Integrative Molecular Phenotyping
INTEGRATIVE MOLECULAR
PHENOTYPING
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY

PubMed

Vaginal epithelial dysfunction is mediated by the microbiome, metabolome, and mTOR signaling

Sun, 07/05/2023 - 12:00
Cell Rep. 2023 May 5;42(5):112474. doi: 10.1016/j.celrep.2023.112474. Online ahead of print.ABSTRACTBacterial vaginosis (BV) is characterized by depletion of Lactobacillus and overgrowth of anaerobic and facultative bacteria, leading to increased mucosal inflammation, epithelial disruption, and poor reproductive health outcomes. However, the molecular mediators contributing to vaginal epithelial dysfunction are poorly understood. Here we utilize proteomic, transcriptomic, and metabolomic analyses to characterize biological features underlying BV in 405 African women and explore functional mechanisms in vitro. We identify five major vaginal microbiome groups: L. crispatus (21%), L. iners (18%), Lactobacillus (9%), Gardnerella (30%), and polymicrobial (22%). Using multi-omics we show that BV-associated epithelial disruption and mucosal inflammation link to the mammalian target of rapamycin (mTOR) pathway and associate with Gardnerella, M. mulieris, and specific metabolites including imidazole propionate. Experiments in vitro confirm that type strain G. vaginalis and M. mulieris supernatants and imidazole propionate directly affect epithelial barrier function and activation of mTOR pathways. These results find that the microbiome-mTOR axis is a central feature of epithelial dysfunction in BV.PMID:37149863 | DOI:10.1016/j.celrep.2023.112474

Mitochondrial citrate metabolism and efflux regulate BeWo differentiation

Sat, 06/05/2023 - 12:00
Sci Rep. 2023 May 6;13(1):7387. doi: 10.1038/s41598-023-34435-x.ABSTRACTCytotrophoblasts fuse to form and renew syncytiotrophoblasts necessary to maintain placental health throughout gestation. During cytotrophoblast to syncytiotrophoblast differentiation, cells undergo regulated metabolic and transcriptional reprogramming. Mitochondria play a critical role in differentiation events in cellular systems, thus we hypothesized that mitochondrial metabolism played a central role in trophoblast differentiation. In this work, we employed static and stable isotope tracing untargeted metabolomics methods along with gene expression and histone acetylation studies in an established BeWo cell culture model of trophoblast differentiation. Differentiation was associated with increased abundance of the TCA cycle intermediates citrate and α-ketoglutarate. Citrate was preferentially exported from mitochondria in the undifferentiated state but was retained to a larger extent within mitochondria upon differentiation. Correspondingly, differentiation was associated with decreased expression of the mitochondrial citrate transporter (CIC). CRISPR/Cas9 disruption of the mitochondrial citrate carrier showed that CIC is required for biochemical differentiation of trophoblasts. Loss of CIC resulted in broad alterations in gene expression and histone acetylation. These gene expression changes were partially rescued through acetate supplementation. Taken together, these results highlight a central role for mitochondrial citrate metabolism in orchestrating histone acetylation and gene expression during trophoblast differentiation.PMID:37149697 | DOI:10.1038/s41598-023-34435-x

Integrative analysis of metabolome and transcriptome profiles to highlight aroma determinants in Aglianico and Falanghina grape berries

Sat, 06/05/2023 - 12:00
BMC Plant Biol. 2023 May 6;23(1):241. doi: 10.1186/s12870-023-04251-6.ABSTRACTBACKGROUND: The biochemical makeup of grape berries at harvest is essential for wine quality and depends on a fine transcriptional regulation occurring during berry development. In this study, we conducted a comprehensive survey of transcriptomic and metabolomic changes occurring in different berry tissues and developmental stages of the ancient grapes Aglianico and Falanghina to establish the patterns of the secondary metabolites contributing to their wine aroma and investigate the underlying transcriptional regulation.RESULTS: Over two hundred genes related to aroma were found, of which 107 were differentially expressed in Aglianico and 99 in Falanghina. Similarly, 68 volatiles and 34 precursors were profiled in the same samples. Our results showed a large extent of transcriptomic and metabolomic changes at the level of isoprenoids (terpenes, norisoprenoids), green leaf volatiles (GLVs), and amino acid pathways, although the terpenoid metabolism was the most distinctive for Aglianico, and GLVs for Falanghina. Co-expression analysis that integrated metabolome and transcriptome data pinpointed 25 hub genes as points of biological interest in defining the metabolic patterns observed. Among them, three hub genes encoding for terpenes synthases (VvTPS26, VvTPS54, VvTPS68) in Aglianico and one for a GDP-L-galactose phosphorylase (VvGFP) in Falanghina were selected as potential active player underlying the aroma typicity of the two grapes.CONCLUSION: Our data improve the understanding of the regulation of aroma-related biosynthetic pathways of Aglianico and Falanghina and provide valuable metabolomic and transcriptomic resources for future studies in these varieties.PMID:37149574 | DOI:10.1186/s12870-023-04251-6

