PubMed

Nat Aging. 2022 Oct;2(10):923-940. doi: 10.1038/s43587-022-00290-0. Epub 2022 Oct 12.ABSTRACTRecent proteome and transcriptome profiling of Alzheimer's disease (AD) brains reveals RNA splicing dysfunction and U1 small nuclear ribonucleoprotein (snRNP) pathology containing U1-70K and its N-terminal 40-KDa fragment (N40K). Here we present a causative role of U1 snRNP dysfunction to neurodegeneration in primary neurons and transgenic mice (N40K-Tg), in which N40K expression exerts a dominant-negative effect to downregulate full-length U1-70K. N40K-Tg recapitulates N40K insolubility, erroneous splicing events, neuronal degeneration and cognitive impairment. Specifically, N40K-Tg shows the reduction of GABAergic synapse components (e.g., the GABA receptor subunit of GABRA2), and concomitant postsynaptic hyperexcitability that is rescued by a GABA receptor agonist. Crossing of N40K-Tg and the 5xFAD amyloidosis model indicates that the RNA splicing defect synergizes with the amyloid cascade to remodel the brain transcriptome and proteome, deregulate synaptic proteins, and accelerate cognitive decline. Thus, our results support the contribution of U1 snRNP-mediated splicing dysfunction to AD pathogenesis.PMID:36636325 | PMC:PMC9833817 | DOI:10.1038/s43587-022-00290-0

J Endocr Soc. 2022 Dec 10;7(3):bvac189. doi: 10.1210/jendso/bvac189. eCollection 2023 Jan 6.ABSTRACTCONTEXT: Identification of insulin resistance (IR) in South Asians, who are at a higher risk for type 2 diabetes, is important. Lack of standardization of insulin assays limits the clinical use of insulin-based surrogate indices. The lipoprotein insulin resistance index (LP-IR), a metabolomic marker, reflects the lipoprotein abnormalities observed in IR. The reliability of the LP-IR index in South Asians is unknown.OBJECTIVE: We evaluated the predictive accuracy of LP-IR compared with other IR surrogate indices in South Asians.METHODS: In a cross-sectional study (n = 55), we used calibration model analysis to assess the ability of the LP-IR score and other simple surrogate indices (Homeostatic Model Assessment of Insulin Resistance, Quantitative insulin sensitivity check index, Adipose insulin resistance index, and Matsuda Index) to predict insulin sensitivity (SI) derived from the reference frequently sampled intravenous glucose tolerance test. LP-IR index was derived from lipoprotein particle concentrations and sizes measured by nuclear magnetic resonance spectroscopy. Predictive accuracy was determined by root mean squared error (RMSE) of prediction and leave-one-out cross-validation type RMSE of prediction (CVPE). The optimal cut-off of the LP-IR index was determined by the area under the receiver operating characteristic curve (AUROC) and the Youden index.RESULTS: The simple surrogate indices showed moderate correlations with SI (r = 0.53-0.69, P < .0001). CVPE and RMSE were not different in any of the surrogate indices when compared with LP-IR. The AUROC was 0.77 (95% CI 0.64-0.89). The optimal cut-off for IR in South Asians was LP-IR >48 (sensitivity: 75%, specificity: 70%).CONCLUSION: The LP-IR index is a simple, accurate, and clinically useful test to assess IR in South Asians.PMID:36636252 | PMC:PMC9830979 | DOI:10.1210/jendso/bvac189

