Integrated Metabolomics and Lipidomics Analysis Reveal Remodeling of Lipid Metabolism and Amino Acid Metabolism in Glucagon Receptor-Deficient Zebrafish

Two NPC1 homologous proteins are involved in asexual reproduction, pathogenicity, and lipid trafficking in Phytophthora sojae

Niemann-Pick type C (NPC) disease is characterized by lysosomal lipid storage disorders and defects in lipid trafficking, primarily due to mutations in the NPC1 protein. Two NPC1 homologous proteins are present in the genome of Phytophthora sojae, named as PsNPC1-1 and PsNPC1-2. Both proteins exhibit high sequence identity, consistent conserved functional domains, similar gene expression patterns, and comparable subcellular localization. Deletion of a single PsNPC1 gene did not result in significant phenotypic changes. However, simultaneous deletion of both PsNPC1 genes led to reduced mycelial growth, decreased sporangial production, impaired pathogenicity, and an inability to release normal zoospores in P. sojae. Furthermore, dysfunction of PsNPC1s did not completely block the absorption and utilization of exogenous sterols by P. sojae. While lipidome analysis revealed that the relative contents of fatty acyls, sphingolipids and saccharolipids were significantly elevated in the double-gene deletion mutant, alongside obvious alterations in glycerophospholipid and glycerolipid metabolism. Additionally, we observed a significant down-regulation of PsCDP-AP protein along with its interactions with both PsNPC1s. Deletion of PsCDP-AP also impaired asexual reproduction and virulence of P. sojae. These findings demonstrate that both PsNPC1 proteins may collaborate with other key regulators to modulate asexual reproduction, pathogenicity and lipid trafficking in P. sojae.

ErbB3 is required for hyperaminoacidemia-induced pancreatic α cell hyperplasia

Blood amino acid levels are maintained in a narrow physiological range. The pancreatic α cells have emerged as the primary aminoacidemia regulator through glucagon secretion to promote hepatic amino acid catabolism. Interruption of glucagon signaling disrupts the liver-α cells axis leading to hyperaminoacidemia, which triggers a compensatory rise in glucagon secretion and α cell hyperplasia. The mechanisms of hyperaminoacidemia-induced α cell hyperplasia remain incompletely understood. Using a mouse α cell line and in vivo studies in zebrafish and mice, we found that hyperaminoacidemia-induced α cell hyperplasia requires ErbB3 signaling. In addition to mechanistic target of rapamycin complex 1, another ErbB3 downstream effector signal transducer and activator of transcription 3 also plays a role in α cell hyperplasia. Mechanistically, ErbB3 may partner with ErbB2 to stimulate cyclin D2 and suppress p27 via mechanistic target of rapamycin complex 1 and signal transducer and activator of transcription 3. Our study identifies ErbB3 as a new regulator for hyperaminoacidemia-induced α cell proliferation and a critical component of the liver-α cells axis that regulates aminoacidemia.

Recycling of animal protein wastes in the formulation of feed for Labeo rohita and Mystus vittatus-a comparative evaluation

Lactic acid bacteria (LAB) are key players in the fermentation of organic wastes and their recycling as feedstuff for fish. Whey, a common dairy byproduct in India, is a cheap source of LAB and can be used to ferment animal byproducts. An experimental study was designed to explore whether the whey fermented animal protein blend (WFAPB) could be used as a fishmeal replacer in the formulation of feed for both stomach-less carp fish Labeo rohita and stomach-bearing catfish Mystus vittatus. Experiments were performed with five isoproteinous, isolipidous, and isoenergetic feeds with WFAPB replacing fishmeal (FM) by 0% (T1), 25% (T2), 50% (T3), 75% (T4), and 100% (T5). Fifteen days of laboratory experiments with these experimental feeds revealed that more than 50% FM replacement level could result in excess postprandial absorption (6 h) of some essential and non-essential amino acids in the plasma of both fish. The postprandial absorption was more in M. vittatus than L. rohita. Ninety-day experiments were conducted in outdoor cement vats to measure growths and deposition of amino acids (AA) in muscle. Regression analysis was performed to find the optimal FM replacement based on four growth parameters and fifteen AA deposition in muscle. A two-phase fuzzy methodology was used to obtain Pareto-optimal replacement levels for each fish. The results demonstrated that FM replacement levels were 7.63% and 36.79% respectively for L. rohita and M. vittatus when only four growth parameters were considered. However, based on the FM replacement level that maximized deposition of 15 amino acids and growth parameters, it was found that 12.23% and 40.02% replacement of FM by the WFAPB was ideal respectively for L. rohita and M. vittatus. The results revealed that only a fraction of both essential and non-essential amino acids absorbed in plasma could be converted into protein and deposited as bound amino acids in the muscle. It is concluded that fermentation by whey is an inexpensive, easily available, and environmentally sustainable technique to recycle animal protein in the formulation of feed for fish, and the stomach-bearing carnivorous fish are more efficient in utilizing fermented animal protein blend than the stomach-less carps.

