PubMed

J Nat Prod. 2023 Jul 6. doi: 10.1021/acs.jnatprod.3c00148. Online ahead of print.ABSTRACTThe saprotrophic filamentous fungus Myrothecium inundatum represents a chemically underexplored ascomycete with a high number of putative biosynthetic gene clusters in its genome. Here, we present new linear lipopeptides from nongenetic gene activation experiments using nutrient and salt variations. Metabolomics studies revealed four myropeptins, and structural analyses by NMR, HRMS, Marfey's analysis, and ECD assessment for their helical properties established their absolute configuration. A myropeptin biosynthetic gene cluster in the genome was identified. The myropeptins exhibit general nonspecific toxicity against all cancer cell lines in the NCI-60 panel, larval zebrafish with EC50 concentrations of 5-30 μM, and pathogenic bacteria and fungi (MICs of 4-32 μg/mL against multidrug-resistant S. aureus and C. auris). In vitro hemolysis, cell viability, and ionophore assays indicate that the myropeptins target mitochondrial and cellular membranes, inducing cell depolarization and cell death. The toxic activity is modulated by the length of the lipid side chain, which provides valuable insight into their structure-activity relationships.PMID:37411007 | DOI:10.1021/acs.jnatprod.3c00148

J Agric Food Chem. 2023 Jul 6. doi: 10.1021/acs.jafc.3c02125. Online ahead of print.ABSTRACTThe potential of probiotics to benefit digestion has been widely reported, while its utilization in high-risk patients and potential adverse reactions have focused interest on postbiotics. A variable data-independent acquisition (vDIA)-based spatial-omics strategy integrated with unsupervised variational autoencoders was applied to profile the functional mechanism underlying the action of Lactobacillus casei-derived postbiotic supplementation in goat milk digestion in an infant digestive system, from a metabolomics-peptidomics-proteomics perspective. Amide and olefin derivatives were proved to elevate the activities of pepsin and trypsin through hydrogen bonding and hydrophobic forces based on allosteric effects, and recognition of nine endopeptidases and their cleavage to serine, proline, and aspartate were introduced by postbiotics, thereby promoting the generation of hydrophilic peptides and elevating the bioaccessibility of goat milk protein. The peptides originating from αs1-casein, β-casein, β-lactoglobulin, Ig-like domain-containing protein, κ-casein, and serum amyloid A protein, with multiple bioactivities including angiotensin I-converting enzyme (ACE)-inhibitory, osteoanabolic, dipeptidyl peptidase IV (DPP-IV) inhibitory, antimicrobial, bradykinin-potentiating, antioxidant, and anti-inflammatory activities, were significantly increased in the postbiotic supplementation group, which was also considered to potentially prevent necrotizing enterocolitis through inhibiting the multiplication of pathogenic bacteria and blocking signal transducer and activator of transcription 1 and nuclear factor kappa-light-chain-enhancer of activated B cells inflammatory pathways. This research deepened the understanding of the mechanism underlying the postbiotics affecting goat milk digestion, which established a critical groundwork for the clinical application of postbiotics in infant complementary foods.PMID:37410960 | DOI:10.1021/acs.jafc.3c02125

