Metabolic Gene Expression Research Articles

Interaction of high lipogenic states with titanium on osteogenesis

As obesity rates continue to rise, the prevalence of metabolic dysfunction and alcohol-associated steatotic liver disease (MetALD), a new term for Nonalcoholic Fatty Liver Disease (NAFLD), also increases. In an aging population, it is crucial to understand the interplay between metabolic disorders, such as MetALD, and bone health. This understanding becomes particularly significant in the context of implant osseointegration. This study introduces an in vitro model simulating high lipogenesis through the use of human Mesenchymal Stroma Cells-derived adipocytes, 3D intrahepatic cholangiocyte organoids (ICO), and Huh7 hepatocytes, to evaluate the endocrine influence on osteoblasts interacting with titanium. We observed a significant increase in intracellular fat accumulation in all three cell types, along with a corresponding elevation in metabolic gene expression compared to the control groups. Notably, osteoblasts undergoing mineralization in this high-lipogenesis environment also displayed lipid vesicle accumulation. The study further revealed that titanium surfaces modulate osteogenic gene expression and impact cell cycle progression, cell survival, and extracellular matrix remodeling under lipogenic conditions. These findings provide new insights into the challenges of implant integration in patients with obesity and MetALD, offering a deeper understanding of the metabolic influences on bone regeneration and implant success.

Transcriptome analysis of Drosophila suzukii reveals molecular mechanisms conferring pyrethroid and spinosad resistance

Drosophila suzukii lay eggs in soft-skinned, ripening fruits, making this insect a serious threat to berry production. Since its 2008 introduction into North America, growers have used insecticides, such as pyrethroids and spinosads, as the primary approach for D. suzukii management, resulting in development of insecticide resistance in this pest. This study sought to identify the molecular mechanisms conferring insecticide resistance in these populations. We sequenced the transcriptomes of two pyrethroid- and two spinosad-resistant isofemale lines. In both pyrethroid-resistant lines and one spinosad-resistant line, we identified overexpression of metabolic genes that are implicated in resistance in other insect pests. In the other spinosad-resistant line, we observed an overexpression of cuticular genes that have been linked to resistance. Our findings enabled the development of molecular diagnostics that we used to confirm persistence of insecticide resistance in California, U.S.A. To validate these findings, we leveraged D. melanogaster mutants with reduced expression of metabolic or cuticular genes that were found to be upregulated in resistant D. suzukii to demonstrate that these genes are involved in promoting resistance. This study is the first to characterize the molecular mechanisms of insecticide resistance in D. suzukii and provides insights into how current management practices can be optimized.

Genes to specialized metabolites: accumulation of scopoletin, umbelliferone and their glycosides in natural populations of Arabidopsis thaliana

BackgroundScopoletin and umbelliferone belong to coumarins, which are plant specialized metabolites with potent and wide biological activities, the accumulation of which is induced by various environmental stresses. Coumarins have been detected in various plant species, including medicinal plants and the model organism Arabidopsis thaliana. In recent years, key role of coumarins in maintaining iron (Fe) homeostasis in plants has been demonstrated, as well as their significant impact on the rhizosphere microbiome through exudates secreted into the soil environment. Several mechanisms underlying these processes require clarification. Previously, we demonstrated that Arabidopsis is an excellent model for studying genetic variation and molecular basis of coumarin accumulation in plants.ResultsHere, through targeted metabolic profiling and gene expression analysis, the gene-metabolite network of scopoletin and umbelliferone accumulation was examined in more detail in selected Arabidopsis accessions (Col-0, Est-1, Tsu-1) undergoing different culture conditions and characterized by variation in coumarin content. The highest accumulation of coumarins was detected in roots grown in vitro liquid culture. The expression of 10 phenylpropanoid genes (4CL1, 4CL2, 4CL3, CCoAOMT1, C3’H, HCT, F6’H1, F6’H2,CCR1 and CCR2) was assessed by qPCR in three genetic backgrounds, cultured in vitro and in soil, and in two types of tissues (leaves and roots). We not only detected the expected variability in gene expression and coumarin accumulation among Arabidopsis accessions, but also found interesting polymorphisms in the coding sequences of the selected genes through in silico analysis and resequencing.ConclusionsTo the best of our knowledge, this is the first study comparing accumulation of simple coumarins and expression of phenylpropanoid-related genes in Arabidopsis accessions grown in soil and in liquid cultures. The large variations we detected in the content of coumarins and gene expression are genetically determined, but also tissue and culture dependent. It is particularly important considering that growing plants in liquid media is a widely used technology that provides a large amount of root tissue suitable for metabolomics. Research on differential accumulation of coumarins and related gene expression will be useful in future studies aimed at better understanding the physiological role of coumarins in roots and the surrounding environments.