A Novel Assessment of Metabolic Pathways in Peritoneal Metastases from Low-Grade Appendiceal Mucinous Neoplasms

Sat, 06/05/2023 - 12:00
Ann Surg Oncol. 2023 May 6. doi: 10.1245/s10434-023-13587-0. Online ahead of print.ABSTRACTBACKGROUND: There is a paucity of targeted therapies for patients with pseudomyxoma peritonei (PMP) secondary to low-grade appendiceal mucinous neoplasms (LAMNs). Dysregulated metabolism has emerged as a hallmark of cancer, and the relationship of metabolomics and cancer is an area of active scientific exploration. We sought to characterize phenotypic differences found in peritoneal metastases (PM) derived from LAMN versus adenocarcinoma.METHODS: Tumors were washed with phosphate-buffered saline (PBS), microdissected, then dissociated in ice-cold methanol dried and reconstituted in pyridine. Samples were derivatized in tert-butyldimethylsilyl (TBDMS) and subjected to gas chromatography-coupled mass spectrometry. Metabolites were assessed based on a standard library. RNA sequencing was performed, with pathway and network analyses on differentially expressed genes.RESULTS: Eight peritoneal tumor samples were obtained and analyzed: LAMNs (4), and moderate to poorly differentiated adenocarcinoma (colon [1], appendix [3]). Decreases in pyroglutamate, fumarate, and cysteine in PM from LAMNs were found compared with adenocarcinoma. Analyses showed the differential gene expression was dominated by the prevalence of metabolic pathways, particularly lipid metabolism. The gene retinol saturase (RETSAT), downregulated by LAMN, was involved in the multiple metabolic pathways that involve lipids. Using network mapping, we found IL1B signaling to be a potential top-level modulation candidate.CONCLUSIONS: Distinct metabolic signatures may exist for PM from LAMN versus adenocarcinoma. A multitude of genes are differentially regulated, many of which are involved in metabolic pathways. Additional research is needed to identify the significance and applicability of targeting metabolic pathways in the potential development of novel therapeutics for these challenging tumors.PMID:37149550 | DOI:10.1245/s10434-023-13587-0

Short-term exposition to acute Cadmium toxicity induces the loss of root gravitropic stimuli perception through PIN2-mediated auxin redistribution in Arabidopsis thaliana (L.) Heynh

Sat, 06/05/2023 - 12:00
Plant Sci. 2023 May 4:111726. doi: 10.1016/j.plantsci.2023.111726. Online ahead of print.ABSTRACTCadmium (Cd), one of the most widespread and water-soluble polluting heavy metals, has been widely studied on plants, even if the mechanisms underlying its phytotoxicity remain elusive. Indeed, most experiments are performed using extensive exposure time to the toxicants, not observing the primary targets affected. The present work studied Cd effects on Arabidopsis thaliana (L.) Heynh's root apical meristem (RAM) exposed for short periods (24h and 48h) to acute phytotoxic concentrations (100 and 150µM). The effects were studied through integrated morpho-histological, molecular, pharmacological and metabolomic analyses, highlighting that Cd inhibited primary root elongation by affecting the meristem zone via altering cell expansion. Moreover, Cd altered Auxin accumulation in RAM and affected PINs polar transporters particularly PIN2. In addition, we observed that high Cd concentration induced accumulation of reactive oxygen species (ROS) in roots, which resulted in an altered organization of cortical microtubules and the starch and sucrose metabolism, altering the statolith formation and, consequently, the gravitropic root response. Our results demonstrated that short Cd exposition (24h) affected cell expansion preferentially, altering auxin distribution and inducing ROS accumulation, which resulted in an alteration of gravitropic response and microtubules orientation pattern.PMID:37149227 | DOI:10.1016/j.plantsci.2023.111726

Analysis of the effect of triclosan on gonadal differentiation of zebrafish based on metabolome

