Journal of proteomics最新文献

{"title":"Urinary proteomics for noninvasive monitoring of biomarkers of chronic mountain sickness in a young adult population using data-independent acquisition (DIA)-based mass spectrometry","authors":"Kaiyuan Fan ,&nbsp;Jin Wang ,&nbsp;Wenqing Zhu ,&nbsp;Xinan Zhang ,&nbsp;Feng Deng ,&nbsp;Yan Zhang ,&nbsp;Shuang Zou ,&nbsp;Lingjia Kong ,&nbsp;He Shi ,&nbsp;Ziling Li ,&nbsp;Guozheng Shen ,&nbsp;Dong Wang ,&nbsp;Zhidong Wu ,&nbsp;Heng Li ,&nbsp;Zhongwei Xu","doi":"10.1016/j.jprot.2024.105195","DOIUrl":"10.1016/j.jprot.2024.105195","url":null,"abstract":"<div><p>Different populations exhibit varying pathophysiological responses to plateau environments. Therefore, it is crucial to identify molecular markers in body fluids with high specificity and sensitivity to aid in determination. Proteomics offers a fresh perspective for investigating protein changes linked to diseases. We utilize urine as a specific biomarker for early chronic mountain sickness (CMS) detection, as it is a simple-to-collect biological fluid. We collected urine samples from three groups: plains health, plateau health and CMS. Using DIA's proteomic approach, we found differentially expressed proteins between these groups, which will be used as a basis for future studies to identify protein markers. Compared with the healthy plain population, 660 altering proteins were identified in plateau health, which performed the resistance to altitude response function by boosting substance metabolism and reducing immune stress function. Compared to the healthy plateau population, the CMS group had 140 different proteins identified, out of which 8 were potential biomarkers for CMS. Our study has suggested that CMS may be closely related to increased thyroid hormone levels, oxidative damage to the mitochondria, impaired cell detoxification function and inhibited hydrolase activity.</p></div><div><h3>Significance</h3><p>Our team has compiled a comprehensive dataset of urine proteomics for AMS disease. We successfully identified differentially expressed proteins between healthy and AMS groups using the DIA proteomic approach. We discovered that 660 proteins were altered in plateau health compared to the healthy plain population, resulting in a heightened resistance to altitude response function by boosting substance metabolism and reducing immune stress function. Additionally, we pinpointed 140 different proteins in the AMS group compared to the healthy plateau population, with 8 showing potential as biomarkers for AMS. Our findings suggest that the onset of AMS may be closely linked to increased thyroid hormone levels, oxidative damage to the mitochondria, impaired cell detoxification function and inhibited hydrolase activity.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1874391924001271/pdfft?md5=4bfdc9f1afbaf67309674e942c4a6136&pid=1-s2.0-S1874391924001271-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140908345","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}

{"title":"Proteomic profiling of FFPE specimens: Discovery of HNRNPA2/B1 and STT3B as biomarkers for determining formalin fixation durations","authors":"Go Kobayashi ,&nbsp;Reiko Ito ,&nbsp;Masataka Taga ,&nbsp;Kazuaki Koyama ,&nbsp;Shiho Yano ,&nbsp;Tatsuya Endo ,&nbsp;Tsutomu Kai ,&nbsp;Takushi Yamamoto ,&nbsp;Takuya Hiratsuka ,&nbsp;Tatsuaki Tsuruyama","doi":"10.1016/j.jprot.2024.105196","DOIUrl":"10.1016/j.jprot.2024.105196","url":null,"abstract":"<div><p>Recent advancements in proteomics technologies using formalin-fixed paraffin-embedded (FFPE) samples have significantly advanced biomarker discovery. Yet, the effects of varying sample preparation protocols on proteomic analyses remain poorly understood. We analyzed mouse liver FFPE samples that varied in fixatives, fixation duration, and storage temperature using LC/MS. We found that variations in fixation duration significantly affected the abundance of specific proteins, showing that HNRNPA2/B1 demonstrated a significant decrease in abundance in samples fixed for long periods, whereas STT3B exhibited a significant increase in abundance in samples fixed for long durations. These findings were supported by immunohistochemical analysis across liver, spleen, and lung tissues, demonstrating a significant decrease in the nuclear staining of HNRNPA2/B1 in long-duration acid formalin(AF)-fixed FFPE samples, and an increase in cytoplasmic staining of STT3B in long-duration neutral buffered formalin-fixed liver and lung tissues and granular staining in all long-duration AF-fixed FFPE tissue types. Similar trends were observed in the long-duration fixed HeLa cells. These results demonstrate that fixation duration critically affects the proteomic integrity of FFPE samples, emphasizing the urgent need for standardized fixation protocols to ensure consistent and reliable proteomic data.