PmLBD3 links auxin and brassinosteroid signalling pathways on dwarfism in Prunus mume

BackgroundGrafting with dwarf rootstock is an efficient method to control plant height in fruit production. However, the molecular mechanism remains unclear. Our previous study showed that plants with Prunus mume (mume) rootstock exhibited a considerable reduction in plant height, internode length, and number of nodes compared with Prunus persica (peach) rootstock. The present study aimed to investigate the mechanism behind the regulation of plant height by mume rootstocks through transcriptomic and metabolomic analyses with two grafting combinations, ‘Longyan/Mume’ and ‘Longyan/Peach’.ResultsThere was a significant decrease in brassinolide levels in plants that were grafted onto mume rootstocks. Plant hormone signal transduction and brassinolide production metabolism gene expression also changed significantly. Flavonoid levels, amino acid and fatty acid metabolites, and energy metabolism in dwarf plants decreased. There was a notable upregulation of PmLBD3 gene expression in plant specimens that were subjected to grafting onto mume rootstocks. Auxin signalling cues promoted PmARF3 transcription, which directly controlled this upregulation. Through its binding to PmBAS1 and PmSAUR36a gene promoters, PmLBD3 promoted endogenous brassinolide inactivation and inhibited cell proliferation.ConclusionsAuxin signalling and brassinolide levels are linked by PmLBD3. Our findings showed that PmLBD3 is a key transcription factor that regulates the balance of hormones through the auxin and brassinolide signalling pathways and causes dwarf plants in stone fruits.

Cross-site reproducibility of human cortical organoids reveals consistent cell type composition and architecture

While guided human cortical organoid (hCO) protocols reproducibly generate cortical cell types at one site, variability in hCO phenotypes across sites using a harmonized protocol has not yet been evaluated. To determine the cross-site reproducibility of hCO differentiation, three independent research groups assayed hCOs in multiple differentiation replicates from one induced pluripotent stem cell (iPSC) line using a harmonized miniaturized spinning bioreactor protocol across 3months. hCOs were mostly cortical progenitor and neuronal cell types in reproducible proportions that were consistently organized in cortical wall-like buds. Cross-site differences were detected in hCO size and expression of metabolism and cellular stress genes. Variability in hCO phenotypes correlated with stem cell gene expression prior to differentiation and technical factors associated with seeding, suggesting iPSC quality and treatment are important for differentiation outcomes. Cross-site reproducibility of hCO cell type proportions and organization encourages future prospective meta-analytic studies modeling neurodevelopmental disorders in hCOs.

Inhibiting miRNA-146a suppresses mouse gallstone formation by regulating LXR/megalin/cubilin-media cholesterol absorption

BackgroundmiRNA has been implicated in regulating cholesterol homeostasis, a critical factor in gallstone formation. Here, we focused on elucidating the role of miR-146a in this pathological process. MethodsC57BL/6 mice were fed with lithogenic diet (LD) and injected with miR-146 antagomir (anta-146) via the tail vein for various weeks. The gallbladders and liver tissues were collected for cholesterol crystal imaging, gallstone mass quantification, and molecular analysis. Levels of cholesterol, bile salt, phospholipids, and metabolic parameters in serum and bile were assessed by ELISA. A 3′ UTR reporter gene assay was used to verify the direct target genes for miR-146. The relative expression of metabolism genes was analyzed by quantitative real-time PCR and immunoblotting. ResultsmiR-146a-5p expression was reduced in mice and clinical samples with gallstones. Anta-146 treatment effectively prevented LD-induced gallstone formation in mice without hepatic and cholecystic damage. The mice treated with anta-146 exhibited beneficial alterations in bile cholesterol and bile acids and lipid levels in the blood. A key biliary cholesterol transporter-Megalin was identified as a direct target of miR-146. Anta-146 administration upregulated megalin expression, thereby ameliorating impaired gallbladder cholesterol absorption associated with the LXR-megalin/cubilin pathway. ConclusionThe data demonstrates that miR-146 modulates gallbladder cholesterol absorption by targeting megalin, and prevents the pathogenesis of cholesterol gallstones.