Sat, 06/05/2023 - 12:00
Chemosphere. 2023 May 4:138856. doi: 10.1016/j.chemosphere.2023.138856. Online ahead of print.ABSTRACTAlthough the previous research confirmed that triclosan (TCS) affects the female proportion at the early stage of zebrafish (Danio rerio) and has an estrogen effect, the mechanism by which TCS affects the sex differentiation of zebrafish is not entirely clear. In this study, zebrafish embryos were exposed to different concentrations of TCS (0, 2, 10, and 50 μg/L) for 50 consecutive days. The expression of sex differentiation related genes and metabolites were then determined in larvae using reverse transcription quantitative polymerase chain reaction (RT-qPCR) and Liquid Chromatography-Mass Spectrometer (LC-MS), respectively. TCS upregulated the expression of the sox9a, dmrt1a and amh genes, down-regulating the expression of wnt4a, cyp19a1b, cyp19a1a, and vtg2 gene. The overlapped classification of Significant Differential Metabolites (SDMs) between the control group and three TCS treated groups related to gonadal differentiation was Steroids and steroid derivatives, including 24 down-regulated SDMs. The enriched pathways related to gonadal differentiation were Steroid hormone biosynthesis, Retinol metabolism, Metabolism of xenobiotics by cytochrome P450, and Cortisol synthesis and secretion. Moreover, SDMs were significantly enriched in Steroid hormone biosynthesis in the 2 μg/L TCS group, which included Dihydrotestosterone, Cortisol, 11beta-hydroxyandrost-4-ene-3, 17-dione, 21-Hydroxypregnenolone, Androsterone, Androsterone glucuronide, Estriol, Estradiol, 19-Hydroxytestosterone, Cholesterol, Testosterone, and Cortisone acetate. Results showed that TCS affects the female proportion mainly through Steroid hormone biosynthesis, in which aromatase plays a key role in zebrafish. Retinol metabolism, metabolism of xenobiotics by cytochrome P450, and cortisol synthesis and secretion may also participate in TCS-mediated sex differentiation. These findings reveal the molecular mechanisms of TCS-induced sex differentiation, and provide theoretical guidance for the maintenance of water ecological balance.PMID:37149099 | DOI:10.1016/j.chemosphere.2023.138856

Xanthine-induced deficits in hippocampal behavior and abnormal expression of hemoglobin genes

Sat, 06/05/2023 - 12:00
Behav Brain Res. 2023 May 4:114476. doi: 10.1016/j.bbr.2023.114476. Online ahead of print.ABSTRACTThe prevalence of mental disorders such as depression and anxiety is high and often comorbid with other diseases. Chronic stress is a common risk factor for these disorders, but the mechanisms behind their development are not yet fully understood. Metabolomics has revealed a close association between purine and pyrimidine metabolism and depression and anxiety, with increased levels of serum xanthine observed in both humans and mice. Xanthine is known as purine metabolism, and this compound shows several biological activities, but the impact of xanthine on our brain function is still unclear. The hippocampus, which plays a crucial role in memory and learning, is also implicated in the pathophysiology of depression and anxiety. Here, we investigated the effects of xanthine intraperitoneal administration on spatial memory and anxiety-like behavior in mice. The findings indicated that xanthine administration induced a deficit of hippocampus-dependent spatial memory and a tendency to anxiety-like behavior in mice. RNA-seq analysis showed that xanthine administration upregulated hemoglobin (Hb) genes involved in oxygen transport in the hippocampus. The upregulated Hb genes occurred in the neuronal cells, and in vitro experiments revealed that both Hba-a1 derived from mice and HBA2 derived from humans were upregulated by xanthine treatment. These observations suggest that the xanthine-induced Hb in the hippocampus could be related to spatial memory deficit and anxiety. This study sheds light on the direct effects of xanthine on the brain and its potential role in the development of depression and anxiety symptoms caused by chronic stress.PMID:37148916 | DOI:10.1016/j.bbr.2023.114476

Vinpocetine mitigates DMH-induce pre-neoplastic colon damage in rats through inhibition of pro-inflammatory cytokines

