The Role of PIK3R1 in Metabolic Function and Insulin Sensitivity

Bioinformatic Analysis of Apoptosis-Related Genes in Preeclampsia Using Public Transcriptomic and Single-Cell RNA Sequencing Datasets

Purpose

Apoptosis, which is crucial in preeclampsia (PE), affects trophoblast survival and placental function. We used transcriptomics and single-cell RNA sequencing (scRNA-seq) to explore apoptosis-related genes (ARGs) and their cellular mechanisms as potential PE biomarkers.

Patients and Methods

All the data included in this study were sourced from public databases. We used scRNA-seq and differential expression analysis, combined with five algorithms from the CytoHubba plugin, to identify ARGs as PE biomarkers. These were integrated into diagnostic nomograms. Mechanistic studies involved enrichment analysis and immune profiling. Biomarker expression was examined at the single-cell level, and verified in clinical samples by RT-qPCR.

Results

Cluster of Differentiation 44 (CD44), Macrophage migration inhibitory factor (MIF), PIK3R1, and Toll-like receptor 4 (TLR4) were identified as PE biomarkers. CD44 and TLR4 were down-regulated, while MIF and PIK3R1 were up-regulated. When integrated into the diagnostic nomogram, they showed clinical utility and affected cell functions. In the immune profile of PE, monocytes decreased, resting NK cells increased, and the activities of APC, checkpoint, T-cell co-stimulation, and MHC class I pathways reduced. ScRNA-seq identified 11 cell types, 10 of which were significantly different. Endothelial cell communication with other cell types decreased, while the interaction between common myeloid progenitors (CMP) and villous cytotrophoblasts (VCT) enhanced. The expression levels of CD44, MIF, and PIK3R1 in VCT were significantly different and key to PE. Their decrease in early PE and increase in late PE reflected the placenta's adaptation to adverse pregnancy conditions.

Conclusion

Four ARGs, CD44, MIF, PIK3R1, and TLR4, identified through comprehensive analyses, served as significant biomarkers for PE and offered insights into PE's cellular mechanisms of PE, providing valuable references for further research.

Role of PI3K/AKT/MAOA in glucocorticoid-induced oxidative stress and associated premature senescence of the trabecular meshwork

The oxidative stress-induced premature senescence of trabecular meshwork (TM) represents a pivotal risk factor for the development of glucocorticoid-induced glaucoma (GIG). This study aimed to elucidate the pathogenesis of TM senescence in GIG. MethodsIntraocular pressure (IOP), transmission electron microscopy and senescence-associated protein expression in TM were evaluated in GIG mice. Protein expression of phosphoinositide-3-kinase regulatory subunit 1 (PIK3R1) and monoamine oxidase A (MAOA), phosphorylation of AKT were quantified. ROS and mitochondrial superoxide levels were measured to evaluate cellular oxidative stress. Cell cycle analysis, β-galactosidase staining, senescence-associated protein expression were employed to assess the aging status of primary human trabecular meshwork cells (pHTMs). ResultsmRNA-seq and KEGG analysis indicating PI3K/AKT pathway as a key regulator in TM of GIG. PI3K inhibitor significantly prevented IOP elevation and abnormal mitochondrial morphology of TM in the GIG mouse model. PI3K inhibitor or selective silencing of PIK3R1 alleviated dexamethasone (DEX)-induced oxidative stress, also mitochondrial dysfunction, inhibiting MAOA expression in pHTMs. The same phenomenon was observed in the GIG models with inhibition of MAOA. Further KEGG analysis indicates that cellular senescence is the key factor in the pathogenesis of GIG. TM senescence was observed in both GIG mouse and cell models. Inhibition of the PI3K/AKT/MAOA pathway significantly alleviated DEX-induced premature cellular senescence of TM in GIG models. Glucocorticoids activated the PI3K/AKT/MAOA pathway, leading to mitochondrial dysfunction, oxidative stress, and premature aging in TM, elevating IOP. This mechanism could be associated with the onset and progression of GIG, providing a potential approach for its treatment.