Neurobiol Pain. 2022 Dec 28;13:100112. doi: 10.1016/j.ynpai.2022.100112. eCollection 2023 Jan-Jul.ABSTRACTAdministration of glyceryl trinitrate (GTN), a donor of nitric oxide, can induce migraine-like attacks in subjects with migraine. Provocation with GTN typically follows a biphasic pattern; it induces immediate headache in subjects with migraine, as well as in healthy controls, whereafter only subjects with migraine may develop a migraine-like headache several hours later. Interestingly, intravenous infusion with prostaglandin-E2 (PGE2) can also provoke a migraine-like headache, but seems to have a more rapid onset compared to GTN. The aim of the study was to shed light on the mechanistic aspect PGE2 has in migraine attack development. Therefore, PGE2 plasma levels were measured towards the (pre)ictal state of an attack, which we provoked with GTN. Blood samples from women with migraine (n = 37) and age-matched female controls (n = 25) were obtained before and ∼ 140 min and ∼ 320 min after GTN infusion. PGE2 levels were measured using liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis. Data was analyzed using a generalized linear mixed-effect model. Immediate headache after GTN infusion occurred in 85 % of migraine participants and in 75 % of controls. A delayed onset migraine-like attack was observed in 82 % of migraine subjects and in none of the controls. PGE2 levels were not different between the interictal and preictal state (P = 0.527) nor between interictal and ictal state (defined as having migraine-like headache) (P = 0.141). Hence, no evidence was found that a rise in PGE2 is an essential step in the initiation of GTN-induced migraine-like attacks.PMID:36636095 | PMC:PMC9829921 | DOI:10.1016/j.ynpai.2022.100112

Phytochem Anal. 2023 Jan 12. doi: 10.1002/pca.3200. Online ahead of print.ABSTRACTINTRODUCTION: The seeds of Cassia obtusifolia L. (Cassiae [C.] semen) have been widely used as both food and traditional Chinese medicine in China.OBJECTIVES: We aimed to analyze the metabolic mechanisms underlying C. semen germination.MATERIALS AND METHODS: Different samples of C. semen at various germination stages were collected. These samples were subjected to 1 H-NMR and UHPLC/Q-Orbitrap-MS-based untargeted metabolomics analysis together with transcriptomics analysis.RESULTS: A total of 50 differential metabolites (mainly amino acids and sugars) and 20 key genes involved in multiple pathways were identified in two comparisons of different groups (36 h vs 12 h and 84 h vs 36 h). The metabolite-gene network for seed germination was depicted. In the germination of C. semen, fructose and mannose metabolism was activated in the testa rupture period, indicating more energy was needed (36 h). In the embryonic axis elongation period (84 h), the pentose and glucuronate interconversions pathway and the phenylpropanoid biosynthesis pathway were activated, which suggested some nutrient sources (nitrogen and sugar) were in demand. Furthermore, oxygen, energy, and nutrition should be supplied throughout the whole germination process. These global views open up an integrated perspective for understanding the complex biological regulatory mechanisms during the germination process of C. semen.PMID:36636016 | DOI:10.1002/pca.3200

Clin Chem Lab Med. 2023 Jan 13. doi: 10.1515/cclm-2022-0805. Online ahead of print.ABSTRACTOBJECTIVES: Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has become a common technique in clinical laboratories in recent years. Because most methods are laboratory-developed tests (LDTs), their reproducibility and quality control (QC) have been controversial. In this study, Westgard Sigma Rules were used to evaluate the analytical performance and establish an individualised internal QC (IQC) strategy for these LDTs.METHODS: Taking the LC-MS/MS LDT method for homocysteine (Hcy) as an example, the 'desirable specifications' from the Biological Variation Database were used as quality goals. Based on the external quality assessment (EQA) samples, bias was calculated and the coefficient of variation (CV) was also calculated by IQC measurements for six consecutive months. The analytical performance was evaluated by calculated sigma metrics and an IQC strategy was designed using the Westgard Sigma Rules with run size.RESULTS: Over 116 days within 6 months, a total of 850 data points were collected for each of IQC 1 and IQC 2. The monthly coefficient of variation CV% was 2.57-4.01%, which was non-significant (p-value: 0.75). The absolute bias% for IQC1 and IQC2 was 1.23 and 1.87%, respectively. The allowable total error (TEa) was selected as 15.5%, Sigma metrics were 4.02 and 4.30, and the analytical performance was 'Good'. The 13s/22s/R4s/41s multi rules (n=4, r=1) with a run size of 200 samples were suggested for the Hcy IQC scheme. The quality goal index (QGI) values were over 1.2, indicating that trueness needed to be improved.CONCLUSIONS: The analytical performance of the Hcy LC-MS/MS LDT conformed to the Six Sigma rating level, achieving 'good' (four Sigma). Clinical practice indicated that calibration bias was the primary factor affecting trueness.PMID:36635945 | DOI:10.1515/cclm-2022-0805