Sat, 06/05/2023 - 12:00
Int Immunopharmacol. 2023 May 4;119:110236. doi: 10.1016/j.intimp.2023.110236. Online ahead of print.ABSTRACTColorectal cancer (CRC) is currently recognized as the third most prevalent cancer worldwide. Vinpocetine is a synthetic derivative of the vinca alkaloid vincamine. It has been found effective in ameliorating the growth and progression of cancerous cells. However, its pharmacological effect on colon damage remains elusive. Hence, in this study, we have shown the role of vinpocetine in DMH-induced colon carcinogenesis. At first, male albino Wistar rats were administered with DMH consistently for four weeks to induce pre-neoplastic colon damage. Afterward, animals were treated with vinpocetine (4.2 and 8.4 mg/kg/day p.o.) for 15 days. Serum samples were collected to assess the physiological parameters, including ELISA and NMR metabolomics. Colon from all the groups was collected and processed separately for histopathology and western blot analysis. Vinpocetine attenuated the altered plasma parameters; lipid profile and showed anti-proliferative action as evidenced by suppressed COX-2 stimulation and decreased levels of IL-1β, IL-2, IL-6, and IL-10. Vinpocetine is significantly effective in preventing CRC which may be associated with its anti-inflammatory and antioxidant potential. Accordingly, vinpocetine could serve as a potential anticancer agent for CRC treatment and thus be considered for future clinical and therapeutic research.PMID:37148772 | DOI:10.1016/j.intimp.2023.110236

CAG Repeat Expansion in THAP11 Is Associated with a Novel Spinocerebellar Ataxia

Sat, 06/05/2023 - 12:00
Mov Disord. 2023 May 6. doi: 10.1002/mds.29412. Online ahead of print.ABSTRACTBACKGROUND: More than 50 loci are associated with spinocerebellar ataxia (SCA), and the most frequent subtypes share nucleotide repeats expansion, especially CAG expansion.OBJECTIVE: The objective of this study was to confirm a novel SCA subtype caused by CAG expansion.METHODS: We performed long-read whole-genome sequencing combined with linkage analysis in a five-generation Chinese family, and the finding was validated in another pedigree. The three-dimensional structure and function of THAP11 mutant protein were predicted. Polyglutamine (polyQ) toxicity of THAP11 gene with CAG expansion was assessed in skin fibroblasts of patients, human embryonic kidney 293 and Neuro-2a cells.RESULTS: We identified THAP11 as the novel causative SCA gene with CAG repeats ranging from 45 to 100 in patients with ataxia and from 20 to 38 in healthy control subjects. Among the patients, the number of CAA interruptions within CAG repeats was decreased to 3 (up to 5-6 in controls), whereas the number of 3' pure CAG repeats was up to 32 to 87 (4-16 in controls), suggesting that the toxicity of polyQ protein was length dependent on the pure CAG repeats. Intracellular aggregates were observed in cultured skin fibroblasts from patients. THAP11 polyQ protein was more intensely distributed in the cytoplasm of cultured skin fibroblasts from patients, which was replicated with in vitro cultured neuro-2a transfected with 54 or 100 CAG repeats.CONCLUSIONS: This study identified a novel SCA subtype caused by intragenic CAG repeat expansion in THAP11 with intracellular aggregation of THAP11 polyQ protein. Our findings extended the spectrum of polyQ diseases and offered a new perspective in understanding polyQ-mediated toxic aggregation. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.PMID:37148549 | DOI:10.1002/mds.29412

Metabolic Signatures of Performance in Elite World Tour Professional Male Cyclists

Sat, 06/05/2023 - 12:00
Sports Med. 2023 May 6. doi: 10.1007/s40279-023-01846-9. Online ahead of print.ABSTRACTBACKGROUND AND OBJECTIVE: Metabolomics studies of recreational and elite athletes have been so far limited to venipuncture-dependent blood sample collection in the setting of controlled training and medical facilities. However, limited to no information is currently available to determine if findings in laboratory settings are translatable to a real-world scenario in elite competitions. The goal of this study was to define molecular signatures of exertion under controlled exercise conditions and use these signatures as a framework for assessing cycling performance in a World Tour competition.METHODS: To characterize molecular profiles of exertion in elite athletes during cycling, we performed metabolomics analyses on blood isolated from 28 international-level, elite, World Tour professional male athletes from a Union Cycliste Internationale World Team taken before and after a graded exercise test to volitional exhaustion and before and after a long aerobic training session. Moreover, established signatures were then used to characterize the metabolic physiology of five of these cyclists who were selected to represent the same Union Cycliste Internationale World Team during a seven-stage elite World Tour race.RESULTS: Using dried blood spot collection to circumvent logistical hurdles associated with field sampling, these studies defined metabolite signatures and fold change ranges of anaerobic or aerobic exertion in elite cyclists, respectively. Blood profiles of lactate, carboxylic acids, fatty acids, and acylcarnitines differed between exercise modes. The graded exercise test elicited significant two- to three-fold accumulations in lactate and succinate, in addition to significant elevations in free fatty acids and acylcarnitines. Conversely, the long aerobic training session elicited a larger magnitude of increase in fatty acids and acylcarnitines without appreciable increases in lactate or succinate. Comparable signatures were revealed after sprinting and climbing stages, respectively, in a World Tour race. In addition, signatures of elevated fatty acid oxidation capacity correlated with competitive performance.CONCLUSIONS: Collectively, these studies provide a unique view of alterations in the blood metabolome of elite athletes during competition and at the peak of their performance capabilities. Furthermore, they demonstrate the utility of dried blood sampling for omics analysis, thereby enabling molecular monitoring of athletic performance in the field during training and competition.PMID:37148487 | DOI:10.1007/s40279-023-01846-9

