The Thioesterase ACOT1 as a Regulator of Lipid Metabolism in Type 2 Diabetes Detected in a Multi-Omics Study of Human Liver

Chromatin accessibility: biological functions, molecular mechanisms and therapeutic application

The dynamic regulation of chromatin accessibility is one of the prominent characteristics of eukaryotic genome. The inaccessible regions are mainly located in heterochromatin, which is multilevel compressed and access restricted. The remaining accessible loci are generally located in the euchromatin, which have less nucleosome occupancy and higher regulatory activity. The opening of chromatin is the most important prerequisite for DNA transcription, replication, and damage repair, which is regulated by genetic, epigenetic, environmental, and other factors, playing a vital role in multiple biological progresses. Currently, based on the susceptibility difference of occupied or free DNA to enzymatic cleavage, solubility, methylation, and transposition, there are many methods to detect chromatin accessibility both in bulk and single-cell level. Through combining with high-throughput sequencing, the genome-wide chromatin accessibility landscape of many tissues and cells types also have been constructed. The chromatin accessibility feature is distinct in different tissues and biological states. Research on the regulation network of chromatin accessibility is crucial for uncovering the secret of various biological processes. In this review, we comprehensively introduced the major functions and mechanisms of chromatin accessibility variation in different physiological and pathological processes, meanwhile, the targeted therapies based on chromatin dynamics regulation are also summarized.

Exploring maternal and developmental toxicity of perfluoroalkyl ether acids PFO4DA and PFO5DoA using hepatic transcriptomics and serum metabolomics

Production of per- and polyfluoroalkyl substances (PFAS) has shifted from long-chain perfluoroalkyl acids to short-chain compounds and those with ether bonds in the carbon chain. Next-generation perfluoroalkylether PFAS include HFPO-DA ("GenX chemicals"), Nafion Byproducts, and the PFOx homologous series that includes perfluoro-3,5,7,9-butaoxadecanoic acid (PFO4DA) and perfluoro-3,5,7,9,11-pentaoxadodecanoic acid (PFO5DoA). PFO4DA and PFO5DoA have been detected in serum and/or tissues from humans and wildlife proximal to contamination point sources. However, toxicity data are extremely limited, with no in vivo developmental toxicology data. To address these data gaps, pregnant Sprague-Dawley rats were exposed via oral gavage to vehicle, PFO4DA, or PFO5DoA across a series of doses (0.1 to 62.5 mg/kg/day) from gestation day (GD) 18-22. Hepatic transcriptomics were assayed in dams and fetuses, and serum metabolomics in dams. These data were overlaid with serum PFO4DA and PFO5DoA concentrations to perform dose-response modeling. Both dams and fetuses exhibited dose-responsive disruption of hepatic gene expression in response to PFO4DA or PFO5DoA, with fetal expression disrupted at lower doses than dams. Several differentially expressed genes were upregulated by every dose of PFO5DoA in both maternal and fetal samples, including genes encoding enzymes that hydrolyze acyl-coA to free fatty acids. Maternal serum metabolomics revealed PFO4DA exposure did not induce significant changes at any tested dose, whereas PFO5DoA exposure resulted in dose-dependent differential metabolite abundance for 149 unique metabolites. Multi-omics pathway analyses of integrated maternal liver transcriptomics and serum metabolomics revealed significant convergent changes as low as 3 mg/kg/d PFO4DA and 0.3 mg/kg/d PFO5DoA exposure. Overall, transcriptomic and metabolomic effects of PFO4DA and PFO5DoA appear consistent with other carboxylic acid PFAS, with primary changes related to lipid metabolism, bile acids, cholesterol, and cellular stress. Importantly, PFO5DoA exposure more potently induced changes in maternal and fetal hepatic gene expression and maternal circulating metabolites, despite high structural similarity. Further, we report in vitro PPARα and PPARγ receptor activation for both compounds as putative molecular mechanisms. This work demonstrates the potential developmental toxicity of alternative moiety perfluoroethers and highlights the developing liver as particularly vulnerable to transcriptomic disruption. Synopsis: Developmental exposure to fluoroether carboxylic acids PFO4DA and PFO5DoA result in differential impacts on hepatic transcriptome in dams and offspring and circulating metabolome in dams, with PFO5DoA exhibiting higher potency than PFO4DA.

Alterations in Blood Methylome as Potential Epigenetic Biomarker in Sporadic Parkinson's Disease

OBJECTIVE

To characterize DNA methylation (DNAm) differences between sporadic Parkinson's disease (PD) and healthy control (HC) individuals enrolled in the Parkinson's Progression Markers Initiative (PPMI).