Mol Oncol. 2023 Jan 12. doi: 10.1002/1878-0261.13374. Online ahead of print.ABSTRACTDysregulation of the adaptor protein Abelson interactor 1 (ABI1) is linked to malignant transformation. To interrogate the role of ABI1 in cancer development, we mapped the ABI1 interactome using proximity-dependent labeling (PDL) with biotin followed by mass spectrometry. Using a novel PDL data filtering strategy, considering both peptide spectral matches and peak areas of detected peptides, we identified 212 ABI1 proximal interactors. These included WAVE2 complex components such as CYFIP1, NCKAP1 or WASF1, confirming the known role of ABI1 in the regulation of actin-polymerization-dependent processes. We also identified proteins associated with the TAK1-IKK pathway, including TAK1, TAB2 and RIPK1, denoting a newly identified function of ABI1 in TAK1-NF-κB inflammatory signaling. Functional assays using TNFα-stimulated, ABI1-overexpressing or ABI1-deficient cells showed effects on TAK1-NF-kB pathway-dependent signaling to RIPK1, with ABI1-knockout cells being less susceptible to TNFα-induced, RIPK1-mediated, TAK1-dependent apoptosis. In sum, our PDL-based strategy enabled mapping of the ABI1 proximal interactome, thus revealing a previously unknown role of this adaptor protein in TAK1/RIPK1-based regulation of cell death and survival.PMID:36635880 | DOI:10.1002/1878-0261.13374

Function (Oxf). 2023 Jan 3;4(1):zqac071. doi: 10.1093/function/zqac071. eCollection 2023.NO ABSTRACTPMID:36632473 | PMC:PMC9830535 | DOI:10.1093/function/zqac071

Nat Microbiol. 2023 Jan 12. doi: 10.1038/s41564-022-01293-8. Online ahead of print.ABSTRACTSpontaneous preterm birth (sPTB) is a leading cause of maternal and neonatal morbidity and mortality, yet its prevention and early risk stratification are limited. Previous investigations have suggested that vaginal microbes and metabolites may be implicated in sPTB. Here we performed untargeted metabolomics on 232 second-trimester vaginal samples, 80 from pregnancies ending preterm. We find multiple associations between vaginal metabolites and subsequent preterm birth, and propose that several of these metabolites, including diethanolamine and ethyl glucoside, are exogenous. We observe associations between the metabolome and microbiome profiles previously obtained using 16S ribosomal RNA amplicon sequencing, including correlations between bacteria considered suboptimal, such as Gardnerella vaginalis, and metabolites enriched in term pregnancies, such as tyramine. We investigate these associations using metabolic models. We use machine learning models to predict sPTB risk from metabolite levels, weeks to months before birth, with good accuracy (area under receiver operating characteristic curve of 0.78). These models, which we validate using two external cohorts, are more accurate than microbiome-based and maternal covariates-based models (area under receiver operating characteristic curve of 0.55-0.59). Our results demonstrate the potential of vaginal metabolites as early biomarkers of sPTB and highlight exogenous exposures as potential risk factors for prematurity.PMID:36635575 | DOI:10.1038/s41564-022-01293-8

