Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics.

Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpreting unannotated spectra, we created a nearest neighbor suspect spectral library, consisting of 87,916 annotated MS/MS spectra derived from hundreds of millions of MS/MS spectra originating from published untargeted metabolomics experiments. Entries in this library, or "suspects," were derived from unannotated spectra that could be linked in a molecular network to an annotated spectrum. Annotations were propagated to unknowns based on structural relationships to reference molecules using MS/MS-based spectrum alignment. We demonstrate the broad relevance of the nearest neighbor suspect spectral library through representative examples of propagation-based annotation of acylcarnitines, bacterial and plant natural products, and drug metabolism. Our results also highlight how the library can help to better understand an Alzheimer's brain phenotype. The nearest neighbor suspect spectral library is openly available for download or for data analysis through the GNPS platform to help investigators hypothesize candidate structures for unknown MS/MS spectra in untargeted metabolomics data.

Urine Excretion, Organ Distribution, and Placental Transfer of 6PPD and 6PPD-Quinone in Mice and Potential Developmental Toxicity through Nuclear Receptor Pathways.

The rubber antioxidant 6PPD has gained significant attention due to its highly toxic transformation product, 6PPD-quinone (6PPDQ). Despite their detection in urines of pregnant women, the placental transfer and developmental toxicity of 6PPD and 6PPDQ are unknown. Here, we treated C57Bl/6 mice with 4 mg/kg 6PPD or 6PPDQ to investigate their urine excretion and placental transfer. Female and male mice exhibited sex difference in excretion profiles of 6PPD and 6PPDQ. Urine concentrations of 6PPDQ were one order of magnitude lower than those of 6PPD, suggesting lower excretion and higher bioaccumulation of 6PPDQ. In pregnant mice treated with 6PPD or 6PPDQ from embryonic day 11.5 to 15.5, 6PPDQ showed ∼1.5-8 times higher concentrations than 6PPD in placenta, embryo body, and embryo brain, suggesting higher placental transfer of 6PPDQ. Using in vitro dual-luciferase reporter assays, we revealed that 6PPDQ activated the human retinoic acid receptor α (RARα) and retinoid X receptor α (RXRα) at concentrations as low as 0.3 µM, which was ∼10-fold higher than the concentrations detected in human urines. 6PPD activated the RXRα at concentrations as low as 1.2 µM. These results demonstrate the exposure risks of 6PPD and 6PPDQ during pregnancy and emphasize the need for further toxicological and epidemiological investigations.

Transfer of antibiotics and their metabolites in human milk: Implications for infant health and microbiota.

Antibiotics are an essential tool for perinatal care. While antibiotics can play a life-saving role for both parents and infants, they also cause collateral damage to the beneficial bacteria that make up the host gut microbiota. This is especially true for infants, whose developing gut microbiota is uniquely sensitive to antibiotic perturbation. Emerging evidence suggests that disruption of these bacterial populations during this crucial developmental window can have long-term effects on infant health and development. Although most current studies have focused on microbial disruptions caused by direct antibiotic administration to infants or prenatal exposure to antibiotics administered to the mother, little is known about whether antibiotics in human milk may pose similar risks to the infant. This review surveys current data on antibiotic transfer during lactation and highlights new methodologies to assess drug transfer in human milk. Finally, we provide recommendations for future work to ensure antibiotic use in lactating parents is safe and effective for both parents and infants.

Trimethylamine N-Oxide Reduces Neurite Density and Plaque Intensity in a Murine Model of Alzheimer's Disease.

BACKGROUND: Alzheimer's disease (AD) is the most common aging-associated neurodegenerative disease; nevertheless, the etiology and progression of the disease is still incompletely understood. We have previously shown that the microbially-derived metabolite trimethylamine N-oxide (TMAO) is elevated in the cerebrospinal fluid (CSF) of individuals with cognitive impairment due to AD and positively correlates with increases in CSF biomarkers for tangle, plaque, and neuronal pathology. OBJECTIVE: We assessed the direct impact of TMAO on AD progression. METHODS: To do so, transgenic 5XFAD mice were supplemented with TMAO for 12 weeks. Neurite density was assessed through quantitative brain microstructure imaging with neurite orientation dispersion and density imaging magnetic resonance imaging (MRI). Label-free, quantitative proteomics was performed on cortex lysates from TMAO-treated and untreated animals. Amyloid-ß plaques, astrocytes, and microglia were assessed by fluorescent immunohistochemistry and synaptic protein expression was quantified via western blot. RESULTS: Oral TMAO administration resulted in significantly reduced neurite density in several regions of the brain. Amyloid-ß plaque mean intensity was reduced, while plaque count and size remained unaltered. Proteomics analysis revealed that TMAO treatment impacted the expression of 30 proteins (1.5-fold cut-off) in 5XFAD mice, including proteins known to influence neuronal health and amyloid-ß precursor protein processing. TMAO treatment did not alter astrocyte and microglial response nor cortical synaptic protein expression. CONCLUSION: These data suggest that elevated plasma TMAO impacts AD pathology via reductions in neurite density.

