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

Bio-molecular map of albumin identifies signatures of severity and early mortality in Acute Liver Failure

Fri, 28/04/2023 - 12:00
J Hepatol. 2023 Apr 26:S0168-8278(23)00241-6. doi: 10.1016/j.jhep.2023.04.018. Online ahead of print.ABSTRACTBACKGROUND AND AIMS: Acute liver failure (ALF) has a high mortality. Alterations in albumin structure and function have been shown to correlate with outcomes in cirrhosis. We undertook a bio-molecular analysis of albumin to determine its correlation with hepatocellular injury and early mortality in ALF.METHOD: Altogether 225 subjects (200-ALF, 25 healthy controls) were enrolled. Albumin was purified from baseline plasma of the training cohort (ALF-40; survivors-8, non-survivors-32, HC-5) and analysed for modifications, functionality, and bound multi-omics signatures and validated in a test cohort [160-ALF; survivors-53, non-survivors-107 and 20-HC].RESULTS: In ALF patients, albumin is more oxidized and glycosylated with a distinct multi-omics profile than controls; more so in non-survivors (p<0.05). In non-survivors, albumin showed increased (p<0.05, FDR<0.01) proteins associated with inflammation, Advanced Glycation End Product; metabolites linked to arginine, proline metabolism, bile acid, and mitochondrial breakdown products. Increased bacterial taxa [Listeria, Clostridium, and others] correlated with lipids [triglycerides (4:0/12:0/12:0) and phosphatidylserine (39:0)] and metabolites (Porphobilinogen, nicotinic acid) in non-survivors (r2>0.7). Multiomics signature-based probability of detection (POD) for non-survival was>90% and showed direct correlation with albumin functionality and clinical parameters (r2>0.85). POD metabolites built on top 5 metabolites; Nicotinic Acid, L-Acetyl carnitine, L-carnitine, Pregnenolone-sulfate, and N-(3-Hydroxybutanoyl)-L-homoserine lactone showed diagnostic efficiency of 98%(AUC=0.98[0.95-1.0]) and segregate ALF patients predisposed to early mortality (log-rank<0.05). On validation using HRMS and five machine learning algorithms in test cohort-1 (plasma and paired one-drop blood), the metabolome panel showed >92% accuracy/sensitivity and specificity for prediction of mortality.CONCLUSION: In ALF, the albumin is hyperoxidised and substantially dysfunctional. Our study outlines distinct 'albuminome' signatures capable of segregating ALF patients predisposed to early mortality or requiring emergency liver transplantation.IMPACTS AND IMPLICATION: Here, we reported the bio-molecular MAP of albumin in Distinct and linked to severity and outcome in acute liver failure (ALF) patients. Detailed structural, functional and Albumin-omics analysis in ALF patients led to the identification and classification of albumin bound biomolecules which could segregate ALF patients predisposed to early mortality. More importantly we found albumin bound metabolites indicative of mitochondrial damage and hyper-inflammation as putative indicator of <30 days mortality in ALF patients. This preclinical study validates the utility of albuminome analysis for understanding the pathophysiology and development of poor outcome indicators in ALF patients.PMID:37116716 | DOI:10.1016/j.jhep.2023.04.018

Dysregulation of steroid metabolome in follicular fluid links phthalate exposure to diminished ovarian reserve of childbearing-age women

