Molecular omics最新文献_第10页

The mechanism of chronic unpredictable mild stress induced high blood pressure in rats: a proteomic and targeted metabolomic analysis† 慢性不可预测的轻度应激诱导大鼠高血压的机制:蛋白质组学和靶向代谢组学分析

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-03-07 DOI: 10.1039/D2MO00332E

Hongxia Zhao, Qiong Wu, Na Li and Yongchun Chen

引用次数: 0

Brain-wide transcriptome-based metabolic alterations in Parkinson's disease: human inter-region and human-experimental model correlations† 帕金森病中基于全脑转录组的代谢改变:人类区域间和人类实验模型相关性

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-03-07 DOI: 10.1039/D2MO00343K

Regan Odongo, Orhan Bellur, Ecehan Abdik and Tunahan Çakır

{"title":"Brain-wide transcriptome-based metabolic alterations in Parkinson's disease: human inter-region and human-experimental model correlations†","authors":"Regan Odongo, Orhan Bellur, Ecehan Abdik and Tunahan Çakır","doi":"10.1039/D2MO00343K","DOIUrl":"10.1039/D2MO00343K","url":null,"abstract":"Alterations in brain metabolism are closely associated with the molecular hallmarks of Parkinson's disease (PD). A clear understanding of the main metabolic perturbations in PD is therefore important. Here, we retrospectively analysed the expression of metabolic genes from 34 PD-control post-mortem human brain transcriptome data comparisons from literature, spanning multiple brain regions. We found high metabolic correlations between the Substantia nigra (SN)- and cerebral cortex-derived tissues. Moreover, three clusters of PD patient cohorts were identified based on perturbed metabolic processes in the SN – each characterised by perturbations in (a) bile acid metabolism (b) omega-3 fatty acid metabolism, and (c) lipoic acid and androgen metabolism – metabolic themes not comprehensively addressed in PD. These perturbations were supported by concurrence between transcriptome and proteome changes in the expression patterns for CBR1, ECI2, BDH2, CYP27A1, ALDH1B1, ALDH9A1, ADH5, ALDH7A1, L1CAM, and PLXNB3 genes, providing a valuable resource for drug targeting and diagnosis. Also, we analysed 58 PD-control transcriptome data comparisons from in vivo/in vitro disease models and identified experimental PD models with significant correlations to matched human brain regions. Collectively, our findings suggest metabolic alterations in several brain regions, heterogeneity in metabolic alterations between study cohorts for the SN tissues and the need to optimize current experimental models to advance research on metabolic aspects of PD.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 7","pages":" 522-537"},"PeriodicalIF":2.9,"publicationDate":"2023-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10026786","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Role of identified proteins in the proteome profiles of CDK4/6 inhibitor-resistant breast cancer cell lines† 鉴定蛋白在CDK4/6抑制剂耐药乳腺癌细胞系蛋白质组谱中的作用

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-03-07 DOI: 10.1039/D2MO00285J

Binayak Kumar, Peeyush Prasad, Ragini Singh, Ram Krishna Sahu, Ashutosh Singh, Srikrishna Jayadev Magani and Suresh Hedau

{"title":"Role of identified proteins in the proteome profiles of CDK4/6 inhibitor-resistant breast cancer cell lines†","authors":"Binayak Kumar, Peeyush Prasad, Ragini Singh, Ram Krishna Sahu, Ashutosh Singh, Srikrishna Jayadev Magani and Suresh Hedau","doi":"10.1039/D2MO00285J","DOIUrl":"10.1039/D2MO00285J","url":null,"abstract":"Abemaciclib (Ab) and palbociclib (Pb) are CDK4/6 inhibitors used to cure advanced breast cancer (BC). However, acquired resistance is a major challenge. The molecular mechanisms and signature proteins of therapy resistance for Ab and Pb drugs need to be explored. Here we developed resistant cells for Ab and Pb drugs in MCF-7 cell lines and explored the mechanisms and signature proteins of therapy resistance in BC. Proteome profiling was performed using the label-free proteome-orbitrap-fusion-MS-MS technique. Gene ontology (GO)-terms, KEGG pathways and network analysis were performed for the proteome data. Drug-resistant cells showed increased drug tolerance, enhanced colony formation potential and an increased gap-healing tendency for the respective drug. Up-regulation of survival genes (BCL-2 and MCL-1) and down-regulation of apoptosis inducers were observed. Drug-resistance markers (MDR-1 and ABCG2 (BCRP)) along with ESR-1, CDK4, CDK6, and cyclin-D1 genes were up-regulated in resistant cells. A total of 237 and 239 proteins were found to be differentially expressed in the Ab and Pb-resistant cells, respectively. Down-regulated proteins induce apoptosis signalling and nucleotide metabolisms and restrict EGFR signalling; however, up-regulated proteins induce Erk, wnt-β-catenin, VEGFR-PI3K-AKT, glucose transportation, and hypoxia signalling pathways and regulate hydrogen peroxide signalling pathways. The panel of identified proteins associated with these pathways might have characteristics of molecular signature and new drug targets for overcoming drug resistance in breast cancer.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 5","pages":" 404-417"},"PeriodicalIF":2.9,"publicationDate":"2023-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9657629","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 1