PLoS One. 2023 Jul 6;18(7):e0286525. doi: 10.1371/journal.pone.0286525. eCollection 2023.ABSTRACTReprogramming metabolism is of great therapeutic interest for reducing morbidity and mortality during sepsis-induced critical illness. Disappointing results from randomized controlled trials targeting glutamine and antioxidant metabolism in patients with sepsis have begged a deeper understanding of the tissue-specific metabolic response to sepsis. The current study sought to fill this gap. We analyzed skeletal muscle transcriptomics of critically ill patients, versus elective surgical controls, which revealed reduced expression of genes involved in mitochondrial metabolism and electron transport, with increases in glutathione cycling, glutamine, branched chain, and aromatic amino acid transport. We then performed untargeted metabolomics and 13C isotope tracing to analyze systemic and tissue specific metabolic phenotyping in a murine polymicrobial sepsis model. We found an increased number of correlations between the metabolomes of liver, kidney, and spleen, with loss of correlations between the heart and quadriceps and all other organs, pointing to a shared metabolic signature within vital abdominal organs, and unique metabolic signatures for muscles during sepsis. A lowered GSH:GSSG and elevated AMP:ATP ratio in the liver underlie the significant upregulation of isotopically labeled glutamine's contribution to TCA cycle anaplerosis and glutamine-derived glutathione biosynthesis; meanwhile, the skeletal muscle and spleen were the only organs where glutamine's contribution to the TCA cycle was significantly suppressed. These results highlight tissue-specific mitochondrial reprogramming to support liver energetic demands and antioxidant synthesis, rather than global mitochondrial dysfunction, as a metabolic consequence of sepsis.PMID:37410734 | DOI:10.1371/journal.pone.0286525

PLoS Comput Biol. 2023 Jul 6;19(7):e1011224. doi: 10.1371/journal.pcbi.1011224. eCollection 2023 Jul.ABSTRACTData are the most important elements of bioinformatics: Computational analysis of bioinformatics data, in fact, can help researchers infer new knowledge about biology, chemistry, biophysics, and sometimes even medicine, influencing treatments and therapies for patients. Bioinformatics and high-throughput biological data coming from different sources can even be more helpful, because each of these different data chunks can provide alternative, complementary information about a specific biological phenomenon, similar to multiple photos of the same subject taken from different angles. In this context, the integration of bioinformatics and high-throughput biological data gets a pivotal role in running a successful bioinformatics study. In the last decades, data originating from proteomics, metabolomics, metagenomics, phenomics, transcriptomics, and epigenomics have been labelled -omics data, as a unique name to refer to them, and the integration of these omics data has gained importance in all biological areas. Even if this omics data integration is useful and relevant, due to its heterogeneity, it is not uncommon to make mistakes during the integration phases. We therefore decided to present these ten quick tips to perform an omics data integration correctly, avoiding common mistakes we experienced or noticed in published studies in the past. Even if we designed our ten guidelines for beginners, by using a simple language that (we hope) can be understood by anyone, we believe our ten recommendations should be taken into account by all the bioinformaticians performing omics data integration, including experts.PMID:37410704 | DOI:10.1371/journal.pcbi.1011224

Microb Biotechnol. 2023 Jul 6. doi: 10.1111/1751-7915.14308. Online ahead of print.ABSTRACTWhitmania pigra is widely used in traditional Chinese medicine. However, W. pigra is being threatened by an edema disease with unknown causes (WPE). In this study, a comprehensive exploration of virome, microbiome, and metabolome aberrations in the intestine of W. pigra was performed to address the aetiology of WPE. Virome analysis indicated that eukaryotic viruses did not contribute to WPE, whereas an expansion of Caudovirales was observed in WPE. Compared to the control, the microbial richness and diversity in diseased W. pigra decreased remarkably. Nine genera, including Aeromonas, Anaerotruncus, Vibrio, Proteocatella, Acinetobacter, and Brachyspira were overrepresented in WPE, whereas eleven genera, including Bifidobacterium, Phascolarctobacterium, Lactobacillus, Bacillus and AF12, were enriched in healthy individuals. Furthermore, certain metabolites, especially amino acids, short-chain fatty acids, and bile acids, were found to be linked to intestinal microbiota alterations in WPE. An integration of the microbiome and metabolome in WPE found that dysbiosis of the gut microbiota or metabolites caused WPE. Notably, W. pigra accepted intestinal microbiota transplantation from WPE donors developed WPE clinical signs eventually, and the dysbiotic intestinal microbiota can be recharacterized in this recipient W. pigra. Strikingly, pathological features of metanephridium and uraemic toxin enrichment in the gut indicated a putative interconnection between the gut and metanephridium in WPE, which represents the prototype of the gut-kidney axis in mammals. These finding exemplify the conservation of "microecological Koch's postulates" from annelids to insects and other vertebrates, which provides a direction of prevention and treatment for WPE and opens a new insight into the pathogenesis of aquatic animal diseases from an ecological perspective.PMID:37410351 | DOI:10.1111/1751-7915.14308