METHODS

Using whole blood, we characterized longitudinal differences in DNAm between sporadic PD patients (n = 196) and HCs (n = 86) enrolled in PPMI. RNA sequencing (RNAseq) was used to conduct gene expression analyses for genes mapped to differentially methylated cytosine-guanine sites (CpGs).

RESULTS

At the time of patient enrollment, 5,178 CpGs were differentially methylated (2,683 hypermethylated and 2,495 hypomethylated) in PD compared to HC. Of these, 579 CpGs underwent significant methylation changes over 3 years. Several differentially methylated CpGs were found near the cytochrome P450 family 2 subfamily E member 1 (CYP2E1) gene. Additionally, multiple hypermethylated CpGs were associated with the N-myc downregulated gene family member 4 (NDRG4) gene. RNA-Seq analyses showed 75 differentially expressed genes in PD patients compared to controls. An integrative analysis of both differentially methylated sites and differentially expressed genes revealed 20 genes that exhibited hypomethylation concomitant with overexpression. Additionally, 1 gene, cathepsin H (CTSH), displayed hypermethylation that was associated with its decreased expression.

INTERPRETATION

We provide initial evidence of alterations in DNAm in blood of PD patients that may serve as potential epigenetic biomarker of disease. To evaluate the significance of these changes throughout the progression of PD, additional profiling at longer intervals and during the prodromal stages of disease will be necessary. ANN NEUROL 2024;95:1162-1172.

Mechanism exploration and biomarker identification of glycemic deterioration in patients with diseases of the exocrine pancreas

The damage to the endocrine pancreas among patients with diseases of the exocrine pancreas (DP) leads to reduced glycemic deterioration, ultimately resulting in diabetes of the exocrine pancreas (DEP). The present research aims to investigate the mechanism responsible for glycemic deterioration in DP patients, and to identify useful biomarkers, with the ultimate goal of enhancing clinical practice awareness. Gene expression profiles of patients with DP in this study were acquired from the Gene Expression Omnibus database. The original study defines DP patients to belong in one of three categories: non-diabetic (ND), impaired glucose tolerance (IGT) and DEP, which correspond to normoglycemia, early and late glycemic deterioration, respectively. After ensuring quality control, the discovery cohort included 8 ND, 20 IGT, and 12 DEP, while the validation cohort included 27 ND, 15 IGT, and 20 DEP. Gene set enrichment analysis (GSEA) employed differentially expressed genes (DEGs), while immunocyte infiltration was determined using single sample gene set enrichment analysis (ssGSEA). Additionally, correlation analysis was conducted to establish the link between clinical characteristics and immunocyte infiltration. The least absolute shrinkage and selection operator regression and random forest combined to identify biomarkers indicating glycemic deterioration in DP patients. These biomarkers were further validated through independent cohorts and animal experiments. With glycemic deterioration, biological processes in the pancreatic islets such as nutrient metabolism and complex immune responses are disrupted in DP patients. The expression of ACOT4, B2M, and ACKR2 was upregulated, whereas the expression of CACNA1F was downregulated. Immunocyte infiltration in the islet microenvironment showed a significant positive correlation with the age, body mass index (BMI), HbA1c and glycemia at the 2-h of patients. It was a crucial factor in glycemic deterioration. Additionally, B2M demonstrated a significant positive correlation with immunocyte infiltration and clinical features. Quantitative real-time PCR (qRT-PCR) and western blotting confirmed the upregulation in B2M. Immunofluorescent staining suggested the alteration of B2M was mainly in the alpha cells and beta cells. Overall, the study showed that gradually increased immunocyte infiltration was a significant contributor to glycemic deterioration in patients with DP, and it also highlighted B2M as a biomarker.

Iron Dysregulation in Cardiovascular Diseases

Iron metabolism plays a crucial role in various physiological functions of the human body, as it is essential for the growth and development of almost all organisms. Dysregulated iron metabolism-manifested either as iron deficiency or overload-is a significant risk factor for the development of cardiovascular disease (CVD). Moreover, emerging evidence suggests that ferroptosis, a form of iron-dependent programed cell death, may also contribute to CVD development. Understanding the regulatory mechanisms of iron metabolism and ferroptosis in CVD is important for improving disease management. By integrating different perspectives and expertise in the field of CVD-related iron metabolism, this overview provides insights into iron metabolism and CVD, along with approaches for diagnosing, treating, and preventing CVD associated with iron dysregulation.