Molecular Mechanisms of Propofol-Induced Cognitive Impairment: Suppression of Critical Hippocampal Pathways

Propofol, a commonly used anesthetic, is known to cause postoperative cognitive dysfunction (POCD), particularly after prolonged or high-dose administration. Its effects on neural remodeling in the hippocampal region, which is vital for cognitive function, remain poorly understood. This study employs single-cell RNA sequencing (scRNA-seq) and high-throughput transcriptomic analysis to elucidate the molecular mechanisms by which propofol impairs hippocampal neural remodeling. Our findings indicate that propofol suppresses the (5-Hydroxytryptamine Receptor 1A/Glutamate Receptor 2/Phosphoinositide 3-Kinase Regulatory Subunit 1) HTR1A/GRIA2/PIK3R1 signaling pathway, contributing to cognitive dysfunction in mice. In vitro experiments reveal that propofol treatment reduces the expression of HTR1A/GRIA2/PIK3R1-related factors, decreases neuronal activity and synaptic plasticity, and increases apoptosis and inflammation. In vivo experiments demonstrate significant impairments in spatial memory and learning abilities in mice treated with propofol. These results provide new insights into the long-term effects of anesthetic drugs and offer a scientific basis for their judicious use in clinical practice. The study highlights potential strategies and targets for preventing and treating POCD, emphasizing the importance of understanding the molecular mechanisms underlying anesthetic-induced cognitive dysfunction.

Unraveling the Mystery of Insulin Resistance: From Principle Mechanistic Insights and Consequences to Therapeutic Interventions

Insulin resistance (IR) is a significant factor in the development and progression of metabolic-related diseases like dyslipidemia, T2DM, hypertension, nonalcoholic fatty liver disease, cardiovascular and cerebrovascular disorders, and cancer. The pathogenesis of IR depends on multiple factors, including age, genetic predisposition, obesity, oxidative stress, among others. Abnormalities in the insulin-signaling cascade lead to IR in the host, including insulin receptor abnormalities, internal environment disturbances, and metabolic alterations in the muscle, liver, and cellular organelles. The complex and multifaceted characteristics of insulin signaling and insulin resistance envisage their thorough and comprehensive understanding at the cellular and molecular level. Therapeutic strategies for IR include exercise, dietary interventions, and pharmacotherapy. However, there are still gaps to be addressed, and more precise biomarkers for associated chronic diseases and lifestyle interventions are needed. Understanding these pathways is essential for developing effective treatments for IR, reducing healthcare costs, and improving quality of patient life.

Targeting cardiotoxicity: the potential of Annona squamosa L. in doxorubicin therapy

Doxorubicin, a potent anthracycline used in chemotherapy, is limited by dose-dependent cardiotoxicity, leading to irreversible heart damage and heart failure. Common symptoms include fatigue, dyspnea, lower limb edema, hypotension, tachycardia, and transient arrhythmias. Annona squamosa L. (AS), traditionally used in medicine, was investigated for its cardioprotective action against doxorubicin-induced cardiotoxicity through computational studies. Phytocompounds were identified using literature reviews, Dr. Duke's, IMPPAT, and PubChem databases. Targets associated with Doxorubicin induced cardiotoxicity were accessed from GeneCards, and protein-protein interactions were analyzed using the STRING database. Cytoscape was used for network visualization, revealing 18 bioactives targeting 67 proteins across 14 pathways. PIK3R1 emerged as a key target with the highest interaction count among 767 targets. Molecular docking showed that the PIK3R1-Rutin complex had the lowest binding energy (- 11.873 kcal/mol), and a 100 ns molecular dynamics (MD) simulation confirmed its stability. LC-MS analysis of the crude extract indicated the presence of bioactives. In vitro antioxidant activity of AS, assessed using the DPPH assay, showed significant radical scavenging activity, correlating with the high total phenol (TPC) and total flavonoid content (TFC) detected. This integrated approach highlights AS's potential in mitigating doxorubicin-induced cardiotoxicity.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-025-00333-5.

A comparative genomic study across 396 liver biopsies provides deep insight into FGF21 mode of action as a therapeutic agent in metabolic dysfunction-associated steatotic liver disease

BACKGROUND

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a systemic disease with insulin resistance at its core. It affects one-third of the world population. Fibroblast growth factor (FGF21)-based therapies are effective in lowering hepatic fat content and fibrosis resolution; yet, its molecular functions remain uncertain. To gain insight into FGF21 mode of action (MoA), we investigated the transcriptomes of MASLD liver biopsies in relation to FGF21 expression.