</p></div><div><h3>Significance</h3><p>The quality of FFPE samples is primarily influenced by the fixation and storage conditions. However, previous studies have mainly focused on their impact on nucleic acids and the extent to which different fixation conditions affect changes in proteins has not been evaluated. In addition, to our knowledge, proteomic research focusing on differences in formalin fixation conditions has not yet been conducted. Here, we analyzed FFPE samples with different formalin fixation and storage conditions using LC/MS and evaluated the impact of different fixation conditions on protein variations. Our study unequivocally established formalin fixation duration as a critical determinant of protein variation in FFPE specimens and successfully identified HNRNPA2/B1 and STT3B as potential biomarkers for predicting formalin fixation duration for the first time. The study findings open new avenues for quality assessment in biomedical research and diagnostics.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1874391924001283/pdfft?md5=f82fe44151223200d64f8782635d2348&pid=1-s2.0-S1874391924001283-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140898218","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}

{"title":"A novel proteomic approach for the identification and relative quantification of disulfide-bridges in the human milk proteome","authors":"Martin Nørmark Thesbjerg ,&nbsp;Ulrik Kræmer Sundekilde ,&nbsp;Nina Aagaard Poulsen ,&nbsp;Lotte Bach Larsen ,&nbsp;Søren Drud-Heydary Nielsen","doi":"10.1016/j.jprot.2024.105194","DOIUrl":"10.1016/j.jprot.2024.105194","url":null,"abstract":"<div><p>This study explores the disulfide bridges present in the human milk proteome by a novel approach permitting both positional identification and relative quantification of the disulfide bridges. Human milk from six donors was subjected to trypsin digestion without reduction. The digested human milk proteins were analyzed by nanoLC-timsTOF Pro combined with data analysis using xiSEARCH. A total of 85 unique disulfide bridges were identified in 25 different human milk proteins. The total relative abundance of disulfide bridge-containing peptides constituted approximately 5% of the total amount of tryptic-peptides. Seven inter-molecular disulfide bridges were identified between either α-lactalbumin and lactotransferrin (5) or α_S1-casein and κ-casein (2). All cysteines involved in the observed disulfide bridges of α-lactalbumin and lactotransferrin were mapped onto protein models using AlphaFold2 Multimer to estimate the length of the observed disulfide bridges. The lengths of the disulfide bridges of lactotransferrin indicate a potential for multi- or poly-merization of lactotransferrin. The high number of intramolecular lactotransferrin disulfide bridges identified, suggests that these are more heterogeneous than previously presumed.</p></div><div><h3>Significance</h3><p>Disulfide-bridges in the human milk proteome are an often overseen post-transaltional modification. Thus, mapping the disulfide-bridges, their positions and relative abundance, are valuable new knowledge needed for an improved understanding of human milk protein behaviour. Although glycosylation and phosphorylation have been described, even less information is available on the disulfide bridges and the disulfide-bridge derived protein complexes. This is important for future work in precision fermentation for recombinant production of human milk proteins, as this will highlight which disulfide-bridges are naturally occouring in human milk proteins. Further, this knowledge would be of value for the infant formula industry as it provides more information on how to humanize bovine-milk based infant formula. The novel method developed here can be broadly applied in other biological systems as the disulfid-brigdes are important for the structure and functionality of proteins.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S187439192400126X/pdfft?md5=83da810057743f85f09d32e16f9317ca&pid=1-s2.0-S187439192400126X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140898251","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}

