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":"<p >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.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":null,"pages":null},"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}
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":null,"pages":null},"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}
{"title":"Cross-talk and integrative post-translational modifications","authors":"Si Wu and Lindsay Pino","doi":"10.1039/D2MO90036J","DOIUrl":"10.1039/D2MO90036J","url":null,"abstract":"<p >A graphical abstract is available for this content</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9094975","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}
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":"<p >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, <small>L</small>-arginine, linoleic acid, <small>L</small>-serine, <small>L</small>-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.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":null,"pages":null},"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}
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":"<p >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 (<em>n</em> = 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 SpO<small><sub>2</sub></small>. 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 <small>L</small>-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.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":null,"pages":null},"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}
{"title":"Omics approaches to better understand the molecular mechanism of necroptosis and their translational implications","authors":"Apoorva J. Pradhan and G. Ekin Atilla-Gokcumen","doi":"10.1039/D2MO00318J","DOIUrl":"10.1039/D2MO00318J","url":null,"abstract":"<p >Necroptosis is a type of programed cell death characterized by an inflammatory phenotype due to extensive membrane permeabilization and rupture. Initiation of necroptosis involves activation of tumor necrosis factor receptors by tumor necrosis factor alpha (TNFα) followed by coordinated activities of receptor-interacting protein kinases and mixed lineage kinase-like protein (MLKL). Subsequently, MLKL undergoes phosphorylation and translocates to the plasma membrane, leading to permeabilization. Such permeabilization results in the release of various cytokines and causes extensive inflammatory activity at the organismal level. This inflammatory activity is one of the major differences between apoptosis and necroptosis and links necroptosis to several human pathologies that exhibit inflammation, in addition to the ultimate cell death phenotype. Given the crosstalk between the activation of cell death pathway and inflammatory activity, approaches that provide insights on the regulation of transcripts, proteins and their processing at the global level have substantially improved our understanding of necroptosis and its involvement in different disease states. In this review, we highlight recent omic studies probing the transcriptome, proteome and lipidome which elucidate potential new mechanisms and signaling pathways during necroptosis and the necroptosis-associated inflammatory activity observed in various diseases. We specifically focus on studies investigating the transcriptome and intracellular and released proteome that contribute to inflammatory nature of necroptotic cells. We also highlight different lipids that have been implicated in necroptosis and lipidomic studies identifying lipid players in necroptosis. Finally, we review studies which suggest certain necroptosis-related genes as potential prognosis markers for different cancers and discuss their translational implications.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9291800","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}
{"title":"Profiling protein targets of cellular toxicant exposure","authors":"Joseph C. Genereux","doi":"10.1039/D2MO00246A","DOIUrl":"10.1039/D2MO00246A","url":null,"abstract":"<p >Environmental agents of exposure can damage proteins, affecting protein function and cellular protein homeostasis. Specific residues are inherently chemically susceptible to damage from individual types of exposure. Amino acid content is not completely predictive of protein susceptibility, as secondary, tertiary, and quaternary structures of proteins strongly influence the reactivity of the proteome to individual exposures. Because we cannot readily predict which proteins will be affected by which chemical exposures, mass spectrometry-based proteomic strategies are necessary to determine the protein targets of environmental toxins and toxicants. This review describes the mechanisms by which environmental exposure to toxins and toxicants can damage proteins and affect their function, and emerging omic methodologies that can be used to identify the protein targets of a given agent. These methods include target identification strategies that have recently revolutionized the drug discovery field, such as activity-based protein profiling, protein footprinting, and protein stability profiling technologies. In particular, we highlight the necessity of multiple, complementary approaches to fully interrogate how protein integrity is challenged by individual exposures.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9296916","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}
Shuainan Huang, Jiahui Zhang, Hua Wan, Kang Wang, Jiayi Wu, Yue Cao, Li Hu, Yanfang Yu, Hao Sun, Youjia Yu, Jie Wang and Feng Chen