METHODS

We compared N = 66 healthy controls with 396 MASLD patients and considered clinical characteristics relative to NAS disease activity scores (steatosis, lobular inflammation and ballooning), fibrosis grades and sex. We performed comparative genomics to identify FGF21-responsive DEGs, utilised information from FGF21-transgenic and FGF21-knockout mice and evaluated DEGs following FGF21 treatment of MASLD animal models. Eventually, we explored 188 validated FGF21 targets, and for ≥10 patients showing the same changes, we constructed MASLD-associated networks to determine the effects of FGF21 in reverting metabolic dysfunction.

RESULTS

We identified patients with increased 30% (N = 117), decreased 40% (N = 159) or unchanged 30% (N = 120) FGF21 expression, and the differences are caused by changes in FGF21 transcriptional control with ATF4 functioning as a key regulator. Based on comparative genomics, we discovered molecular circuitries of FGF21 in MASLD, notably FGF21-dependent induction of autophagy and oxidative phosphorylation/mitochondrial respiration. Conversely, FGF21 repressed hepatic glycogen-storage, its glucose release and gluconeogenesis, and therefore reduced glucose flux in conditions of insulin resistance. Furthermore, FGF21 repressed lipid transporters, and acetyl-CoA carboxylase-β to attenuate hepatic lipid overload and lipogenesis. Strikingly, FGF21 dampened immune response by repressing complement factors, MARCO, CD163, MRC1/CD206, CD4, CD45 and pro-inflammatory cytokine receptors. It also reverted procoagulant imbalance in MASLD, stimulated extracellular matrix degradation, repressed TGFβ- and integrin-signalling and lessened liver sinusoidal endothelial cell defenestration in support of fibrosis resolution.

CONCLUSIONS

We gained deep insight into FGF21-MoA in MASLD. However, heterogeneity in FGF21 expression calls for molecular stratifications as to identify patients which likely benefit from FGF21-based therapies.

KEY POINTS

Performed comprehensive genomics across liver biopsies of 396 MASLD patients and identified patients with increased, decreased and unchanged FGF21 expression. Used genomic data from FGF21 transgenic, knock-out and animal MASLD models treated with synthetic FGF21 analogues to identify FGF21-mode-of-action and metabolic networks in human MASLD. Given the significant heterogeneity in FGF21 expression, not all patients will benefit from FGF21-based therapies.

Identification and verification of autophagy-related gene signatures and their association with immune infiltration and drug responsiveness in epilepsy

Background

Epilepsy, a common neurological disorder, is characterized by susceptibility to recurrent seizures. Increasing evidence suggests that autophagy plays a crucial role in the initiation and progression of epilepsy. However, the precise mechanisms by which autophagy deficiencies involved in epileptogenesis are still not fully understood.

Methods

Two datasets of epilepsy (GSE143272 and GSE256068) were downloaded from the Gene Expression Omnibus (GEO) database. Differential expression genes (DEGs) analysis and weighted gene co-expression network analysis (WGCNA) were employed to screen for autophagy related differential expression genes (ARDEGs) in GSE143272 database. Subsequently, protein-protein interaction, transcription factors and miRNAs networks were constructed. Additionally, the functional enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were applied. The hub ARDEGs were identified through CytoHubba, followed by the LASSO analysis. The Immune Cell Abundance Identifier (ImmuCellAI) was used to estimate peripheral immune cells abundance of epilepsy. Furthermore, the expression level of hub ARDEGs were detected in patients treated with different epilepsy monotherapies to explore the role of autophagy in the responsiveness of antiepileptic drug therapy. Finally, the expression level of hub ARDEGs were further validated in hippocampus of GSE256068 to enhance the reliability of the results.

