Combined metabolomic and transcriptomic profiling approaches reveal the cardiac response to high-fat diet

Whole-Genome Sequence Analysis, Probiotic Potential, and Safety Assessment of the Marine Bacterium Paraliobacillus zengyii CGMCC1.16464

Paraliobacillus zengyii CGMCC1.16464 (P. zengyii) is a novel antiviral probiotic candidate strain. To ensure its safety as a potential probiotic, a safety evaluation was conducted in this study. The safety and functional potential of P. zengyii were systematically assessed through genomic bioinformatics analysis, in vitro experiments, and acute oral toxicity tests in mice. Genomic analysis revealed that P. zengyii is rich in genes related to carbohydrate and amino acid metabolisms and carries genes encoding antimicrobial and antiviral agents (such as ectoine, type III polyketide synthase, and lasso peptides). It also expresses gastrointestinal tolerance-related proteins (ClpC, GroEL, and ClpP). Its resistance to polymyxins is an inherent trait with no risk of plasmid-mediated transfer. In vitro experiments confirmed that P. zengyii is somewhat tolerant to bile salts and acidic environments and does not exhibit hemolytic or gelatinase activity. Importantly, an acute oral toxicity test in mice revealed that after intervention with high, medium, or low doses, no significant abnormalities in the body weight, organ index, or tissue morphology of the mice were observed. In conclusion, P. zengyii exhibited good safety and probiotic potential in terms of genomic safety, metabolic function, and in vitro and in vivo toxicities, providing a theoretical basis for the development of novel functional probiotics.

Multi-omics insights into the pathogenesis of diabetic cardiomyopathy: epigenetic and metabolic profiles

AIM

Diabetic cardiomyopathy (DbCM), a complex metabolic disease, greatly threatens human health due to therapeutic limitations. Multi-omics approaches facilitate the elucidation of its intrinsic pathological changes.

METHODS

Metabolomics, RNA-seq, proteomics, and assay of transposase-accessible chromatin (ATAC-seq) were utilized to elucidate multidimensional molecular alterations in DbCM.

RESULTS

In the heart and plasma of mice with DbCM, metabolomic analysis demonstrated significant differences in branched-chain amino acids (BCAAs) and lipids. Subsequent RNA-seq and proteomics showed that the key genes, including BCKDHB, PPM1K, Cpt1b, Fabp4, Acadm, Acadl, Acadvl, HADH, HADHA, HADHB, Eci1, Eci2, PDK4, and HMGCS2, were aberrantly regulated, contributing to the disorder of BCAAs and fatty acids. ATAC-seq analysis underscored the pivotal role of epigenetic regulation by revealing dynamic shifts in chromatin accessibility and a robust positive correlation with gene expression patterns in diabetic cardiomyopathy mice. Furthermore, motif analysis identified that KLF15 as a critical transcription factor in DbCM, regulating the core genes implicated with BCAAs metabolism.

CONCLUSION

Our research delved into the metabolic alterations and epigenetic landscape and revealed that KLF15 may be a promising candidate for therapeutic intervention in DbCM.

Senescent cell depletion alleviates obesity-related metabolic and cardiac disorders

Obesity is a major contributor to metabolic and cardiovascular disease. Although senescent cells have been shown to accumulate in adipose tissue, the role of senescence in obesity-induced metabolic disorders and in cardiac dysfunction is not yet clear; therefore, the therapeutic potential of managing senescence in obesity-related metabolic and cardiac disorders remains to be fully defined.

OBJECTIVE

We investigated the beneficial effects of a senolytic cocktail (dasatinib and quercetin) on senescence and its influence on obesity-related parameters.

METHODS AND RESULTS

We found that the increase in body weight and adiposity, glucose intolerance, insulin resistance, dyslipidemia, hyperleptinemia, and hepatic disorders which were induced by an obesogenic diet were alleviated by senolytic cocktail treatment in mice. Treatment with senolytic compounds eliminated senescent cells, counteracting the activation of the senescence program and DNA damage in white adipose tissue (WAT) observed with an obesogenic diet. Moreover, the senolytic cocktail prevented the brown adipose tissue (BAT) whitening and increased the expression of the thermogenic gene profile in BAT and pWAT. In the hearts of obese mice, senolytic combination abolished myocardial maladaptation, reducing the senescence-associated secretory phenotype (SASP) and DNA damage, repressing cardiac hypertrophy, and improving diastolic dysfunction. Additionally, we showed that treatment with the senolytic cocktail corrected gene expression programs associated with fatty acid metabolism, oxidative phosphorylation, the P53 pathway, and DNA repair, which were all downregulated in obese mice.

