Search Results (43)

Background: Ramulus Mori (Sangzhi) Alkaloids (SZ-A) are natural hypoglycemic compounds known to enhance insulin secretion. Given the emerging role of the gut microbiota in regulating β-cell function, in this study, we aimed to investigate whether SZ-A exert their beneficial effects through modulating the gut microbiota and its metabolites. Methods: A diabetic mouse model was established using a high-fat diet and streptozotocin, followed by 20 weeks of SZ-A treatment. Gut microbiota and metabolites were profiled via 16S rRNA sequencing and liquid chromatography–mass spectrometry, respectively. Spearman’s correlation analysis was used to explore associations between gut microbiota and metabolites. Single-cell RNA sequencing (scRNA-seq) was used to assess gene expression and signaling pathway changes in β cells. Results: Our results demonstrate that SZ-A alleviated hyperglycemia and increased islet numbers in T2DM mice. SZ-A treatment also reshaped the gut microbiota, notably enriching quantities of Lactobacillus and norank_f__Eubacterium_coprostanoligenes_group, which may contribute to increasing levels of 2-methoxyestradiol (2-ME), a bioactive metabolite. Moreover, scRNA-seq revealed an increased proportion of COMT⁺ cells in the islets, suggesting that 2-ME may also be synthesized within the islets. In vitro, 2-ME suppressed HIF-1α signaling and promoted insulin secretion, indicating that 2-ME may act as a crucial mediator of the beneficial effects of SZ-A. Conclusions: SZ-A improve β-cell function by increasing 2-ME levels via gut microbiota modulation and islet production, ultimately suppressing HIF-1α signaling and restoring β-cell homeostasis. Full article

Abiotic stress can reprogram the gametophytic pathway; the mechanisms by which floral bud pre-treatment influences microspore embryogenesis initiation remain unclear. In this study, we use bisulfite sequencing, sRNA-seq, and RNA-seq to analyze the dynamic changes in rice microspores under different cold treatment durations. Our results showed that a 10-day cold treatment is essential for CXJ microspore embryogenesis initiation. DNA methylation levels showed a slight change at CG, CHG, and CHH sites under cold treatment. The number of both hyper- and hypomethylated DMRs increased over cold treatment, with more hypermethylated DMRs at 5 and 10 dpt. Hypermethylated DMRs were more frequently in the TSS region compared to hypomethylated DMRs. The proportion of 24 nt sRNAs increased upon cold stress, with more downregulated than upregulated sRNAs at 10 dpt. The number of DMR target DEGs increased from 5 to 10 dpt. Promoter hypomethylation at the CHH site was more frequently associated with DEGs. These outcomes suggested that the RdDM pathway participates in the initiation of rice ME. GO analysis indicated that DMR target DEGs at 10 dpt were enriched in responses to chemical stimuli, biological processes, and stress responses. An auxin-related gene, OsHOX28, was further identified. Its upregulation, potentially mediated by the RdDM pathway, may play a crucial role in the initiation of rice ME. This study provides more information on epigenetic mechanisms during rice ME. Full article

Sporadic colorectal cancer (CRC), the third leading cause of cancer-related death globally, arises through a continuum from normal tissue to adenomas, progressing from low-grade (LGD) to high-grade dysplasia (HGD); yet, the early epigenetic drivers of this transition remain unclear. To investigate these events, we profiled LGD and HGD adenomas using EM-seq, and identified a consensus differential methylation signature (DMS) of 626 regions through two independent bioinformatics pipelines. This signature effectively distinguished LGD from HGD in both tissue and plasma-derived cell-free DNA (cfDNA), highlighting specific methylation patterns. Functional annotation indicated enrichment for regulatory elements associated with transcription factor activity and cell signaling. Applying the DMS to the TCGA CRC dataset revealed three tumor subtypes with increasing hypermethylation and one normal cluster. The most hypermethylated subtype exhibited poor survival, high mutation burden, and disrupted transcriptional networks. While overlapping with classical CpG Island Methylator Phenotype (CIMP) categories, the DMS captured a broader spectrum of methylation alterations. These findings suggest that the DMS captures functionally relevant, antecedent epigenetic alterations in CRC progression, enabling the robust stratification of dysplasia severity and tumor subtypes. This signature holds promise for enhancing preclinical detection and molecular classification, and warrants further evaluation in larger prospective cohorts. Full article