Fri, 28/04/2023 - 12:00
Environ Pollut. 2023 Apr 26:121730. doi: 10.1016/j.envpol.2023.121730. Online ahead of print.ABSTRACTThe widespread use of phthalates (PAEs) has drawn increasing attention due to their endocrine disruption and reproductive toxicity, while the steroid metabolome is essential for follicular development. However, the mechanism by which PAE exposure affects ovarian reserve through the steroid metabolome remains unclear. This study recruited 264 childbearing-age women in Tianjin (China) from April 2019 to August 2020 in a cross-sectional design. Target metabolome analysis of 16 steroids was performed in follicular fluid (FF) to compare diminished ovarian reserve (DOR) against normal ovarian reserve (NOR) women and differential steroids were identified using binary logistic analyses. Further analysis of eleven PAE metabolites (mPAEs) in FF was conducted, and the retrieved oocyte number (RON) representing ovarian reserve was counted. Multiple linear regression and quantile-based g-computation (qgcomp) models were used to associate individual mPAEs and mPAE mixture with the DOR-related differential steroids in FF. Mediation analysis was used to discuss the mediating effect of DOR-related steroids on the association between mPAEs and RON. Androstenedione (A4), corticosterone (CORT), cortisol (COR) and cortisone were significantly down-regulated in FF from women with DOR. Nine mPAEs with detection frequencies greater than 60% and median concentrations of 0.02-4.86 ng/mL were incorporated into statistical models. Negative associations with COR and CORT were found for mono-ethyl phthalate (mEP), mono-(2-ethyl-5-oxohexyl) phthalate (mEOHP), and mono-2-ethylhexyl phthalate (mEHP). A positive association with cortisone was found for mEOHP, mEHP, monobutyl phthalate (mBP), and mono (2-isobutyl) phthalate (miBP). The qgcomp and mediation analyses revealed that mEP and mEOHP not only significantly contributed to the decline of COR and CORT in the mixed exposure but also indirectly reduced RON through the mediating effects of COR and CORT. In conclusion, PAE exposure may decrease ovarian reserve by downregulating COR and CORT.PMID:37116568 | DOI:10.1016/j.envpol.2023.121730

Aflatoxin B1 disrupts testicular development via the cell cycle-related Ras/PI3K/Akt signaling in mice and pig

Fri, 28/04/2023 - 12:00
Environ Pollut. 2023 Apr 26:121729. doi: 10.1016/j.envpol.2023.121729. Online ahead of print.ABSTRACTAflatoxins B1 (AFB1), a type I carcinogen widely present in the environment, not only poses a danger to animal husbandry, but also poses a potential threat to human reproductive health, but its mechanism is still unclear. To address this question, multi-omics were performed on porcine Sertoli cells and mice testis. The data suggest that AFB1 induced testicular damage manifested as decreased expression of GJA1, ZO1 and OCCLUDIN in mice (p < 0.01) and inhibition of porcine Sertoli cell proliferation. Transcriptomic analysis suggested changes in noncoding RNA expression profiles that affect the cell cycle-related Ras/PI3K/Akt signaling pathway after AFB1 exposure both in mice and pigs. Specifically, AFB1 caused abnormal cell cycle of testis with the characterization of decreased expressions of CCNA1, CCNB1 and CDK1 (p < 0.01). Flow cytometry revealed that the G2/M phase was significantly increased after AFB1 exposure. Meanwhile, AFB1 downregulated the expressions of Ras, PI3K and AKT both in porcine Sertoli cell (p < 0.01) and mice testis (p < 0.01). Metabolome analysis verified the alterations in the PI3K/Akt signaling pathway (p < 0.05). Moreover, the joint analysis of metabolome and microbiome found that the changes of metabolites were correlated with the expression of flora. In conclusion, we have demonstrated that AFB1 impairs spermatogenesis via the cell cycle-related Ras/PI3K/Akt signaling and gut imbalance.PMID:37116564 | DOI:10.1016/j.envpol.2023.121729

Sotrovimab restores neutralization against current Omicron subvariants in patients with blood cancer

Fri, 28/04/2023 - 12:00
Cancer Cell. 2023 Apr 13:S1535-6108(23)00131-9. doi: 10.1016/j.ccell.2023.04.005. Online ahead of print.ABSTRACTWu et al. report that patients with hematologic malignancies have reduced immunity against SARS-CoV-2 Omicron subvariants and Sotrovimab retains neutralizing capacity against all tested Omicron subvariants.PMID:37116490 | DOI:10.1016/j.ccell.2023.04.005

Simultaneous targeting of PD-1 and IL-2Rβγ with radiation therapy inhibits pancreatic cancer growth and metastasis