Sebacic acid as a potential age-related biomarker of liver aging: evidence linking mice and human

Sat, 06/05/2023 - 12:00
J Gerontol A Biol Sci Med Sci. 2023 May 6:glad121. doi: 10.1093/gerona/glad121. Online ahead of print.ABSTRACTThe aging process is complicated and involves diverse organ dysfunction; furthermore, the biomarkers that are able to reflect biological aging are eagerly sought after in order to monitor the system-wide decline associated with the aging process. To address this, we performed a metabolomics analysis using a longitudinal cohort study from Taiwan (N=710) and established plasma metabolomic age using a machine learning algorithm. The resulting estimation of age acceleration among the older adults was found to be correlated with HOMA-insulin resistance. In addition, a sliding window analysis was used to investigate the undulating decrease in hexanoic and heptanoic acids that occurs among the older adults at different ages. A comparison of the metabolomic alterations associated with aging between humans and mice implied that ω-oxidation of medium chain fatty acids was commonly dysregulated in older subjects. Among these fatty acids, sebacic acid, an ω-oxidation product produced by the liver, was significantly decreased in the plasma of both older humans and aged mice. Notably, an increase in the production and consumption of sebacic acid within the liver tissue of aged mice was observed, along with an elevation of pyruvate-to-lactate conversion. Taken together, our study reveals that sebacic acid and metabolites of ω-oxidation are the common aging biomarkers in both humans and mice. The further analysis suggests that sebacic acid may play an energetic role to supporting the production of acetyl-CoA during liver aging, and thus its alteration in plasma concentration potentially reflects the aging process.PMID:37148322 | DOI:10.1093/gerona/glad121

Integrated genetic and metabolic characterization of Latin American cassava (Manihot esculenta) germplasm

Sat, 06/05/2023 - 12:00
Plant Physiol. 2023 May 6:kiad269. doi: 10.1093/plphys/kiad269. Online ahead of print.ABSTRACTCassava (Manihot esculenta Crantz) is an important staple crop for food security in Africa and South America. The present study describes an integrated genomic and metabolomic approach to the characterization of Latin American cassava germplasm. Classification based on genotyping correlated with the leaf metabolome and indicated a key finding of adaption to specific eco-geographical environments. In contrast the root metabolome did not relate to genotypic clustering, suggesting different spatial regulation of this tissue's metabolome. The data were used to generate pan-metabolomes for specific tissues, and the inclusion of phenotypic data enabled the identification of metabolic sectors underlying traits of interest. For example, tolerance to whiteflies (Aleurotrachelus socialis) was not linked directly to cyanide content but to cell wall-related phenylpropanoid or apocarotenoid content. Collectively, these data advance the community resources and provide valuable insight into new candidate parental breeding materials with traits of interest directly related to combating food security.PMID:37148300 | DOI:10.1093/plphys/kiad269

Integrated multi-omics analysis reveals unique signatures of paclitaxel-loaded poly(lactide-co-glycolide) nanoparticles treatment of head and neck cancer cells

Sat, 06/05/2023 - 12:00
Proteomics. 2023 May 6:e2200380. doi: 10.1002/pmic.202200380. Online ahead of print.ABSTRACTThe use of poly(lactide-co-glycolide) (PLGA) nanoparticles (NPs) as carriers for chemotherapeutic drugs is regarded as an actively targeted nano-therapy for the specific delivery of anti-cancer drugs to target cells. However, the exact mechanism by which PLGA NPs boost anticancer cytotoxicity at the molecular level remains largely unclear. This study employed different molecular approaches to define the response of carcinoma FaDu cells to different types of treatment, specifically: paclitaxel (PTX) alone, drug free PLGA NPs, and PTX-loaded PTX-PLGA NPs. Functional cell assays revealed that PTX-PLGA NPs treated cells had a higher level of apoptosis than PTX alone, whereas the complementary, UHPLC-MS/MS (TIMS-TOF) based multi-omics analyses revealed that PTX-PLGA NPs treatment resulted in increased abundance of proteins associated with tubulin, as well as metabolites such as 5-thymidylic acid, PC(18:1(9Z)/18:1(9Z0), vitamin D, and sphinganine among others. The multi-omics analyses revealed new insights about the molecular mechanisms underlying the action of novel anticancer NP therapies. In particular, PTX-loaded NPs appeared to exacerbate specific changes induced by both PLGA-NPs and PTX as a free drug. Hence, the PTX-PLGA NPs' molecular mode of action, seen in greater detail, depends on this synergy that ultimately accelerates the apoptotic process, resulting in cancer cell death.PMID:37148169 | DOI:10.1002/pmic.202200380

