collect the best quality data possible. Data are available on Panorama Public and ProteomeXchange under the identifier PXD051318.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142152543","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

Comprehensive Glycomic and Glycoproteomic Analyses of Human Programmed Cell Death Protein 1 Extracellular Domain. 人类程序性细胞死亡蛋白 1 细胞外结构域的综合糖组学和糖蛋白组学分析。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-09-06 Epub Date: 2024-08-05 DOI: 10.1021/acs.jproteome.4c00292

Qiushi Chen, Zhiwu Tan, Yang Tang, Yi Man Eva Fung, Sheng Chen, Zhiwei Chen, Xuechen Li

{"title":"Comprehensive Glycomic and Glycoproteomic Analyses of Human Programmed Cell Death Protein 1 Extracellular Domain.","authors":"Qiushi Chen, Zhiwu Tan, Yang Tang, Yi Man Eva Fung, Sheng Chen, Zhiwei Chen, Xuechen Li","doi":"10.1021/acs.jproteome.4c00292","DOIUrl":"10.1021/acs.jproteome.4c00292","url":null,"abstract":"Human programmed cell death protein 1 (hPD-1) is an essential receptor in the immune checkpoint pathway. It has played an important role in cancer therapy. However, not all patients respond positively to the PD-1 antibody treatment, and the underlying mechanism remains unknown. PD-1 is a transmembrane glycoprotein, and its extracellular domain (ECD) is reported to be responsible for interactions and signal transduction. This domain contains 4 N-glycosylation sites and 25 potential O-glycosylation sites, which implicates the importance of glycosylation. The structure of hPD-1 has been intensively studied, but the glycosylation of this protein, especially the glycan on each glycosylation site, has not been comprehensively illustrated. In this study, hPD-1 ECD expressed by human embryonic kidney 293 (HEK 293) and Chinese hamster ovary (CHO) cells was analyzed; not only N- and O-glycosylation sites but also the glycans on these sites were comprehensively analyzed using mass spectrometry. In addition, hPD-1 ECD binding to different anti-hPD-1 antibodies was tested, and N-glycans were found functioned differently. All of this glycan information will be beneficial for future PD-1 studies.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141887533","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

The Study of Metalloproteome of DNA Viruses: Identification, Functional Annotation, and Diversity Analysis of Viral Metal-Binding Proteins. DNA 病毒金属蛋白质组的研究：病毒金属结合蛋白的鉴定、功能注释和多样性分析。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-09-06 Epub Date: 2024-08-12 DOI: 10.1021/acs.jproteome.4c00358

Himisha Dixit, Vipin Upadhyay, Mahesh Kulharia, Shailender Kumar Verma

{"title":"The Study of Metalloproteome of DNA Viruses: Identification, Functional Annotation, and Diversity Analysis of Viral Metal-Binding Proteins.","authors":"Himisha Dixit, Vipin Upadhyay, Mahesh Kulharia, Shailender Kumar Verma","doi":"10.1021/acs.jproteome.4c00358","DOIUrl":"10.1021/acs.jproteome.4c00358","url":null,"abstract":"Metalloproteins are fundamental to diverse biological processes but still lack extensive investigation in viral contexts. This study reveals the prevalence and functional diversity of metal-binding proteins in DNA viruses. Among a subset of 1432 metalloproteins, zinc and magnesium-binding proteins are notably abundant, indicating their importance in viral biology. Furthermore, significant numbers of proteins binding to iron, manganese, copper, nickel, mercury, and cadmium were also detected. Human-infecting viral proteins displayed a rich landscape of metalloproteins, with MeBiPred (964 proteins) and Pfam (666) yielding the highest numbers. Interestingly, many essential viral proteins exhibited metal-binding capabilities, including polymerases, DNA binding proteins, helicases, dUPTase, thymidine kinase, and various structural and accessory proteins. This study sheds light on the ubiquitous presence of metalloproteins, their functional signatures, subcellular placements, and metal-utilization patterns, providing valuable insights into viral biology. A similar metal utilization pattern was observed in similar functional proteins across the various DNA viruses. Furthermore, these findings provide a foundation for identifying potential drug targets for combating viral infections.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141969949","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

A New Evaluation Metric for Quantitative Accuracy of LC-MS/MS-Based Proteomics with Data-Independent Acquisition. 基于数据独立采集的 LC-MS/MS 蛋白质组学定量准确性的新评估指标。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-09-06 Epub Date: 2024-08-28 DOI: 10.1021/acs.jproteome.4c00088