Curr Osteoporos Rep. 2023 Jul 6. doi: 10.1007/s11914-023-00812-8. Online ahead of print.ABSTRACTPURPOSE OF REVIEW: Recent advancements in "omics" technologies and bioinformatics have afforded researchers new tools to study bone biology in an unbiased and holistic way. The purpose of this review is to highlight recent studies integrating multi-omics data gathered from multiple molecular layers (i.e.; trans-omics) to reveal new molecular mechanisms that regulate bone biology and underpin skeletal diseases.RECENT FINDINGS: Bone biologists have traditionally relied on single-omics technologies (genomics, transcriptomics, proteomics, and metabolomics) to profile measureable differences (both qualitative and quantitative) of individual molecular layers for biological discovery and to investigate mechanisms of disease. Recently, literature has grown on the implementation of integrative multi-omics to study bone biology, which combines computational and informatics support to connect multiple layers of data derived from individual "omic" platforms. This emerging discipline termed "trans-omics" has enabled bone biologists to identify and construct detailed molecular networks, unveiling new pathways and unexpected interactions that have advanced our mechanistic understanding of bone biology and disease. While the era of trans-omics is poised to revolutionize our capacity to answer more complex and diverse questions pertinent to bone pathobiology, it also brings new challenges that are inherent when trying to connect "Big Data" sets. A concerted effort between bone biologists and interdisciplinary scientists will undoubtedly be needed to extract physiologically and clinically meaningful data from bone trans-omics in order to advance its implementation in the field.PMID:37410317 | DOI:10.1007/s11914-023-00812-8

Methods Mol Biol. 2023;2688:173-186. doi: 10.1007/978-1-0716-3319-9_15.ABSTRACTMatrix-assisted laser desorption/ionization mass spectrometry imaging with laser-induced postionization (MALDI-2-MSI) has proven a powerful tool for the in situ analysis of N-linked glycosylation, or N-glycans, directly from clinical tissue samples. Here we describe a sample preparation protocol for the analysis of N-glycans from formalin-fixed, paraffin-embedded tissue sections.PMID:37410293 | DOI:10.1007/978-1-0716-3319-9_15

Methods Mol Biol. 2023;2688:161-172. doi: 10.1007/978-1-0716-3319-9_14.ABSTRACTMolecular visualization of metabolites, lipids, and proteins by matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) is becoming an in-demand analytical approach to aid the histopathological analysis of breast cancer. Particularly, proteins seem to play a role in cancer progression, and specific proteins are currently used in the clinic for staging. Formalin-fixed paraffin-embedded (FFPE) tissues are ideal for correlating the molecular markers with clinical outcomes due to their long-term storage. So far, to obtain proteomic information by MSI from this kind of tissue, antigen retrieval and tryptic digestion steps are required. In this chapter, we present a protocol to spatially detect small proteins in tumor and necrotic regions of patient-derived breast cancer xenograft FFPE tissues without employing any on-tissue digestion. This protocol can be used for other kinds of FFPE tissue following specific optimization of the sample preparation phases.PMID:37410292 | DOI:10.1007/978-1-0716-3319-9_14