Fri, 28/04/2023 - 12:00
Cancer Cell. 2023 Apr 24:S1535-6108(23)00117-4. doi: 10.1016/j.ccell.2023.04.001. Online ahead of print.ABSTRACTIn pancreatic ductal adenocarcinoma (PDAC) patients, we show that response to radiation therapy (RT) is characterized by increased IL-2Rβ and IL-2Rγ along with decreased IL-2Rα expression. The bispecific PD1-IL2v is a PD-1-targeted IL-2 variant (IL-2v) immunocytokine with engineered IL-2 cis targeted to PD-1 and abolished IL-2Rα binding, which enhances tumor-antigen-specific T cell activation while reducing regulatory T cell (Treg) suppression. Using PD1-IL2v in orthotopic PDAC KPC-driven tumor models, we show marked improvement in local and metastatic survival, along with a profound increase in tumor-infiltrating CD8+ T cell subsets with a transcriptionally and metabolically active phenotype and preferential activation of antigen-specific CD8+ T cells. In combination with single-dose RT, PD1-IL2v treatment results in a robust, durable expansion of polyfunctional CD8+ T cells, T cell stemness, tumor-specific memory immune response, natural killer (NK) cell activation, and decreased Tregs. These data show that PD1-IL2v leads to profound local and distant response in PDAC.PMID:37116489 | DOI:10.1016/j.ccell.2023.04.001

Metabolomics of mature honey formation

Fri, 28/04/2023 - 12:00
Nat Food. 2021 Apr;2(4):223. doi: 10.1038/s43016-021-00273-1.NO ABSTRACTPMID:37118468 | DOI:10.1038/s43016-021-00273-1

Healthy aging and muscle function are positively associated with NAD<sup>+</sup> abundance in humans

Fri, 28/04/2023 - 12:00
Nat Aging. 2022 Mar;2(3):254-263. doi: 10.1038/s43587-022-00174-3. Epub 2022 Feb 17.ABSTRACTSkeletal muscle is greatly affected by aging, resulting in a loss of metabolic and physical function. However, the underlying molecular processes and how (lack of) physical activity is involved in age-related metabolic decline in muscle function in humans is largely unknown. Here, we compared, in a cross-sectional study, the muscle metabolome from young to older adults, whereby the older adults were exercise trained, had normal physical activity levels or were physically impaired. Nicotinamide adenine dinucleotide (NAD+) was one of the most prominent metabolites that was lower in older adults, in line with preclinical models. This lower level was even more pronounced in impaired older individuals, and conversely, exercise-trained older individuals had NAD+ levels that were more similar to those found in younger individuals. NAD+ abundance positively correlated with average number of steps per day and mitochondrial and muscle functioning. Our work suggests that a clear association exists between NAD+ and health status in human aging.PMID:37118369 | DOI:10.1038/s43587-022-00174-3

Microbiota from young mice counteracts selective age-associated behavioral deficits

Fri, 28/04/2023 - 12:00
Nat Aging. 2021 Aug;1(8):666-676. doi: 10.1038/s43587-021-00093-9. Epub 2021 Aug 9.ABSTRACTThe gut microbiota is increasingly recognized as an important regulator of host immunity and brain health. The aging process yields dramatic alterations in the microbiota, which is linked to poorer health and frailty in elderly populations. However, there is limited evidence for a mechanistic role of the gut microbiota in brain health and neuroimmunity during aging processes. Therefore, we conducted fecal microbiota transplantation from either young (3-4 months) or old (19-20 months) donor mice into aged recipient mice (19-20 months). Transplant of a microbiota from young donors reversed aging-associated differences in peripheral and brain immunity, as well as the hippocampal metabolome and transcriptome of aging recipient mice. Finally, the young donor-derived microbiota attenuated selective age-associated impairments in cognitive behavior when transplanted into an aged host. Our results reveal that the microbiome may be a suitable therapeutic target to promote healthy aging.PMID:37117767 | DOI:10.1038/s43587-021-00093-9

Author Correction: Nutriome-metabolome relationships provide insights into dietary intake and metabolism

Fri, 28/04/2023 - 12:00
Nat Food. 2021 Jul;2(7):541-542. doi: 10.1038/s43016-021-00309-6.NO ABSTRACTPMID:37117689 | DOI:10.1038/s43016-021-00309-6

