Distinct roles for Notch1 and Notch3 in human adipose-derived stem/stromal cell adipogenesis

Genetic variation in NOTCH1 is associated with overweight and obesity in Brazilian elderly

Excessive weight (overweight and obesity) is a common disorder involving genetic and environmental factors, associated with cardiovascular diseases, type-2 diabetes, and others. NOTCH1 is critical for the maintenance of stem cells and adult tissues, being reported as a key player in metabolism and adipogenesis in animals. Thus, we test the hypothesis that NOTCH1 Single Nucleotide Polymorphisms (SNPs) are associated with excessive weight. Participants from the census-based cohort SABE (Saúde, Bem Estar e Envelhecimento-Health, Well-Being, and Aging), carried out in the city of São Paulo-Brazil, were stratified into cases and controls according to BMI. We filter the SNPs located at the start and end positions of NOTCH1 and 50 Kb on both sides. We selected SNPs with minor allelic frequency (MAF) greater than or equal to 0.01 and Hardy-Weinberg equilibrium (p > 0.05) and r2 ≥ 0.8. We performed an association study with genotypes and haplotypes, as well as in silico functional analysis of the identified SNPs. We observed an association of the SNP rs9411207 with the risk of excessive weight, under log-additive model, and the genotype distribution showed an increased frequency of homozygous TT (OR 1.50, CI 1.20-1.88; p = 0.0002). The haplotype GAT constructed from this and other SNPs in high Linkage Disequilibrium was more frequent in excessive-weight individuals (p = 0.003). In silico analyses suggested that these SNPs are likely to affect the transcription of NOTCH1 and other genes involved in adipogenesis and metabolism. This is the first study reporting association between NOTCH1 SNPs and the risk of excessive weight. Considering the possibility of NOTCH1 modulation, additional population studies are important to replicate these data and confirm the usefulness of risk genotypes for management strategies of excessive weight.

Transcriptomic analysis reveals regulation of adipogenesis via long non-coding RNA, alternative splicing, and alternative polyadenylation

Obesity is characterized by dysregulated adipogenesis that leads to increased number and/or size of adipocytes. Understanding the molecular mechanisms governing adipogenesis is therefore key to designing therapeutic interventions against obesity. In our study, we analyzed 3'-end sequencing data that we generated from human preadipocytes and adipocytes, as well as previously published RNA-seq datasets, to elucidate mechanisms of regulation via long non-coding RNA (lncRNA), alternative splicing (AS) and alternative polyadenylation (APA). We discovered lncRNAs that have not been previously characterized but may be key regulators of white adipogenesis. We also detected 100 AS events and, using motif enrichment analysis, identified RNA binding proteins (RBPs) that could mediate exon skipping-the most prevalent AS event. In addition, we show that usage of alternative poly(A) sites in introns or 3'-UTRs of key adipogenesis genes leads to isoform diversity, which can have significant biological consequences on differentiation efficiency. We also identified RBPs that may modulate APA and defined how 3'-UTR APA can regulate gene expression through gain or loss of specific microRNA binding sites. Taken together, our bioinformatics-based analysis reveals potential therapeutic avenues for obesity through manipulation of lncRNA levels and the profile of mRNA isoforms via alternative splicing and polyadenylation.

Targeted Proteomics Reveals Functional Targets for Early Diabetes Susceptibility in Young Adults

BACKGROUND

The circulating proteome may encode early pathways of diabetes susceptibility in young adults for surveillance and intervention. Here, we define proteomic correlates of tissue phenotypes and diabetes in young adults.

METHODS

We used penalized models and principal components analysis to generate parsimonious proteomic signatures of diabetes susceptibility based on phenotypes and on diabetes diagnosis across 184 proteins in >2000 young adults in the CARDIA (Coronary Artery Risk Development in Young Adults study; mean age, 32 years; 44% women; 43% Black; mean body mass index, 25.6±4.9 kg/m2), with validation against diabetes in >1800 individuals in the FHS (Framingham Heart Study) and WHI (Women's Health Initiative).

RESULTS

In 184 proteins in >2000 young adults in CARDIA, we identified 2 proteotypes of diabetes susceptibility-a proinflammatory fat proteotype (visceral fat, liver fat, inflammatory biomarkers) and a muscularity proteotype (muscle mass), linked to diabetes in CARDIA and WHI/FHS. These proteotypes specified broad mechanisms of early diabetes pathogenesis, including transorgan communication, hepatic and skeletal muscle stress responses, vascular inflammation and hemostasis, fibrosis, and renal injury. Using human adipose tissue single cell/nuclear RNA-seq, we demonstrate expression at transcriptional level for implicated proteins across adipocytes and nonadipocyte cell types (eg, fibroadipogenic precursors, immune and vascular cells). Using functional assays in human adipose tissue, we demonstrate the association of expression of genes encoding these implicated proteins with adipose tissue metabolism, inflammation, and insulin resistance.