Effect of Ca2+ signal on the activity of key enzymes of carbon metabolism and related gene expression in yeast under high sugar fermentation.

Saccharomyces cerevisiae is a fungus widely used in the food industry and biofuel industry, whereas it is usually exposed to high sugar stress during the fermentation process. Ca2+ is a key second messenger of the cell, it can regulate cell metabolism. The present study investigated the effect of the Ca2+ signal on the activity of key enzymes of carbon metabolism and related gene expression in yeast under high sugar fermentation. The expression of genes encoding hexokinase was up-regulated in the high sugar environment, the activity of hexokinase was increased, glucose transmembrane transport capacity was enhanced, the ability of glucose to enter into glycolytic metabolism was increased, and the expression of genes related to pentose phosphate metabolism, glycerol metabolism and trehalose metabolism was up-regulated in the high glucose with Ca2+ group. Ca2+ signal regulates the cellular metabolism of glycerol and trehalose and optimizes the allocation of carbon flow by regulating the key enzymes and related gene expression to enhance the resistance of yeast to high sugar stress. © 2024 Society of Chemical Industry.

Ontogeny and organ-specific steroidal glycoside diversity is associated with differential expression of steroidal glycoside pathway genes in two Solanum dulcamara leaf chemotypes.

Solanaceous plants, such as Solanum dulcamara, produce steroidal glycosides (SGs). Leaf SG profiles vary among S. dulcamara individuals, leading to distinct phytochemical phenotypes ('chemotypes') and intraspecific phytochemical diversity ('chemodiversity'). However, if and how SG chemodiversity varies among organs and across ontogeny, and how this relates to SG metabolism gene expression is unknown. Among organs and across ontogeny, S. dulcamara plants with saturated (S) and unsaturated (U) SG leaf chemotypes were selected and clonally propagated. Roots, stems and leaves were harvested from vegetative and flowering plants. Extracts were analysed using untargeted LC-MS. Expression of candidate genes in SG metabolism (SdGAME9, SdGAME4, SdGAME25, SdS5αR2 and SdDPS) was analysed using RT-qPCRs. Our analyses showed that SG chemodiversity varies among organs and across ontogeny in S. dulcamara; SG richness (Dmg) was higher in flowering than vegetative plants. In vegetative plants, Dmg was higher for leaves than for roots. Lack of SdGAME25 expression in U-chemotype leaves, while readily expressed in roots and stems, suggests a pivotal role for SdGAME25 in differentiation of leaf chemotypes in vegetative and flowering plants. By acting as an ontogeny-dependent chemotypic switch, differential regulation of SdGAME25 enables adaptive allocation of SGs, thereby increasing SG chemodiversity in leaves. This indicates that differential expression and/or regulation of glycoalkaloid metabolism genes, rather than their presence or absence, explains observed chemotypic variation in SG chemodiversity among organs and across ontogeny.

Dietary manganese supplementation decreases hepatic lipid deposition by regulating gene expression and enzyme activity involved in lipid metabolism in the liver of broilers.