Results

Twenty ARDEGs in epilepsy were screened out by integrating DEGs and WGCNA analysis. KEGG enrichment analysis showed that the ARDEGs in epilepsy were not only involved in the autophagy, but also apoptosis, the NOD-like receptor signaling pathway, the neurotrophin signaling pathway, etc. Four hub ARDEGs (PIK3R1, TRIM21, TRIM22, and ITPR3) were screened through integrating CytoHubba plug and LASSO analysis. The immune infiltration analysis showed that there was a significantly increased abundance of macrophages and a decreased abundance of CD4 and CD8 T cells, including Tr1, nTreg, Tfh, CD8 naïve, cytotoxic T cells and effector memory T cells in the epilepsy group. Furthermore, the hub ARDEGs were significantly correlated with the abundance of differential immune cells. In expression level validation and anti-epileptic drug responsiveness analysis, PIK3R1 and ITPR3 had significant differences in the hippocampus of patients with epilepsy. PIK3R1 expression level was found to be related with carbamazepine resistance.

Conclusion

This study elucidated the autophagy-related gene signatures in epilepsy and clarified their association with immune infiltration and anti-epileptic drug responsiveness, providing a novel target for future therapeutic interventions and disease markers in epilepsy.

Baicalin Mitigates Cardiac Hypertrophy and Fibrosis by Inhibiting the p85a Subunit of PI3K

Background: Heart failure (HF) is a serious public health concern. Baicalin is one of the major active ingredients of a traditional Chinese herbal medicine, Huang Qin, which is used to treat patients with chest pain or cardiac discomfort. However, the underlying mechanism(s) of the cardioprotective effect of baicalin are still not fully understood. Methods: Isoprenaline injection or transverse aortic constriction-induced animal models and isoprenaline or angiotensin 2 administration-induced cell models of heart failure were established. Baicalin (15 mg/kg/day or 25 mg/kg/day) was administered in vivo, and 10 μM baicalin was administered in vitro. Potential pharmacological targets of baicalin and genes related to heart failure were identified via different databases, which suggested that PI3K-Akt may be involved in the effects of baicalin. Molecular docking was carried out to reveal the effect of baicalin on p85a. Results: We observed significant antihypertrophic and antifibrotic effects of baicalin both in vivo and in vitro. The mean cross-sectional area of cardiomyocytes recovered from 390 μm2 in the HF group to 195 μm2 in the baicalin-treated group. The area of fibrosis was reduced from 2.8-fold in the HF group to 1.62-fold in the baicalin-treated group. Baicalin displayed a significant cardioprotective effect via the inhibition of the PI3K signaling pathway by binding with five amino acid residues of the p85a regulatory subunit of PI3K. The combination treatment of baicalin and an inhibitor of PI3K p110 demonstrated a stronger cardioprotective effect. The mean ejection fraction increased from 54% in the baicalin-treated group to 67% in the combination treatment group. Conclusions: Our work identified baicalin as a new active herbal ingredient that is able to treat isoprenaline-induced heart dysfunction and suggests that p85a is a pharmacological target. These findings reveal the significant potential of baicalin combined with an inhibitor of PI3K p110 for the treatment of heart failure and support more clinical trials in the future.

Integrated transcriptome and metabolome analysis of liver reveals unsynchronized growth mechanisms in blunt-snout bream (Megalobrama amblycephala)

BACKGROUND

Megalobrama amblycephala presents unsynchronized growth, which affects its productivity and profitability. The liver is essential for substance exchange and energy metabolism, significantly influencing the growth of fish.

RESULTS

To investigate the differential metabolites and genes governing growth, and understand the mechanism underlying their unsynchronized growth, we conducted comprehensive transcriptomic and metabolomic analyses of liver from fast-growing (FG) and slow-growing (SG) M. amblycephala individuals. A total of 2,097 differentially expressed genes (DEGs) were identified between FG and SG, with 830 genes exhibiting significantly higher expression level in FG. KEGG and GO enrichment analysis indicated that the DEGs with higher expression level were significantly correlated with insulin signaling pathway, steroid hormone and lipid metabolism related pathway (PPAR signaling pathway and fatty acid degradation). In the metabolomic analysis, 224 differentially expressed metabolites (DEMs) were detected, of which 128 were significantly more abundant in FG. These more abundant DEMs were prominently enriched in pathways associated with cell proliferation and energy metabolism (Oxidative phosphorylation, mTOR signaling pathway and FoxO signaling pathway). In addition, DEGs and DEMs in adenosine diphosphate (ATP) hydrolysis activity and associate with fatty acid metabolism, glucose metabolism, and amino acid metabolism pathways were both found in the transcriptomic and metabolomic integrated data. These findings suggest that the large amounts of energy generated by fatty acid, glucose metabolism and other energy metabolism pathway promote the rapid growth of FG.

