Proteomes最新文献

{"title":"Enzymatic Investigation of <i>Spongospora subterranea</i> Zoospore Attachment to Roots of Potato Cultivars Resistant or Susceptible to Powdery Scab Disease.","authors":"Xian Yu,&nbsp;Richard Wilson,&nbsp;Alieta Eyles,&nbsp;Sadegh Balotf,&nbsp;Robert Stephen Tegg,&nbsp;Calum Rae Wilson","doi":"10.3390/proteomes11010007","DOIUrl":"https://doi.org/10.3390/proteomes11010007","url":null,"abstract":"<p><p>For potato crops, host resistance is currently the most effective and sustainable tool to manage diseases caused by the plasmodiophorid <i>Spongospora subterranea</i>. Arguably, zoospore root attachment is the most critical phase of infection; however, the underlying mechanisms remain unknown. This study investigated the potential role of root-surface cell-wall polysaccharides and proteins in cultivars resistant/susceptible to zoospore attachment. We first compared the effects of enzymatic removal of root cell-wall proteins, <i>N</i>-linked glycans and polysaccharides on <i>S. subterranea</i> attachment. Subsequent analysis of peptides released by trypsin shaving (TS) of root segments identified 262 proteins that were differentially abundant between cultivars. These were enriched in root-surface-derived peptides but also included intracellular proteins, e.g., proteins associated with glutathione metabolism and lignin biosynthesis, which were more abundant in the resistant cultivar. Comparison with whole-root proteomic analysis of the same cultivars identified 226 proteins specific to the TS dataset, of which 188 were significantly different. Among these, the pathogen-defence-related cell-wall protein stem 28 kDa glycoprotein and two major latex proteins were significantly less abundant in the resistant cultivar. A further major latex protein was reduced in the resistant cultivar in both the TS and whole-root datasets. In contrast, three glutathione <i>S</i>-transferase proteins were more abundant in the resistant cultivar (TS-specific), while the protein glucan endo-1,3-beta-glucosidase was increased in both datasets. These results imply a particular role for major latex proteins and glucan endo-1,3-beta-glucosidase in regulating zoospore binding to potato roots and susceptibility to <i>S. subterranea</i>.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"11 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2023-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9944879/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10823006","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive Kinase Activity Profiling Revealed the Kinase Activity Patterns Associated with the Effects of EGFR Tyrosine Kinase Inhibitor Therapy in Advanced Non-Small-Cell Lung Cancer Patients with Sensitizing EGFR Mutations.","authors":"Rei Noguchi,&nbsp;Akihiro Yoshimura,&nbsp;Junji Uchino,&nbsp;Takayuki Takeda,&nbsp;Yusuke Chihara,&nbsp;Takayo Ota,&nbsp;Osamu Hiranuma,&nbsp;Hiroshi Gyotoku,&nbsp;Koichi Takayama,&nbsp;Tadashi Kondo","doi":"10.3390/proteomes11010006","DOIUrl":"https://doi.org/10.3390/proteomes11010006","url":null,"abstract":"<p><p>EGFR mutations are strong predictive markers for EGFR tyrosine kinase inhibitor (EGFR-TKI) therapy in patients with non-small-cell lung cancer (NSCLC). Although NSCLC patients with sensitizing EGFR mutations have better prognoses, some patients exhibit worse prognoses. We hypothesized that various activities of kinases could be potential predictive biomarkers for EGFR-TKI treatment among NSCLC patients with sensitizing EGFR mutations. In 18 patients with stage IV NSCLC, EGFR mutations were detected and comprehensive kinase activity profiling was performed using the peptide array PamStation12 for 100 tyrosine kinases. Prognoses were observed prospectively after the administration of EGFR-TKIs. Finally, the kinase profiles were analyzed in combination with the prognoses of the patients. Comprehensive kinase activity analysis identified specific kinase features, consisting of 102 peptides and 35 kinases, in NSCLC patients with sensitizing EGFR mutations. Network analysis revealed seven highly phosphorylated kinases: CTNNB1, CRK, EGFR, ERBB2, PIK3R1, PLCG1, and PTPN11. Pathway analysis and Reactome analysis revealed that the PI3K-AKT and RAF/ MAPK pathways were significantly enriched in the poor prognosis group, being consistent with the outcome of the network analysis. Patients with poor prognoses exhibited high activation of EGFR, PIK3R1, and ERBB2. Comprehensive kinase activity profiles may provide predictive biomarker candidates for screening patients with advanced NSCLC harboring sensitizing EGFR mutations.