Metabolomics. 2023 Jan 12;19(1):5. doi: 10.1007/s11306-022-01970-z.ABSTRACTINTRODUCTION: Blast induced Traumatic brain injury (BI-TBI) is common among military personnels as well as war affected civilians. In the war zone, people can also encounter repeated exposure of blast wave, which may affect their cognition and metabolic alterations.OBJECTIVE: In this study we assess the metabolic and histological changes in the hippocampus of rats at 24 h post injury.METHOD: Rats were divided into four groups: (i) Sham; (ii) Mild TBI (mi); (iii) Moderate TBI (mo); and (iv) Repetitive mild TBI (rm TBI) and then subjected to different intensities of blast exposure. Hippocampal tissues were collected after 24 h of injury for proton nuclear magnetic resonance spectroscopy (1H NMR spectroscopy) and immunohistochemical (IHC) analysis.RESULTS: The metabolic alterations were found in the hippocampal tissue samples and these alterations showed significant change in glutamate, N-Acetylaspartic acid (NAA), acetate, creatine, phosphoethanolamine (PE), ethanolamine and PC/choline concentrations in rmTBI rats only. IHC studies revealed that AH3 (Acetyl histone) positive cells were decreased in rm TBI tissue samples in comparison to other TBI groups and sham rats. This might reflect an epigenetic alteration due to repeated blast exposure at 24 h post injury. Additionally, astrogliosis was observed in miTBI and moTBI hippocampal tissue while no change was observed in rmTBI tissues.CONCLUSION: The present study reports altered acetylation in the presence of altered metabolism in hippocampal tissue of blast induced rmTBI at 24 h post injury. Mechanistic understanding of these intertwined processes may help in the development of better therapeutic pathways and agents for blast induced TBI in near future.PMID:36635559 | DOI:10.1007/s11306-022-01970-z

J Nat Med. 2023 Jan 12. doi: 10.1007/s11418-022-01673-8. Online ahead of print.ABSTRACTThe genus Claviceps (Clavicipitaceae) is famous for producing ergot alkaloids (EAs) in sclerotia. EAs can cause ergotism, resulting in convulsions and necrosis when ingested, making these compounds a serious concern for food safety. Agroclavine (2), a typical Clavine-type EA, is a causative agent of ergotism and is listed as a compound to be monitored by the European Food Safety Authority. Clavine-type EAs are known to cause cytotoxicity, but the mechanism has not been elucidated. We performed annexin V and PI double-staining followed by flow cytometric analysis to detect apoptosis in HepG2 and PANC-1 cells after exposure to Clavine-type EAs. Clavine-type EAs reduced cell viability and induced apoptosis in both cell lines. We then performed LC-MS analysis of EAs from 41 sclerotia samples of Claviceps collected in Japan. 24 out of 41 sclerotia extracts include peptide-type EAs (ergosine/inine: 4/4', ergotamine: 5, ergocornine/inine: 6/6', α-ergocryptine/inine: 8/8', and ergocristine/inine: 9/9') and 19 sclerotia extracts among 24 sclerotia detected peptide type EAs include Clavine-type EAs (pyroclavine: 1, agroclavine: 2, festuclavine: 3) by LC-MS. We then performed a metabolomic analysis of the EAs in the sclerotia using principal component analysis (PCA). The PCA score plots calculated for EAs suggested the existence of four groups with different EA production patterns. One of the groups was formed by the contribution of Clavine-type EAs. These results suggest that Clavine-type EAs are a family of compounds requiring attention in food safety and livestock production in Japan.PMID:36635416 | DOI:10.1007/s11418-022-01673-8

Nat Genet. 2023 Jan 12. doi: 10.1038/s41588-022-01270-1. Online ahead of print.ABSTRACTMetabolic processes can influence disease risk and provide therapeutic targets. By conducting genome-wide association studies of 1,091 blood metabolites and 309 metabolite ratios, we identified associations with 690 metabolites at 248 loci and associations with 143 metabolite ratios at 69 loci. Integrating metabolite-gene and gene expression information identified 94 effector genes for 109 metabolites and 48 metabolite ratios. Using Mendelian randomization (MR), we identified 22 metabolites and 20 metabolite ratios having estimated causal effect on 12 traits and diseases, including orotate for estimated bone mineral density, α-hydroxyisovalerate for body mass index and ergothioneine for inflammatory bowel disease and asthma. We further measured the orotate level in a separate cohort and demonstrated that, consistent with MR, orotate levels were positively associated with incident hip fractures. This study provides a valuable resource describing the genetic architecture of metabolites and delivers insights into their roles in common diseases, thereby offering opportunities for therapeutic targets.PMID:36635386 | DOI:10.1038/s41588-022-01270-1

