Journal of proteomics最新文献

{"title":"Multi-omics analysis reveals the regulatory mechanism of branching development in Quercus fabri","authors":"Shifa Xiong ,&nbsp;Liwen Wu ,&nbsp;Yicun Chen ,&nbsp;Xiang Shi ,&nbsp;Yangdong Wang","doi":"10.1016/j.jprot.2024.105373","DOIUrl":"10.1016/j.jprot.2024.105373","url":null,"abstract":"<div><div>The ability of axillary meristems to form axillary buds and subsequently develop into branches is influenced by phytohormones, environmental conditions, and genetic factors. The main trunk of <em>Quercus fabri</em> is prone to branching, which not only impacts the appearance and density of the wood and significantly reduces the yield rate. This study conducted transcriptomic, proteomic, and metabolomic analyses on three stages of axillary bud development in <em>Q. fabri</em>. A total of 12,888 differentially expressed genes (DEGs), 8193 differentially accumulated proteins (DAPs), and 1788 differentially accumulated metabolites (DAMs) were identified through comparisons among the stages and subjected to multi-omics joint analysis. Conduct interaction network analysis on DEGs and DAPs to identify the significant transcription factor family (AP2/ERF) involved in the regulation of axillary bud development. Furthermore, KEGG enrichment analysis of DEGs, DAPs and DAMs indicated significant enrichment in plant hormone signaling pathways. The analysis of endogenous hormone levels and qRT-PCR results for pathway genes demonstrated that the expression levels of IAA and tZ significantly increased during late developmental stages, whereas the expression levels of ABA, ACC and JA significantly decreased. In summary, these findings contribute to a comprehensive understanding of the regulatory networks underlying the branching development of <em>Q. fabri</em>.</div></div><div><h3>Significance</h3><div><em>Q. fabri</em> exhibits robust vegetative growth, and its primary trunk is prone to branching, significantly influencing the wood yield rate. Through a joint analysis of transcriptomics, proteomics, and metabolomics, we comprehensively examined the regulatory network governing the axillary bud development of <em>Q. fabri</em>. Our findings revealed the crucial roles of the AP2/ERF transcription factor family and plant hormone signal transduction pathways in branch development. These insights contribute to a deeper understanding of the mechanisms regulating branch development.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"313 ","pages":"Article 105373"},"PeriodicalIF":2.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142950537","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":"Molecular insights into myelomeningocele via proteomic analysis of amniotic fluid","authors":"Lucie Guilbaud ,&nbsp;Kévin Roger ,&nbsp;Andree Schmidt ,&nbsp;Cerina Chhuon ,&nbsp;Stephan Breimann ,&nbsp;Joanna Lipecka ,&nbsp;Sophie Dreux ,&nbsp;Stephan A. Müller ,&nbsp;Michel Zérah ,&nbsp;Jérôme Larghero ,&nbsp;Jean-Marie Jouannic ,&nbsp;Stefan F. Lichtenthaler ,&nbsp;Ida C. Guerrera","doi":"10.1016/j.jprot.2024.105372","DOIUrl":"10.1016/j.jprot.2024.105372","url":null,"abstract":"<div><div>Despite numerous studies on fetal therapy for myelomeningoceles (MMC), the pathophysiology of this malformation remains poorly understood.</div><div>This study aimed to analyze the biochemical profile and proteome of amniotic fluid (AF) supernatants from MMC fetuses to explore the prenatal pathophysiology.</div><div>Biochemical analysis of 61 AF samples from MMC fetuses was compared with 45 healthy fetuses' samples. Proteome analysis was conducted in 18 MMC and 18 healthy singleton fetuses, and in 5 dichorionic pregnancies with MMC fetuses and their healthy co-twins. ELISA tests were used to validate proteome results.</div><div>Biochemical analysis revealed anal incontinence in 37 % of MMC cases, absent in controls (<em>p</em> &lt; 0.0001). Proteomics identified 2453 quantified proteins with 39 significantly up-regulated and 10 down-regulated in the MMC group. Up-regulated proteins included ectodomains of CHL1, APLP1, SEZ6, SEZ6L, known targets of the protease BACE1. We explored the overlap of neonatal cerebrospinal fluid (CSF) and AF proteome and highlighted 411 proteins in common, mostly upregulated in MMC AF compared to controls.</div><div>Our study thoroughly characterizes the AF proteome and reveals numerous proteins to be changed as a consequence of MMC. Many of these proteins are typical constituents of CSF. No difference in AF inflammation markers were observed between MMC and healthy fetuses.