Methods Mol Biol. 2023;2688:135-146. doi: 10.1007/978-1-0716-3319-9_12.ABSTRACTMetabolites reflect the biological state of cells and tissue, and metabolomics is therefore a field of high interest both to understand normal physiological functions and disease development. When studying heterogeneous tissue samples, mass spectrometry imaging (MSI) is a valuable tool as it conserves the spatial distribution of analytes on tissue sections. A large proportion of metabolites are, however, small and polar, making them vulnerable to delocalizing through diffusion during sample preparation. Here we present a sample preparation method optimized to limit diffusion and delocalization of small polar metabolites in fresh frozen tissue sections. This sample preparation protocol includes cryosectioning, vacuum frozen storage, and matrix application. The methods described were primely developed for matrix-assisted laser desorption/ionization (MALDI) MSI, but the protocol describing cryosectioning and vacuum freezing storage can also be applied before desorption electrospray ionization (DESI) MSI. Our vacuum drying and vacuum packing approach offers a particular advantage to limit delocalization and safe storage.PMID:37410290 | DOI:10.1007/978-1-0716-3319-9_12

Methods Mol Biol. 2023;2688:95-105. doi: 10.1007/978-1-0716-3319-9_9.ABSTRACTThe application of innovative spatial omics approaches in the context of cytological specimens may open new frontiers for their diagnostic assessment. In particular, spatial proteomics using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) represents one of the most promising avenues, owing to its capability to map the distribution of hundreds of proteins within a complex cytological background in a multiplexed and relatively high-throughput manner. This approach may be particularly beneficial in the heterogeneous context of thyroid tumors where certain cells may not present clear-cut malignant morphology upon fine-needle aspiration biopsy, highlighting the necessity for additional molecular tools which are able to improve their diagnostic performance.This chapter aims to provide a detailed overview of a cytospin-based preparation workflow that has been optimized to facilitate the reliable spatial proteomics analysis of cytological thyroid specimens using MALDI-MSI, indicating the key aspects which should be considered when handling such samples.PMID:37410287 | DOI:10.1007/978-1-0716-3319-9_9

J Gastroenterol. 2023 Jul 6. doi: 10.1007/s00535-023-02016-4. Online ahead of print.ABSTRACTBACKGROUND: Ferroptosis, a type of programmed cell death triggered by oxidative stress, was suspected to play a role in ulcerative colitis. Indigo naturalis is highly effective against ulcerative colitis, but its mechanism is unclear. This study found that indigo naturalis treatment suppressed ferroptosis.METHODS: We analyzed 770 mRNA expressions of patients with ulcerative colitis. Suppression of ferroptosis by indigo naturalis treatment was shown using a cell death assay. Malondialdehyde levels and reactive oxygen species were analyzed in CaCo-2 cells treated with indigo naturalis. Glutathione metabolism was shown by metabolomic analysis. Extraction of the ingredients indigo naturalis from the rectal mucosa was performed using liquid chromatograph-mass spectrometry.RESULTS: Gene expression profiling showed that indigo naturalis treatment increased antioxidant genes in the mucosa of patients with ulcerative colitis. In vitro analysis showed that nuclear factor erythroid-2-related factor 2-related antioxidant gene expression was upregulated by indigo naturalis. Indigo naturalis treatment rendered cells resistant to ferroptosis. Metabolomic analysis suggested that an increase in reduced glutathione by indigo naturalis. The protein expression of CYP1A1 and GPX4 was increased in the rectum by treatment with indigo naturalis. The main ingredients of indigo naturalis, indirubin and indigo inhibited ferroptosis. Indirubin was detected in the rectal mucosa of patients with ulcerative colitis who were treated with indigo naturalis.CONCLUSIONS: Suppression of ferroptosis by indigo naturalis in the intestinal epithelium could be therapeutic target for ulcerative colitis. The main active ingredient of indigo naturalis may be indirubin.PMID:37410250 | DOI:10.1007/s00535-023-02016-4