CONCLUSIONS

This research is the first to integrate metabolomic and transcriptomic analyses of liver to identify key genes, metabolites, and pathways to uncover the molecular and metabolic mechanisms of unsynchronized growth in M. amblycephala. The identified metabolic and genes can be potential targets for selective breeding programs to improve growth performance in aquaculture.

Effects of defined voluntary running distances coupled with high-fat diet consumption on the skeletal muscle transcriptome of male mice

Exercise counters many adverse health effects of consuming a high-fat diet (HFD). However, complex molecular changes that occur in skeletal muscle in response to exercising while consuming a HFD are not yet known. We investigated the interplay between diverse exercise regimes and HFD consumption on the adaptation of skeletal muscle transcriptome. C57BL/6 male mice were randomized into five groups-one sedentary control group and four exercise groups. The exercise groups consisted of an unrestricted running group (8.3 km/day) and three groups that were restricted to 75%, 50%, or 25% of unrestricted running (6.3, 4.2, and 2.1 km/day, respectively). Total RNA was extracted from frozen gastrocnemius muscle for transcriptome analyses. DEG counts were 1347, 1823, 1103, and 1107 and there were 107, 169, 67, and 89 unique genes present in the HFD-25%, HFD-50%, HFD-75%, and HFD-U, respectively. Comparing exercise groups, we found that exercising at 50% resulted in the most differentially expressed transcripts with the MAPK and PPAR signaling pathways enriched in down- and up-regulated genes, respectively. These results demonstrate that running distance impacts the adaptation of the skeletal muscle transcriptome to exercise and suggest that middle-distance running may provide the greatest protection against high-fat diet-induced stress coupled with exercise.

β-Carotene Impacts the Liver MicroRNA Profile in a Sex-Specific Manner in Mouse Offspring of Western Diet-Fed Mothers: Results from Microarray Analysis by Direct Hybridization

Maternal unbalanced diets cause adverse metabolic programming and affect the offspring's liver microRNA (miRNA) profile. The liver is a site of β-carotene (BC) metabolism and a target of BC action. We studied the interaction of maternal Western diet (WD) and early-life BC supplementation on the epigenetic remodeling of offspring's liver microRNAs. Mouse offspring of WD-fed mothers were given a daily placebo (controls) or BC during suckling. Biometric parameters and liver miRNAome by microarray hybridization were analyzed in newly weaned animals. BC sex-dependently impacted the liver triacylglycerol content. The liver miRNAome was also differently affected in male and female offspring, with no overlap in differentially expressed (DE) miRNAs between sexes and more impact in females. Bioinformatic analysis of DE miRNA predicted target genes revealed enrichment in biological processes/pathways related to metabolic processes, regulation of developmental growth and circadian rhythm, liver homeostasis and metabolism, insulin resistance, and neurodegeneration, among others, with differences between sexes. Fifty-five percent of the overlapping target genes in both sexes identified were targeted by DE miRNAs changed in opposite directions in males and females. The results identify sex-dependent responses of the liver miRNA expression profile to BC supplementation during suckling and may sustain further investigations regarding the long-term impact of early postnatal life BC supplementation on top of an unbalanced maternal diet.

Unveiling the role of PIK3R1 in cancer: A comprehensive review of regulatory signaling and therapeutic implications