Background/Objectives: Type 2 diabetes mellitus (T2DM) is a major global health challenge, primarily driven by insulin resistance and beta-cell dysfunction. This study investigated the roles of p21-activated kinase 1 (PAK1) and calcium/calmodulin-dependent protein kinase II (CAMKII) in insulin secretion, aiming to elucidate their involvement in this process and their implications in T2DM pathophysiology. Methods: Using the Beta-TC-6 insulinoma cell line, we assessed colocalization and interaction of PAK1 and CAMKII under glucose stimulation through indirect immuno-fluorescence (IFI) and proximity ligation assays (PLA). To examine their expression dynamics in a physiological context, we performed immunohistochemistry (IHC) on pancreatic sections from wild-type (WT), prediabetic, and T2DM murine models. Additionally, bioinformatic analysis of publicly available RNA sequencing (RNA-Seq) data from human islets of healthy donors, prediabetic individuals, and T2DM patients provided translational validation. Results: High glucose conditions significantly increased PAK1-CAMKII colocalization, correlating with enhanced insulin secretion. Pharmacological inhibition of these kinases reduced insulin release, confirming their regulatory roles. Murine and human islet analyses showed a progressive increase in kinase expression from prediabetes to T2DM, highlighting their relevance in disease progression. Conclusions: The coordinated function of PAK1 and CaMKII in insulin secretion suggests their potential as biomarkers and therapeutic targets in T2DM. Further studies are warranted to explore their mechanistic roles and therapeutic applications in preserving beta-cell function. Full article

Background/Objectives: Eggshell quality is a critical factor influencing consumer preference and the economic benefits of poultry enterprises, and the uterus is the key site for eggshell synthesis. Yaoshan chicken (YS), an indigenous chicken breed in China, is renowned for its flavorful meat and high-quality eggs. However, its egg production is lower compared to specialized strains. Therefore, the GYR crossbreed was developed by three-line hybridization for YS chicken, which can produce green-shelled eggs with better eggshell thickness and strength than YS chicken (p < 0.01). To explore the molecular mechanisms underlying the differences in eggshell quality between GYR and YS chickens, we conducted an integrated transcriptomic and metabolomic analysis. Methods: Twelve uterus samples (six from GYR and six from YS chickens) were collected during the period of eggshell calcification at 260 days of age. RNA sequencing (RNA-seq) and liquid chromatography–mass spectrometry (LC-MS/MS) were performed to identify differentially expressed genes (DEGs) and differential metabolites (DMs), respectively. Results: A total of 877 DEGs were identified in the GYR group, including 196 upregulated and 681 downregulated genes (|log₂ (fold change)| > 1, p-value < 0.05). Additionally, 79 DMs were detected, comprising 50 upregulated and 29 downregulated metabolites (|log₂ (fold change)| > 1, VIP > 1). Notably, the key DEGs (SLCO1B3, SLCO1B1, PTGR1, LGR6, MELTF, CRISP2, GVINP1, and OVSTL), important DMs (prostaglandin-related DMs and biliverdin) and signaling pathways (calcium signaling, neuroactive ligand–receptor interaction, arachidonic acid metabolism, bile secretion, and primary bile acid biosynthesis) were major regulators of the eggshell quality. Furthermore, an integrated transcriptomic and metabolomic analysis revealed two significant gene–metabolite pairs associated with eggshell quality: PTGDS–prostaglandin E2 and PTGS1–prostaglandin E2. Conclusions: This study provides a theoretical foundation for the improved eggshell quality of Yaoshan chicken. Full article

Background/Objectives: Our lab has previously reported that Grifola frondosa (maitake mushroom) GF5000 has antidiabetic potential owing to its ability to improve insulin resistance. This study aimed to gain insight into the system-level hypoglycemic mechanisms of GF5000 using transcriptomics, proteomics, and network pharmacology. This study provides new insights into the hypoglycemic mechanisms of GF5000, identifying key molecular targets involved in mitigating insulin resistance in T2DM. Methods: Liver protein and gene expression in normal control (NC), diabetic control (DC), and GF5000-treated (GF5000) rats were analyzed via iTRAQ and RNA-seq. The relationships between differentially expressed genes (DEGs), differentially expressed proteins (DEPs), and type 2 diabetes (T2DM) disease targets were studied using Metascape and the Cytoscape GeneMANIA plug-in. Results: One hundred and fifty-two DEGs and sixty-two DEPs were identified; twenty DEGs/DEPs exhibited the same trend in mRNA and protein expression levels when comparing the GF5000 vs. DC groups. The Metascape analysis revealed that the T2DM disease targets included four DEGs—Gck, Scd, Abcb4, and Cyp3a9—and two DEPs—glucokinase and acetyl-CoA carboxylase 2. A Cytoscape–GeneMANIA analysis of thirteen DEGs/DEPs related to T2DM showed that Apoa1/Apolipoprotein A-I, Gckr/glucokinase regulatory protein, and Gck/glucokinase had the highest connectivity and centrality in the topological network. The qPCR results confirmed that GF5000 increased the mRNA expression of GCK in GCK-knockdown HepG2 cells. Conclusions: These results provide theoretical evidence for the use of GF5000 as a potential active nutritional ingredient for the prevention and treatment of T2DM. Our findings suggest that GF5000 targets multiple pathways implicated in T2DM, offering a multi-faceted approach to disease management and prevention. Full article