{"title":"Comparative proteomics analysis of samples from hepatic cystic echinococcosis patients using data-independent acquisition approach","authors":"Kahaer Tuerxun ,&nbsp;Rong-Hua Tang ,&nbsp;Aabudouxikuer Abudoumijiti ,&nbsp;Zainuer Yusupu ,&nbsp;Aizemaiti Aikebaier ,&nbsp;Salamu Mijiti ,&nbsp;Irshat Ibrahim ,&nbsp;Yan-Long Cao ,&nbsp;Abudoukeyimu Yasheng ,&nbsp;Yuan-Quan Wu","doi":"10.1016/j.jprot.2024.105191","DOIUrl":"https://doi.org/10.1016/j.jprot.2024.105191","url":null,"abstract":"<div><p>Cystic echinococcosis is a zoonotic disease resulting from infection caused by the larval stage of <em>Echinococcus granulosus</em>. This study aimed to assess the specific proteins that are potential candidates for the development of a vaccine against <em>E. granulosus</em>. The data-independent acquisition approach was employed to identify differentially expressed proteins (DEPs) in <em>E. granulosus</em> samples. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was employed to identify several noteworthy proteins. <strong>Results:</strong> The DEPs in <em>E. granulosus</em> samples were identified (245 pericystic wall <em>vs.</em> parasite-free yellowish granuloma (PYG, 1725 PY <em>vs.</em> PYG, 2274 PN <em>vs.</em> PYG). Further examination of these distinct proteins revealed their predominant enrichment in metabolic pathways, amyotrophic lateral sclerosis, and neurodegeneration-associated pathways. Notably, among these DEPs, SH3BGRL, MST1, TAGLN2, FABP5, UBE2V2, and RARRES2 exhibited significantly higher expression levels in the PYG group compared with the PY group (<em>P</em> &lt; 0.05). The findings may contribute to the understanding of the pathological mechanisms underlying echinococcosis, providing valuable insights into the development of more effective diagnostic tools, treatment modalities, and preventive strategies.</p></div><div><h3>Significance</h3><p>CE is a major public health hazard in the western regions of China, Central Asia, South America, the Mediterranean countries, and eastern Africa. Echinococcus granulosus is responsible for zoonotic disease through infection Our analysis focuses on the proteins in various samples by data-dependent acquisition (DIA) for proteomic analysis. The importance of this research is to develop new strategies and targets to protect against <em>E. granulosus</em> infections in humans.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140844150","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}

{"title":"Calpain 8 as a potential biomarker regulates the progression of pancreatic cancer via EMT and AKT/ERK pathway","authors":"Na Song ,&nbsp;Kai Cui ,&nbsp;Liqun Zeng ,&nbsp;Yanwu Fan ,&nbsp;Ziwei Wang ,&nbsp;Pingyu Shi ,&nbsp;Wei Su ,&nbsp;Haijun Wang","doi":"10.1016/j.jprot.2024.105182","DOIUrl":"https://doi.org/10.1016/j.jprot.2024.105182","url":null,"abstract":"<div><p>Calpain is a non-lysozyme, calcium-dependent intracellular cysteine protease that has been shown to play a role in tumor proliferation, survival, migration, invasion, and apoptosis. Dysregulation of calpain expression is closely related to tumorigenesis. However, the role of calpain-8 (CAPN8), as a member of the calpain family, in pancreatic cancer (PC) is remains unclear. In elucidating the mechanism of CAPN8 in PC, a comprehensive bioinformatics analysis and in vitro experiments were conducted. The TCGA database was used to explore the expression level of CAPN8, and the results in PC tissues and cell lines were verified. Then, the correlation between CAPN8 and clinicopathological features was analyzed. Additionaly, promoter methylation, immune infiltration, and GO/KEGG enrichment analyses were performed. Lastly, the molecular mechanism of CAPN8 in PC was investigated by using cell counting kit (CCK) 8, transwell, wound healing, Western blot assays, and so on. Results indicate that CAPN8 was highly expressed in PC and correlated with poor prognosis and advanced TNM stage. In addition, a low level of immune infiltration was closely associated with the high expression level of CAPN8. Based on these findings, we hypothesized that CAPN8 is a potential biomarker that regulates progression of PC via EMT and the AKT/ERK pathway.</p></div><div><h3>Significance</h3><p>Through comprehensive biological information and in vitro experiments, CAPN8 has been confirmed to play an important role in regulating pancreatic cancer (PC) proliferation, migration and invasion. CAPN8 is found to be closely related to the diagnosis, survival and prognosis of PC. Above all, CAPN8 may be a potential biomarker for the diagnosis and prognosis of PC.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140824404","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}