Cancer Epidemiol Biomarkers Prev. 2023 Jul 6:EPI-23-0045. doi: 10.1158/1055-9965.EPI-23-0045. Online ahead of print.ABSTRACTAn increasing number of cancer epidemiology studies use metabolomics assays. This scoping review characterizes trends in the literature in terms of study design, population characteristics, and metabolomics approaches and identifies opportunities for future growth and improvement. We searched PubMed/MEDLINE, Embase, Scopus, and Web of Science: Core Collection databases and included research articles that used metabolomics to primarily study cancer, contained minimum 100 cases in each main analysis stratum, used an epidemiological study design, and were published in English from 1998-June 2021. 2048 articles were screened of which 314 full texts were further assessed resulting in 77 included articles. The most well-studied cancers were colorectal (19.5%), prostate (19.5%), and breast (19.5%). Most studies used a nested case-control design to estimate associations between individual metabolites and cancer risk and a liquid chromatography-tandem mass spectrometry untargeted or semi-targeted approach to measure metabolites in blood. Studies were geographically diverse, including countries in Asia, Europe, and North America; 27.3% of studies reported on participant race, majority reporting White participants. Most studies (70.2%) included fewer than 300 cancer cases in their main analysis. This scoping review identified key areas for improvement, including needs for standardized race and ethnicity reporting, more diverse study populations, and larger studies.PMID:37410086 | DOI:10.1158/1055-9965.EPI-23-0045

Microbiol Spectr. 2023 Jul 6:e0062823. doi: 10.1128/spectrum.00628-23. Online ahead of print.ABSTRACTThe constant, ever-increasing antibiotic resistance crisis leads to the announcement of "urgent, novel antibiotics needed" by the World Health Organization. Our previous works showed a promising synergistic antibacterial activity of silver nitrate with potassium tellurite out of thousands of other metal/metalloid-based antibacterial combinations. The silver-tellurite combined treatment not only is more effective than common antibiotics but also prevents bacterial recovery, decreases the risk of future resistance chance, and decreases the effective concentrations. We demonstrate that the silver-tellurite combination is effective against clinical isolates. Further, this study was conducted to address knowledge gaps in the available data on the antibacterial mechanism of both silver and tellurite, as well as to give insight into how the mixture provides synergism as a combination. Here, we defined the differentially expressed gene profile of Pseudomonas aeruginosa under silver, tellurite, and silver-tellurite combination stress using an RNA sequencing approach to examine the global transcriptional changes in the challenged cultures grown in simulated wound fluid. The study was complemented with metabolomics and biochemistry assays. Both metal ions mainly affected four cellular processes, including sulfur homeostasis, reactive oxygen species response, energy pathways, and the bacterial cell membrane (for silver). Using a Caenorhabditis elegans animal model we showed silver-tellurite has reduced toxicity over individual metal/metalloid salts and provides increased antioxidant properties to the host. This work demonstrates that the addition of tellurite would improve the efficacy of silver in biomedical applications. IMPORTANCE Metals and/or metalloids could represent antimicrobial alternatives for industrial and clinical applications (e.g., surface coatings, livestock, and topical infection control) because of their great properties, such as good stability and long half-life. Silver is the most common antimicrobial metal, but resistance prevalence is high, and it can be toxic to the host above a certain concentration. We found that a silver-tellurite composition has antibacterial synergistic effect and that the combination is beneficial to the host. So, the efficacy and application of silver could increase by adding tellurite in the recommended concentration(s). We used different methods to evaluate the mechanism for how this combination can be so incredibly synergistic, leading to efficacy against antibiotic- and silver-resistant isolates. Our two main findings are that (i) both silver and tellurite mostly target the same pathways and (ii) the coapplication of silver with tellurite tends not to target new pathways but targets the same pathways with an amplified change.PMID:37409940 | DOI:10.1128/spectrum.00628-23