This study aimed to characterize the effects of different dietary forms of supplemental manganese (Mn) on hepatic lipid deposition, gene expression, and enzyme activity in liver fat metabolism in 42-d-old broiler chickens. In total 420 one-day-old Arbor Acres (AA) broilers (rooster:hen = 1:1) were assigned randomly based on body weight and sex to 1 of 6 treatments (10 replicate cages per treatment and 7 broilers per replicate cage) in a completely randomized design using a 2 (sex) × 3 (diet) factorial arrangement. The 3 diets were basal control diets without Mn supplementation and basal diets supplemented with either Mn sulfate or Mn proteinate. No sex × diet interactions were observed in any of the measured indexes; thus, the effect of diet alone was presented in this study. Dietary Mn supplementation increased Mn content in the plasma and liver, adipose triglyceride lipase (ATGL) activity, and ATGL mRNA and its protein expression in the liver by 5.3% to 24.0% (P < 0.05), but reduced plasma triglyceride (TG), total cholesterol, and low-density lipoprotein (LDL-C) levels, liver TG content, fatty acid synthase (FAS) and malic enzyme (ME) activities, mRNA expression of sterol-regulatory element-binding protein 1 (SREBP1), FAS, stearoyl-coA desaturase (SCD), and ME, as well as the protein expression of SREBP1 and SCD in the liver by 5.5% to 22.8% (P < 0.05). No differences were observed between the 2 Mn sources in all of the determined parameters. Therefore, it was concluded that dietary Mn supplementation, regardless of Mn source, decreased hepatic lipid accumulation in broilers by inhibiting SREBP1 and SCD expression, FAS and ME activities, and enhancing ATGL expression and activity.

Expression of sialic acid metabolism genes during LDL desialylation in blood

Expression of sialic acid metabolism genes during LDL desialylation in blood

Abstract Tu116: Neurofibromin 2 regulates metabolic gene expression and cardiac responses to pressure overload stress

Background: Neurofibromin 2 (NF2) is a tumor suppressor that can engage multiple signaling pathways to modulate cell proliferation and survival. We previously demonstrated that NF2 mediates cardiomyocyte apoptosis and cardiac injury caused by acute myocardial infarction. Research Aim: The role of NF2 in heart failure remains uncharacterized. This study sought to determine whether NF2 modulates heart failure due to chronic stress. Approach: We generated cardiomyocyte-specific NF2 knockout (cKO) mice, and used transverse aortic constriction (TAC) to generate chronic pressure overload (PO) stress, which elicits cardiac remodeling and failure. Complementary cell-based experiments were performed in neonatal rat ventricular myocytes (NRVMs). We analyzed cardiac function by echocardiographic and hemodynamic analysis. We used RNAseq, ChIP, Seahorse metabolic profiling, and biochemical analyses to investigate underlying mechanisms. Results: We found that NF2 is transiently upregulated in wild-type mouse myocardium in response to early phase of PO, but is downregulated during heart failure. Following TAC, NF2 cKO hearts unexpectedly showed significantly worsened cardiac function, compared to controls. RNAseq analysis indicated downregulation of several metabolic pathways and impaired ERR activity in NF2 cKO hearts. qPCR confirmed significantly reduced ERRβ and ERRγ transcripts and decreased metabolic gene expression. Experiments employing NRMVs confirmed that NF2 promoted expression of ERRβ and ERRγ, and DNA pulldown assays demonstrated NF2 association with ERRβ and ERRγ proximal promoters. Analysis of NRVM bioenergetics demonstrated that NF2 depletion impaired mitochondrial respiration, which was reversed by concomitant expression of ERRγ. Moreover, AAV9-mediated restoration of ERRγ in NF2 cKO mice normalized cardiac function in response to PO. Because NF2 does not directly bind DNA, ongoing studies are leveraging a proteomics-based approach to identify the mediator linking NF2 to ERR isoform expression. Conclusion: Based on these findings, we conclude that transient upregulation of myocardial NF2 expression during PO stress is compensatory and regulates metabolic gene expression according to energy demand.

Abstract We087: The mitochondrial citrate carrier SLC25A1 is a regulator of metabolic reprogramming and morphogenesis in the developing heart