{"title":"Integrative proteomic and transcriptomic analysis in the female goat ovary to explore the onset of puberty","authors":"Ping Qin ,&nbsp;Zhihao Pan ,&nbsp;Wei Zhang ,&nbsp;Rui Wang ,&nbsp;Xiaoqian Li ,&nbsp;Juntai Lu ,&nbsp;Shuangshuang Xu ,&nbsp;Xinbao Gong ,&nbsp;Jing Ye ,&nbsp;Xu Yan ,&nbsp;Ya Liu ,&nbsp;Yunsheng Li ,&nbsp;Yunhai Zhang ,&nbsp;Fugui Fang","doi":"10.1016/j.jprot.2024.105183","DOIUrl":"https://doi.org/10.1016/j.jprot.2024.105183","url":null,"abstract":"<div><p>Puberty is considered a prerequisite for affecting reproductive performance and productivity. Little was known about molecular changes in pubertal goat ovaries. Therefore, we measured and performed a correlation analysis of the mRNA and proteins changes in the pre-pubertal and pubertal goat ovaries. The results showed that only six differentially expressed genes and differentially abundant proteins out of 18,139 genes and 7550 proteins quantified had significant correlations. <em>CNTN2</em> and <em>THBS1</em>, discovered in the mRNA-mRNA interaction network, probably participated in pubertal and reproductive regulation by influencing GnRH receptor signals, follicular development, and ovulation. The predicted core transcription factors may either promote or inhibit the expression of reproductive genes and act synergistically to maintain normal reproductive function in animals. The interaction between PKM and TIMP3 with other proteins may impact animal puberty through energy metabolism and ovarian hormone secretion. Pathway enrichment analyses revealed that the co-associated key pathways between ovarian genes and proteins at puberty included calcium signalling pathway and olfactory transduction. These pathways were associated with gonadotropin-releasing hormone synthesis and secretion, signal transmission, and cell proliferation. In summary, these results enriched the potential molecules and signalling pathways that affect puberty and provided new insights for regulating and promoting the onset of puberty.</p></div><div><h3>Significance</h3><p>This study conducted the first transcriptomic and proteomic correlation analysis of pre-pubertal and pubertal goat ovaries and identified six significantly correlated molecules at both the gene and protein levels. Meanwhile, we were drawn to several molecules and signalling pathways that may play a regulatory role in the onset of puberty and reproduction by influencing reproductive-related gene expression, GnRH receptor signals, energy metabolism, ovarian hormone secretion, follicular development, and ovulation. This information contributed to identify potential biomarkers in pubertal goat ovaries, which was vital for predicting the onset of puberty and improving livestock performance.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140824403","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}

{"title":"Proteomic analysis revealed that the oomyceticide phosphite exhibits multi-modal action in an oomycete pathosystem","authors":"Christina E. Andronis ,&nbsp;Silke Jacques ,&nbsp;Francisco J. Lopez-Ruiz ,&nbsp;Richard Lipscombe ,&nbsp;Kar-Chun Tan","doi":"10.1016/j.jprot.2024.105181","DOIUrl":"10.1016/j.jprot.2024.105181","url":null,"abstract":"<div><p>Phytopathogenic oomycetes constitute some of the most devastating plant pathogens and cause significant crop and horticultural yield and economic losses. The phytopathogen <em>Phytophthora cinnamomi</em> causes dieback disease in native vegetation and several crops. The most commonly used chemical to control <em>P. cinnamomi</em> is the oomyceticide phosphite. Despite its widespread use, the mode of action of phosphite is not well understood and it is unclear whether it targets the pathogen, the host, or both. Resistance to phosphite is emerging in <em>P. cinnamomi</em> isolates and other oomycete phytopathogens. The mode of action of phosphite on phosphite-sensitive and resistant isolates of the pathogen and through a model host was investigated using label-free quantitative proteomics. <em>In vitro</em> treatment of sensitive <em>P. cinnamomi</em> isolates with phosphite hinders growth by interfering with metabolism, signalling and gene expression; traits that are not observed in the resistant isolate. When the model host <em>Lupinus angustifolius</em> was treated with phosphite, proteins associated with photosynthesis, carbon fixation and lipid metabolism in the host were enriched. Increased production of defence-related proteins was also observed in the plant. We hypothesise the multi-modal action of phosphite and present two models constructed using comparative proteomics that demonstrate mechanisms of pathogen and host responses to phosphite.