Antibiotic-induced gut microbiota dysbiosis altered host metabolism† 抗生素诱导的肠道菌群失调改变了宿主代谢†

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-02-28 DOI: 10.1039/D2MO00284A

Mengxue He, Jiachen Shi, Aiyang Liu, Yong-Jiang Xu and Yuanfa Liu

引用次数: 1

Label-free serum proteomics for the identification of the putative biomarkers of postoperative pain in patients with gastric cancer† 无标记血清蛋白质组学用于鉴定胃癌患者术后疼痛的推定生物标志物

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-02-27 DOI: 10.1039/D2MO00296E

Jianing Li, Shuo Li, Tianzhuo Zhang, Ling Yu, Jin Wei, Mengge Wu, Yining Xie and Hongyu Tan

{"title":"Label-free serum proteomics for the identification of the putative biomarkers of postoperative pain in patients with gastric cancer†","authors":"Jianing Li, Shuo Li, Tianzhuo Zhang, Ling Yu, Jin Wei, Mengge Wu, Yining Xie and Hongyu Tan","doi":"10.1039/D2MO00296E","DOIUrl":"10.1039/D2MO00296E","url":null,"abstract":" Background: Individualized pain therapy conforms to the concept of precision medicine and contributes to adequate pain management after surgery. Preoperative biomarkers associated with postoperative pain may instruct anesthesiologists to improve personalized suitable analgesia. Therefore, it is essential to explore the association between preoperative proteins and postoperative acute pain using the proteomics platform. Methods: In this study, the 24 hours postoperative sufentanil consumption of 80 male patients with gastric cancer was ranked. Patients with sufentanil consumption in the lowest 12% were included in the sufentanil low consumption group, while patients with sufentanil consumption in the highest 12% were included in the sufentanil high consumption group. The secretion of serum proteins in both groups was analyzed using label-free proteomics technology. The results were validated by ELISA. Results: Proteomics identified 29 proteins that were significantly differentially expressed between groups. ELISA confirmed that secretion of TNC and IGFBP2 was down-regulated in the SLC group. The differential proteins were mainly extracellular and were involved in several terms, including calcium ion binding, laminin-1 binding, and so on. Pathway analysis showed that they were mainly enriched in focal adhesion and extracellular matrix-receptor interaction. The protein–protein interaction network analysis showed 22 proteins that interacted with other proteins. F13B had the strongest correlation with sufentanil consumption and its AUC value was 0.859. Conclusions: Several differential proteins are associated with postoperative acute pain and are involved in ECM-related processes, inflammation, and blood coagulation cascades. F13B may be a novel marker for postoperative acute pain. Our results may benefit postoperative pain management.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 4","pages":" 351-361"},"PeriodicalIF":2.9,"publicationDate":"2023-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9490814","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 1

Multi-omics insights into the interplay between gut microbiota and colorectal cancer in the “microworld” age 在“微观世界”时代，肠道微生物群与结直肠癌之间相互作用的多组学见解

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-02-16 DOI: 10.1039/D2MO00288D