Correction: McMillen et al. Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood. Nutrients 2022, 14, 412.

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An untargeted metabolomics analysis of exogenous chemicals in human milk and transfer to the infant.

Human milk is the optimal infant nutrition. However, although human-derived metabolites (such as lipids and oligosaccharides) in human milk are regularly reported, the presence of exogenous chemicals (such as drugs, food, and synthetic compounds) are often not addressed. To understand the types of exogenous compounds that might be present, human milk (n = 996) was analyzed by untargeted metabolomics. This analysis revealed that lifestyle molecules, such as medications and their metabolites, and industrial sources, such as plasticizers, cosmetics, and other personal care products, are found in human milk. We provide further evidence that some of these lifestyle molecules are also detectable in the newborn's stool. Thus, this study gives important insight into the types of exposures infants receiving human milk might ingest due to the lifestyle choices, exposure, or medical status of the lactating parent.

Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood.

The gut microbiota is implicated in the adverse developmental outcomes of postnatal iron supplementation. To generate hypotheses on how changes to the gut microbiota by iron adversely affect development, and to determine whether the form of iron influences microbiota outcomes, we characterized gut microbiome and metabolome changes in Sprague-Dawley rat pups given oral supplements of ferrous sulfate (FS), ferrous bis-glycinate chelate (FC), or vehicle control (CON) on postnatal day (PD) 2−14. Iron supplementation reduced microbiome alpha-diversity (p < 0.0001) and altered short-chain fatty acids (SCFAs) and trimethylamine (TMA) in a form-dependent manner. To investigate the long-term effects of iron provision in early life, an additional cohort was supplemented with FS, FC, or CON until PD 21 and then weaned onto standard chow. At ~8 weeks of age, young adult (YA) rats that received FS exhibited more diverse microbiomes compared to CON (p < 0.05), whereas FC microbiomes were less diverse (p < 0.05). Iron provision resulted in 10,000-fold reduced abundance of Lactobacilli in pre-weanling and YA animals provided iron in early life (p < 0.0001). Our results suggest that in pre-weanling rats, supplemental iron form can generate differential effects on the gut microbiota and microbial metabolism that persist into adulthood.

Oropharyngeal Carcinoma Treated with Surgery Alone: Outcomes and Predictors of Failure.

OBJECTIVE: To analyze the oncologic outcomes and risk factors for recurrence in patients who underwent surgery for oropharyngeal squamous cell carcinoma (OPSCC), and in whom adjuvant therapy was not recommended or was declined. METHODS: Retrospective cohort study of patients with OPSCC who were treated with transoral surgery only at a tertiary care academic medical center from April 2010 to March 2019. RESULTS: Seventy-four patients met inclusion criteria. In 16, adjuvant therapy was recommended but declined. There were 8 recurrences, of which 6 had been given recommendations for adjuvant therapy. Of the 8 recurrences, 2 died, 2 are alive with disease, and 4 were successfully salvaged. Five patients died of unrelated causes. Lymphovascular invasion (LVI, P = .016) had a significant impact on recurrence, while other pathologic features of the primary tumor such as size, location, human papillomavirus (HPV) status, and margin status did not. Margins were classified as "positive" in 4 patients, "close" in 54, and "negative" in 16. There were 3 local recurrences (4.1%), each of whom had declined adjuvant therapy. Lymph node features such as N-stage (P = .0004), number of positive nodes (P = .0005), and presence of extra-nodal extension (ENE, P = .0042) had a statistically significant impact on relapse. Smoking history and surgical approach showed no significant impact on recurrence. CONCLUSION: Patients who undergo surgery for HPV-positive OPSCC with negative margins, no PNI, no LVI, and ≤1 positive lymph node without ENE have low risk for recurrence. These patients can likely be safely treated with surgery alone. Patients with these risk factors who decline adjuvant therapy are at risk for recurrence, and should be monitored.

Short-chain fatty acids activate acetyltransferase p300.