</p></div><div><h3>Significance</h3><p><em>Phytophthora cinnamomi</em> is a significant phytopathogenic oomycete that causes root rot (dieback) in a number of horticultural crops and a vast range of native vegetation. Historically, areas infected with phosphite have been treated with the oomyceticide phosphite despite its unknown mode of action. Additionally, overuse of phosphite has driven the emergence of phosphite-resistant isolates of the pathogen. We conducted a comparative proteomic study of a sensitive and resistant isolate of <em>P. cinnamomi</em> in response to treatment with phosphite, and the response of a model host, <em>Lupinus angustifolius,</em> to phosphite and its implications on infection. The present study has allowed for a deeper understanding of the bimodal action of phosphite, suggested potential biochemical factors contributing to chemical resistance in <em>P. cinnamomi</em>, and unveiled possible drivers of phosphite-induced host plant immunity to the pathogen.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1874391924001131/pdfft?md5=d90b2cfd99b96d215e05dd0e91ce1bae&pid=1-s2.0-S1874391924001131-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140773614","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}

{"title":"Screening of lung cancer serum biomarkers based on Boruta-shap and RFC-RFECV algorithms","authors":"Guangcheng Yue","doi":"10.1016/j.jprot.2024.105180","DOIUrl":"10.1016/j.jprot.2024.105180","url":null,"abstract":"<div><h3>Objective</h3><p>This study aimed to identify a set of serum miRNAs as potential biomarkers for lung cancer diagnosis using algorithmic approaches.</p></div><div><h3>Methods</h3><p>Serum miRNA expression data from lung cancer patients and non-tumor controls were obtained. The top six miRNAs were selected using Boruta-shap and RFC-RFECV algorithms. A Gaussian Naive Bayes (NB) classifier was trained and evaluated using cross-validation, ROC curve analysis, and evaluation metrics.</p></div><div><h3>Results</h3><p>Six miRNAs (hsa-miRNA-144, hsa-miRNA-107, hsa-miRNA-484, hsa-miRNA-103, hsa-miRNA-26b, and hsa-miRNA-641) were identified as feature genes. The NB classifier achieved an area under curve (AUC) of 0.8966 and a mean AUC of 0.88 in cross-validation. Accuracy, recall, and F1 scores exhibited promising results, with an accuracy of 82%. In the validation set, the AUC values for the NB and SVC classifiers were 0.9345 and 0.9423, respectively, with a mean AUC of 0.95 in cross-validation. The classifiers demonstrated an accuracy of 89% in diagnosing lung cancer.</p></div><div><h3>Conclusion</h3><p>This study identified a panel of six serum miRNAs with potential as non-invasive biomarkers for lung cancer diagnosis. These miRNAs show promise in providing sensitive and specific tools for detecting lung cancer.</p></div><div><h3>Significance</h3><p>Lung cancer is one of the top cancers worldwide, threatening the health and lives of tens of thousands of people. miRNA is a biomarker, which can be used as a potential clinical tool for diagnosis and prognosis of cancer patients. Therefore, the use of multiple miRNAs to construct diagnostic models may be one of the future methods of accurate diagnosis of lung cancer. In this study, we used the Boruta-shap and RFC-RFECV algorithms to automatically identify and extract characteristic miRNAs highly associated with lung cancer, thereby establishing an accurate classifier for the diagnosis of lung cancer with characteristic miRNAs.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140784185","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}

{"title":"Delineating molecular regulatory network of meat quality of longissimus dorsi indicated by transcriptomic, proteomic, and metabolomics analysis in rabbit","authors":"Liangde Kuang ,&nbsp;Jianhong Zeng ,&nbsp;Yuying Li ,&nbsp;Jie Zheng ,&nbsp;Yongjun Ren ,&nbsp;Zhiqiang Guo ,&nbsp;Xiangyu Zhang ,&nbsp;Cuixia Zhang ,&nbsp;Chao Yang ,&nbsp;Xiuli Mei ,&nbsp;Rui Yang ,&nbsp;Li Tang ,&nbsp;Yang Ji ,&nbsp;Xiaohong Xie ,&nbsp;Min Lei ,&nbsp;Congyan Li","doi":"10.1016/j.jprot.2024.105179","DOIUrl":"10.1016/j.jprot.2024.105179","url":null,"abstract":"<div><p>This study aims to investigate the potential regulatory network responsible for the meat quality using multi-omics to help developing better varieties. Slaughter performance and meat quality of Shuxing No.1 rabbit outperformed IRA rabbit according to the tested rabbit parameters. Differentially expressed genes (DEGs) and differentially abundance proteins (DAPs) were involved in meat quality-related pathways, such as PI3K − Akt and MAPK signaling pathways. Only SMTNL1 and PM20D2 shared between DEGs and DAPs. Olfactory-sensitive undecanal, a differentially abundant metabolite (DAM) in volatilomics (vDAMs), correlated with all of the remaining 11 vDAMs, and most of 12 vDAMs were associated with amino acid metabolism. Integration revealed that 829 DEGs/DAPs were associated with 15 DAMs in four KEGG pathways, such as melatonin (a DAM in widely targeted metabolomics) was significantly positively correlated with ALDH and negatively correlated with RAB3D and CAT in the tryptophan metabolism pathway. This study sheds light on the potential mechanisms that contribute to the improved meat quality and flavor.