</div></div><div><h3>Significance</h3><div>This study provides good evidence that neuroepithelial destruction in MMC is independent of inflammation or presumed meconium toxicity.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"313 ","pages":"Article 105372"},"PeriodicalIF":2.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142950535","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":"A comprehensive proteomic analysis reveals novel inflammatory biomarkers in intracranial aneurysms","authors":"Siqi Chen ,&nbsp;Ziliang Hu ,&nbsp;Mingyue Zhao ,&nbsp;Jie Sun ,&nbsp;Sheng Nie ,&nbsp;Xiang Gao ,&nbsp;Yi Huang","doi":"10.1016/j.jprot.2025.105374","DOIUrl":"10.1016/j.jprot.2025.105374","url":null,"abstract":"<div><div>Inflammation is a complex factor in the pathogenesis of intracranial aneurysms (IA), but its specific cellular inflammatory factors remain uncertain. We collected two cohorts and measured the representation of vascular inflammation-related proteins using the Olink CVD II Vascular Inflammation Panel. We subsequently validated our findings using ELISA and RT-qPCR. Our proteomic analysis identified 11 vascular inflammation-related markers that were significantly differentially represented between the IA and control groups. These markers were implicated in leukocyte migration, immune response, triglyceride and lipoprotein metabolism, acute phase response, T cell regulation, and several key biological pathways, including PPAR, HIF-1, cytokine-cytokine interactions, and PI3K-AKT signaling. Further validation with ELISA and RT-qPCR confirmed the differential representation of IL6, PTX3, LPL, and OLR1 between the two groups. Notably, a combination marker incorporating these four factors demonstrated high diagnostic potential for the early detection of IA. Our study has identified a set of informative biomarkers (IL6, PTX3, LPL, and OLR1) that could be valuable for the early diagnosis of IA. Importantly, this is the first report of significantly elevated OLR1 representation in the plasma of IA patients. Further investigation into the role of OLR1 in the pathogenesis of IA is warranted.</div></div><div><h3>Significance</h3><div>This study significantly advances our understanding of the molecular mechanisms underlying intracranial aneurysm (IA) pathogenesis. By identifying a panel of novel biomarkers, including the previously unreported elevated expression of OLR1 in IA patients, we provide crucial insights into the inflammatory processes involved in aneurysm formation and development. These findings have important clinical implications, as the identified biomarkers could serve as valuable tools for early diagnosis and potentially targeted therapeutic interventions. Furthermore, the study highlights the complex interplay of inflammatory pathways in IA, suggesting that a multi-faceted approach may be necessary for effective management.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"313 ","pages":"Article 105374"},"PeriodicalIF":2.8,"publicationDate":"2025-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143080457","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":"Cardio-metabolic and cytoskeletal proteomic signatures differentiate stress hypersensitivity in dystrophin-deficient mdx mice","authors":"Gretel S. Major ,&nbsp;Craig W. Herbold ,&nbsp;Flora Cheng ,&nbsp;Albert Lee ,&nbsp;Shuzhao Zhuang ,&nbsp;Aaron P. Russell ,&nbsp;Angus Lindsay","doi":"10.1016/j.jprot.2024.105371","DOIUrl":"10.1016/j.jprot.2024.105371","url":null,"abstract":"<div><div>Extreme heterogeneity exists in the hypersensitive stress response exhibited by the dystrophin-deficient <em>mdx</em> mouse model of Duchenne muscular dystrophy. Because stress hypersensitivity can impact dystrophic phenotypes, this research aimed to understand the peripheral pathways driving this inter-individual variability. Male and female <em>mdx</em> mice were phenotypically stratified into “stress-resistant” or “stress-sensitive” groups based on their response to two laboratory stressors. Quantitative proteomics of striated muscle revealed that stress-resistant females were most dissimilar from all other groups, with over 250 proteins differentially regulated with stress hypersensitivity. Males showed less proteomic variation with stress hypersensitivity; however, these changes were associated with pathway enrichment. In the heart, stress-sensitive males had significant enrichment of pathways related to mitochondrial ATP synthesis, suggesting that increased cardio-metabolic capacity is associated with stress hypersensitivity in male <em>mdx</em> mice. In both sexes, stress hypersensitivity was associated with greater expression of beta-actin-like protein 2, indicative of altered cytoskeletal organisation. Despite identifying proteomic signatures associated with stress hypersensitivity, these did not correlate with differences in the serum metabolome acutely after a stressor. These data suggest that the heterogeneity in stress hypersensitivity in <em>mdx</em> mice is partially driven by cytoskeletal organisation, but that sex-specific cardio-metabolic reprogramming may also underpin this phenotype.