Short-chain fatty acids (SCFAs) acetate, propionate, and butyrate are produced in large quantities by the gut microbiome and contribute to a wide array of physiological processes. While the underlying mechanisms are largely unknown, many effects of SCFAs have been traced to changes in the cell's epigenetic state. Here, we systematically investigate how SCFAs alter the epigenome. Using quantitative proteomics of histone modification states, we identified rapid and sustained increases in histone acetylation after the addition of butyrate or propionate, but not acetate. While decades of prior observations would suggest that hyperacetylation induced by SCFAs are due to inhibition of histone deacetylases (HDACs), we found that propionate and butyrate instead activate the acetyltransferase p300. Propionate and butyrate are rapidly converted to the corresponding acyl-CoAs which are then used by p300 to catalyze auto-acylation of the autoinhibitory loop, activating the enzyme for histone/protein acetylation. This data challenges the long-held belief that SCFAs mainly regulate chromatin by inhibiting HDACs, and instead reveals a previously unknown mechanism of HAT activation that can explain how an influx of low levels of SCFAs alters global chromatin states.

Gut microbiome variation modulates the effects of dietary fiber on host metabolism.

BACKGROUND: There is general consensus that consumption of dietary fermentable fiber improves cardiometabolic health, in part by promoting mutualistic microbes and by increasing production of beneficial metabolites in the distal gut. However, human studies have reported variations in the observed benefits among individuals consuming the same fiber. Several factors likely contribute to this variation, including host genetic and gut microbial differences. We hypothesized that gut microbial metabolism of dietary fiber represents an important and differential factor that modulates how dietary fiber impacts the host. RESULTS: We examined genetically identical gnotobiotic mice harboring two distinct complex gut microbial communities and exposed to four isocaloric diets, each containing different fibers: (i) cellulose, (ii) inulin, (iii) pectin, (iv) a mix of 5 fermentable fibers (assorted fiber). Gut microbiome analysis showed that each transplanted community preserved a core of common taxa across diets that differentiated it from the other community, but there were variations in richness and bacterial taxa abundance within each community among the different diet treatments. Host epigenetic, transcriptional, and metabolomic analyses revealed diet-directed differences between animals colonized with the two communities, including variation in amino acids and lipid pathways that were associated with divergent health outcomes. CONCLUSION: This study demonstrates that interindividual variation in the gut microbiome is causally linked to differential effects of dietary fiber on host metabolic phenotypes and suggests that a one-fits-all fiber supplementation approach to promote health is unlikely to elicit consistent effects across individuals. Overall, the presented results underscore the importance of microbe-diet interactions on host metabolism and suggest that gut microbes modulate dietary fiber efficacy. Video abstract.

Spring-Assisted Surgery for Treatment of Sagittal Craniosynostosis.

ABSTRACT: Craniosynostosis (CSS), the premature fusion of calvarial sutures, most commonly involves the sagittal suture. Cranial vault remodeling (CVR) is a traditional method of CSS correction. Minimally invasive methods are becoming widely accepted, including spring-assisted surgery (SAS). The equipment required for SAS is minimal therefore adaptable to resource challenged health systems. This paper outlines the experience of SAS in Moldova.A retrospective study was performed for patients treated with SAS for sagittal CSS from 2011 to 2018 in Moldova. Perioperative data were recorded including age, length of surgery, blood loss, volume transfused and length of stay. Four patients had pre- and post-operative computed tomography (CT) scans which were used to calculate changes in cephalic index, normative cephalic index, and intracranial volume.Thirteen patients underwent SAS. Diagnoses were made clinically and confirmed with CT. Mean age at surgery was 4.0 months, and length of surgery 62.7 minutes. All but one patient received a blood transfusion, as is standard of practice in Moldova. The mean length of post-operative recovery in ICU was 30.9 hours. No complications required surgical revision. Springs were removed after 4 to 5 months. All patients had a subjective improvement in scaphocephaly. Based on the available CT scans, an increase in cephalic index (7.3%), normative cephalic index (11.8%), and intracranial volume (38.1%) was observed. One patient underwent SAS at 11 months and required cranioplasty for asymmetry at the time of spring removal.SAS is a safe and cost-effective method of CSS correction that can be utilized in countries with limited health system resources.

Hypoalbuminemia in children with cancer treated with chemotherapy.

BACKGROUND: Hypoalbuminemia is a well-recognized finding associated with cancer, but its prevalence and prognostic significance have not been well studied in children with cancer. OBJECTIVE: To determine the prevalence of hypoalbuminemia prior to starting chemotherapy in children with cancer and its association with relapse-free survival (RFS) and overall survival (OS). DESIGN/METHOD: We performed a single institution, IRB-approved, retrospective review of pediatric oncology patients diagnosed between 1998 and 2012. Five-year survival was estimated using the Kaplan-Meier method; groups were compared using Cox regression. RESULTS: We identified 659 pediatric patients with a first diagnosis of cancer and a serum albumin level prior to starting chemotherapy. Mean age was 8.6 years (SD = 5.8); 62% were male and 92% were non-Hispanic. Hypoalbuminemia prior to starting chemotherapy was present at least once in 302 (45.8%). The five-year RFS and OS of those with hypoalbuminemia and without hypoalbuminemia were not significantly different. However, patients with severe hypoalbuminemia (defined as a value 10% or more below the lower limit of normal) had inferior RFS and OS for patients with hematologic/lymphatic malignancies, and inferior RFS for patients with metstatic Ewing sarcoma. CONCLUSION: Hypoalbuminemia prior to starting chemotherapy in pediatric oncology patients is common (nearly half in this cohort). Severe hypoalbuminemia was associated with inferior 5-year RFS in some subgroups.