Sci Rep. 2023 Jan 12;13(1):629. doi: 10.1038/s41598-022-26156-4.ABSTRACTEvidence shows that individuals infected by SARS-CoV-2 experience an altered metabolic state in multiple organs. Metabolic activities are directly involved in modulating immune responses against infectious diseases, yet our understanding of how host metabolism relates to inflammatory responses remains limited. To better elucidate the underlying biochemistry of the leukocyte response, we focused our analysis on possible relationships between SARS-CoV-2 post-infection stages and distinct metabolic pathways. Indeed, we observed a significant altered metabolism of tryptophan and urea cycle pathways in cultures of peripheral blood mononuclear cells obtained 60-90 days after infection and showing in vitro IgG antibody memory for spike-S1 antigen (n = 17). This work, for the first time, identifies metabolic routes in cell metabolism possibly related to later stages of immune defence against SARS-CoV-2 infection, namely, when circulating antibodies may be absent but an antibody memory is present. The results suggest reprogramming of leukocyte metabolism after viral pathogenesis through activation of specific amino acid pathways possibly related to protective immunity against SARS-CoV-2.PMID:36635345 | DOI:10.1038/s41598-022-26156-4

Nat Commun. 2023 Jan 12;14(1):173. doi: 10.1038/s41467-023-35798-5.ABSTRACTβ2-agonist treatment improves skeletal muscle glucose uptake and whole-body glucose homeostasis in rodents, likely via mTORC2-mediated signalling. However, human data on this topic is virtually absent. We here investigate the effects of two-weeks treatment with the β2-agonist clenbuterol (40 µg/day) on glucose control as well as energy- and substrate metabolism in healthy young men (age: 18-30 years, BMI: 20-25 kg/m2) in a randomised, placebo-controlled, double-blinded, cross-over study (ClinicalTrials.gov-identifier: NCT03800290). Randomisation occurred by controlled randomisation and the final allocation sequence was seven (period 1: clenbuterol, period 2: placebo) to four (period 1: placebo, period 2: clenbuterol). The primary and secondary outcome were peripheral insulin-stimulated glucose disposal and skeletal muscle GLUT4 translocation, respectively. Primary analyses were performed on eleven participants. No serious adverse events were reported. The study was performed at Maastricht University, Maastricht, The Netherlands, between August 2019 and April 2021. Clenbuterol treatment improved peripheral insulin-stimulated glucose disposal by 13% (46.6 ± 3.5 versus 41.2 ± 2.7 µmol/kg/min, p = 0.032), whereas skeletal muscle GLUT4 translocation assessed in overnight fasted muscle biopsies remained unaffected. These results highlight the potential of β2-agonist treatment in improving skeletal muscle glucose uptake and underscore the therapeutic value of this pathway for the treatment of type 2 diabetes. However, given the well-known (cardiovascular) side-effects of systemic β2-agonist treatment, further exploration on the underlying mechanisms is needed to identify viable therapeutic targets.PMID:36635304 | DOI:10.1038/s41467-023-35798-5

Free Radic Biol Med. 2023 Jan 9:S0891-5849(23)00008-4. doi: 10.1016/j.freeradbiomed.2023.01.007. Online ahead of print.ABSTRACTStudies of the Arabidopsis cat2 mutant lacking the major leaf isoform of catalase have allowed the potential impact of intracellular H2O2 on plant function to be studied. Here, we report a robust analysis of modified gene expression associated with key families involved in metabolite modification in cat2. Though a combined transcriptomic and metabolomic analysis focused on the salicylic acid (SA) and jasmonic acid (JA) pathways, we report key features of the metabolic signatures linked to oxidative stress-induced signaling via these defence hormones and discuss the enzymes that are likely to be involved in determining these features. We provide evidence that specific UDP-glycosyl transferases contribute to the glucosylation of SA that accumulates as a result of oxidative stress in cat2. Glycosides of dihydroxybenzoic acids that accumulate alongside SA in cat2 are identified and, based on the expression of candidate genes, likely routes for their production are discussed. We also report that enhanced intracellular H2O2 triggers induction of genes encoding different enzymes that can metabolize JA. Integrated analysis of metabolite and transcript profiles suggests that a gene network involving specific hydrolases, hydroxylases, and sulfotransferases functions to limit accumulation of the most active jasmonates during oxidative stress.PMID:36634883 | DOI:10.1016/j.freeradbiomed.2023.01.007