Chromatin remodeling due to degradation of citrate carrier impairs osteogenesis of aged mesenchymal stem cells

Fri, 28/04/2023 - 12:00
Nat Aging. 2021 Sep;1(9):810-825. doi: 10.1038/s43587-021-00105-8. Epub 2021 Sep 13.ABSTRACTAging is accompanied by a general decline in the function of many cellular pathways. However, whether these are causally or functionally interconnected remains elusive. Here, we study the effect of mitochondrial-nuclear communication on stem cell aging. We show that aged mesenchymal stem cells exhibit reduced chromatin accessibility and lower histone acetylation, particularly on promoters and enhancers of osteogenic genes. The reduced histone acetylation is due to impaired export of mitochondrial acetyl-CoA, owing to the lower levels of citrate carrier (CiC). We demonstrate that aged cells showed enhanced lysosomal degradation of CiC, which is mediated via mitochondrial-derived vesicles. Strikingly, restoring cytosolic acetyl-CoA levels either by exogenous CiC expression or via acetate supplementation, remodels the chromatin landscape and rescues the osteogenesis defects of aged mesenchymal stem cells. Collectively, our results establish a tight, age-dependent connection between mitochondrial quality control, chromatin and stem cell fate, which are linked together by CiC.PMID:37117628 | DOI:10.1038/s43587-021-00105-8

Microbiota-dependent increase in δ-valerobetaine alters neuronal function and is responsible for age-related cognitive decline

Fri, 28/04/2023 - 12:00
Nat Aging. 2021 Dec;1(12):1127-1136. doi: 10.1038/s43587-021-00141-4. Epub 2021 Dec 20.ABSTRACTUnderstanding the physiological origins of age-related cognitive decline is of critical importance given the rising age of the world's population1. Previous work in animal models has established a strong link between cognitive performance and the microbiota2-5, and it is known that the microbiome undergoes profound remodeling in older adults6. Despite growing evidence for the association between age-related cognitive decline and changes in the gut microbiome, the mechanisms underlying such interactions between the brain and the gut are poorly understood. Here, using fecal microbiota transplantation (FMT), we demonstrate that age-related remodeling of the gut microbiota leads to decline in cognitive function in mice and that this impairment can be rescued by transplantation of microbiota from young animals. Moreover, using a metabolomic approach, we found elevated concentrations of δ-valerobetaine, a gut microbiota-derived metabolite, in the blood and brain of aged mice and older adults. We then demonstrated that δ-valerobetaine is deleterious to learning and memory processes in mice. At the neuronal level, we showed that δ-valerobetaine modulates inhibitory synaptic transmission and neuronal network activity. Finally, we identified specific bacterial taxa that significantly correlate with δ-valerobetaine levels in the brain. Based on our findings, we propose that δ-valerobetaine contributes to microbiota-driven brain aging and that the associated mechanisms represent a promising target for countering age-related cognitive decline.PMID:37117525 | DOI:10.1038/s43587-021-00141-4

Studying protein structure and function by native separation-mass spectrometry

Fri, 28/04/2023 - 12:00
Nat Rev Chem. 2022 Mar;6(3):215-231. doi: 10.1038/s41570-021-00353-7. Epub 2022 Jan 20.ABSTRACTAlterations in protein structure may have profound effects on biological function. Analytical techniques that permit characterization of proteins while maintaining their conformational and functional state are crucial for studying changes in the higher order structure of proteins and for establishing structure-function relationships. Coupling of native protein separations with mass spectrometry is emerging rapidly as a powerful approach to study these aspects in a reliable, fast and straightforward way. This Review presents the available native separation modes for proteins, covers practical considerations on the hyphenation of these separations with mass spectrometry and highlights the involvement of affinity-based separations to simultaneously obtain structural and functional information of proteins. The impact of these approaches is emphasized by selected applications addressing biomedical and biopharmaceutical research questions.PMID:37117432 | DOI:10.1038/s41570-021-00353-7

Comparison of betalain compounds in two Beta vulgaris var. cicla and BvCYP76AD27 function identification in betalain biosynthesis