A practical guide for analysis of histone post-translational modifications by mass spectrometry: Best practices and pitfalls.

Advances in mass spectrometry (MS) have revolutionized the ability to measure global changes in histone post-translational modifications (PTMs). The method routinely quantifies over 60 modification states in a single sample, far exceeding the capabilities of traditional western blotting. Thus, MS-based histone analysis has become an increasingly popular tool for understanding how genetic and environmental factors influence epigenetic states. However, histone proteomics experiments exhibit unique challenges, such as batch-to-batch reproducibility, accurate peak integration, and noisy data. Here, we discuss the steps of histone PTM analysis, from sample preparation and peak integration to data analysis and validation. We outline a set of best practices for ensuring data quality, accurate normalization, and robust statistics. Using these practices, we quantify histone modifications in 5 human cell lines, revealing that each cell line exhibits a unique epigenetic signature. We also provide a reproducible workflow for histone PTM analysis in the form of an R script, which is freely available at https://github.com/DenuLab/HistoneAnalysisWorkflow.

Effect of menstrual cycle on ethanol drinking in rhesus monkeys.

BACKGROUND: Sex differences in the abuse-related effects of alcohol have been demonstrated in the clinic and in preclinical animal models. Less is known about the influence of menstrual cycle phase on drinking. METHODS: In this study, we examined the relationship between menstrual cycle phase and intake of ethanol (EtOH) in five adult female rhesus monkeys. Subjects consumed a 4% EtOH solution in their home cage 6 h per day, 5 days per week and pressed a lever to receive food pellets during the drinking session. Menstrual cycle was determined with vaginal swabs 5-7 days per week. To facilitate comparison with previous studies, the cycle was divided three different ways for analysis. RESULTS: First, no significant difference was observed when EtOH intake was compared between phases defined as "follicular" (days 5-10) and "luteal" (19-24). Second, when the cycle was further divided into four phases [early follicular (days 1-7), late follicular (8-14), early luteal (15-21) and late luteal (22-next cycle)], significant differences were detected, with intake highest in phases that bracket menses and lowest in the late follicular phase. Finally, EtOH intake during "mid-cycle" (days 12-16) was significantly lower than during "menses" (days 1-5) and "late luteal" (last 5 days). Effect sizes were small to moderate, although absolute differences in EtOH intake (g/kg) were <15%. Food-maintained responding was not different across phases. CONCLUSIONS: Menstrual cycle has modest but statistically significant and selective effects on EtOH drinking, with higher EtOH intake observed in the peri-menstrual period compared to the middle of the cycle.

Human angiogenin is a potent cytotoxin in the absence of ribonuclease inhibitor.

Angiogenin (ANG) is a secretory ribonuclease that promotes the proliferation of endothelial cells, leading to angiogenesis. This function relies on its ribonucleolytic activity, which is low for simple RNA substrates. Upon entry into the cytosol, ANG is sequestered by the ribonuclease inhibitor protein (RNH1). We find that ANG is a potent cytotoxin for RNH1-knockout HeLa cells, belying its inefficiency as a nonspecific catalyst. The toxicity does, however, rely on the ribonucleolytic activity of ANG and a cytosolic localization, which lead to the accumulation of particular tRNA fragments (tRFs), such as tRF-5 Gly-GCC. These up-regulated tRFs are highly cytotoxic at physiological concentrations. Although ANG is well-known for its promotion of cell growth, our results reveal that ANG can also cause cell death.

Knockout of the Ribonuclease Inhibitor Gene Leaves Human Cells Vulnerable to Secretory Ribonucleases.

Ribonuclease inhibitor (RNH1) is a cytosolic protein that binds with femtomolar affinity to human ribonuclease 1 (RNase 1) and homologous secretory ribonucleases. RNH1 contains 32 cysteine residues and has been implicated as an antioxidant. Here, we use CRISPR-Cas9 to knock out RNH1 in HeLa cells. We find that cellular RNH1 affords marked protection from the lethal ribonucleolytic activity of RNase 1 but not from oxidants. We conclude that RNH1 protects cytosolic RNA from invading ribonucleases.