Anim Biosci. 2023 Jan 11. doi: 10.5713/ab.22.0249. Online ahead of print.ABSTRACTOBJECTIVE: Cow urine possesses several bioactive properties but the responsible components behind these bioactivities are still far from identified. In our study, we tried to identify the possible components behind the antimicrobial activity of cow urine by exploring the peptidome and metabolome.METHODS: We extracted peptides from the urine of Sahiwal cows belonging to three different physiological states viz heifer, lactation, and pregnant, each group consisting of 10 different animals. The peptides were extracted using the Solid Phase Extraction technique followed by further extraction using ethyl acetate. The antimicrobial activity of the aqueous extract was evaluated against different pathogenic strains like S. aureus, E. coli, and S. agalactiae. The safety of urinary aqueous extract was evaluated by haemolysis and cytotoxicity assay on BuMEC cell line. The urinary peptides were further fractionated using HPLC to identify the fraction(s) containing the antimicrobial activity. The HPLC fractions and ethyl acetate extract were analysed using nLC-MS/MS for the identification of the peptides and metabolites.RESULTS: A total of three fractions were identified with antimicrobial activity, nLC-MS/MS analysis of fractions resulted in the identification of 511 sequences. While 46 compounds were identified in the metabolite profiling of organic extract. The urinary aqueous extract showed significant activity against E.coli as compared to S.aureus and S.agalactiae and was relatively safe against mammalian cells.CONCLUSIONS: The antimicrobial activity of cow urine is a consequence of the feeding habit. The metabolites of plant origin with several bioactivities are eliminated through urine and are responsible for its antimicrobial nature. Secondly, and the plethora of peptides generated from the activity of endogenous proteases on protein shed from different parts of tissues also find their way to urine. Some of these sequences possess antimicrobial activity due to their amino acid composition.PMID:36634651 | DOI:10.5713/ab.22.0249

J Magn Reson. 2022 Dec 31;347:107365. doi: 10.1016/j.jmr.2022.107365. Online ahead of print.ABSTRACTRobust annotation of metabolites is a challenging task in metabolomics. Among available applications, 13C NMR experiment INADEQUATE determines direct 13C-13C connectivity unambiguously, offering indispensable information on molecular structure. Despite its great utility, it is not always practical to collect INADEQUATE data on every sample in a large metabolomics study because of its relatively long experiment time. Here, we propose an alternative approach that maintains the quality of information but saves experiment time. In this approach, individual samples in a study are first screened by 13C homonuclear J-resolved experiment (JRES). Next, JRES data are processed by statistical total correlation spectroscopy (STOCSY) to extract peaks that behave similarly among samples. Finally, INADEQUATE is collected on one internal pooled sample to select STOCSY peaks that originate from the same compound. We tested this concept using the 13C-labeled endometabolome of a model marine diatom strain incubated under various settings, intending to cover a range of metabolites produced under different external conditions. This scheme was able to extract known diatom metabolites proline, 2,3-dihydroxypropane-1-sulfonate (DHPS), β-1,3-glucan, choline, and glutamate. This pipeline also detected unknown compounds with structural information, which is valuable in metabolomics where a priori knowledge of metabolites is not always available. The ability of this scheme was seen even in sugar regions, which are usually challenging in 1H NMR due to severe peak overlap. JRES and INADEQUATE were highly complementary; INADEQUATE provided directly-bonded 13C networks, whereas JRES linked INADEQUATE networks within the same compound but broken by nitrogen or sulfur atoms, highlighting the advantage of this integrated approach.PMID:36634594 | DOI:10.1016/j.jmr.2022.107365