Population divergence in heat and drought responses of a coastal plant: from metabolic phenotypes to plant morphology and growth

Sat, 06/05/2023 - 12:00
J Exp Bot. 2023 May 6:erad147. doi: 10.1093/jxb/erad147. Online ahead of print.ABSTRACTStudying intra-specific variation in multi-stress responses is central for predicting and managing the population dynamics of wild plant species under rapid global change. Yet, it remains a challenging goal in this field to integrate knowledge on the complex biochemical underpinnings for the targeted 'non-model' species. Here, we studied divergence in combined drought and heat responses among Northern and Southern European populations of the dune plant Cakile maritima, by combining comprehensive plant phenotyping with metabolic profiling via FT-ICR-MS and UPLC-TQ-MS/MS. We observed pronounced constitutive divergence in growth phenology, leaf functional traits and defence chemistry (glucosinolates, alkaloids) among population origins. Most importantly, the magnitude of growth reduction under drought was partly weaker in southern plants and associated with divergence in plastic growth responses (leaf abscission) and the modulation of primary and specialized metabolites with known central functions not only in plant abiotic but also biotic stress responses. Our study indicates that divergent selection has shaped the constitutive and drought/heat-induced expression of numerous morphological and biochemical functional traits to mediate higher abiotic stress resistance in southern Cakile populations, and highlights that metabolomics can be a powerful tool to explore the mechanistic underpinnings of local adaptation in 'non-model' species.PMID:37147850 | DOI:10.1093/jxb/erad147

Multi-omics approaches for revealing the etiology of cancer: from genomics, exposomics, metabolomics to system epidemiology

Sat, 06/05/2023 - 12:00
Zhonghua Liu Xing Bing Xue Za Zhi. 2023 Apr 10;44(4):521-528. doi: 10.3760/cma.j.cn112338-20221201-01026.ABSTRACTIdentifying risk factors of the disease are one of the main tasks of epidemiology. With the advancement of omics technologies (e.g., genome, transcriptome, proteome, metabolome, and exposome), cancer etiology research has entered the stage of systems epidemiology. Genomic research identifies cancer susceptibility loci and uncovers their biological mechanisms. Exposomic research investigates the impact of environmental factors on biological processes and disease risks. The metabolome is downstream of biological regulatory networks, reflecting the effects of the gene, environment, and their interactions, which can help elucidate the biological mechanisms of genetic and environmental risk factors and identify new biomarkers. Here, we reviewed the applications of genomic, exposomic, and metabolomic studies in the etiologic research on cancer. We summarized the importance of multi-omics approaches and systems epidemiology in cancer etiology research and outlined future perspectives.PMID:37147821 | DOI:10.3760/cma.j.cn112338-20221201-01026

Analysis of defense-related gene expression and leaf metabolome in wheat during the early infection stages of Blumeria graminis f.sp. tritici

Fri, 05/05/2023 - 12:00
Phytopathology. 2023 May 5. doi: 10.1094/PHYTO-10-22-0364-R. Online ahead of print.ABSTRACTBlumeria graminis f.sp. tritici (Bgt) is an obligate biotrophic fungal pathogen responsible for powdery mildew in bread wheat (Triticum aestivum L.). Upon Bgt infection, the wheat plant activates basal defense mechanisms namely PAMP-triggered immunity (PTI) in the leaves during the first few days. Understanding this early stage of quantitative resistance is crucial for developing new breeding tools and evaluating plant resistance inducers for sustainable agricultural practices. In this sense, we used a combination of transcriptomic and metabolomic approaches to analyze the early steps of the interaction between Bgt and the moderately susceptible wheat cultivar Pakito. Bgt infection resulted in an increasing expression of genes encoding pathogenesis-related proteins (PR-proteins, PR1, PR4, PR5 and PR8), known to target the pathogen, during the first 48 hours post-inoculation. Moreover, RT-qPCR and metabolomic analyses pointed out the importance of the phenylpropanoid pathway in quantitative resistance against Bgt. Among metabolites linked to this pathway, hydroxycinnamic acid amides containing agmatine and putrescine as amine component accumulated from the second to the fourth day after inoculation. This suggests their involvement in quantitative resistance via cross-linking processes in cell wall for reinforcement, what is supported by the up-regulation of PAL (phenylalanine ammonia-lyase), PR15 (encoding an oxalate oxidase) and POX (peroxidase) after inoculation. Finally, pipecolic acid, which is considered as a signal involved in systemic acquired resistance (SAR), accumulated after inoculation. These new insights lead to a better understanding of basal defense in wheat leaves after Bgt infection.PMID:37147741 | DOI:10.1094/PHYTO-10-22-0364-R