{"title":"Plasma extracellular vesicles microRNA-208b-3p and microRNA-143-3p as novel biomarkers for sudden cardiac death prediction in acute coronary syndrome†","authors":"Shuainan Huang, Jiahui Zhang, Hua Wan, Kang Wang, Jiayi Wu, Yue Cao, Li Hu, Yanfang Yu, Hao Sun, Youjia Yu, Jie Wang and Feng Chen","doi":"10.1039/D2MO00257D","DOIUrl":"10.1039/D2MO00257D","url":null,"abstract":"<p >Acute coronary syndrome (ACS) occurs as a result of myocardial ischemia that can give rise to a variety of acute cardiovascular events, including arrhythmia, heart failure and sudden cardiac death (SCD). Currently, there are challenges and insufficient innovations regarding early diagnosis and therapeutic approaches within ACS patients experiencing SCD. Plasma extracellular vesicles (EVs) might serve as biomarkers of many diseases depending on the biological molecules of their cargo, such as miRNAs. This study aims to identify the plasma EVs containing miRNAs as novel biomarkers for the prediction of SCD in ACS patients. A total of 39 ACS patients experiencing SCD and 39 healthy control individuals (HC) were enrolled, among which 9 samples in each group were randomly selected as testing groups for miRNA sequencing in plasma EVs, and the remaining samples were assigned to the validation group. The top 10 significant expression miRNAs were verified by the real-time quantitative polymerase chain reaction. Upregulation of miR-208b-3p, miR-143-3p, miR-145-3p and miR-152-3p, and down-regulation of miR-183-5p were further validated in the validation group. Spearman's correlation analysis and the receiver operating characteristic (ROC) curve showed that both miR-208b-3p and miR-143-3p levels were positively correlated with myoglobin (MYO), and their predictive power for SCD was confirmed. In conclusion, our findings indicate that plasma EVs miR-208b-3p and miR-143-3p may serve as promising biomarkers in predicting SCD in patients with ACS, as well as postmortem forensic diagnosis of the cause of death due to ACS.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9344795","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}
Rojalin Nayak, Trisha Chattopadhyay, Pooja Gupta and Bibekanand Mallick
{"title":"Integrative analysis of small non-coding RNAs predicts a piRNA/miRNA-CCND1/BRAF/HRH1/ATXN3 regulatory circuit that drives oncogenesis in glioblastoma†","authors":"Rojalin Nayak, Trisha Chattopadhyay, Pooja Gupta and Bibekanand Mallick","doi":"10.1039/D2MO00245K","DOIUrl":"10.1039/D2MO00245K","url":null,"abstract":"<p >The high-grade astrocytoma, glioblastoma multiforme (GBM), is the most common primary tumour of the brain, known for being aggressive and developing drug resistance. The non-coding RNAs (ncRNAs), such as microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), have critical functions in tumorigenesis and cancer drug resistance. Hence, we profiled miRNAs, piRNAs, and genes in U-87 MG GBM cells by next-generation sequencing and performed target prediction, pathway enrichment, protein–protein interaction, co-expression studies, and qRT-PCR validations to predict their possible roles in the malignancy. The study identified 335 miRNAs, 665 piRNAs, and 4286 genes differentially expressed (DE) in GBM. Among them 128 DE genes (DEGs) were targeted by both miRNAs and piRNAs, while 1817 and 192 were targeted solely by miRNAs or piRNAs, respectively. Interestingly, all the DEG targets enriched in cancer processes were overexpressed in GBM. Among these, BRAF was solely targeted by two piRNAs and this was found to be co-expressed with 19 sole targets of 5 miRNAs, including CCND1, and both were found to regulate cell proliferation in cancer. We conjectured that upregulated HRH1 and ATXN3 were targeted by both piRNAs and miRNAs, and along with BRAF and CCND1 might induce cell proliferation in GBM through G-protein-coupled receptor or Akt signalling pathways due to downregulation of the respective targeting small RNAs. These targets were also linked to the progression and overall survival of GBM patients, suggesting that they could be used as biomarkers. Overall, this study has identified a few novel ncRNA targets, which might aid in a better understanding of GBM pathogenesis.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9660778","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}
{"title":"Focus on the molecular mechanisms of cisplatin resistance based on multi-omics approaches","authors":"Ping Yue, Bingjie Han and Yi Zhao","doi":"10.1039/D2MO00220E","DOIUrl":"10.1039/D2MO00220E","url":null,"abstract":"<p >Cisplatin is commonly used in combination with other cytotoxic agents as a standard treatment regimen for a variety of solid tumors, such as lung, ovarian, testicular, and head and neck cancers. However, the effectiveness of cisplatin is accompanied by toxic side effects, for instance, nephrotoxicity and neurotoxicity. The response of tumors to cisplatin treatment involves multiple physiological processes, and the efficacy of chemotherapy is limited by the intrinsic and acquired resistance of tumor cells. Although enormous efforts have been made toward molecular mechanisms of cisplatin resistance, the development of omics provides new insights into the understanding of cisplatin resistance at genome, transcriptome, proteome, metabolome and epigenome levels. Mechanism studies using different omics approaches revealed the necessity of multi-omics applications, which provide information at different cellular function levels and expand our recognition of the peculiar genetic and phenotypic heterogeneity of cancer. The present work systematically describes the underlying mechanisms of cisplatin resistance in different tumor types using multi-omics approaches. In addition to the classical mechanisms such as enhanced drug efflux, increased DNA damage repair and changes in the cell cycle and apoptotic pathways, other changes like increased protein damage clearance, increased protein glycosylation, enhanced glycolytic process, dysregulation of the oxidative phosphorylation pathway, ferroptosis suppression and mRNA m6A methylation modification can also induce cisplatin resistance. Therefore, utilizing the integrated omics to identify key signaling pathways, target genes and biomarkers that regulate chemoresistance are essential for the development of new drugs or strategies to restore tumor sensitivity to cisplatin.</p>","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9427752","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}