An-Jun Wang, Dingka Song, Yue-Mei Hong and Ning-Ning Liu

{"title":"Multi-omics insights into the interplay between gut microbiota and colorectal cancer in the “microworld” age","authors":"An-Jun Wang, Dingka Song, Yue-Mei Hong and Ning-Ning Liu","doi":"10.1039/D2MO00288D","DOIUrl":"10.1039/D2MO00288D","url":null,"abstract":"Colorectal cancer (CRC) is a multifactorial heterogeneous disease largely due to both genetic predisposition and environmental factors including the gut microbiota, a dynamic microbial ecosystem inhabiting the gastrointestinal tract. Elucidation of the molecular mechanisms by which the gut microbiota interacts with the host may contribute to the pathogenesis, diagnosis, and promotion of CRC. However, deciphering the influence of genetic variants and interactions with the gut microbial ecosystem is rather challenging. Despite recent advancements in single omics analysis, the application of multi-omics approaches to integrate multiple layers of information in the microbiome and host to introduce effective prevention, diagnosis, and treatment strategies is still in its infancy. Here, we integrate host- and microbe-based multi-omics studies, respectively, to provide a strategy to explore potential causal relationships between gut microbiota and colorectal cancer. Specifically, we summarize the recent multi-omics studies such as metagenomics combined with metabolomics and metagenomics combined with genomics. Meanwhile, the sample size and sample types commonly used in multi-omics research, as well as the methods of data analysis, were also generalized. We highlight multiple layers of information from multi-omics that need to be verified by different types of models. Together, this review provides new insights into the clinical diagnosis and treatment of colorectal cancer patients.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 4","pages":" 283-296"},"PeriodicalIF":2.9,"publicationDate":"2023-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9490821","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Re-mining serum proteomics data reveals extensive post-translational modifications upon Zika and dengue infection† 重新挖掘血清蛋白质组学数据揭示了寨卡病毒和登革热感染的广泛翻译后修饰†

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-02-15 DOI: 10.1039/D2MO00258B

Kristina Allgoewer, Shaohuan Wu, Hyungwon Choi and Christine Vogel

{"title":"Re-mining serum proteomics data reveals extensive post-translational modifications upon Zika and dengue infection†","authors":"Kristina Allgoewer, Shaohuan Wu, Hyungwon Choi and Christine Vogel","doi":"10.1039/D2MO00258B","DOIUrl":"10.1039/D2MO00258B","url":null,"abstract":"Zika virus (ZIKV) and dengue virus (DENV) are two closely related flaviviruses with similar symptoms. However, due to the implications of ZIKV infections for pregnancy outcomes, understanding differences in their molecular impact on the host is of high interest. Viral infections change the host proteome, including post-translational modifications. As modifications are diverse and of low abundance, they typically require additional sample processing which is not feasible for large cohort studies. Therefore, we tested the potential of next-generation proteomics data in its ability to prioritize specific modifications for later analysis. We re-mined published mass spectra from 122 serum samples from ZIKV and DENV patients for the presence of phosphorylated, methylated, oxidized, glycosylated/glycated, sulfated, and carboxylated peptides. We identified 246 modified peptides with significantly differential abundance in ZIKV and DENV patients. Amongst these, methionine-oxidized peptides from apolipoproteins and glycosylated peptides from immunoglobulin proteins were more abundant in ZIKV patient serum and generate hypotheses on the potential roles of the modification in the infection. The results demonstrate how data-independent acquisition techniques can help prioritize future analyses of peptide modifications.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 4","pages":" 308-320"},"PeriodicalIF":2.9,"publicationDate":"2023-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2023/mo/d2mo00258b?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9449190","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Cross-talk and integrative post-translational modifications 串音与综合翻译后修饰

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-02-02 DOI: 10.1039/D2MO90036J

Si Wu and Lindsay Pino

引用次数: 0

Untargeted metabolomics reveals altered branch chain amino acids, glucose and fat metabolism contributing to coronary artery disease among Indian diabetic patients† 非靶向代谢组学揭示了支链氨基酸、葡萄糖和脂肪代谢的改变与印度糖尿病患者冠状动脉疾病有关†

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-01-31 DOI: 10.1039/D2MO00320A

Ramu Adela, Siva Swapna Kasarla, Najmuddin Saquib, Sonu Kumar Gupta, Sneh Bajpai, Yashwant Kumar and Sanjay K Banerjee