J Bone Miner Res. 2023 Jul 6. doi: 10.1002/jbmr.4876. Online ahead of print.ABSTRACTIn a 36 month RCT examining the effect of high dose vitamin D3 on radial and tibial total bone mineral density (TtBMD), measured by high resolution peripheral quantitative tomography (HR-pQCT), participants (311 healthy males and females aged 55-70 years with DXA T-scores > -2.5, without vitamin D deficiency) were randomized to receive 400 IU (N = 109); 4,000 IU (N = 100); 10,000 IU (N = 102) daily. Participants had HR-pQCT radius and tibia scans and blood sampling at baseline, 6, 12, 24 and 36 months. This secondary analysis examined the effect of vitamin D dose on plasma measurements of the vitamin D metabolome by liquid chromatography-tandem mass spectrometry (LC-MS/MS), exploring whether the observed decline in TtBMD was associated with changes in four key metabolites [25-(OH)D3 ; 24,25-(OH)2 D3 ; 1,25-(OH)2 D3 ; and 1,24,25-(OH)3 D3 ]. Relationship between peak values in vitamin D metabolites and change in TtBMD over 36 months was assessed using linear regression, controlling for sex. Increasing vitamin D dose was associated with a marked increase in 25-(OH)D3 , 24,25-(OH)2 D3 and 1,24,25-(OH)3 D3 , but no dose-related change in plasma 1,25-(OH)2 D3 was observed. There was a significant negative slope for radius TtBMD and 1,24,25-(OH)3 D3 (-0.05, 95%CI -0.08, -0.03, p < 0.001) after controlling for sex. A significant interaction between TtBMD and sex was seen for 25-(OH)D3 (female: -0.01, 95%CI -0.12,-0.07; male: -0.04, 95%CI -0.06,-0.01, p = 0.001) and 24,25-(OH)2 D3 (female: -0.75, 95%CI -0.98, -0.52; male: -0.35, 95%CI -0.59, -0.11, p < 0.001). For the tibia there was a significant negative slope for 25-(OH)D3 (-0.03, 95%CI -0.05, -0.01, p < 0.001), and 24,25-(OH)2 D3 (-0.30, 95%CI -0.44, -0.16, p < 0.001), and 1,24,25-(OH)3 D3 (-0.03, 95%CI -0.05, -0.01, p = 0.01) after controlling for sex. These results suggest vitamin D metabolites other than 1,25-(OH)2 D3 may be responsible for the bone loss seen in the Calgary vitamin D Study. Although plasma 1,25-(OH)2 D3 did not change with vitamin D dose, it is possible rapid catabolism to 1,24,25-(OH)3 D3 prevented detection of a dose-related rise in plasma 1,25-(OH)2 D3 . This article is protected by copyright. All rights reserved.PMID:37409797 | DOI:10.1002/jbmr.4876

Biofactors. 2023 Jul 6. doi: 10.1002/biof.1988. Online ahead of print.ABSTRACTReduction in oxygen levels is a key feature in the physiology of the bone marrow (BM) niche where hematopoiesis occurs. The BM niche is a highly vascularized tissue and endothelial cells (ECs) support and regulate blood cell formation from hematopoietic stem cells (HSCs). While in vivo studies are limited, ECs when cultured in vitro at low O2 (<5%), fail to support functional HSC maintenance due to oxidative environment. Therefore, changes in EC redox status induced by antioxidant molecules may lead to alterations in the cellular response to hypoxia likely favoring HSC self-renewal. To evaluate the impact of redox regulation, HUVEC, exposed for 1, 6, and 24 h to 3% O2 were treated with N-(N-acetyl-l-cysteinyl)-S-acetylcysteamine (I-152). Metabolomic analyses revealed that I-152 increased glutathione levels and influenced the metabolic profiles interconnected with the glutathione system and the redox couples NAD(P)+/NAD(P)H. mRNA analysis showed a lowered gene expression of HIF-1α and VEGF following I-152 treatment whereas TRX1 and 2 were stimulated. Accordingly, the proteomic study revealed the redox-dependent upregulation of thioredoxin and peroxiredoxins that, together with the glutathione system, are the main regulators of intracellular ROS. Indeed, a time-dependent ROS production under hypoxia and a quenching effect of the molecule were evidenced. At the secretome level, the molecule downregulated IL-6, MCP-1, and PDGF-bb. These results suggest that redox modulation by I-152 reduces oxidative stress and ROS level in hypoxic ECs and may be a strategy to fine-tune the environment of an in vitro BM niche able to support functional HSC maintenance.PMID:37409789 | DOI:10.1002/biof.1988