Fri, 28/04/2023 - 12:00
Plant Physiol Biochem. 2023 Apr 15;199:107711. doi: 10.1016/j.plaphy.2023.107711. Online ahead of print.ABSTRACTBeta vulgaris var. cicla is an edible, ornamental and horticultural plant. However, the difference of components and contents of betalain in beets with different leaf color are not well understood. Here, the stress resistance and metabolites of two B. vulgaris var. cicla cultivars were determined. The differences in stress resistance between red leaf-colored chard (RC) and yellow leaf-colored chard (YC) were positively related to betacyanins (BC) and betaxathins (BX) content in the leaves. Furthermore, a total of 3615 distinct metabolites were identified by UPLC-QTOF-MS in two cultivars, including 70 alkaloids and their derivatives, 249 flavonoids, and 264 terpenoids. There were 17 metabolites attributed to betalain biosynthesis pathway, seven of nine BC were up-regulated, and eight BX showed no significant difference in RC compared with YC. The contents of celosianin II and betanin were the highest BC in RC, at approximately 84.38 and 19.97 times that of YC, respectively. The content of portulacaxanthin II was the highest BX in two beets. Additionally, the BvCYP450 genes were identified based on genome, and the members that might be involved in betalain biosynthesis were screened. BvCYP76AD27, a member of the BvCYP76AD subfamily, had a higher expression level in RC than YC under freezing, drought and shading stress. In yeast Saccharomyces cerevisiae, BvCYP76AD5 and BvCYP76AD27 only hydroxylated tyrosine to L-DOPA, which was transformed into portulacaxanthin II by 4,5-DOPA extradiol dioxygenase. The results contribute to illustrating the molecular mechanism of betalain biosynthesis and provide useful information for further investigation of beet chemistry and sufficient utilization of this species.PMID:37116227 | DOI:10.1016/j.plaphy.2023.107711

Sex-specific effects of CD248 on metabolism and the adipose tissue lipidome

Fri, 28/04/2023 - 12:00
PLoS One. 2023 Apr 28;18(4):e0284012. doi: 10.1371/journal.pone.0284012. eCollection 2023.ABSTRACTCd248 has recently been associated with adipose tissue physiology, demonstrated by reduced weight gain in high fat diet-fed mice with genetic deletion of Cd248 relative to controls. Here we set out to determine the metabolic consequences of loss of Cd248. Strikingly, we find these to be sex specific; By subjecting Cd248-/- and Cd248+/+ mice to a high fat diet and indirect calorimetry study, we identified that only male Cd248-/- mice show reduced weight gain compared to littermate control wildtype mice. In addition, male (but not female) mice showed a lower respiratory exchange ratio on both chow and high fat diets, indicating a predisposition to metabolise lipid. Lipidomic studies on specific fat depots found reduced triglyceride and diglyceride deposition in male Cd248-/- mice, and this was supported by reduced expression of lipogenic and adipogenic genes. Finally, metabolomic analysis of isolated, differentiated preadipocytes found alterations in metabolic pathways associated with lipid deposition in cells isolated from male, but not female, Cd248-/- mice. Overall, our results highlight the importance of sex controls in animal studies and point to a role for Cd248 in sex- and depot-specific regulation of lipid metabolism.PMID:37115796 | DOI:10.1371/journal.pone.0284012

Pressure overload induces ISG15 to facilitate adverse ventricular remodeling and promote heart failure