ACOT1 deficiency attenuates high-fat diet-induced fat mass gain by increasing energy expenditure

Acyl-CoA thioesterase 1 (ACOT1) catalyzes the hydrolysis of long-chain acyl-CoAs to free fatty acids and CoA and is typically upregulated in obesity. Whether targeting ACOT1 in the setting of high-fat diet-induced (HFD-induced) obesity would be metabolically beneficial is not known. Here we report that male and female ACOT1KO mice are partially protected from HFD-induced obesity, an effect associated with increased energy expenditure without alterations in physical activity or food intake. In males, ACOT1 deficiency increased mitochondrial uncoupling protein-2 (UCP2) protein abundance while reducing 4-hydroxynonenal, a marker of oxidative stress, in white adipose tissue and liver of HFD-fed mice. Moreover, concurrent knockdown (KD) of UCP2 with ACOT1 in hepatocytes prevented increases in oxygen consumption observed with ACOT1 KD during high lipid loading, suggesting that UCP2-induced uncoupling may increase energy expenditure to attenuate weight gain. Together, these data indicate that targeting ACOT1 may be effective for obesity prevention during caloric excess by increasing energy expenditure.

Integration of proteomics and network toxicology reveals the mechanism of mercury chloride induced hepatotoxicity, in mice and HepG2 cells

Mercury is one heavy metal toxin that could cause severe health impairments. Mercury exposure has become a global environmental issue. Mercury chloride (HgCl₂) is one of mercury's main chemical forms, but it lacks detailed hepatotoxicity data. The present study aimed to investigate the mechanism of hepatotoxicity induced by HgCl₂ through proteomics and network toxicology at the animal and cellular levels. HgCl₂ showed apparent hepatotoxicity after being administrated with C57BL/6 mice (16 mg/kg.bw, oral once a day, 28 days) and HepG2 cells (100 μmol/L, 12 h). Otherwise, oxidative stress, mitochondrial dysfunction and inflammatory infiltration play an important role in HgCl₂-induced hepatotoxicity. The differentially expressed proteins (DEPs) after HgCl₂ treatment and enriched pathways were obtained through proteomics and network toxicology. Western blot and RT-qPCR results showed Acyl-CoA thioesterase 1 (ACOT1), Acyl-CoA synthetase short chain family member 3 (ACSS3), Epidermal growth factor receptor (EGFR), Apolipoprotein B (APOB), Signal transducer and activator of transcription 3 (STAT3), Alanine--glyoxylate aminotransferase (AGXT), cytochrome P450 3A5(CYP3A5), CYP2E1 and CYP1A2 may be the major biomarkers for HgCl₂-induced hepatotoxicity, which involved chemical carcinogenesis, fatty acid metabolism, CYPs-mediated metabolism, GSH metabolism and others. Therefore, this study can provide scientific evidence for the biomarkers and mechanism of HgCl₂-induced hepatotoxicity.

Reversal of the diabetic bone signature with anabolic therapies in mice

The mechanisms underlying the bone disease induced by diabetes are complex and not fully understood; and antiresorptive agents, the current standard of care, do not restore the weakened bone architecture. Herein, we reveal the diabetic bone signature in mice at the tissue, cell, and transcriptome levels and demonstrate that three FDA-approved bone-anabolic agents correct it. Diabetes decreased bone mineral density (BMD) and bone formation, damaged microarchitecture, increased porosity of cortical bone, and compromised bone strength. Teriparatide (PTH), abaloparatide (ABL), and romosozumab/anti-sclerostin antibody (Scl-Ab) all restored BMD and corrected the deteriorated bone architecture. Mechanistically, PTH and more potently ABL induced similar responses at the tissue and gene signature levels, increasing both formation and resorption with positive balance towards bone gain. In contrast, Scl-Ab increased formation but decreased resorption. All agents restored bone architecture, corrected cortical porosity, and improved mechanical properties of diabetic bone; and ABL and Scl-Ab increased toughness, a fracture resistance index. Remarkably, all agents increased bone strength over the healthy controls even in the presence of severe hyperglycemia. These findings demonstrate the therapeutic value of bone anabolic agents to treat diabetes-induced bone disease and suggest the need for revisiting the approaches for the treatment of bone fragility in diabetes.

The underlying pathological mechanism of ferroptosis in the development of cardiovascular disease

Cardiovascular diseases (CVDs) have been attracting the attention of academic society for decades. Numerous researchers contributed to figuring out the core mechanisms underlying CVDs. Among those, pathological decompensated cellular loss posed by cell death in different kinds, namely necrosis, apoptosis and necroptosis, was widely regarded to accelerate the pathological development of most heart diseases and deteriorate cardiac function. Recently, apart from programmed cell death revealed previously, ferroptosis, a brand-new cellular death identified by its ferrous-iron-dependent manner, has been demonstrated to govern the occurrence and development of different cardiovascular disorders in many types of research as well. Therefore, clarifying the regulatory function of ferroptosis is conducive to finding out strategies for cardio-protection in different conditions and improving the prognosis of CVDs. Here, molecular mechanisms concerned are summarized systematically and categorized to depict the regulatory network of ferroptosis and point out potential therapeutic targets for diverse cardiovascular disorders.