Cancer Med. 2023 Jul 6. doi: 10.1002/cam4.6283. Online ahead of print.ABSTRACTBACKGROUND: The aim of this study is to investigate the profiles of gut microbiota and metabolites in acute myelocytic leukemia (AML) patients treated with/without chemotherapy.METHODS: Herein, high-throughput 16S rRNA gene sequencing was performed to analysis gut microbiota profiles, and liquid chromatography and mass spectrometry were performed to analysis metabolites profiles. The correlation between gut microbiota biomarkers identified by LEfSe and differentially expressed metabolites were determined by spearman association analysis.RESULTS: The results showed the distinguished gut microbiota and metabolites profiles between AML patients and control individuals or AML patients treated with chemotherapy. Compared to normal populations, the ratio of Firmicutes to Bacteroidetes was increased at the phylum level than that in AML patients, and LEfSe analysis identified Collinsella and Coriobacteriaceae as biomarkers of AML patients. Differential metabolite analysis indicated that, compared to AML patients, numerous differential amino acids and analogs could be observed in control individuals and AML patients treated with chemotherapy. Interestingly, spearman association analysis demonstrated that plenty of bacteria biomarkers shows statistical correlations with differentially expressed amino acid metabolites. In addition, we found that both Collinsella and Coriobacteriaceae demonstrate remarkable positive correlation with hydroxyprolyl-hydroxyproline, prolyl-tyrosine, and tyrosyl-proline.CONCLUSION: In conclusion, our present study investigated the role of the gut-microbiome-metabolome axis in AML and revealed the possibility of AML treatment by gut-microbiome-metabolome axis in the further.PMID:37409640 | DOI:10.1002/cam4.6283

J Med Virol. 2023 Jul;95(7):e28898. doi: 10.1002/jmv.28898.ABSTRACTOvarian cancers, especially high-grade serous ovarian cancer (HGSOC), are one of the most lethal age-independent gynecologic malignancies. Although pathogenic microorganisms have been demonstrated to participate in the pathogenesis of multiple types of tumors, their potential roles in the development of ovarian cancer remain unclear. To gain an insight into the microbiome-associated pathogenesis of ovarian cancer and identify potential diagnostic biomarkers, we applied different techniques to analyse the microbiome and serum metabolome of different resources. We found that the vaginal microbiota in ovarian cancer mouse models was under dysbiosis, with altered metabolite configurations that may result from amino acid or lysophospholipid metabolic processes. Local therapeutic intervention with a broad spectrum of antibiotics was effective in reversing microbiota dysbiosis and suppressing carcinogenic progression. As the ovary is situated deeply in the pelvis, it is difficult to directly monitor the ovarian microbial community. Our findings provide alternative options for utilizing the vaginal bacteria as noninvasive biomarkers, such as Burkholderia (area under the curve = 0.8843, 95% confidence interval: 0.743-1.000), which supplement the current invasive diagnostic methods for monitoring ovarian cancer progression and contribute to the development of advanced microbe-based diagnosis and adjuvant therapies.PMID:37409619 | DOI:10.1002/jmv.28898