Lung Cancer. 2022 Dec 27;176:121-131. doi: 10.1016/j.lungcan.2022.12.015. Online ahead of print.ABSTRACTTTF-1-expressing non-small cell lung cancer (NSCLC) is one of the most prevalent lung cancer types worldwide. However, theparadoxical activity of TTF-1 in both lung carcinogenesis and tumor suppression is believed to be context-dependentwhich calls for a deeper understanding about the pathological expression of TTF-1. In addition, the expression circuitry of TTF-1-target genes in NSCLC has not been well examined which necessitates to revisit the involvement of TTF-1- in a multitude of oncologic pathways. We used RNA-seq and clinical data of patients from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx), including ChIP-seq data from different NSCLC cell lines, and mapped the proteome of NSCLC tumor. Our analysis showed significant variability in TTF-1 expression among NSCLC,and further clarified that this variability is orchestrated at the transcriptional level. We also found that high TTF-1 expression could negatively influence the survival outcomes of stage 1 LUAD which may be attributed to growth factor receptor-driven activation of mitogenic and angiogenic pathways. Mechanistically, TTF-1 may also control the genes associated with pathways involved in acquired TKI drug resistance or response to immune checkpoint inhibitors. Lastly, proteome-based biomarker discovery in stage 1 LUAD showed that TTF-1 positivity is potentially associated with the upregulation of several oncogenes which includes interferon proteins, MUC1, STAT3, and EIF2AK2. Collectively, this study highlights the potential involvement of TTF-1 in cell proliferation, immune evasion, and angiogenesis in early-stage NSCLC.PMID:36634573 | DOI:10.1016/j.lungcan.2022.12.015

EBioMedicine. 2023 Jan 10;88:104430. doi: 10.1016/j.ebiom.2022.104430. Online ahead of print.ABSTRACTBACKGROUND: Patients with inflammatory bowel disease (IBD) treated with anti-TNF therapy exhibit attenuated humoral immune responses to vaccination against SARS-CoV-2. The gut microbiota and its functional metabolic output, which are perturbed in IBD, play an important role in shaping host immune responses. We explored whether the gut microbiota and metabolome could explain variation in anti-SARS-CoV-2 vaccination responses in immunosuppressed IBD patients.METHODS: Faecal and serum samples were prospectively collected from infliximab-treated patients with IBD in the CLARITY-IBD study undergoing vaccination against SARS-CoV-2. Antibody responses were measured following two doses of either ChAdOx1 nCoV-19 or BNT162b2 vaccine. Patients were classified as having responses above or below the geometric mean of the wider CLARITY-IBD cohort. 16S rRNA gene amplicon sequencing, nuclear magnetic resonance (NMR) spectroscopy and bile acid profiling with ultra-high-performance liquid chromatography mass spectrometry (UHPLC-MS) were performed on faecal samples. Univariate, multivariable and correlation analyses were performed to determine gut microbial and metabolomic predictors of response to vaccination.FINDINGS: Forty-three infliximab-treated patients with IBD were recruited (30 Crohn's disease, 12 ulcerative colitis, 1 IBD-unclassified; 26 with concomitant thiopurine therapy). Eight patients had evidence of prior SARS-CoV-2 infection. Seventeen patients (39.5%) had a serological response below the geometric mean. Gut microbiota diversity was lower in below average responders (p = 0.037). Bilophila abundance was associated with better serological response, while Streptococcus was associated with poorer response. The faecal metabolome was distinct between above and below average responders (OPLS-DA R2X 0.25, R2Y 0.26, Q2 0.15; CV-ANOVA p = 0.038). Trimethylamine, isobutyrate and omega-muricholic acid were associated with better response, while succinate, phenylalanine, taurolithocholate and taurodeoxycholate were associated with poorer response.INTERPRETATION: Our data suggest that there is an association between the gut microbiota and variable serological response to vaccination against SARS-CoV-2 in immunocompromised patients. Microbial metabolites including trimethylamine may be important in mitigating anti-TNF-induced attenuation of the immune response.FUNDING: JLA is the recipient of an NIHR Academic Clinical Lectureship (CL-2019-21-502), funded by Imperial College London and The Joyce and Norman Freed Charitable Trust. BHM is the recipient of an NIHR Academic Clinical Lectureship (CL-2019-21-002). The Division of Digestive Diseases at Imperial College London receives financial and infrastructure support from the NIHR Imperial Biomedical Research Centre (BRC) based at Imperial College Healthcare NHS Trust and Imperial College London. Metabolomics studies were performed at the MRC-NIHR National Phenome Centre at Imperial College London; this work was supported by the Medical Research Council (MRC), the National Institute of Health Research (NIHR) (grant number MC_PC_12025) and infrastructure support was provided by the NIHR Imperial Biomedical Research Centre (BRC). The NIHR Exeter Clinical Research Facility is a partnership between the University of Exeter Medical School College of Medicine and Health, and Royal Devon and Exeter NHS Foundation Trust. This project is supported by the National Institute for Health Research (NIHR) Exeter Clinical Research Facility. The views expressed are those of the authors and not necessarily those of the NIHR or the UK Department of Health and Social Care.PMID:36634565 | DOI:10.1016/j.ebiom.2022.104430