</div></div><div><h3>Significance</h3><div>Duchenne muscular dystrophy (DMD) is a fatal muscle wasting disease which is associated with a premature loss of ambulation and neurocognitive dysfunction. The hypersensitive stress response in DMD is a heterogeneous phenotype which is poorly understood. This study provided the first investigation of the peripheral mechanisms regulating the hypersensitive stress response by undertaking multi-omics analysis of phenotypically stratified <em>mdx</em> mice. Variations in behaviour and the striated muscle proteomic profiles suggest that cardio-metabolic remodelling and cytoskeletal organisation may contribute to this phenotype. This research offers significant insights into understanding how peripheral dystrophin deficiency relates to the cognitive abnormalities seen in patients with DMD.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"312 ","pages":"Article 105371"},"PeriodicalIF":2.8,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142895528","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":"Untargeted fast proteomics analysis using UPLC-Orbitrap HRMS for halal authentication of meat and meat products","authors":"Suratno Suratno ,&nbsp;Anjar Windarsih ,&nbsp;Ayu Septi Anggraeni ,&nbsp;Lucky Prabowo Miftachul Alam ,&nbsp;Hendy Dwi Warmiko ,&nbsp;Siti Nurul Aisyiyah Jenie ,&nbsp;Hilda Novianty ,&nbsp;Yaya Ihya Ulumuddin ,&nbsp;Ade Marmita ,&nbsp;Ni Putu Sri Ayuni ,&nbsp;Anastasia Wheni Indrianingsih ,&nbsp;Abdul Rohman","doi":"10.1016/j.jprot.2024.105369","DOIUrl":"10.1016/j.jprot.2024.105369","url":null,"abstract":"<div><div>The authenticity of halal meat is a global issue because pork adulteration occurs. Certain religions, such as Islam and Judaism, prohibit the use of pork in food products. The purpose of this study was to evaluate the volume of trypsin with 10, 50 and 100 μL (20 μg/100 μL) and the digestion time from overnight to 30–120 min to establish a fast and straightforward procedure on proteomic analysis for halal authentication of meat and meat products. The method was applied to raw meat and processed pork products. The results show that 30 min digestion time and 50 μL of trypsin could detect specific peptides from pork. The proteins such as L-lactate dehydrogenase (D2SW96), haemoglobin subunit beta (F1RII7), carbonic anhydrase (A0A4XIUCS1), and myosin-1 (A0A481AX92) could be the alternative protein that contains specific peptide from pork that could be used as peptide biomarker in raw pork meat. Two peptides from haemoglobin subunit beta (F1RII7) protein heat stable peptide biomarkers were not previously reported. The method is proven for fast analysis, simple protein extraction, and rapid identification of specific pork peptides in raw meat and processed pork products.</div></div><div><h3>Significance</h3><div>The authenticity of halal meat is a global issue because pork adulteration occurs. Certain religions, such as Islam and Judaism, prohibit the use of pork in food products. Pork is frequently used as an adulterant in high-quality, high-priced meats such as beef, fish meat slices, lamb, or other meat to increase profits because pork is less expensive than the other meats. The purpose of this study was to evaluate the volume of trypsin and the digestion time to establish a fast and straightforward procedure on proteomic analysis for halal authentication of meat and meat products. The results show that 30 min digestion time and 50 μL of trypsin could detect specific peptides from pork. The proteins such as L-lactate dehydrogenase (D2SW96), haemoglobin subunit beta (F1RII7), carbonic anhydrase (A0A4XIUCS1), and myosin-1 (A0A481AX92) could be the alternative protein that contains specific peptide from pork that could be used as peptide biomarker in raw pork meat. To the best of our knowledge, this is the first report that studied on fast analysis, simple protein extraction, and rapid identification of specific pork peptides in raw meat and processed pork products.