Background: Congenital heart defects (CHDs) are the most common type of birth defect, yet the etiology of most CHDs are unknown. A major genetic risk factor for CHD is 22q11.2 deletion syndrome (22q11.2DS), a multisystem chromosomal microdeletion disorder where ~75% of patients present with CHD. SLC25A1 is a gene found within the 22q11.2DS microdeletion region that encodes for the mitochondrial citrate carrier, an inner membrane transporter that regulates intracellular citrate compartmentalization. Through this role, SLC25A1 is thought to contribute to cytosolic acetyl-CoA availability, and processes like protein acetylation and the epigenetic regulation of gene expression. We have previously found that SLC25A1 is a central gene contributing to the neurodevelopmental presentation of 22q11.2DS and importantly, neuronal mitochondrial function. Because the heart, like the brain, is highly reliant on energy derived from mitochondria, and the developing heart must undergo metabolic maturation whereby metabolism is reprogrammed from primary reliance on glycolysis towards mitochondrial oxidative metabolism, we hypothesized that SLC25A1 plays a key role in the metabolic maturation that is required for proper cardiac development. Objective: Here, we studied the role of Slc25a1 in the developing heart to examine the link between mitochondria and cardiac morphogenesis. Methods and Results: By studying mice with the systemic knockout of SLC25A1, we discovered that Slc25a1 null embryos displayed impaired growth, cardiac malformations, mitochondrial ultrastructural defects and impaired mitochondrial oxygen consumption. Transcriptomics analyses of metabolism-related genes revealed that Slc25a1 deletion causes widespread alterations in metabolic gene expression. Further, metabolic modelling predicted that loss of SLC25A1 downregulates oxidative phosphorylation, while increasing reliance on glucose. Finally, we found that loss of SLC25A1 decreases cardiac H3K9 acetylation levels at promoter regions of dysregulated metabolic genes. Mechanistically, SLC25A1 may regulating mitochondrial function and metabolism through epigenetic control of gene expression to promote metabolic remodeling in the developing heart. Conclusions: Our work suggests that SLC25A1 as an an important mitochondrial regulator of gene expression in the developing heart. Importantly, it positions SLC25A1 as a novel mitochondrial regulator of ventricular morphogenesis as well as cardiac metabolic maturation.

Abstract Tu036: Adipose tissue plasticity in response to early pathological stress on the heart and mediation by adipose thermogenic activation

Background: Cardiovascular diseases (CVD) are the leading cause of death globally, accounting for approximately 17.9 million mortalities per year. Previous studies have shown that there is an early response of white and brown adipose tissue (WAT and BAT, respectively) to pathological stress on the heart prior to cardiac dysfunction. Interestingly, human subjects with detectable BAT activity (a thermogenic tissue) exhibit a reduced risk of Congestive Heart Failure, but the mechanism for this is unclear. We hypothesized that increasing the thermogenic acitivity of adipose tissue would be beneficial during the initial cardiac hypertrophic signaling prior to the development of compensatory hypertrophy. Methods: We studied both WAT and BAT in male and female C57BL/6J mice subjected to cardiac pressure overload via transaortic constriction (TAC). 24 hours post-surgery, mice were subjected to room temperature (RT) 22° C or mild cold 16°C to stimulate BAT activation for 48 hours after which tissues were collected. The study groups included: SHAM RT, TAC RT, SHAM COLD, TAC COLD. We used uncoupling protein 1 knockout (UCP1-KO) mice, with impaired thermogenic activity as a negative control. Results: At 72 hours post tac surgery, expression of thermogenic and metabolic genes remained unchanged in BAT and WAT of both sexes. However, mild cold exposure resulted in an increase in UCP1 expression in BAT of male, but not female mice while other metabolic and thermogenic gene markers’ expression was increased in a sex-specific manner. Adaptations to scWAT were more moderate than BAT, with an increase in Ucp1 after cold exposure in both sexes. Moreover, 48 hours of cold exposure attenuated expression of gene markers for hypertrophic signaling in the heart during TAC. Importantly, these adaptations were absent in UCP1-KO mice, signifying that intact thermogenic activity in adipose tissue was required for the attenuated expression of hypertrophic markers in the heart. Interestingly, cardiac fibrosis markers were downregulated with TAC-Cold in male mice only, suggesting a stronger response compared to female mice. Conclusions: Our findings demonstrate that pathological stress on the heart during TAC does not impact adipose tisse thermogenesis. Additionally, activating thermogenic gene expression of adipose tissue via cold exposure mediates the early induction of hypertrophic signaling in the heart within 72 hours of TAC. Notably, adipose tissue plasticity is sex-specific.