Protective mechanisms of a microbial oil against hypercholesterolemia: evidence from a zebrafish model

A Western diet elevates the circulating lipoprotein and triglyceride levels which are the major risk factors in cardiovascular disease (CVD) development. Consumption of long-chain omega-3 fatty acids can stall the disease progression. Although these fatty acids can significantly impact the intestine under a hypercholesterolemic condition, the associated changes have not been studied in detail. Therefore, we investigated the alterations in the intestinal transcriptome along with the deviations in the plasma lipids and liver histomorphology of zebrafish offered DHA- and EPA-rich oil. Fish were allocated to 4 dietary treatments: a control group, a high cholesterol group and microbial oil groups with low (3.3%) and high (6.6%) inclusion levels. We quantified the total cholesterol, lipoprotein and triglyceride levels in the plasma. In addition, we assessed the liver histology, intestinal transcriptome and plasma lipidomic profiles of the study groups. The results suggested that higher levels of dietary microbial oil could control the CVD risk factor indices in zebrafish plasma. Furthermore, microbial oil-fed fish had fewer liver vacuoles and higher mRNA levels of genes involved in β-oxidation and HDL maturation. Analyses of the intestine transcriptome revealed that microbial oil supplementation could influence the expression of genes altered by a hypercholesterolemic diet. The plasma lipidomic profiles revealed that the higher level of microbial oil tested could elevate the long-chain poly-unsaturated fatty acid content of triglyceride species and lower the concentration of several lysophosphatidylcholine and diacylglycerol molecules. Our study provides insights into the effectiveness of microbial oil against dyslipidemia in zebrafish.

Evaluation of extraction methods for untargeted metabolomic studies for future applications in zebrafish larvae infection models

Sample preparation in untargeted metabolomics should allow reproducible extractions of as many molecules as possible. Thus, optimizing sample preparation is crucial. This study compared six different extraction procedures to find the most suitable for extracting zebrafish larvae in the context of an infection model. Two one-phase extractions employing methanol (I) and a single miscible phase of methanol/acetonitrile/water (II) and two two-phase methods using phase separation between chloroform and methanol/water combinations (III and IV) were tested. Additional bead homogenization was used for methods III and IV (III_B and IV_B). Nine internal standards and 59 molecules of interest (MoInt) related to mycobacterial infection were used for method evaluation. Two-phase methods (III and IV) led to a lower feature count, higher peak areas of MoInt, especially amino acids, and higher coefficients of variation in comparison to one-phase extractions. Adding bead homogenization increased feature count, peak areas, and CVs. Extraction I showed higher peak areas and lower CVs than extraction II, thus being the most suited one-phase method. Extraction III and IV showed similar results, with III being easier to execute and less prone to imprecisions. Thus, for future applications in zebrafish larvae metabolomics and infection models, extractions I and III might be chosen.

Ram sperm cryopreservation disrupts metabolism of unsaturated fatty acids

In ram sperm, metabolites are important components of the plasma membrane, energy metabolism cycle, and precursors for other membrane lipids, and they may have important roles in maintaining plasma membrane integrity, energy metabolism, and regulation of cryotolerance. In this study, the ejaculates from 6 Dorper rams were pooled and sperm were systematically investigated by metabolomics at various steps of cryopreservation (37 °C, fresh [F]; from 37 to 4 °C, cooling [C]; and from 4 to -196 to 37 °C, frozen-thawed [FT]) to identify differential metabolites (DM). There were 310 metabolites identified, of which 86 were considered DMs. Regarding the DMs, there were 23 (0 up and 23 down), 25 (12 up and 13 down), and 38 (7 up and 31 down) identified during cooling (C vs F), freezing (FT vs C), and cryopreservation (FT vs F), respectively. Furthermore, some key polyunsaturated fatty acids (FAs), particularly, linoleic acid (LA), docosahexaenoic acid (DHA), and arachidonic acid (AA) were down-regulated during cooling and cryopreservation. Significant DMs were enriched in several metabolic pathways including biosynthesis of unsaturated FAs, LA metabolism, mammalian target of rapamycin (mTOR), forkhead box transcription factors (FoxO), adenosine monophosphate-activated protein kinase (AMPK), phosphatidylinositol 3-kinase/protein kinase B (PI3K-Akt) signaling pathways, regulation of lipolysis in adipocytes, and FA biosynthesis. This was apparently the first report to compare metabolomics profiles of ram sperm during cryopreservation and provided new knowledge to improve this process.