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"11 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2023-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9944465/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10823010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Double-Edged Proteins in Cancer Proteomes and the Generation of Induced Tumor-Suppressing Cells (iTSCs).","authors":"Kexin Li, Qingji Huo, Bai-Yan Li, Hiroki Yokota","doi":"10.3390/proteomes11010005","DOIUrl":"10.3390/proteomes11010005","url":null,"abstract":"<p><p>Unlike a prevalent expectation that tumor cells secrete tumor-promoting proteins and stimulate the progression of neighboring tumor cells, accumulating evidence indicates that the role of tumor-secreted proteins is double-edged and context-dependent. Some of the oncogenic proteins in the cytoplasm and cell membranes, which are considered to promote the proliferation and migration of tumor cells, may inversely act as tumor-suppressing proteins in the extracellular domain. Furthermore, the action of tumor-secreted proteins by aggressive \"super-fit\" tumor cells can be different from those derived from \"less-fit\" tumor cells. Tumor cells that are exposed to chemotherapeutic agents could alter their secretory proteomes. Super-fit tumor cells tend to secrete tumor-suppressing proteins, while less-fit or chemotherapeutic agent-treated tumor cells may secrete tumor-promotive proteomes. Interestingly, proteomes derived from nontumor cells such as mesenchymal stem cells and peripheral blood mononuclear cells mostly share common features with tumor cell-derived proteomes in response to certain signals. This review introduces the double-sided functions of tumor-secreted proteins and describes the proposed underlying mechanism, which would possibly be based on cell competition.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"11 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2023-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9944087/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10823013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Acknowledgment to the Reviewers of <i>Proteomes</i> in 2022.","authors":"Proteomes Editorial Office","doi":"10.3390/proteomes11010004","DOIUrl":"https://doi.org/10.3390/proteomes11010004","url":null,"abstract":"<p><p>High-quality academic publishing is built on rigorous peer review [...].</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"11 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2023-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9844453/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10549900","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterisation of Colorectal Cancer Cell Lines through Proteomic Profiling of Their Extracellular Vesicles.","authors":"Kathleen A Heck,&nbsp;Håvard T Lindholm,&nbsp;Barbara Niederdorfer,&nbsp;Eirini Tsirvouli,&nbsp;Martin Kuiper,&nbsp;Åsmund Flobak,&nbsp;Astrid Lægreid,&nbsp;Liv Thommesen","doi":"10.3390/proteomes11010003","DOIUrl":"https://doi.org/10.3390/proteomes11010003","url":null,"abstract":"<p><p>Colorectal cancer (CRC) is one of the most prevalent cancers, driven by several factors including deregulations in intracellular signalling pathways. Small extracellular vesicles (sEVs) are nanosized protein-packaged particles released from cells, which are present in liquid biopsies. Here, we characterised the proteome landscape of sEVs and their cells of origin in three CRC cell lines HCT116, HT29 and SW620 to explore molecular traits that could be exploited as cancer biomarker candidates and how intracellular signalling can be assessed by sEV analysis instead of directly obtaining the cell of origin itself. Our findings revealed that sEV cargo clearly reflects its cell of origin with proteins of the PI3K-AKT pathway highly represented in sEVs. Proteins known to be involved in CRC were detected in both cells and sEVs including KRAS, ARAF, mTOR, PDPK1 and MAPK1, while TGFB1 and TGFBR2, known to be key players in epithelial cancer carcinogenesis, were found to be enriched in sEVs. Furthermore, the phosphopeptide-enriched profiling of cell lysates demonstrated a distinct pattern between cell lines and highlighted potential phosphoproteomic targets to be investigated in sEVs. The total proteomic and phosphoproteomics profiles described in the current work can serve as a source to identify candidates for cancer biomarkers that can potentially be assessed from liquid biopsies.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"11 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2023-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9844407/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10555094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice.","authors":"Ankita Punetha,&nbsp;Deepak Kotiya","doi":"10.3390/proteomes11010002","DOIUrl":"10.3390/proteomes11010002","url":null,"abstract":"<p><p>Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset and progression involve multiple dysregulated proteoforms and their downstream signaling pathways. These are modulated by various factors such as molecular, genetic, tissue, cellular, ethnic/racial, socioeconomic status, environmental, and demographic differences that vary with time. The knowledge of cancer has improved the treatment and clinical management; however, the survival rates have not increased significantly, and cancer remains a