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"312 ","pages":"Article 105369"},"PeriodicalIF":2.8,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142895533","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":"A scoping review of circulating peptides assessments in anorexia nervosa: Uncovering diversity and nuanced findings","authors":"Sandra Doua ,&nbsp;Natacha Germain ,&nbsp;Amale Geandrot ,&nbsp;Cloé Defour ,&nbsp;Aurélia Gay ,&nbsp;Catherine Massoubre ,&nbsp;Francois Lang ,&nbsp;Bruno Estour ,&nbsp;Bogdan Galusca","doi":"10.1016/j.jprot.2024.105370","DOIUrl":"10.1016/j.jprot.2024.105370","url":null,"abstract":"<div><div>Understanding biological mechanisms underlying anorexia nervosa (AN) is necessary to develop care strategies. Despite many articles dedicated to peptides assessment in AN, there is no systematic review. A scoping review of circulating peptides published in relation to AN, comparing their results with those of controls, was conducted. Embase and PubMed databases were search from 1966 to 2022 (PROSPERO CRD42022323716). All original English articles, assessing peptides in AN (except classical markers) were analyzed. 1151 studies for 207 peptides, in 486 published articles were selected, and evidences/trends in AN were compared to controls. Fifteen clusters of function gathering peptides covering physiopathological aspects of AN were identified. This scoping review revealed a large variety of circulating peptides explored in AN. Some peptides presented with convincing results and helped understanding pathophysiologic aspects. Other peptides presented with nuanced results, partly due to insufficient number of studies, multiple assay techniques, inadequate sampling time, and lack of phenotyping. Conversion from bench-to-bed remains difficult and may explain why peptides evaluations did not currently lead to specific international recommendations or tailored therapeutic/preventive strategies. Peptide evaluation in anorexia nervosa could explore secretion profiles, and test it in well-phenotyped patients with AN, to conclude for potential clinical use, and finally design therapeutic tests.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"312 ","pages":"Article 105370"},"PeriodicalIF":2.8,"publicationDate":"2024-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142882281","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":"Optimized pipeline for personalized neurobiological insights from single patient-derived Neurospheres","authors":"Guillaume Nugue ,&nbsp;Michele Martins ,&nbsp;Gabriela Vitória ,&nbsp;Beatriz Luzia De Mello Lima Guimaraes ,&nbsp;Mauricio Quiñones-Vega ,&nbsp;Stevens Rehen ,&nbsp;Marilia Z. Guimarães ,&nbsp;Magno Junqueira","doi":"10.1016/j.jprot.2024.105368","DOIUrl":"10.1016/j.jprot.2024.105368","url":null,"abstract":"<div><div>This pipeline presents a refined approach for deriving personalized neurobiological insights from iPSC-derived neurospheres. By employing Tandem Mass Tag (TMT) labeling, we optimized sample pooling and multiplexing for robust comparative analysis across experimental conditions, maximizing data yield per sample. Through single-patient-derived neurospheres—composed of neural progenitor cells, early neurons, and radial glia—this study explores proteomic profiling to mirror the cellular complexity of neurodevelopment more accurately than traditional 2D cultures. Given their enhanced relevance, these 3D neurospheres serve as a valuable model for elucidating neurogenesis, differentiation, and neuropathological mechanisms, contributing to the advancement of in vitro neural models and reducing dependency on animal models.</div></div><div><h3>Significance</h3><div>This study evaluates ten protein extraction protocols using TMT 10-plex labeling to optimize proteomic analysis from single neurospheres. It compares cost, protein yield, and the ability to detect differentially expressed proteins, identifying methods like SPEED and S-Trap as efficient for high-throughput studies, while FASP excels in peptide yield. TMT labeling enhances protein identification, particularly for low-abundance proteins, and allows pre-fractionation to maximize analysis from limited samples. However, challenges such as limited PTM analysis and the potential loss of minor proteins highlight the importance of selecting protocols based on specific research goals. This work contributes to optimizing proteomic workflows for in vitro neural models, advancing single-cell analysis with minimal reliance on animal models.