Mengtian Shi, Chiyuan Huang, Renhui Chen, David Da Yong Chen, Binjun Yan

{"title":"A New Evaluation Metric for Quantitative Accuracy of LC-MS/MS-Based Proteomics with Data-Independent Acquisition.","authors":"Mengtian Shi, Chiyuan Huang, Renhui Chen, David Da Yong Chen, Binjun Yan","doi":"10.1021/acs.jproteome.4c00088","DOIUrl":"10.1021/acs.jproteome.4c00088","url":null,"abstract":"Data-independent acquisition (DIA) has improved the identification and quantitation coverage of peptides and proteins in liquid chromatography-tandem mass spectrometry-based proteomics. However, different DIA data-processing tools can produce very different identification and quantitation results for the same data set. Currently, benchmarking studies of DIA tools are predominantly focused on comparing the identification results, while the quantitative accuracy of DIA measurements is acknowledged to be important but insufficiently investigated, and the absence of suitable metrics for comparing quantitative accuracy is one of the reasons. A new metric is proposed for the evaluation of quantitative accuracy to avoid the influence of differences in false discovery rate control stringency. The part of the quantitation results with high reliability was acquired from each DIA tool first, and the quantitative accuracy was evaluated by comparing quantification error rates at the same number of accurate ratios. From the results of four benchmark data sets, the proposed metric was shown to be more sensitive to discriminating the quantitative performance of DIA tools. Moreover, the DIA tools with advantages in quantitative accuracy were consistently revealed by this metric. The proposed metric can also help researchers in optimizing algorithms of the same DIA tool and sample preprocessing methods to enhance quantitative accuracy.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142078350","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

FANS Unfixed: Isolation and Proteomic Analysis of Mouse Cell Type-Specific Brain Nuclei. FANS Unfixed：小鼠细胞类型特异性脑核的分离和蛋白质组分析。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-09-06 Epub Date: 2024-07-26 DOI: 10.1021/acs.jproteome.4c00161

Lucy Bedwell, Myrto Mavrotas, Nikita Demchenko, Reuben M Yaa, Brittannie Willis, Zuzana Demianova, Nelofer Syed, Harry J Whitwell, Alexi Nott

{"title":"FANS Unfixed: Isolation and Proteomic Analysis of Mouse Cell Type-Specific Brain Nuclei.","authors":"Lucy Bedwell, Myrto Mavrotas, Nikita Demchenko, Reuben M Yaa, Brittannie Willis, Zuzana Demianova, Nelofer Syed, Harry J Whitwell, Alexi Nott","doi":"10.1021/acs.jproteome.4c00161","DOIUrl":"10.1021/acs.jproteome.4c00161","url":null,"abstract":"Epigenetic-mediated gene regulation orchestrates brain cell-type gene expression programs, and epigenetic dysregulation is a major driver of aging and disease-associated changes. Proteins that mediate gene regulation are mostly localized to the nucleus; however, nuclear-localized proteins are often underrepresented in gene expression studies and have been understudied in the context of the brain. To address this challenge, we have optimized an approach for nuclei isolation that is compatible with proteomic analysis. This was coupled to a mass spectrometry protocol for detecting proteins in low-concentration samples. We have generated nuclear proteomes for neurons, microglia, and oligodendrocytes from the mouse brain cortex and identified cell-type nuclear proteins associated with chromatin structure and organization, chromatin modifiers such as transcription factors, and RNA-binding proteins, among others. Our nuclear proteomics platform paves the way for assessing brain cell type changes in the nuclear proteome across health and disease, such as neurodevelopmental, aging, neurodegenerative, and neuroinflammatory conditions. Data are available via ProteomeXchange with the identifier PXD053515.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11385383/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141755616","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 Endogenous Serum Peptides as Potential Biomarkers for Hepatocellular Carcinoma in Patients with Liver Cirrhosis. 揭示作为肝硬化患者肝细胞癌潜在生物标记物的内源性血清肽

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-09-06 Epub Date: 2024-08-23 DOI: 10.1021/acs.jproteome.4c00269

Muhammad Salman Sajid, Yuansong Ding, Rency S Varghese, Alexander Kroemer, Habtom W Ressom

{"title":"Unveiling Endogenous Serum Peptides as Potential Biomarkers for Hepatocellular Carcinoma in Patients with Liver Cirrhosis.","authors":"Muhammad Salman Sajid, Yuansong Ding, Rency S Varghese, Alexander Kroemer, Habtom W Ressom","doi":"10.1021/acs.jproteome.4c00269","DOIUrl":"10.1021/acs.jproteome.4c00269","url":null,"abstract":"Hepatocellular carcinoma (HCC) is a leading cause of cancer-related deaths worldwide, mainly associated with liver cirrhosis. Current diagnostic methods for HCC have limited sensitivity and specificity, highlighting the need for improved early detection and intervention. In this study, we used a comprehensive approach involving endogenous peptidome along with bioinformatics analysis to identify and evaluate potential biomarkers for HCC. Serum samples from 40 subjects, comprising 20 HCC cases and 20 patients with liver cirrhosis (CIRR), were analyzed. Among 2568 endogenous peptides, 67 showed significant differential expression between the HCC vs CIRR. Further analysis revealed three endogenous peptides (VMHEALHNHYTQKSLSLSPG, NRFTQKSLSLSPG, and SARQSTLDKEL) that showed far better performance compared to AFP in terms of area under the receiver operating characteristic curve (AUC), showcasing their potential as biomarkers for HCC. Additionally, endogenous peptide IAVEWESNGQPENNYKT that belongs to the precursor protein Immunoglobulin heavy constant gamma 4 was detected in 100% of the HCC group and completely absent in the CIRR group, suggesting a promising diagnostic biomarker. Gene ontology and pathway analysis revealed the potential involvement of these dysregulated peptides in HCC. These findings provide valuable insights into the molecular basis of HCC and may contribute to the development of improved diagnostic methods and therapeutic targets for HCC.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11385380/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142034501","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