major cause of mortality. Oncoproteomics studies help to develop and validate proteomics technologies for routine application in clinical laboratories for (1) diagnostic and prognostic categorization of cancer, (2) real-time monitoring of treatment, (3) assessing drug efficacy and toxicity, (4) therapeutic modulations based on the changes with prognosis and drug resistance, and (5) personalized medication. Investigation of tumor-specific proteomic profiles in conjunction with healthy controls provides crucial information in mechanistic studies on tumorigenesis, metastasis, and drug resistance. This review provides an overview of proteomics technologies that assist the discovery of novel drug targets, biomarkers for early detection, surveillance, prognosis, drug monitoring, and tailoring therapy to the cancer patient. The information gained from such technologies has drastically improved cancer research. We further provide exemplars from recent oncoproteomics applications in the discovery of biomarkers in various cancers, drug discovery, and clinical treatment. Overall, the future of oncoproteomics holds enormous potential for translating technologies from the bench to the bedside.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"11 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2023-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9844371/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10541401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Need for Biomarkers in the ALS-FTD Spectrum: A Clinical Point of View on the Role of Proteomics.","authors":"Francesca Vignaroli,&nbsp;Angelica Mele,&nbsp;Giacomo Tondo,&nbsp;Veronica De Giorgis,&nbsp;Marcello Manfredi,&nbsp;Cristoforo Comi,&nbsp;Letizia Mazzini,&nbsp;Fabiola De Marchi","doi":"10.3390/proteomes11010001","DOIUrl":"https://doi.org/10.3390/proteomes11010001","url":null,"abstract":"<p><p>Frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) are severely debilitating and progressive neurodegenerative disorders. A distinctive pathological feature of several neurodegenerative diseases, including ALS and FTD, is the deposition of aberrant protein inclusions in neuronal cells, which leads to cellular dysfunction and neuronal damage and loss. Despite this, to date, the biological process behind developing these protein inclusions must be better clarified, making the development of disease-modifying treatment impossible until this is done. Proteomics is a powerful tool to characterize the expression, structure, functions, interactions, and modifications of proteins of tissue and biological fluid, including plasma, serum, and cerebrospinal fluid. This protein-profiling characterization aims to identify disease-specific protein alteration or specific pathology-based mechanisms which may be used as markers of these conditions. Our narrative review aims to highlight the need for biomarkers and the potential use of proteomics in clinical practice for ALS-FTD spectrum disorders, considering the emerging rationale in proteomics for new drug development. Certainly, new data will emerge in the near future in this regard and support clinicians in the development of personalized medicine.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"11 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2023-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9844364/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10555101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-Omics of <i>Corynebacterium Pseudotuberculosis</i> 12CS0282 and an In Silico Reverse Vaccinology Approach Reveal Novel Vaccine and Drug Targets.","authors":"Jens Möller,&nbsp;Mona Bodenschatz,&nbsp;Vartul Sangal,&nbsp;Jörg Hofmann,&nbsp;Andreas Burkovski","doi":"10.3390/proteomes10040039","DOIUrl":"https://doi.org/10.3390/proteomes10040039","url":null,"abstract":"<p><p><i>Corynebacterium pseudotuberculosis</i> is an important animal pathogen, which is also able to infect humans. An optimal treatment of infections with this pathogen is not available today and consequently, more research is necessary to understand the infection process. Here, we present a combined -omics and bioinformatics approach to characterize <i>C. pseudotuberculosis</i> 12CS0282. The genome sequence of strain 12CS0282 was determined, analyzed in comparison with the available 130 <i>C. pseudotuberculosis</i> sequences and used as a basis for proteome analyses. In a reverse vaccinology approach, putative vaccine and drug targets for 12CS0208 were identified. Mass spectrometry analyses revealed the presence of multiple virulence factors even without host contact. In macrophage interaction studies, <i>C. pseudotuberculosis</i> 12CS0282 was highly resistant against human phagocytes and even multiplied within human THP-1 cells. Taken together, the data indicate a high pathogenic potential of the strain.