Abstract Tu120: Sarm1 promotes diabetic cardiomyopathy by regulating HIF signaling, lipotoxicity and mitochondrial dysfunction

Heart failure occurs at twice the rate in diabetic patients as compared to normal patients, and reduced NAD levels are associated with diabetic cardiomyopathy. Sterile Alpha and Tir Motif Containing 1 (SARM1) is an intracellular NAD hydrolase. We hypothesized that SARM1 promotes NAD decline and diabetic cardiomyopathy. We subjected wild type (WT) and global SARM1 knockout mice to chronic diabetic stress induced by streptozotocin injections. We showed that 16-week diabetic stress promoted progressive decline in systolic and diastolic function, and in NAD levels, which were ameliorated by SARM1 deficiency despite similar plasma glucose and lipid levels. Gene Module Network Analysis of cardiac transcriptomics identified upregulation of genes in fatty acid and glucose metabolic processes, and suppression of genes in mitochondrial processes in diabetic WT hearts. SARM1 deficiency reversed upregulated fatty acid metabolic genes but had no impact on glucose metabolic and mitochondrial gene expressions in diabetic hearts. By transmission electron microscopy and Oil Red O staining, we observed increases in lipid droplet sizes and lipid accumulation in diabetic WT hearts, which were suppressed by SARM1 deficiency. SARM1 deficiency did not reverse mitochondrial gene expression, but it mitigated the reduction in ADP-driven respiration, mitochondrial fragmentation, and abnormal cristae structure in diabetic WT hearts. Diabetic WT hearts had increased phospho-PDH and PDK4 levels as well as activated HIF signaling, exhibiting an increase in expression of HIF-1a target genes (55 genes) , many of which were related to lipid storage. SARM1 deficiency suppressed expression of HIF1-a target genes (53 genes) , and reduced phospho-PDH and PDK4 levels. These data suggest that SARM1 regulates pseudohypoxic HIF-dependent signaling in diabetic hearts. In summary, our current data support the hypothesis that SARM1 regulates HIF-dependent transcription events, particularly those influencing lipid metabolism of diabetic hearts. However, SARM1 promotes mitochondrial dysfunction in diabetic hearts independent of transcription of mitochondrial genes. Further studies will continue to elucidate the role of SARM1 in diabetic cardiomyopathy, and its potential as a novel therapeutic target.

Abstract Mo092: Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes as an In Vitro Model to Evaluate the Efficacy of a Gene Replacement Therapy for Plakophilin-2- Associated Arrhythmogenic Right Ventricular Cardiomyopathy

Background: Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a genetic cardiac disorder characterized by severe arrhythmias and heart dysfunction. Mutations in desmosome gene Plakophilin-2 ( PKP2 ) account for 40% of ARVC cases, with current palliative therapies failing to address the genetic cause. Herein, we generated an in vitro ARVC model using human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CM) harboring a pathogenic PKP2 variant (c.2146G&gt;C), as a platform to test a PKP2 -gene replacement approach developed at Tenaya Therapeutics for the treatment of PKP2 -associated ARVC patients. Methods: Three isogenic human iPSC lines (wild-type, heterozygous and homozygous PKP2 mutant) were differentiated to iPSC-CM; and monolayers and engineered heart tissues (EHTs) were generated. Gene and protein expression were assessed by RNA-Seq/RT-qPCR, and immunocytochemistry, respectively. Contractility, electrophysiology and calcium handling were measured. A proprietary adeno-associated virus gene therapy (AAV9: PKP2 ) was used to transduce human iPSC-CM, and changes in gene and protein expression, and contractile function were evaluated. Results: A human iPSC-CM beating monolayer was achieved for all three lines. PKP2 expression was depleted in a genotype-dependent manner, and desmosome structure was disrupted in the mutant lines. Functional assessment of human iPSC-CM monolayers showed impaired contractile properties and abnormal electrophysiological and calcium transients in the mutant lines, such as decreased contraction amplitude and prolonged field and action potential duration. Transcriptional analysis revealed changes in desmosome, gap junctions, sarcomere, ion channels, metabolic and apoptosis gene expression. Characterization of EHTs displayed a deficit in contractility, slower action and field potential kinetics and irregular calcium homeostasis in the mutant lines. The administration of AAV9: PKP2 to the mutant lines restored ion channel and desmosome gene and protein expression, and contractile function. Conclusions: Our PKP2 human iPSC-CM disease model recapitulated the main hallmarks of ARVC phenotype. Administration of AAV9: PKP2 restored desmosome protein expression and contractility. This model lays a foundation for the understanding of the underlying molecular pathophysiological mechanisms of PKP2 -ARVC, and the potential for AAV9: PKP2 as a one-time dose to correct the genetic cause of disease in individuals with PKP2 -associated ARVC.