Food Chem. 2023 Jan 3;410:135396. doi: 10.1016/j.foodchem.2023.135396. Online ahead of print.ABSTRACTHigh-performance liquid chromatography (HPLC), headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS) and ultra-high performance liquid chromatography-Q-Exactive HF-X mass spectrometer (UHPLC-Q-Exactive HF/MS) were carried out to reveal dynamic changes of volatile and non-volatile compounds during the withering process of black tea. A total of 118 volatile organic compounds (VOCs) and 648 metabolites were identified in fresh and withered tea-leaves, respectively. Among them, 47 VOCs (OAV > 1.0) for the aroma formation, and 46 characteristic metabolites (VIP > 1.50, p < 0.01) selected through orthonormal partial least squares-discriminant analysis, indicated the withering contribution during black tea processing. Overall, the withering promoted alcohols, aldehydes, phenols, heterocyclic oxygen, hydrocarbons and halogenated hydrocarbons through relevant hydrolyzation, decomposition, terpene synthesis, and O-methylation. The hydrolyzation, O-methylation, condensation and N-acylation of kaempferol glycosides, quercetin glycosides, ester catechins, and gallic acid generated the accumulation of methoxyl flavonoids and flavonoid glucosides, dihydrokaempferol, syringic acid, theaflavins, and N-acylated amino acids, respectively.PMID:36634561 | DOI:10.1016/j.foodchem.2023.135396

Redox Biol. 2023 Jan 6;60:102603. doi: 10.1016/j.redox.2023.102603. Online ahead of print.ABSTRACTInflammatory bowel diseases (IBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), are intimately associated with inflammation and overproduction of reactive oxygen species (ROS). Temporal and inter-individual variabilities in disease activity and response to therapy pose significant challenges to diagnosis and patient care. Discovery and validation of truly integrative biomarkers would benefit from embracing redox metabolomics approaches with prioritization of central regulatory hubs. We here make a case for applying a personalized redox medicine approach that aims to selectively inhibit pathological overproduction and/or altered expression of specific enzymatic sources of ROS without compromising physiological function. To this end, improved 'clinical-omics integration' may help to better understand which particular redox signaling pathways are disrupted in what patient. Pharmacological interventions capable of activating endogenous antioxidant defense systems may represent viable therapeutic options to restore local/systemic redox status, with HIF-1α and NRF2 holding particular promise in this context. Achieving the implementation of clinically meaningful mechanism-based biomarkers requires development of easy-to-use, robust and cost-effective tools for secure diagnosis and monitoring of treatment efficacy. Ultimately, matching redox-directed pharmacological interventions to individual patient phenotypes using predictive biomarkers may offer new opportunities to break the therapeutic ceiling in IBD.PMID:36634466 | DOI:10.1016/j.redox.2023.102603