Compared to Fishmeal, Dietary Soybean Meal Improves the Reproductive Performance of Female Yellow Catfish (Pelteobagrus fulvidraco) Broodstock

To investigate the effects of different dietary protein sources on the reproductive performance of female broodstock, yellow catfish (Pelteobagrus fulvidraco) were fed with three experimental diets using fishmeal (FM), soybean meal (SBM), and rapeseed meal (RSM) as main protein sources, respectively. Females (initial weight: 64.56 ± 0.45 g) were distributed into 9 net cages for feeding trial. Results indicated that 30% dietary SBM improved the reproductive performance for higher gonadosomatic index (GSI), relative fecundity, total egg production, egg diameter, and hatching rate. In addition, SBM and RSM diets resulted in higher estradiol (E2), vitellogenin (VTG), luteinizing hormones (LH), and lower follicle-stimulating hormone (FSH) and testosterone (T) in plasma (P < 0.05) of female broodstock. Dietary SBM and RSM also resulted in lower mesenteric fat index (MFI), plasma total cholesterol (TC), plasma total bilirubin (T-Bil) contents, and gonadal cortisol concentrations, while dietary SBM downregulated the transcription levels of steroidogenesis-related proteins by negative feedback (P < 0.05). The results demonstrated that dietary SBM and RSM could promote sex steroid hormone and VTG biosynthesis and showed hypocholesterolemic effects. Besides, 30% dietary SBM inclusion could improve the reproductive performance of female yellow catfish broodstock.

Integrated ONT Full-Length Transcriptome and Metabolism Reveal the Mechanism Affecting Ovulation in Muscovy Duck (Cairina moschata)

Ovulation is a complicated physiological process that is regulated by a multitude of different pathways. In comparison to mammalian studies, there are few reports of ovulation in Muscovy ducks, and the molecular mechanism of ovarian development remained unclear. In order to identify candidate genes and metabolites related to Muscovy duck follicular ovulation, the study combined Oxford Nanopore Technologies (ONT) full-length transcriptome and metabolomics to analyze the differences in gene expression and metabolite accumulation in the ovaries between pre-ovulation (PO) and consecutive ovulation (CO) Muscovy ducks. 83 differentially accumulated metabolites (DAMs) were identified using metabolomics analysis, 33 of which are related to lipids. Combined with data from previous transcriptomic analyses found that DEGs and DAMs were particularly enriched in processes including the regulation of glycerophospholipid metabolism pathway, arachidonic acid metabolic pathway and the steroid biosynthetic pathway. In summary, the novel potential mechanisms that affect ovulation in Muscovy ducks may be related to lipid metabolism, and the findings provide new insights into the mechanisms of ovulation in waterfowl and will contribute to a better understanding of changes in the waterfowl ovarian development regulatory network.

Association Among the Gut Microbiome, the Serum Metabolomic Profile and RNA m6A Methylation in Sepsis-Associated Encephalopathy

Objective: To investigate the relationship among the gut microbiome, serum metabolomic profile and RNA m6A methylation in patients with sepsis-associated encephalopathy (SAE), 16S rDNA technology, metabolomics and gene expression validation were applied.

Methods: Serum and feces were collected from patients with and without (SAE group and non-SAE group, respectively, n = 20). The expression of serum markers and IL-6 was detected by enzyme-linked immunosorbent assay (ELISA), and blood clinical indicators were detected using a double antibody sandwich immunochemiluminescence method. The expression of RNA m⁶A regulator were checked by Q-RTPCR. The gut microbiome was analyzed by 16S rDNA sequencing and the metabolite profile was revealed by liquid chromatography-mass spectrometry (LC-MS/MS).

Results: In the SAE group, the IL-6, ICAM-5 and METTL3 levels were significantly more than those in the non-SAE group, while the FTO levels were significantly decreased in the SAE group. The diversity was decreased in the SAE gut microbiome, as characterized by a profound increase in commensals of the Acinetobacter, Methanobrevibacter, and Syner-01 genera, a decrease in [Eubacterium]_hallii_group, while depletion of opportunistic organisms of the Anaerofilum, Catenibacterium, and Senegalimassilia genera were observed in both groups. The abundance of Acinetobacter was positively correlated with the expression of METTL3. The changes between the intestinal flora and the metabolite profile showed a significant correlation. Sphingorhabdus was negatively correlated with 2-ketobutyric acid, 9-decenoic acid, and l-leucine, and positively correlated with Glycyl-Valine [Eubacterium]_hallii_group was positively correlated with 2-methoxy-3-methylpyazine, acetaminophen, and synephrine acetonide.