Uncovering the Fate and Risks of Intravenously Injected Prussian Blue Nanoparticles in mice by an Integrated Methodology of Toxicology, Pharmacokinetics, Proteomics, and Metabolomics

Fri, 05/05/2023 - 12:00
Part Fibre Toxicol. 2023 May 5;20(1):18. doi: 10.1186/s12989-023-00529-7.ABSTRACTBACKGROUND: Prussian blue (PB) nanoparticles (NPs) have been intensively investigated for medical applications, but an in-depth toxicological investigation of PB NPs has not been implemented. In the present study, a comprehensive investigation of the fate and risks of PB NPs after intravenous administration was carried out by using a mouse model and an integrated methodology of pharmacokinetics, toxicology, proteomics, and metabolomics.RESULTS: General toxicological studies demonstrated that intravenous administration of PB NPs at 5 or 10 mg/kg could not induce obvious toxicity in mice, while mice treated with a relatively high dose of PB NPs at 20 mg/kg exhibited loss of appetite and weight decrease in the first two days postinjection. Pharmacokinetic studies revealed that intravenously administered PB NPs (20 mg/kg) underwent fast clearance from blood, highly accumulated in the liver and lungs of mice, and finally cleared from tissues. By further integrated proteomics and metabolomics analysis, we found that protein expression and metabolite levels changed significantly in the liver and lungs of mice due to the high accumulation of PB NPs, leading to slight inflammatory responses and intracellular oxidative stress.CONCLUSIONS: Collectively, our integrated experimental data imply that the high accumulation of PB NPs may cause potential risks to the liver and lungs of mice, which will provide detailed references and guidance for further clinical application of PB NPs in the future.PMID:37147710 | DOI:10.1186/s12989-023-00529-7

Cardiac-targeted delivery of nuclear receptor RORα via ultrasound targeted microbubble destruction optimizes the benefits of regular dose of melatonin on sepsis-induced cardiomyopathy

Fri, 05/05/2023 - 12:00
Biomater Res. 2023 May 5;27(1):41. doi: 10.1186/s40824-023-00377-8.ABSTRACTBACKGROUND: Large-dose melatonin treatment in animal experiments was hardly translated into humans, which may explain the dilemma that the protective effects against myocardial injury in animal have been challenged by clinical trials. Ultrasound-targeted microbubble destruction (UTMD) has been considered a promising drug and gene delivery system to the target tissue. We aim to investigate whether cardiac gene delivery of melatonin receptor mediated by UTMD technology optimizes the efficacy of clinically equivalent dose of melatonin in sepsis-induced cardiomyopathy.METHODS: Melatonin and cardiac melatonin receptors in patients and rat models with lipopolysaccharide (LPS)- or cecal ligation and puncture (CLP)-induced sepsis were assessed. Rats received UTMD-mediated cardiac delivery of RORα/cationic microbubbles (CMBs) at 1, 3 and 5 days before CLP surgery. Echocardiography, histopathology and oxylipin metabolomics were assessed at 16-20 h after inducing fatal sepsis.RESULTS: We observed that patients with sepsis have lower serum melatonin than healthy controls, which was observed in the blood and hearts of Sprague-Dawley rat models with LPS- or CLP-induced sepsis. Notably, a mild dose (2.5 mg/kg) of intravenous melatonin did not substantially improve septic cardiomyopathy. We found decreased nuclear receptors RORα, not melatonin receptors MT1/2, under lethal sepsis that may weaken the potential benefits of a mild dose of melatonin treatment. In vivo, repeated UTMD-mediated cardiac delivery of RORα/CMBs exhibited favorable biosafety, efficiency and specificity, significantly strengthening the effects of a safe dose of melatonin on heart dysfunction and myocardial injury in septic rats. The cardiac delivery of RORα by UTMD technology and melatonin treatment improved mitochondrial dysfunction and oxylipin profiles, although there was no significant influence on systemic inflammation.CONCLUSIONS: These findings provide new insights to explain the suboptimal effect of melatonin use in clinic and potential solutions to overcome the challenges. UTMD technology may be a promisingly interdisciplinary pattern against sepsis-induced cardiomyopathy.PMID:37147703 | DOI:10.1186/s40824-023-00377-8