Through the identification and expression pattern analysis of potato Laccase (LAC) gene family members, the characteristics of the StLAC gene family were elucidated, and the biological function of potato StLACs was further analyzed. In this study, bioinformatics approaches were employed to identify the members of the potato LAC family at the whole-genome level. Subsequently, their physicochemical properties, chromosomal localizations, gene structures, gene duplication events, and expression patterns were thoroughly analyzed. By leveraging the RNA-seq data retrieved from the PGSC database, the expression patterns of StLACs in diploid monoploid (DM) potatoes under various tissue, stress, and hormone treatments were investigated. Moreover, real-time fluorescence quantitative polymerase chain reaction (qPCR) was utilized to analyze the relative expression levels of StLACs in the “Atlantic” potato cultivar under salt stress treatments at different time points (zero hours, one hour, three hours, twelve hours, and twenty-four hours), aiming to screen for the StLAC genes potentially involved in the potato’s response to salt stress. Forty-five members of the potato StLAC gene family were identified, unevenly distributed across 12 chromosomes. Through the analysis of their gene structures and phylogenetic characteristics, the 45 StLACs members were classified into five subgroups. Collinearity analysis indicated that segmental duplication and tandem repeats played major roles in the expansion of the StLAC genes. Using RNA-seq and qPCR analyses, two candidate StLAC genes (Soltu09G001990 and Soltu04G028320) involved in the potato’s response to salt stress were screened out. This study provides a theoretical basis for further understanding StLAC gene family characteristics and an in-depth analysis of StLAC gene function in potato. Full article

The etiology of type 1 diabetes mellitus (T1DM) is intricate, leading to its classification as an autoimmune metabolic disorder. T1DM often coexists with various visceral diseases. N-acetylcysteine (NAC) is widely acknowledged for its potent antioxidant properties. Studies have demonstrated that the combination of NAC and insulin can effectively alleviate iron-induced nephropathy in T1DM and mitigate oxidative stress injury in skeletal muscle associated with the condition. However, the potential impact of NAC alone on liver disease in individuals with T1DM remains uncertain. In this study, a beagle model was established to simulate T1DM, enabling investigation into the role of NAC in liver disease using RNA-seq biogenic analysis and subsequent validation through molecular biological methods. The findings revealed suppressed expression of CXCL12 chemokine in the livers of individuals with T1DM, while treatment with NAC induced specific activation of CXCL12 within the liver affected by T1DM. These results suggest that CXCL12 may serve as a regulatory factor involved in the therapeutic effects of NAC on liver disease associated with TIDM. This discovery holds significant implications for utilizing NAC as an adjunctive therapy for managing complicated liver diseases accompanying type 1 diabetes mellitus. Full article

O-acetylserine (thiol) lyase is a pivotal enzyme in plant cysteine biosynthesis, which is crucial for promoting plant growth, development, and resisting abiotic stress. However, the related studies on the potato OASTL gene family (StOASTL) have not been reported. In the present study, we identified 11 members of the StOASTL gene family, conducting a thorough analysis encompassing chromosome distribution, protein physicochemical properties, gene structure, protein-conserved motifs, and gene replication events. Phylogenetic scrutiny delineated these 11 StOASTLs into five distinct subfamilies. Using RNA-seq from the Potato Genome Sequencing Consortium (PGSC), we investigated the expression profile of StOASTLs in different tissues of DM (double-monoploid) potato and under abiotic/biotic stress, hormone treatment, and biostimulant treatment. The results showed that one of the StOASTLs (Soltu09G024390) was differentially expressed under different abiotic stresses and hormone treatments. Our findings showcased the differential response of one StOASTL (Soltu09G024390) to a spectrum of abiotic stresses and hormone treatments. Soltu09G024390 was earmarked as a candidate gene and successfully cloned. Functional validation through yeast stress assays demonstrated that the heterologous expression of Soltu09G024390 bolstered yeast tolerance to salt and cadmium stresses. This study provides a theoretical basis for revealing the role of the StOASTL family in potato response to abiotic stress and valuable insights for further study of the biological functions of StOASTL. Full article