Food Funct. 2023 Jul 6. doi: 10.1039/d3fo01810e. Online ahead of print.ABSTRACTThe Maillard reaction (MR) is inevitable in food processing and daily cooking, but whether the MR degree would affect the biological activity of the protein in vivo remains unknown. In this study, we used untargeted metabolomics techniques to explore the effects of two different levels of Maillard reaction products (MRPs) of ovalbumin (OVA) on metabolites in colitis mice. Studies have shown that MR could affect protein metabolites in vivo and MRPs of OVA could reduce the concentrations of IL-6 and IL-1β and intestinal permeability. Metabolomics results showed that the degree of MR affected the abundance of oligopeptides and bile acids in vivo. This study revealed that MRPs could regulate the abundance of metabolites such as taurocholic acid and putrescine, and repair the intestinal barrier in colitis mice through signaling pathways such as secondary bile acid biosynthesis, bile secretion and ABC transporters. The investigation has significant implications for the digestion properties and metabolite regulation of MRPs in vivo, and also promotes the application of MRPs in functional foods.PMID:37409580 | DOI:10.1039/d3fo01810e

Psychiatry Investig. 2023 Jul 7. doi: 10.30773/pi.2022.0336. Online ahead of print.ABSTRACTPsychiatric disorders remain one of the most debilitating conditions; however, most patients are never diagnosed and do not seek treatment. Despite its massive burden on modern society and the health system, many hurdles prevent proper diagnosis and management of these disorders. The diagnosis is primarily based on clinical symptoms, and efforts to find appropriate biomarkers have not been practical. Through the past years, researchers have put a tremendous effort into finding biomarkers in "omics" fields: genomics, transcriptomics, proteomics, metabolomics, and epigenomics. This article reviews the evolving field of radiomics and its role in diagnosing psychiatric disorders as the sixth potential "omics." The first section of this paper elaborates on the definition of radiomics and its potential to provide a detailed structural study of the brain. Following that, we have provided the latest promising results of this novel approach in a broad range of psychiatric disorders. Radiomics fits well within the concept of psychoradiology. Besides volumetric analysis, radiomics takes advantage of many other features. This technique may open a new field in psychiatry for diagnosing and classifying psychiatric disorders and treatment response prediction in the era of precision and personalized medicine. The initial results are encouraging, but radiomics in psychiatry is still in its infancy. Despite the extensive burden of psychiatric disorders, there are very few published studies in this field, with small patient populations. The lack of prospective multi-centric studies and heterogeneity of studies in design are the significant barriers against the clinical adaptation of radiomics in psychoradiology.PMID:37409371 | DOI:10.30773/pi.2022.0336

Front Plant Sci. 2023 Jun 12;14:1088537. doi: 10.3389/fpls.2023.1088537. eCollection 2023.ABSTRACTINTRODUCTION: Cotton (Gossypium hirsutum L.) is susceptible to long-term waterlogging stress; however, genomic information of cotton response mechanisms toward long days of waterlogging is quite elusive.METHODS: Here, we combined the transcriptome and metabolome expression level changes in cotton roots after 10 and 20 days of waterlogging stress treatment pertaining to potential resistance mechanisms in two cotton genotypes.RESULTS AND DISCUSSION: Numerous adventitious roots and hypertrophic lenticels were induced in CJ1831056 and CJ1831072. Transcriptome analysis revealed 101,599 differentially expressed genes in cotton roots with higher gene expression after 20 days of stress. Reactive oxygen species (ROS) generating genes, antioxidant enzyme genes, and transcription factor genes (AP2, MYB, WRKY, and bZIP) were highly responsive to waterlogging stress among the two genotypes. Metabolomics results showed higher expressions of stress-resistant metabolites sinapyl alcohol, L-glutamic acid, galactaric acid, glucose 1-phosphate, L-valine, L-asparagine, and melibiose in CJ1831056 than CJ1831072. Differentially expressed metabolites (adenosine, galactaric acid, sinapyl alcohol, L-valine, L-asparagine, and melibiose) significantly correlated with the differentially expressed PRX52, PER1, PER64, and BGLU11 transcripts. This investigation reveals genes for targeted genetic engineering to improve waterlogging stress resistance to enhance abiotic stress regulatory mechanisms in cotton at the transcript and metabolic levels of study.PMID:37409297 | PMC:PMC10319419 | DOI:10.3389/fpls.2023.1088537