Phosphoinositide 3-kinase (PI3K) is responsible for phosphorylating phosphoinositides to generate secondary signaling molecules crucial for regulating various cellular processes, including cell growth, survival, and metabolism. The PI3K is a heterodimeric enzyme complex comprising of a catalytic subunit (p110α, p110β, or p110δ) and a regulatory subunit (p85). The binding of the regulatory subunit, p85, with the catalytic subunit, p110, forms an integral component of the PI3K enzyme. PIK3R1 (phosphoinositide-3-kinase regulatory subunit 1) belongs to class IA of the PI3K family. PIK3R1 exhibits structural complexity due to alternative splicing, giving rise to distinct isoforms, prominently p85α and p55α. While the primary p85α isoform comprises multiple domains, including Src homology 3 (SH3) domains, a Breakpoint Cluster Region Homology (BH) domain, and Src homology 2 (SH2) domains (iSH2 and nSH2), the shorter isoform, p55α, lacks certain domains present in p85α. In this review, we will highlight the intricate regulatory mechanisms governing PI3K signaling along with the impact of PIK3R1 alterations on cellular processes. We will further delve into the clinical significance of PIK3R1 mutations in various cancer types and their implications for prognosis and treatment outcomes. Additionally, we will discuss the evolving landscape of targeted therapies aimed at modulating PI3K-associated pathways. Overall, this review will provide insights into the dynamic interplay of PIK3R1 in cancer, fostering advancements in precision medicine and the development of targeted interventions.

Cepharanthine inhibits African swine fever virus replication by suppressing AKT-associated pathways through disrupting Hsp90-Cdc37 complex

African swine fever (ASF) represents one of the most economically important viral infectious diseases in the swine industry worldwide. Presently, there is an absence of commercially available therapeutic drugs and safe vaccines. Cepharanthine (CEP), one of the naturally occurring bisbenzylisoquinoline alkaloids, has been approved as a drug to treat various diseases such as leukopenia, bronchial asthma, and snake bites for 70 years in Japan. Most recently, CEP was reported to inhibit ASFV replication by suppressing endosomal/lysosomal function although the specific molecular mechanisms were not elucidated. In this study, we demonstrate for the first time that ASFV infection promotes co-chaperone Cdc37 expression and its binding to Hsp90, leading to increased AKT phosphorylation to benefit viral replication. Notably, CEP disrupts the Hsp90-Cdc37 complex, subsequently decreasing p-AKT and inhibiting ASFV replication. Furthermore, our investigation reveals that enhanced AKT phosphorylation amplifies glycolysis, resulting in increased lactate production, while it upregulates the NF-κB signaling pathway, resulting in increased expression of IL-1β and other inflammatory cytokines. Elevated lactate enhances ASFV replication, and IL-1β acts synergistically on the proviral effect of lactate. CEP reduces ASFV replication by disrupting the formation of the Hsp90-Cdc37 complex and suppressing its downstream AKT/glycolysis axis and AKT/NF-κB pathway, leading to reduced lactate and IL-1β production. Our findings suggest that CEP could serve as a promising ASFV inhibitor, and the Hsp90-Cdc37 complex and glycolysis represent novel antiviral targets against ASFV infections, offering novel avenues for further exploration in antiviral therapeutic strategies. As the in vivo environment is largely complicated from ex vivo PAMs, anti-ASFV efficacy evaluation of CEP in pigs is the most imperative work in the future.

Combining bioinformatics, network pharmacology, and artificial intelligence to predict the mechanism of resveratrol in the treatment of rheumatoid arthritis

Background

Rheumatoid arthritis (RA) is a chronic autoimmune disorder that causes joint inflammation and destruction, resulting in significant physical and economic burdens. Finding effective and targeted therapy for RA remains a top priority. Resveratrol is a potential candidate with anti-inflammatory and immunomodulatory properties for RA treatment. This study aims to determine the therapeutic targets and signaling pathways of resveratrol in the treatment of RA.

Methods

The GSE205962 dataset downloaded from The Gene Expression Omnibus (GEO) database was used to obtain the differentially expressed genes (DEGs) in blood samples from the patients and the healthy. PharmMapper database and Cytoscape (v3.9.1) were applied to construct the resveratrol pharmacophore target network. Gene functional enrichment analysis, including the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, was based on the BiNGo plug-in of Cytoscape and David's online tool. The intersection of the target genes of resveratrol and the DEGs were considered potential therapeutic genes (PT-genes). The Protein-Protein Interaction (PPI) network of PT-genes was constructed using the STRING tool, and the key therapeutic genes (KT-genes) were determined using the cytoHubba plug-in based on the Maximal Clique Centrality (MCC) algorithms. Molecular docking validation of resveratrol and therapeutic targets was performed based on the protein structure of KT-genes predicted by AlphaFold.