Cellular therapies exhibit immense potential in treating complex diseases with sustained responses. The manufacture of cell therapies involves the purification and engineering of specific cells from a donor or patient to achieve a therapeutic response upon injection. Magnetic cell sorting targeting the presence or absence of surface markers is commonly used for upfront purification. However, emerging research shows that optimal therapeutic phenotypes are characterized not only by the presence or absence of specific antigens but also by antigen density. Unfortunately, current cell purification tools like magnetic or fluorescence-activated cell sorting (FACS) lack the resolution to differentiate populations based on antigen density while maintaining scalability. Utilizing a technique known as digital magnetic sorting (DMS), we demonstrate proof of concept for a scalable, magnetic-based approach to fractionate cell populations based on antigen density level. Targeting CD4 on human leukocytes, DMS demonstrated fractionation into CD4^Hi T cells and CD4^Low monocytes and neutrophils as quantified by flow cytometry and single-cell RNA seq. DMS also demonstrated high throughput processing at throughputs 3–10× faster than FACS. We believe DMS can be leveraged and scaled to enable antigen density-based sorting in cell therapy manufacturing, leading to the production of more potent and sustainable cellular therapies. Full article

Diabetic foot ulcers (DFUs) are a severe complication of diabetes mellitus (DM), which often lead to hospitalization and non-traumatic amputations in the United States. Diabetes prevalence estimates in South Texas exceed the national estimate and the number of diagnosed cases is higher among Hispanic adults compared to their non-Hispanic white counterparts. San Antonio, a predominantly Hispanic city, reports significantly higher annual rates of diabetic amputations compared to Texas. The late identification of severe foot ulcers minimizes the likelihood of reducing amputation risk. The aim of this study was to identify molecular factors related to the severity of DFUs by leveraging a multimodal approach. We first utilized electronic health records (EHRs) from two large demographic groups, encompassing thousands of patients, to identify blood tests such as cholesterol, blood sugar, and specific protein tests that are significantly associated with severe DFUs. Next, we translated the protein components from these blood tests into their ribonucleic acid (RNA) counterparts and analyzed them using public bulk and single-cell RNA sequencing datasets. Using these data, we applied a machine learning pipeline to uncover cell-type-specific and molecular factors associated with varying degrees of DFU severity. Our results showed that several blood test results, such as the Albumin/Creatinine Ratio (ACR) and cholesterol and coagulation tissue factor levels, correlated with DFU severity across key demographic groups. These tests exhibited varying degrees of significance based on demographic differences. Using bulk RNA-Sequenced (RNA-Seq) data, we found that apolipoprotein E (APOE) protein, a component of lipoproteins that are responsible for cholesterol transport and metabolism, is linked to DFU severity. Furthermore, the single-cell RNA-Seq (scRNA-seq) analysis revealed a cluster of cells identified as keratinocytes that showed overexpression of APOE in severe DFU cases. Overall, this study demonstrates how integrating extensive EHRs data with single-cell transcriptomics can refine the search for molecular markers and identify cell-type-specific and molecular factors associated with DFU severity while considering key demographic differences. Full article

The goal of our study was to identify and assess the functionally significant SNPs with potentially important roles in the development of type 2 diabetes mellitus (T2DM) and/or their effect on individual response to antihyperglycemic medication with metformin. We applied a bioinformatics approach to identify the regulatory SNPs (rSNPs) associated with allele-asymmetric binding and expression events in our paired ChIP-seq and RNA-seq data for peripheral blood mononuclear cells (PBMCs) of nine healthy individuals. The rSNP outcomes were analyzed using public data from the GWAS (Genome-Wide Association Studies) and Genotype-Tissue Expression (GTEx). The differentially expressed genes (DEGs) between healthy and T2DM individuals (GSE221521), including metformin responders and non-responders (GSE153315), were searched for in GEO RNA-seq data. The DEGs harboring rSNPs were analyzed using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). We identified 14,796 rSNPs in the promoters of 5132 genes of human PBMCs. We found 4280 rSNPs to associate with both phenotypic traits (GWAS) and expression quantitative trait loci (eQTLs) from GTEx. Between T2DM patients and controls, 3810 rSNPs were detected in the promoters of 1284 DEGs. Based on the protein-protein interaction (PPI) network, we identified 31 upregulated hub genes, including the genes involved in inflammation, obesity, and insulin resistance. The top-ranked 10 enriched KEGG pathways for these hubs included insulin, AMPK, and FoxO signaling pathways. Between metformin responders and non-responders, 367 rSNPs were found in the promoters of 131 DEGs. Genes encoding transcription factors and transcription regulators were the most widely represented group and many were shown to be involved in the T2DM pathogenesis. We have formed a list of human rSNPs that add functional interpretation to the T2DM-association signals identified in GWAS. The results suggest candidate causal regulatory variants for T2DM, with strong enrichment in the pathways related to glucose metabolism, inflammation, and the effects of metformin. Full article