Abstract Mo045: The metabolic landscape of Fontan-associated liver disease

Introduction: Congenital heart diseases (CHDs) are the most common birth defects in the U.S. There are growing numbers of infants and children living with single ventricle congenital heart disease (SVCHD), a unique congenital cardiac anomaly in which there is only one functional ventricle. The Fontan surgery is the current standard of care for SVCHD. Although operative survival has improved over the years, it is now evident that these surviving patients are facing new life-threatening challenges: severe complications resulting from the Fontan operation, including one of the most evident consequences-hepatic fibrosis, which is now recognized as Fontan-Associated Liver Disease (FALD). Unfortunately, the mechanisms underlying FALD remain little understood. Improved understanding in this knowledge gap will offer crucial insights into FALD pathophysiology that can lead to targeted therapies for SVCHD patients. Goal: To determine if liver metabolism changes significantly in FALD and compare these liver metabolomics changes to metabolic gene expression (our snRNA-ATAC-seq data) and reported plasma metabolomics results, and validate the key findings. Methods: We recently generated the first single-cell transcriptomic landscape of human FALD using snRNA-ATAC-seq, which revealed profound metabolic reprogramming in FALD. Here we utilized metabolomics to further understand this. Liver samples/biopsies were collected from healthy donors and FALD patients. The extracted metabolites were analyzed using C18 and HILIC HPLC/MS columns. Raw data files were acquired by high resolution MS on Orbitrap and processed by Compound Discoverer. Further statistical and bioinformatics analyses were performed to identify altered metabolites and potential metabolic pathways involved in FALD. Results: Significant changes of metabolite levels of multiple metabolic pathways were observed in Fontan livers, often consistent with the gene expression results. Overall, these data unveiled profound metabolic abnormalities in livers of patients with early-stage FALD. Conclusions: In conclusion, our investigation revealed alterations in metabolites involved in glycolysis/gluconeogenesis, mitochondrial electron transport chain, and amino acids in early-stage FALD. The observed correlations between the metabolomics and gene expression results reveal new insights into the mechanisms underlying FALD. FALD is not only a hepatic fibrosis disease, but also features severe dysregulation of liver metabolism.

The abscisic acid-responsive transcriptional regulatory module CsERF110–CsERF53 orchestrates citrus fruit coloration

Carotenoid biosynthesis is closely associated with abscisic acid (ABA) during the ripening process of non-climacteric fruits, but the regulatory mechanism that links ABA signaling to carotenoid metabolism remains largely unclear. Here, we identified two master regulators of ABA-mediated citrus fruit coloration, CsERF110 and CsERF53, which activate the expression of carotenoid metabolism genes (CsGGPPS, CsPSY, CsPDS, CsCRTISO, CsLCYB2, CsLCYE, CsHYD, CsZEP, and CsNCED2) to facilitate carotenoid accumulation. Further investigations showed that CsERF110 not only activates the expression of CsERF53 by binding to its promoter but also interacts with CsERF53 to form the transcriptional regulatory module CsERF110–CsERF53. We also discovered a positive feedback regulatory loop between the ABA signal and carotenoid metabolism regulated by the transcriptional regulatory module CsERF110–CsERF53. Our results reveal that the CsERF110–CsERF53 module responds to ABA signaling, thereby orchestrating citrus fruit coloration. Considering the importance of carotenoid content for citrus and many other carotenoid-rich crops, the revelation of molecular mechanisms that underlie ABA-mediated carotenoid biosynthesis in plants will facilitate the development of transgenic/gene-editing approaches, further contributing to improving the quality of citrus and other carotenoid-rich crops.

TLCD4 as Potential Transcriptomic Biomarker of Cold Exposure.