{"title":"Untargeted metabolomics reveals altered branch chain amino acids, glucose and fat metabolism contributing to coronary artery disease among Indian diabetic patients†","authors":"Ramu Adela, Siva Swapna Kasarla, Najmuddin Saquib, Sonu Kumar Gupta, Sneh Bajpai, Yashwant Kumar and Sanjay K Banerjee","doi":"10.1039/D2MO00320A","DOIUrl":"10.1039/D2MO00320A","url":null,"abstract":"Type 2 diabetes mellitus (T2DM) is a chronic metabolic disorder characterised by increased blood glucose levels. Patients with T2DM have a high risk of developing atherosclerotic coronary artery disease (CAD). CAD with T2DM has a complex etiology and the understanding of the pathophysiology of coronary artery disease (CAD) in the presence of diabetes is poor. Here, we have used LC-MS/MS-based untargeted metabolomics to unveil the alterations of metabolites in the serum of South-Indian patients diagnosed with T2DM, CAD and T2DM along with CAD (T2DM-CAD) compared with the healthy subjects (CT). Using untargeted metabolomics and network-based approaches, a set of metabolites highly co-expressed with T2DM-CAD pathogenesis were identified. Our results revealed that these metabolites belong to essential pathways such as amino acid metabolism, fatty acid metabolism and carbohydrate metabolism. The candidate metabolites identified by metabolomics study are branch chain amino acids, L-arginine, linoleic acid, L-serine, L-cysteine, fructose-6-phosphate, glycerol, creatine and 3-phosphoglyceric acid, and explain the pathogenesis of T2DM-assisted CAD. The identified metabolites could be used as potential prognostic markers to predict CAD in patients diagnosed with T2DM.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 4","pages":" 321-329"},"PeriodicalIF":2.9,"publicationDate":"2023-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9436612","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Effect of short-term use of FFP2 (N95) masks on the salivary metabolome of young healthy volunteers: a pilot study† 短期使用FFP2 (N95)面罩对年轻健康志愿者唾液代谢组的影响:一项初步研究

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-01-21 DOI: 10.1039/D2MO00232A

Sk Ramiz Islam, Debasish Prusty, Subhadip Maiti, Raju Dutta, Partha Chattopadhyay and Soumen Kanti Manna

{"title":"Effect of short-term use of FFP2 (N95) masks on the salivary metabolome of young healthy volunteers: a pilot study†","authors":"Sk Ramiz Islam, Debasish Prusty, Subhadip Maiti, Raju Dutta, Partha Chattopadhyay and Soumen Kanti Manna","doi":"10.1039/D2MO00232A","DOIUrl":"10.1039/D2MO00232A","url":null,"abstract":"The use of face masks has become an integral part of public life in the post-pandemic era. However, the understanding of the effect of wearing masks on physiology remains incomplete and is required for informing public health policies. For the first time, we report the effects of wearing FFP2 masks on the metabolic composition of saliva, a proximal matrix to breath, along with cardiopulmonary parameters. Un-induced saliva was collected from young (31.2 ± 6.3 years) healthy volunteers (n = 10) before and after wearing FFP2 (N95) masks for 30 minutes and analyzed using GCMS. The results showed that such short-term mask use did not cause any significant change in heart rate, pulse rate or SpO2. Three independent data normalization approaches were used to analyze the changes in metabolomic signature. The individuality of the overall salivary metabotype was found to be unaffected by mask use. However, a trend of an increase in the salivary abundance of L-fucose, 5-aminovaleric acid, putrescine and phloretic acid was indicated irrespective of the method of data normalization. Quantitative analysis confirmed increases in concentrations of these metabolites in saliva of paired samples amid high inter-individual variability. The results showed that while there was no significant change in measured physiological parameters and individual salivary metabotypes, mask use was associated with correlated changes in these metabolites plausibly originating from altered microbial metabolic activity. These results might also explain the change in odour perception reported to be associated with mask use. Potential implications of these changes on mucosal health and immunity warrants further investigation to evolve more prudent mask use policies.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 5","pages":" 383-394"},"PeriodicalIF":2.9,"publicationDate":"2023-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9665604","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 1