Conclusion: The gut microbiota diversity was decreased. The serum metabolites and expression of RNA m6A regulators in PBMC were significantly changed in the SAE group compared to the non-SAE group. The results revealed that serum and fecal biomarkers could be used for SAE screening.

Plasma lipidomics analysis reveals altered lipids signature in patients with osteonecrosis of the femoral head

INTRODUCTION

Although studies have established a link between lipid metabolism disorder and osteonecrosis of the femoral head (ONFH), the characteristics of the circulating lipidome signature of ONFH have not yet been investigated and need to be explored.

OBJECTIVES

We aimed to explore the plasma lipidome signatures in patients with ONFH, and to identify specific lipid biomarkers of ONFH.

METHODS

In this study, a comprehensive detection and analysis of plasma lipidomics was conducted in clinical human cohort, including 32 healthy normal control (NC) subjects and 91 ONFH patients in different subgroups [alcohol-induced ONFH (AONFH), steroid-induced ONFH (SONFH), and traumatic-induced ONFH (TONFH)] or at different disease stages (stage I, II, III and IV of ONFH) using ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS).

RESULTS

Overall, the plasma lipidome profile differs between ONFH and NC samples. Lipidome signature including 22 common differentially expressed lipids (DELs) in all three subgroups (variable importance in projection > 1, P < 0.05, fold change > 1.5 or < 0.67, compared to the NC group) was identified. Besides, the subtype-specific lipidome profiles for each ONFH subgroup were also analyzed. Generally, the AONFH subgroup has the largest number of DELs, and the plasma levels of triacylglycerol lipid compounds increased obviously in the AONFH samples. In the subgroup of SONFH, the relative abundance of lipid 4-Aminobenzoic acid increased significantly with changes in the expression of several of its interactive genes. We have identified that 9 stage-positive and 2 stage-negative lipids may function as novel biomarkers predicting the progression of ONFH.

CONCLUSION

Our study presents an overview of the phenotype-related plasma lipidome signature of patients with ONFH. The results will provide insight into the mechanisms underlying the metabolism of lipids in the pathogenesis and progression of ONFH and help identify novel lipids biomarkers or disease diagnosis and treatment targets.

Newly discovered endocrine functions of the liver

The liver, the largest solid visceral organ of the body, has numerous endocrine functions, such as direct hormone and hepatokine production, hormone metabolism, synthesis of binding proteins, and processing and redistribution of metabolic fuels. In the last 10 years, many new endocrine functions of the liver have been discovered. Advances in the classical endocrine functions include delineation of mechanisms of liver production of endocrine hormones [including 25-hydroxyvitamin D, insulin-like growth factor 1 (IGF-1), and angiotensinogen], hepatic metabolism of hormones (including thyroid hormones, glucagon-like peptide-1, and steroid hormones), and actions of specific binding proteins to glucocorticoids, sex steroids, and thyroid hormones. These studies have furthered insight into cirrhosis-associated endocrinopathies, such as hypogonadism, osteoporosis, IGF-1 deficiency, vitamin D deficiency, alterations in glucose and lipid homeostasis, and controversially relative adrenal insufficiency. Several novel endocrine functions of the liver have also been unraveled, elucidating the liver’s key negative feedback regulatory role in the pancreatic α cell-liver axis, which regulates pancreatic α cell mass, glucagon secretion, and circulating amino acid levels. Betatrophin and other hepatokines, such as fetuin-A and fibroblast growth factor 21, have also been discovered to play important endocrine roles in modulating insulin sensitivity, lipid metabolism, and body weight. It is expected that more endocrine functions of the liver will be revealed in the near future.

Mass Spectrometry-Based Zebrafish Toxicometabolomics: A Review of Analytical and Data Quality Challenges

Metabolomics has achieved great progress over the last 20 years, and it is currently considered a mature research field. As a result, the number of applications in toxicology, biomarker, and drug discovery has also increased. Toxicometabolomics has emerged as a powerful strategy to provide complementary information to study molecular-level toxic effects, which can be combined with a wide range of toxicological assessments and models. The zebrafish model has gained importance in recent decades as a bridging tool between in vitro assays and mammalian in vivo studies in the field of toxicology. Furthermore, as this vertebrate model is a low-cost system and features highly conserved metabolic pathways found in humans and mammalian models, it is a promising tool for toxicometabolomics. This short review aims to introduce zebrafish researchers interested in understanding the effects of chemical exposure using metabolomics to the challenges and possibilities of the field, with a special focus on toxicometabolomics-based mass spectrometry. The overall goal is to provide insights into analytical strategies to generate and identify high-quality metabolomic experiments focusing on quality management systems (QMS) and the importance of data reporting and sharing.