Vitamin K2 supplementation improves impaired glycemic homeostasis and insulin sensitivity for type 2 diabetes through gut microbiome and fecal metabolites

Fri, 05/05/2023 - 12:00
BMC Med. 2023 May 5;21(1):174. doi: 10.1186/s12916-023-02880-0.ABSTRACTBACKGROUND: There is insufficient evidence for the ability of vitamin K2 to improve type 2 diabetes mellitus symptoms by regulating gut microbial composition. Herein, we aimed to demonstrate the key role of the gut microbiota in the improvement of impaired glycemic homeostasis and insulin sensitivity by vitamin K2 intervention.METHODS: We first performed a 6-month RCT on 60 T2DM participants with or without MK-7 (a natural form of vitamin K2) intervention. In addition, we conducted a transplantation of the MK-7-regulated microbiota in diet-induced obesity mice for 4 weeks. 16S rRNA sequencing, fecal metabolomics, and transcriptomics in both study phases were used to clarify the potential mechanism.RESULTS: After MK-7 intervention, we observed notable 13.4%, 28.3%, and 7.4% reductions in fasting serum glucose (P = 0.048), insulin (P = 0.005), and HbA1c levels (P = 0.019) in type 2 diabetes participants and significant glucose tolerance improvement in diet-induced obesity mice (P = 0.005). Moreover, increased concentrations of secondary bile acids (lithocholic and taurodeoxycholic acid) and short-chain fatty acids (acetic acid, butyric acid, and valeric acid) were found in human and mouse feces accompanied by an increased abundance of the genera that are responsible for the biosynthesis of these metabolites. Finally, we found that 4 weeks of fecal microbiota transplantation significantly improved glucose tolerance in diet-induced obesity mice by activating colon bile acid receptors, improving host immune-inflammatory responses, and increasing circulating GLP-1 concentrations.CONCLUSIONS: Our gut-derived findings provide evidence for a regulatory role of vitamin K2 on glycemic homeostasis, which may further facilitate the clinical implementation of vitamin K2 intervention for diabetes management.TRIAL REGISTRATION: The study was registered at https://www.chictr.org.cn (ChiCTR1800019663).PMID:37147641 | DOI:10.1186/s12916-023-02880-0

Sleep insufficiency, circadian rhythms, and metabolomics: the connection between metabolic and sleep disorders

Fri, 05/05/2023 - 12:00
Sleep Breath. 2023 May 6. doi: 10.1007/s11325-023-02828-x. Online ahead of print.ABSTRACTPURPOSE: US adults who report experiencing insufficient sleep are more likely to suffer from metabolic disorders such as hyperlipidemia, diabetes, and obesity than those with sufficient sleep. Less is understood about the underlying molecular mechanisms connecting these phenomena. A systematic, qualitative review of metabolomics studies exploring metabolic changes in response to sleep insufficiency, sleep deprivation, or circadian disruption was conducted in accordance with PRISMA guidelines.METHODS: An electronic literature review in the PubMed database was performed considering publications through May 2021 and screening and eligibility criteria were applied to articles retrieved. The following keywords were used: "metabolomics" and "sleep disorders" or "sleep deprivation" or "sleep disturbance" or "circadian rhythm." After screening and addition of studies included from reference lists of retrieved studies, 16 records were identified for review.RESULTS: Consistent changes in metabolites were observed across studies between individuals experiencing sleep deprivation compared to non-sleep deprived controls. Significant increases in phosphatidylcholines, acylcarnitines, sphingolipids, and other lipids were consistent across studies. Increased levels of amino acids such as tryptophan and phenylalanine were also noted. However, studies were limited to small samples of young, healthy, mostly male participants conducted in short inpatient sessions, limiting generalizability.CONCLUSION: Changes in lipid and amino acid metabolites accompanying sleep deprivation and/or circadian rhythms may indicate cellular membrane and protein breakdown underlying the connection between sleep disturbance, hyperlipidemia, and other metabolic disorders. Larger epidemiological studies examining changes in the human metabolome in response to chronic insufficient sleep would help elucidate this relationship.PMID:37147557 | DOI:10.1007/s11325-023-02828-x

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