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"313 ","pages":"Article 105368"},"PeriodicalIF":2.8,"publicationDate":"2024-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807388","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":"Identification of biological pathways and putative candidate genes for residual feed intake in a tropically adapted beef cattle breed by plasma proteome analysis","authors":"Jessica M. Malheiros ,&nbsp;Henrique G. Reolon ,&nbsp;Bruna G. Bosquini ,&nbsp;Fernando Baldi ,&nbsp;Daniela Lourenco ,&nbsp;Breno O. Fragomeni ,&nbsp;Rafael M.O. Silva ,&nbsp;Claudia C.P. Paz ,&nbsp;Nedenia B. Stafuzza","doi":"10.1016/j.jprot.2024.105361","DOIUrl":"10.1016/j.jprot.2024.105361","url":null,"abstract":"<div><div>This study identified potential biomarkers for feed efficiency by blood plasma proteome analysis of a tropically adapted beef cattle breed. Two experimental groups were selected based on residual feed intake (RFI). The proteome was investigated by LC-MS/MS in a data-dependent acquisition mode. After quality control, 123 differentially abundant proteins (DAPs) were identified between the two experimental groups. Among DAPs with the highest absolute log-fold change values, the <em>PRDM2</em>, <em>KRT5</em>, <em>UGGT1</em>, <em>DENND5B</em>, <em>B2M</em>, <em>SLC44A2</em>, <em>SLC7A2</em>, <em>PTPRC</em>, and <em>FETUB</em> were highlighted as potential biomarkers because of their functions that may contribute to RFI. Furthermore, functional enrichment analysis revealed several biological processes, molecular functions and pathways that contributes to RFI, such as cell signaling, cellular responses to stimuli, immune system, calcium, hormones, metabolism and functions of proteins, lipids and carbohydrates. Protein-protein interaction analysis identified 32 and 11 DAPs as important nodes based on their interactions in the high- and low-RFI groups, respectively. This study represents the first comprehensive profiling of the blood plasma proteome of a tropically adapted beef cattle breed and provides valuable insights into the potential roles of these DAPs in key biological processes and pathways, contributing to our understanding of the mechanisms underlying feed efficiency in tropically adapted beef cattle.</div></div><div><h3>Significance</h3><div>LC-MS/MS analysis was performed to investigate changes in the blood plasma proteome associated with residual feed intake (RFI) in a tropically adapted beef cattle breed (<em>Bos taurus taurus</em>). Some putative biomarkers were identified to distinguish the high-RFI to low-RFI animals, based on their log-fold change value or on their protein-protein interaction network, which provide helpful sources in developing novel selection strategies for breeding programs. Our findings also revealed valuable insights into the metabolic pathways and biological processes that contribute to RFI in beef cattle, such as those closely linked to cell signaling, cellular responses to stimuli, immune system, calcium, hormones, metabolism and functions of proteins, lipids and carbohydrates.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"312 ","pages":"Article 105361"},"PeriodicalIF":2.8,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142785990","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":"Probiotic Bacillus cereus regulates metabolic disorders and activates the cholic acid-FXR axis to alleviate DSS-induced colitis","authors":"Yixiao Liao ,&nbsp;Shihui Wu ,&nbsp;Guixian Zhou ,&nbsp;Shihui Mei ,&nbsp;Bingmin Ou ,&nbsp;Ming Wen ,&nbsp;Ying Yang ,&nbsp;Guilan Wen","doi":"10.1016/j.jprot.2024.105360","DOIUrl":"10.1016/j.jprot.2024.105360","url":null,"abstract":"<div><div>Inflammatory bowel disease is characterized by severe imbalance of intestinal flora and metabolic disorders. Recent studies have demonstrated that probiotics can effectively alleviate inflammatory bowel disease by restoring the intestinal flora structure and modulating the immune response. However, the role of probiotics in regulating intestinal metabolism disorders is still unclear. This study explores the role of probiotic <em>B. cereus</em> in alleviating DSS-induced colitis. The findings indicated probiotic <em>B. cereus</em> treatment mitigated tissue damage and apoptosis during inflammation. Metabolome and transcriptome analysis revealed <em>B. cereus</em> activated the cholic acid-FXR axis by increasing cholic acid levels, which promoted the gene expression level of NF-κB inhibitor α, reduced the IL-1β, IL-6, IL-18 and TNF-α concentrations. Furthermore, it effectively mitigated the DSS-induced disruption of bile acid metabolism, arginine metabolism, and linoleic acid metabolism. This study explores the effect and mechanisms of probiotic <em>B. cereus</em> on alleviating DSS-induced colitis. It aims to provide a theoretical basis for microbial therapy in inflammatory bowel disease.