(1) Background: Cold exposure induces metabolic adaptations that can promote health benefits, including increased energy disposal due to lipid mobilization in adipose tissue (AT). This study aims to identify easily measurable biomarkers mirroring the effect of cold exposure on AT. (2) Methods: Transcriptomic analysis was performed in peripheral blood mononuclear cells (PBMCs) and distinct AT depots of two animal models (ferrets and rats) exposed to cold, and in PBMCs of cold-exposed humans. (3) Results: One week of cold exposure (at 4 °C) affected different metabolic pathways and gene expression in the AT of ferrets, an animal model with an AT more similar to humans than that of rodents. However, only one gene, Tlcd4, was affected in the same way (overexpressed) in aortic perivascular and inguinal AT depots and in PBMCs, making it a potential biomarker of interest. Subsequent targeted analysis in rats showed that 1 week at 4 °C also induced Tlcd4 expression in brown AT and PBMCs, while 1 h at 4 °C resulted in reduced Tlcd4 mRNA levels in retroperitoneal white AT. In humans, no clear effects were observed. Nevertheless, decreased PBMC TLCD4 expression was observed after acute cold exposure in women with normal weight, although this effect could be attributed to short-term fasting during the procedure. No effect was evident in women with overweight or in normal-weight men. (4) Conclusions: Our results obtained for different species point toward TLCD4 gene expression as a potential biomarker of cold exposure/fat mobilization that could tentatively be used to address the effectiveness of cold exposure-mimicking therapies.

Multiomics Analyses Explore the Immunometabolic Interplay in the Liver of White Crucian Carp (Carassius cuvieri) After Aeromonas veronii Challenge.

Aeromonas veronii is one of the predominant pathogenic species that can imperil the survival of farmed fish. However, the interactive networks of immune regulation and metabolic response in A. veronii-infected fish are still unclear. In this investigation, we aimed to explore immunometabolic interplay in white crucian carp (WCC) after the A. veronii challenge. Elevated levels of immune-related genes were observed in various tissues after A. veronii infection, along with the sharp alteration of disease-related enzymatic activities. Besides, decreased levels of antioxidant status were observed in the liver, but most metabolic gene expressions increased dramatically. Multiomics analyses revealed that metabolic products of amino acids, such as formiminoglutamic acid (FIGLU), L-glutamate (L-Glu), and 4-hydroxyhippuric acid, were considered the crucial liver biomarkers in A. veronii-infected WCC. In addition, A. veronii infection may dysregulate endoplasmic reticulum (ER) function to affect the metabolic process of lipids, carbohydrates, and amino acids in the liver of WCC. These results may have a comprehensive implication for understanding immunometabolic response in WCC upon A. veronii infection.

Transitions in chromatin conformation shaped by fatty acids and the circadian clock underlie hepatic transcriptional reorganization in obese mice

The circadian clock system coordinates metabolic, physiological, and behavioral functions across a 24-h cycle, crucial for adapting to environmental changes. Disruptions in circadian rhythms contribute to major metabolic pathologies like obesity and Type 2 diabetes. Understanding the regulatory mechanisms governing circadian control is vital for identifying therapeutic targets. It is well characterized that chromatin remodeling and 3D structure at genome regulatory elements contributes to circadian transcriptional cycles; yet the impact of rhythmic chromatin topology in metabolic disease is largely unexplored. In this study, we explore how the spatial configuration of the genome adapts to diet, rewiring circadian transcription and contributing to dysfunctional metabolism. We describe daily fluctuations in chromatin contacts between distal regulatory elements of metabolic control genes in livers from lean and obese mice and identify specific lipid-responsive regions recruiting the clock molecular machinery. Interestingly, under high-fat feeding, a distinct interactome for the clock-controlled gene Dbp strategically promotes the expression of distal metabolic genes including Fgf21. Alongside, new chromatin loops between regulatory elements from genes involved in lipid metabolism control contribute to their transcriptional activation. These enhancers are responsive to lipids through CEBPβ, counteracting the circadian repressor REVERBa. Our findings highlight the intricate coupling of circadian gene expression to a dynamic nuclear environment under high-fat feeding, supporting a temporally regulated program of gene expression and transcriptional adaptation to diet.