CONCLUSIONS

Collectively, these data suggest that a senolytic cocktail can prevent the activation of the senescence program in the heart and WAT and activate the thermogenic program in BAT. Our results suggest that targeting senescent cells may be a novel therapeutic strategy for alleviating obesity-related metabolic and cardiac disorders.

Sex-based differences in short- and longer-term diet-induced metabolic heart disease

Sex-based differences in the development of obesity-induced cardiometabolic dysfunction are well documented, however, the specific mechanisms are not completely understood. Obesity has been linked to dysregulation of the epitranscriptome, but the role of N6-methyladenosine (m6A) RNA methylation has not been investigated in relation to the sex differences during obesity-induced cardiac dysfunction. In the current study, male and female C57BL/6J mice were subjected to short- and long-term high-fat/high-sucrose (HFHS) diet to induce obesogenic stress. Cardiac echocardiography showed males developed systolic and diastolic dysfunction after 4 mo of diet, but females maintained normal cardiac function despite both sexes being metabolically dysfunctional. Cardiac m6A machinery gene expression was differentially regulated by duration of HFHS diet in male, but not female mice, and left ventricular ejection fraction correlated with RNA machinery gene levels in a sex- and age-dependent manner. RNA-sequencing of cardiac transcriptome revealed that females, but not males may undergo protective cardiac remodeling early in the course of obesogenic stress. Taken together, our study demonstrates for the first time that cardiac RNA methylation machinery genes are regulated early during obesogenic stress in a sex-dependent manner and may play a role in the sex differences observed in cardiometabolic dysfunction.NEW & NOTEWORTHY Sex differences in obesity-associated cardiomyopathy are well documented but incompletely understood. We show for the first time that RNA methylation machinery genes may be regulated in response to obesogenic diet in a sex- and age-dependent manner and levels may correspond to cardiac systolic function. Our cardiac RNA-seq analysis suggests female, but not male mice may be protected from cardiac dysfunction by a protective cardiac remodeling response early during obesogenic stress.

OmicsSuite: a customized and pipelined suite for analysis and visualization of multi-omics big data

With the advancements in high-throughput sequencing technologies such as Illumina, PacBio, and 10X Genomics platforms, and gas/liquid chromatography-mass spectrometry, large volumes of biological data in multiple formats can now be obtained through multi-omics analysis. Bioinformatics is constantly evolving and seeking breakthroughs to solve multi-omics problems; however, it is challenging for most experimental biologists to analyse data using command-line interfaces, coding, and scripting. Based on experience with multi-omics, we have developed OmicsSuite, a desktop suite that comprehensively integrates statistics and multi-omics analysis and visualization. The suite has 175 sub-applications in 12 categories, including Sequence, Statistics, Algorithm, Genomics, Transcriptomics, Enrichment, Proteomics, Metabolomics, Clinical, Microorganism, Single Cell, and Table Operation. We created the user interface with Sequence View, Table View, and intelligent components based on JavaFX and the popular Shiny framework. The multi-omics analysis functions were developed based on BioJava and 300+ packages provided by the R CRAN and Bioconductor communities, and it encompasses over 3000 adjustable parameter interfaces. OmicsSuite can directly read multi-omics raw data in FastA, FastQ, Mutation Annotation Format, mzML, Matrix, and HDF5 formats, and the programs emphasize data transfer directions and pipeline analysis functions. OmicsSuite can produce pre-publication images and tables, allowing users to focus on biological aspects. OmicsSuite offers multi-omics step-by-step workflows that can be easily applied to horticultural plant breeding and molecular mechanism studies in plants. It enables researchers to freely explore the molecular information contained in multi-omics big data (Source: https://github.com/OmicsSuite/, Website: https://omicssuite.github.io, v1.3.9).