CONCLUSIONS

A multifaceted discovery effort uniting proteomics, underlying clinical susceptibility phenotypes, and tissue expression patterns may uncover potentially novel functional biomarkers of early diabetes susceptibility in young adults for future mechanistic evaluation.

Screening for genes, miRNAs and transcription factors of adipogenic differentiation and dedifferentiation of mesenchymal stem cells

BACKGROUND

The purpose of present study was to reveal the molecular mechanisms responsible for both adipogenic differentiation and dedifferentiation of mesenchymal stem cells (MSCs).

METHODS

Microarray data GSE36923 were obtained from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) between adipogenically differentiated cells vs undifferentiated bone marrow-derived MSCs, adipogenically differentiated cells vs dedifferentiated cells samples at day 7 and adipogenically differentiated cells vs dedifferentiated cells samples at day 35 were screened, and overlapped DEGs across the three groups were analyzed. The underlying functions of the upregulated and downregulated DEGs were investigated by Gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analysis. The protein-protein interaction network was constructed, and hub genes were obtained subsequently. Hub genes were verified with GSE113253 dataset, and then miRNA-gene network and TF-gene network were constructed.

RESULTS

A total of 284 upregulated DEGs and 376 downregulated DEGs overlapped across the three groups. PPAR signaling pathway, AMPK signaling pathway, insulin signaling pathway, carbon metabolism, pyruvate metabolism, fatty acid metabolism, regulation of lipolysis in adipocytes, biosynthesis of amino acids, citrate cycle (TCA cycle) and 2-Oxocarboxylic acid metabolism were the top 10 pathways involving in the upregulated DEGs, and graft-versus-host disease, allograft rejection, viral myocarditis, cell adhesion molecules, phagosome, type I diabetes mellitus, antigen processing and presentation, autoimmune thyroid disease, intestinal immune network for IgA production and rheumatoid arthritis were the top 10 pathways in downregulated DEGs. After validation, the 8 hub genes were IL6, PPARG, CCL2, FASN, CEBPA, ADIPOQ, FABP4 and LIPE. Ten key miRNAs were hsa-mir-27a-3p, hsa-mir-182-5p, hsa-mir-7-5p, hsa-mir-16-5p, hsa-mir-1-3p, hsa-mir-155-5p, hsa-mir-21-3p, hsa-mir-34a-5p, hsa-mir-27a-5p and hsa-mir-30c-5p, and 10 key TFs were TFDP1, GTF2A2, ZNF584, NRF1, ZNF512, NFRKB, CEBPG, KLF16, GLIS2 and MXD4.

CONCLUSION

Our study constructed miRNA-gene network and TF-gene network involved in both adipogenic differentiation and dedifferentiation of MSCs, contributing to enhancing the efficiency of MSCs transplantation in soft tissue defect repair and developing more potent remedies for adipogenesis-related skeletal disorders.

Molecular Regulation of Yak Preadipocyte Differentiation and Proliferation by LncFAM200B and ceRNA Regulatory Network Analysis

The positive regulatory role of lncFAM200B in differentiation and lipid deposition in yak intramuscular preadipocytes has been demonstrated in our previous study. However, the regulatory mechanisms remain unclear. In this study, we aimed to produce complete mRNA and microRNA (miRNA) profiles after adenovirus-mediated lncFAM200B overexpression in yak preadipocytes using high-throughput sequencing. We constructed a competing endogenous RNA (ceRNA) network with lncFAM200B as the core and identified the functions of the selected target miRNA during cell proliferation and differentiation. We obtained 118 differentially expressed genes (DEGs) after lncFAM200B overexpression, 76 of which were up-regulated, including Notch signaling members NOTCH3, DTX3L, and HES4, and 42 DEGs were down-regulated, including genes related to the cell cycle (CCNA2, BUB1, CDC20, TOP2A, and KIF20A). Additionally, many ubiquitin-mediated proteolysis pathway members were also significantly up-regulated (BUA7, PML, TRIM21, and TRIM25). MiRNA sequencing showed that 13 miRNAs were significantly up-regulated, and 12 miRNAs were down-regulated. Among them, 29 targets of 10 differentially expressed miRNAs (DEMs) were differentially expressed, including miR-152-FBXO33, miR-6529a-TRIM21, miR-148c-NOTCH3, and the miR-6529b-HES4 axis. We further verified that overexpression and inhibition of miR-6529a can inhibit and promote, respectively, the proliferation and differentiation of preadipocytes. Taken together, our study not only revealed the regulatory network of lncFAM200B during yak preadipocytes differentiation but also laid a foundation for elucidating the cause for lower intramuscular fat content in yaks at the molecular level.