</div></div><div><h3>Significance</h3><div>This study used metabolome and transcriptome to reveal the roles and mechanisms, which probiotic <em>Bacillus cereus</em> modulates metabolic disorders and alleviate DSS-induced colitis. We identified the cholic acid-FXR axis as an important target for alleviating DSS-induced colitis. These findings provide new insights into microbial treatment strategies for IBD.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"312 ","pages":"Article 105360"},"PeriodicalIF":2.8,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142779037","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 interrogation of complex biomedical samples using the rapid denaturing organic digestion (DOD) method","authors":"Jonathan Oyler ,&nbsp;Raymond F. Sullivan ,&nbsp;Bao Q. Tran ,&nbsp;Dhanwin Baker ,&nbsp;Clare Coveney ,&nbsp;David Boocock ,&nbsp;Benjamin Oyler ,&nbsp;Carole C. Perry ,&nbsp;David P.A. Kilgour","doi":"10.1016/j.jprot.2024.105359","DOIUrl":"10.1016/j.jprot.2024.105359","url":null,"abstract":"<div><div>Limitations to many current aqueous-based tryptic digestion methods include lengthy digestion times and both relatively high inter- and intra-day variability for both characteristic peptides identified and sequence coverages. This report describes results from digestion of some complex biomedical samples using the rapid Denaturing Organic Digestion method (DOD), an organic solvent-modified digestion method previously optimized for targeted protein digestion. Advantages of the DOD method included a very rapid digestion only requiring inexpensive solvents and reagents generally available in the laboratory, with no requirement for specialized equipment or expensive, specialized consumables. For this study, samples of <em>E. coli</em> and murine ileum protein extracts, and K562, a mass spectrometry-compatible human protein extract and reference standard routinely used to evaluate methods, were digested. Sequence coverage and characteristic peptide identification results were compared to those from 18 and 24 h conventional aqueous-based digestion methods. Across the samples tested, though the number of characteristic peptides and sequence coverages produced by the 5 min DOD method were very similar to those produced by the aqueous-based digestion methods, the specific characteristic proteins and their corresponding tryptic peptides identified following DOD method digestion included more hydrophilic and less hydrophobic species. In addition, we explored the effect of increasing digestion times with complex samples from 5 to 30 and 90 min for the DOD method. Increasing the digestion time to ≥30 min resulted in improved intra-day precision and the identification of many more peptide products than the currently used aqueous methods to which it was compared. These results suggest that the DOD organic-modified digestion method could, while markedly reducing protein digestion time, also provide more precise analysis and access to a somewhat different area of the proteome than that provided by current aqueous-based digestion methods.</div></div><div><h3>Significance</h3><div>The DOD tryptic digest method is a very simple and rapid process with no requirement for expensive equipment or consumables. The method markedly reduces tryptic digestion time and cost, and substantially improves within-batch and across-analyst precision for peptide and sequence coverage results over methods to which it was compared. Importantly, it also provides access to a somewhat different subset of the proteome with different peptide products identified as compared to aqueous solvent-based digestion providing potential for increased proteome coverage for bottom-up analysis if used in conjunction with aqueous-based methods.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"312 ","pages":"Article 105359"},"PeriodicalIF":2.8,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142755264","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}