The relationship between type 2 diabetes mellitus (T2DM) and colorectal cancer (CRC) has long been extensively recognized, but their crosstalk mechanisms based on gene regulation remain elusive. In our study, for the first time, bulk RNA-seq and single-cell RNA-seq data were used to explore the shared molecular mechanisms between T2DM and CRC. Moreover, Connectivity Map and molecular docking were employed to determine potential drugs targeting the candidate targets. Eight genes (EVPL, TACSTD2, SOX4, ETV4, LY6E, MLXIPL, ENTPD3, UGP2) were identified as characteristic comorbidity genes for T2DM and CRC, with EVPL and ENTPD3 further identified as core comorbidity genes. Our results demonstrated that upregulation of EVPL and downregulation of ENTPD3 were intrinsic molecular features throughout T2DM and CRC and were significantly associated with immune responses, immune processes, and abnormal immune landscapes in both diseases. Single-cell analysis highlighted a cancer-associated fibroblast (CAF) subset that specifically expressed ENTPD3 in CRC, which exhibited high heterogeneity and unique tumor-suppressive features that were completely different from classical cancer-promoting CAFs. Furthermore, ENTPD3⁺ CAFs could notably predict immunotherapy response in CRC, holding promise to be an immunotherapy biomarker at the single-cell level. Finally, we identified that droperidol may be a novel drug simultaneously targeting EVPL and ENTPD3. In conclusion, previous studies have often focused solely on metabolic alterations common to T2DM and CRC. Our study establishes EVPL and ENTPD3 as characteristic molecules and immune biomarkers of comorbidity in T2DM and CRC patients, and emphasizes the importance of considering immunological mechanisms in the co-development of T2DM and CRC. Full article

Diabetic cardiomyopathy (DCM) represents a common pathological state brought about by diabetes mellitus (DM). Patchouli alcohol (PatA) is known for its diverse advantageous effects, notably its anti-inflammatory properties and protective role against metabolic disorders. Despite this, the influence of PatA on DCM remains relatively unexplored. To explore the effect of PatA on diabetes-induced cardiac injury and dysfunction in mice, streptozotocin (STZ) was used to mimic type 1 diabetes in mice. Serological markers and echocardiography show that PatA treatment protects the heart against cardiomyopathy by controlling myocardial fibrosis but not by reducing hyperglycemia in diabetic mice. Discovery Studio 2017 software was used to perform reverse target screening of PatA, and we found that JAK2 may be a potential target of PatA. RNA-seq analysis of heart tissues revealed that PatA activity in the myocardium was primarily associated with the inflammatory fibrosis through the Janus tyrosine kinase 2 (JAK2)/signal transducer and activator of the transcription 3 (STAT3) pathway. In vitro, we also found that PatA alleviates high glucose (HG) + palmitic acid (PA)-induced fibrotic and inflammatory responses via inhibiting the JAK2/STAT3 signaling pathway in H9C2 cells. Our findings illustrate that PatA mitigates the effects of HG + PA- or STZ-induced cardiomyopathy by acting on the JAK2/STAT3 signaling pathway. These insights indicate that PatA could potentially serve as a therapeutic agent for DCM treatment. Full article

The lipoxygenases (LOXs) are non-heme iron-containing dioxygenases that play an important role in plant growth and defense responses. There is scarce knowledge regarding the LOX gene family members and their involvement in biotic and abiotic stresses in potato. In this study, a total of 17 gene family members (StLOXs) in potato were identified and clustered into three subfamilies: 9-LOX type I, 13-LOX type I, and 13-LOX type II, with eleven, one, and five members in each subfamily based on phylogenetic analysis. By exploiting the RNA-seq data in the Potato Genome Sequencing Consortium (PGSC) database, the tissue-specific expressed and stress-responsive StLOX genes in double-monoploid (DM) potato were obtained. Furthermore, six candidate StLOX genes that might participate in drought and salt response were determined via qPCR analysis in tetraploid potato cultivars under NaCl and PEG treatment. Finally, the involvement in salt stress response of two StLOX genes, which were significantly up-regulated in both DM and tetraploid potato under NaCl and PEG treatment, was confirmed via heterologous expression in yeast under salt treatment. Our comprehensive analysis of the StLOX family provides a theoretical basis for the potential biological functions of StLOXs in the adaptation mechanisms of potato to stress conditions. Full article