Results

A total of 2202 DEGs and 47PT-genes were identified. GO analysis showed that the three groups of genes, the DEGs, the resveratrol target genes, and the PT-genes, have similar results for the top-five gene functional enrichment. PT-genes were closely related to the pathways of metabolic pathways, pathways in cancer, proteoglycans in cancer, insulin signaling pathway, and chemokine signaling pathway. The common pathway enriched by KEGG for the DEGs, and the resveratrol target genes was up to 36 %. The nine KT-genes were ABL1, ANXA5, CASP3, HSP90AA1, LCK, MAP2K1, MAPK1, PIK3R1, and RAC1, and the lowest free energy indicating the resveratrol/protein affinity were -8.4, -7.4, -6.4, -6.7, -8.0, -7.9, -7.4, -6.7, and -7.9, respectively.

Conclusion

Nine KT-genes were identified and validated as the most potential therapeutic targets in the treatment of RA with resveratrol, which provide new insights into therapeutic mechanisms and may improve the efficiency of drug development.

Integrating network pharmacology, molecular docking and non-targeted serum metabolomics to illustrate pharmacodynamic ingredients and pharmacologic mechanism of Haizao Yuhu Decoction in treating hyperthyroidism

Objective

To explore the pharmacodynamic ingredients and pharmacologic mechanism of Haizao Yuhu Decoction (HYD) in treating hyperthyroidism via an analysis integrating network pharmacology, molecular docking, and non-targeted serum metabolomics.

Methods

Therapeutic targets of hyperthyroidism were searched through multi-array analyses in the Gene Expression Omnibus (GEO) database. Hub genes were subjected to the construction of a protein-protein interaction (PPI) network, and GO and KEGG enrichment analyses. Targets of active pharmaceutical ingredients (APIs) in HYD and those of hyperthyroidism were intersected to yield hub genes, followed by validations via molecular docking and non-targeted serum metabolomics.

Results

112 hub genes were identified by intersecting APIs of HYD and therapeutic targets of hyperthyroidism. Using ultra-high performance liquid chromatography with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) in both negative and positive ion polarity modes, 279 compounds of HYD absorbed in the plasma were fingerprinted. Through summarizing data yielded from network pharmacology and non-targeted serum metabolomics, 214 common targets were identified from compounds of HYD absorbed in the plasma and therapeutic targets of hyperthyroidism, including PTPN11, PIK3CD, EGFR, HRAS, PIK3CA, AKT1, SRC, PIK3CB, and PIK3R1. They were mainly enriched in the biological processes of positive regulation of gene expression, positive regulation of MAPK cascade, signal transduction, protein phosphorylation, negative regulation of apoptotic process, positive regulation of protein kinase B signaling and positive regulation of MAP kinase activity; and molecular functions of identical protein binding, protein serine/threonine/tyrosine kinase activity, protein kinase activity, RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding and protein binding. A total of 185 signaling pathways enriched in the 214 common targets were associated with cell proliferation and angiogenesis.

Conclusion

HYD exerts a pharmacological effect on hyperthyroidism via inhibiting pathological angiogenesis in the thyroid and rebalancing immunity.

The Interlinking Metabolic Association between Type 2 Diabetes Mellitus and Cancer: Molecular Mechanisms and Therapeutic Insights

Type 2 diabetes mellitus (T2DM) and cancer share common risk factors including obesity, inflammation, hyperglycemia, and hyperinsulinemia. High insulin levels activate the PI3K/Akt/mTOR signaling pathway promoting cancer cell growth, survival, proliferation, metastasis, and anti-apoptosis. The inhibition of the PI3K/Akt/mTOR signaling pathway for cancer remains a promising therapy; however, drug resistance poses a major problem in clinical settings resulting in limited efficacy of agents; thus, combination treatments with therapeutic inhibitors may solve the resistance to such agents. Understanding the metabolic link between diabetes and cancer can assist in improving the therapeutic strategies used for the management of cancer patients with diabetes and vice versa. This review provides an overview of shared molecular mechanisms between diabetes and cancer as well as discusses established and emerging therapeutic anti-cancer agents targeting the PI3K/Akt/mTOR pathway in cancer management.