</p></div><div><h3>Significance</h3><p>Shuxing No.1 rabbit is a new breed of meat rabbit in the Chinese market. In meat marketing, meat quality usually determines the purchase intention of consumers. Determining the biological and molecular mechanisms of meat quality in meat rabbit is essential for developing strategies to improve meat quality. According to the tested rabbit parameters, this study ascertained that the slaughter performance and meat quality of Shuxing No.1 rabbit surpasses that of IRA rabbit. The present study profiled the transcriptome, proteome, widely targeted metabolome, and volatilome of longissimus dorsi from Shuxing No.1 rabbit and IRA rabbit. The study found that meat quality and flavor-related tryptophan metabolism pathway is enriched with many DEGs/DAPs (including ALDH, RAB3D, and CAT), as well as a DAM, melatonin. This study sheds light on the potential mechanisms that contribute to the improved meat quality and flavor.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140785617","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}

{"title":"Insights into the differential proteome landscape of a newly isolated Paramecium multimicronucleatum in response to cadmium stress","authors":"Itrat Zahra ,&nbsp;Lauren DeVine ,&nbsp;Robert Cole ,&nbsp;Hafiza Aroosa Malik ,&nbsp;Jinke Wu ,&nbsp;Junneng Wen ,&nbsp;Amor Hedfi ,&nbsp;Ayesha Liaqat ,&nbsp;Roohi Ijaz ,&nbsp;Uzma Ramzan ,&nbsp;Abdul Rauf Shakoori ,&nbsp;Farah Rauf Shakoori ,&nbsp;Michael J. Betenbaugh","doi":"10.1016/j.jprot.2024.105178","DOIUrl":"https://doi.org/10.1016/j.jprot.2024.105178","url":null,"abstract":"<div><p>Employing microbial systems for the bioremediation of contaminated waters represent a potential option, however, limited understanding of the underlying mechanisms hampers the implication of microbial-mediated bioremediation. The omics tools offer a promising approach to explore the molecular basis of the bioremediation process. Here, a mass spectrometry-based quantitative proteome profiling approach was conducted to explore the differential protein levels in cadmium-treated <em>Paramecium multimicronucleatum</em>. The Proteome Discoverer software was used to identify and quantify differentially abundant proteins. The proteome profiling generated 7,416 peptide spectral matches, yielding 2824 total peptides, corresponding to 989 proteins. The analysis revealed that 29 proteins exhibited significant (<em>p</em> ≤ 0.05) differential levels, including a higher abundance of 6 proteins and reduced levels of 23 proteins in Cd^<em>2+</em> treated <em>samples.</em> These differentially abundant proteins were associated with stress response, energy metabolism, protein degradation, cell growth, and hormone processing. Briefly, a comprehensive proteome profile in response to cadmium stress of a newly isolated <em>Paramecium</em> has been established that will be useful in future studies identifying critical proteins involved in the bioremediation of metals in ciliates.</p></div><div><h3>Significance</h3><p>Ciliates are considered a good biological indicator of chemical pollution and relatively sensitive to heavy metal contamination. A prominent ciliate, <em>Paramecium</em> is a promising candidate for the bioremediation of polluted water. The proteins related to metal resistance in <em>Paramecium</em> species are still largely unknown and need further exploration. In order to identify and reveal the proteins related to metal resistance in Paramecia, we have reported differential protein abundance in <em>Paramecium multimicronucleatum</em> in response to cadmium stress. The proteins found in our study play essential roles during stress response, hormone processing, protein degradation, energy metabolism, and cell growth. It seems likely that Paramecia are not a simple sponge for metals but they could also transform them into less toxic derivatives or by detoxification by protein binding. This data will be helpful in future studies to identify critical proteins along with their detailed mechanisms involved in the bioremediation and detoxification of metal ions in <em>Paramecium</em> species.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140646635","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}