Fri, 28/04/2023 - 12:00
J Clin Invest. 2023 May 1;133(9):e161453. doi: 10.1172/JCI161453.ABSTRACTInflammation promotes adverse ventricular remodeling, a common antecedent of heart failure. Here, we set out to determine how inflammatory cells affect cardiomyocytes in the remodeling heart. Pathogenic cardiac macrophages induced an IFN response in cardiomyocytes, characterized by upregulation of the ubiquitin-like protein IFN-stimulated gene 15 (ISG15), which posttranslationally modifies its targets through a process termed ISGylation. Cardiac ISG15 is controlled by type I IFN signaling, and ISG15 or ISGylation is upregulated in mice with transverse aortic constriction or infused with angiotensin II; rats with uninephrectomy and DOCA-salt, or pulmonary artery banding; cardiomyocytes exposed to IFNs or CD4+ T cell-conditioned medium; and ventricular tissue of humans with nonischemic cardiomyopathy. By nanoscale liquid chromatography-tandem mass spectrometry, we identified the myofibrillar protein filamin-C as an ISGylation target. ISG15 deficiency preserved cardiac function in mice with transverse aortic constriction and led to improved recovery of mouse hearts ex vivo. Metabolomics revealed that ISG15 regulates cardiac amino acid metabolism, whereas ISG15 deficiency prevented misfolded filamin-C accumulation and induced cardiomyocyte autophagy. In sum, ISG15 upregulation is a feature of pathological ventricular remodeling, and protein ISGylation is an inflammation-induced posttranslational modification that may contribute to heart failure development by altering cardiomyocyte protein turnover.PMID:37115698 | DOI:10.1172/JCI161453

iPSC-derived retinal pigmented epithelial cells from patients with macular telangiectasia show decreased mitochondrial function

Fri, 28/04/2023 - 12:00
J Clin Invest. 2023 May 1;133(9):e163771. doi: 10.1172/JCI163771.ABSTRACTPatient-derived induced pluripotent stem cells (iPSCs) provide a powerful tool for identifying cellular and molecular mechanisms of disease. Macular telangiectasia type 2 (MacTel) is a rare, late-onset degenerative retinal disease with an extremely heterogeneous genetic architecture, lending itself to the use of iPSCs. Whole-exome sequencing screens and pedigree analyses have identified rare causative mutations that account for less than 5% of cases. Metabolomic surveys of patient populations and GWAS have linked MacTel to decreased circulating levels of serine and elevated levels of neurotoxic 1-deoxysphingolipids (1-dSLs). However, retina-specific, disease-contributing factors have yet to be identified. Here, we used iPSC-differentiated retinal pigmented epithelial (iRPE) cells derived from donors with or without MacTel to screen for novel cell-intrinsic pathological mechanisms. We show that MacTel iRPE cells mimicked the low serine levels observed in serum from patients with MacTel. Through RNA-Seq and gene set enrichment pathway analysis, we determined that MacTel iRPE cells are enriched in cellular stress pathways and dysregulation of central carbon metabolism. Using respirometry and mitochondrial stress testing, we functionally validated that MacTel iRPE cells had a reduction in mitochondrial function that was independent of defects in serine biosynthesis and 1-dSL accumulation. Thus, we identified phenotypes that may constitute alternative disease mechanisms beyond the known serine/sphingolipid pathway.PMID:37115691 | DOI:10.1172/JCI163771

Concordance-Based Batch Effect Correction for Large-Scale Metabolomics

Fri, 28/04/2023 - 12:00
Anal Chem. 2023 Apr 28. doi: 10.1021/acs.analchem.2c05748. Online ahead of print.ABSTRACTFor a large-scale metabolomics study, sample collection, preparation, and analysis may last several days, months, or even (intermittently) over years. This may lead to apparent batch effects in the acquired metabolomics data due to variability in instrument status, environmental conditions, or experimental operators. Batch effects may confound the true biological relationships among metabolites and thus obscure real metabolic changes. At present, most of the commonly used batch effect correction (BEC) methods are based on quality control (QC) samples, which require sufficient and stable QC samples. However, the quality of the QC samples may deteriorate if the experiment lasts for a long time. Alternatively, isotope-labeled internal standards have been used, but they generally do not provide good coverage of the metabolome. On the other hand, BEC can also be conducted through a data-driven method, in which no QC sample is needed. Here, we propose a novel data-driven BEC method, namely, CordBat, to achieve concordance between each batch of samples. In the proposed CordBat method, a reference batch is first selected from all batches of data, and the remaining batches are referred to as "other batches." The reference batch serves as the baseline for the batch adjustment by providing a coordinate of correlation between metabolites. Next, a Gaussian graphical model is built on the combined dataset of reference and other batches, and finally, BEC is achieved by optimizing the correction coefficients in the other batches so that the correlation between metabolites of each batch and their combinations are in concordance with that of the reference batch. Three real-world metabolomics datasets are used to evaluate the performance of CordBat by comparing it with five commonly used BEC methods. The present experimental results showed the effectiveness of CordBat in batch effect removal and the concordance of correlation between metabolites after BEC. CordBat was found to be comparable to the QC-based methods and achieved better performance in the preservation of biological effects. The proposed CordBat method may serve as an alternative BEC method for large-scale metabolomics that lack proper QC samples.PMID:37115661 | DOI:10.1021/acs.analchem.2c05748