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"10 4","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9784263/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10427698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impact of CHIKV Replication on the Global Proteome of <i>Aedes albopictus</i> Cells.","authors":"Ramesh Kumar,&nbsp;Divya Mehta,&nbsp;Sakshi Chaudhary,&nbsp;Debasis Nayak,&nbsp;Sujatha Sunil","doi":"10.3390/proteomes10040038","DOIUrl":"https://doi.org/10.3390/proteomes10040038","url":null,"abstract":"<p><p>Arboviruses are some of the important causative agents of mosquito-mediated viral diseases. These viruses are transmitted between vector and host during the blood meal. Upon viral entry, host replication machinery is hijacked, supporting new virus particle production and thereby allowing viral survival in the host. In this process, host proteins interact with viral proteins to either facilitate viral replication, or they may provide antiviral defense mechanisms. In this study, we analyzed the impact of chikungunya virus (CHIKV) infection on the global proteome of Dicer active <i>Aedes albopictus</i> cells during the early and late time points of infection. We utilized a bottom-up approach of global proteomics analysis, and we used label-free quantitative mass spectrometry to identify the global protein signatures of <i>Ae. albopictus</i> at two different time points upon CHIKV infection. The mass spectrometry data analysis of the early time point revealed that proteins belonging to pathways such as translation, RNA processing, and cellular metabolic processes were less in abundance, whereas those belonging to pathways such as cellular catabolic process and organic substance transport were significantly abundant. At later time points, proteins belonging to pathways such as cellular metabolic processes, primary metabolic process, organonitrogen compound metabolic process, and organic substance metabolic process were found to be decreased in their presence, whereas those belonging to pathways such as RNA processing, gene expression, macromolecule metabolic processing, and nitrogen compound metabolic processing were found to be abundant during CHIKV infection, indicating that modulation in gene expression favoring cell survival occurs at a later time point, suggesting a survival strategy of <i>Aedes</i> cells to counter prolonged CHIKV infection.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"10 4","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9680348/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10689970","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Salivary Biomarkers in Oral Squamous Cell Carcinoma: A Proteomic Overview.","authors":"Gabriele Riccardi,&nbsp;Mario Giuseppe Bellizzi,&nbsp;Irene Fatuzzo,&nbsp;Federica Zoccali,&nbsp;Luca Cavalcanti,&nbsp;Antonio Greco,&nbsp;Marco de Vincentiis,&nbsp;Massimo Ralli,&nbsp;Marco Fiore,&nbsp;Carla Petrella,&nbsp;Antonio Minni,&nbsp;Christian Barbato","doi":"10.3390/proteomes10040037","DOIUrl":"https://doi.org/10.3390/proteomes10040037","url":null,"abstract":"<p><strong>Background: </strong>Oral squamous cell carcinoma (OSCC) is one of the most frequent cancers worldwide. Endoscopic methods may be useful in the evaluation of oral injuries even though the diagnostic gold standard is a biopsy. Targeted screenings could be considered the best way to prevent the occurrence of oral cancer. Aimed to elucidate the potential identification of specific biomarkers of OSCC, the use of saliva is convenient and noninvasive. Many studies reported more than a hundred putative saliva biomarkers for OSCC, and proteogenomic approaches were fundamental to disclosing this issue.</p><p><strong>Methods: </strong>Relevant literature published in the last few years was systematically searched on PubMed and we focused on articles about the use and study of salivary biomarkers in the diagnostics of head and neck cancer (n = 110). Thereafter, we performed a selection focusing on diagnosis with salivary proteomics in OSCC (n = 8).</p><p><strong>Results: </strong>Saliva proteomics can be a source of biomarkers for OSCC. We reviewed literature of biomarker proteins in saliva that could also be evaluated as probable targets for non-invasive screening of oral neoplasm such as cytokines, matrix metalloproteinases, and acute-phase response proteins.</p><p><strong>Conclusions: </strong>The measurement of salivary biomarkers is a highly hopeful technique for the diagnosis of OSCC. Proteogenomic approaches could permit an accurate and early diagnosis of OSCC. This review seeks to generate an up-to-date view on translational OSCC issues by raising awareness of researchers, physicians, and surgeons. Renewed clinical studies, which will validate the sensitivity and specificity of salivary biomarkers, are necessary to translate these results into possible strategies for early diagnosis of OSCC, thus improving patient outcomes.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"10 4","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9680331/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10689972","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}