Quantifying Cell Heterogeneity and Subpopulations Using Single Cell Metabolomics

Fri, 28/04/2023 - 12:00
Anal Chem. 2023 Apr 28. doi: 10.1021/acs.analchem.2c05245. Online ahead of print.ABSTRACTMass spectrometry (MS) has become an indispensable tool for metabolomics studies. However, due to the lack of applicable experimental platforms, suitable algorithm, software, and quantitative analyses of cell heterogeneity and subpopulations, investigating global metabolomics profiling at the single cell level remains challenging. We combined the Single-probe single cell MS (SCMS) experimental technique with a bioinformatics software package, SinCHet-MS (Single Cell Heterogeneity for Mass Spectrometry), to characterize changes of tumor heterogeneity, quantify cell subpopulations, and prioritize the metabolite biomarkers of each subpopulation. As proof of principle studies, two melanoma cancer cell lines, the primary (WM115; with a lower drug resistance) and the metastatic (WM266-4; with a higher drug resistance), were used as models. Our results indicate that after the treatment of the anticancer drug vemurafenib, a new subpopulation emerged in WM115 cells, while the proportion of the existing subpopulations was changed in the WM266-4 cells. In addition, metabolites for each subpopulation can be prioritized. Combining the SCMS experimental technique with a bioinformatics tool, our label-free approach can be applied to quantitatively study cell heterogeneity, prioritize markers for further investigation, and improve the understanding of cell metabolism in human diseases and response to therapy.PMID:37115510 | DOI:10.1021/acs.analchem.2c05245

Integrative analysis of metabolomic, genomic, and imaging-based phenotypes identify very-low-density lipoprotein as a potential risk factor for lumbar Modic changes

Fri, 28/04/2023 - 12:00
Eur Spine J. 2023 Apr 28. doi: 10.1007/s00586-023-07704-6. Online ahead of print.NO ABSTRACTPMID:37115279 | DOI:10.1007/s00586-023-07704-6

Evolution-guided multiomics provide insights into the strengthening of bioactive flavone biosynthesis in medicinal pummelo

Fri, 28/04/2023 - 12:00
Plant Biotechnol J. 2023 Apr 28. doi: 10.1111/pbi.14058. Online ahead of print.ABSTRACTPummelo (Citrus maxima or Citrus grandis) is a basic species and an important type for breeding in Citrus. Pummelo is used not only for fresh consumption but also for medicinal purposes. However, the molecular basis of medicinal traits is unclear. Here, compared with wild citrus species/Citrus-related genera, the content of 43 bioactive metabolites and their derivatives increased in the pummelo. Furthermore, we assembled the genome sequence of a variety for medicinal purposes with a long history, Citrus maxima 'Huazhouyou-tomentosa' (HZY-T), at the chromosome level with a genome size of 349.07 Mb. Comparative genomics showed that the expanded gene family in the pummelo genome was enriched in flavonoids-, terpenoid-, and phenylpropanoid biosynthesis. Using the metabolome and transcriptome of six developmental stages of HZY-T and Citrus maxima 'Huazhouyou-smooth' (HZY-S) fruit peel, we generated the regulatory networks of bioactive metabolites and their derivatives. We identified a novel MYB transcription factor, CmtMYB108, as an important regulator of flavone pathways. Both mutations and expression of CmtMYB108, which targets the genes PAL (phenylalanine ammonia-lyase) and FNS (flavone synthase), displayed differential expression between Citrus-related genera, wild citrus species and pummelo species. This study provides insights into the evolution-associated changes in bioactive metabolism during the origin process of pummelo.PMID:37115171 | DOI:10.1111/pbi.14058

Pages