Comprehensive next-generation sequencing identifies novel putative pathogenic or likely pathogenic germline variants in patients with concurrent tubo-ovarian and endometrial serous and endometrioid carcinomas or precursors

BACKGROUND

Endometrial serous carcinoma (ESC) and tubo-ovarian high-grade serous carcinoma (HGSC) are characterized by late-stage presentation and high mortality. Current guidelines for prevention recommend risk-reducing salpingo-oophorectomy (RRSO) in patients with hereditary mutations in cancer susceptibility genes. However, HGSC displays extensive genetic heterogeneity with alterations in 168 genes identified in TCGA study, but current germline testing panels are often limited to the handful of recurrently mutated genes, leaving families with rare hereditary gene mutations potentially at-risk.

OBJECTIVE

To determine if there are rare germline mutations that may aid in early identification of more patients at-risk for ESC and/or HGSC by evaluating patients with concurrent ESC, HGSC or precursor lesions, and endometrial atypical hyperplasia (CAH) or low-grade endometrial endometrioid adenocarcinoma (LGEEA).

METHODS

We performed targeted next-generation sequencing using TSO 500, a 523 gene panel, on formalin-fixed paraffin-embedded tumor and matched benign non-tumor tissue blocks from 5 patients with concurrent ESC, HGSC or precursor lesions, and CAH or LGEEA.

RESULTS

We identified germline pathogenic, likely pathogenic or uncertain significance variants in cancer susceptibility genes in 4 of 5 patients - affected genes included GLI1, PIK3R1, FOXP1, FANCD2, INPP4B and H3F3C. Notably, none of these genes were included in the commercially available germline testing panels initially used to evaluate the patients at the time of their diagnoses.

CONCLUSION

Comprehensive germline testing of patients with concurrent LGEEA or CAH and ESC, HGSC or precursor lesions may aid in early identification of relatives at-risk for cancer who may be candidates for RRSO with hysterectomy.

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.

Illuminating Genetic Diversity and Selection Signatures in Matou Goats through Whole-Genome Sequencing Analysis

(1) Background: Matou goats, native to Hunan and Hubei provinces in China, are renowned for their exceptional meat and skin quality. However, a comprehensive whole-genome-based exploration of the genetic architecture of this breed is scant in the literature. (2) Methods: To address this substantial gap, we used whole-genome sequences of 20 Matou goats and compared them with published genomic data of 133 goats of different breeds across China. This comprehensive investigation sought to assess genetic diversity, population structure, and the presence of genomic selection signals. (3) Results: The whole genome of Matou goat populations yielded a substantial catalog of over 19 million single nucleotide polymorphisms (SNPs), primarily distributed within intergenic and intron regions. The phylogenetic tree analysis revealed distinct clades corresponding to each goat population within the dataset. Notably, this analysis positioned Matou goats in a closer genetic affinity with Guizhou White goats, compared to other recognized goat breeds. This observation was corroborated by principal component analysis (PCA) and admixture analysis. Remarkably, Matou goats exhibited diminished genetic diversity and a notable degree of inbreeding, signifying a reduced effective population size. Moreover, the study employed five selective sweep detection methods (including PI, CLR, PI-Ratio, Fst, and XP-EHH) to screen top signal genes associated with critical biological functions, encompassing cardiomyocytes, immunity, coat color, and meat quality. (4) Conclusions: In conclusion, this study significantly advances our understanding of the current genetic landscape and evolutionary dynamics of Matou goats. These findings underscore the importance of concerted efforts in resource conservation and genetic enhancement for this invaluable breed.

Transcriptome sequencing and bioinformatics analysis of gastrocnemius muscle in type 2 diabetes mellitus rats

OBJECTIVE

Type 2 diabetes mellitus (T2DM) is one of the high risk factors for sarcopenia. However, the pathogenesis of diabetic sarcopenia has not been fully elucidated. This study obtained transcriptome profiles of gastrocnemius muscle in normal and T2DM rats based on high-throughput sequencing technology, which may provide new ideas for exploring the pathogenesis of diabetic sarcopenia.

METHODS

Twelve adult male Sprague-Dawley rats were randomly divided into Control group and T2DM group, and gastrocnemius muscle tissue was retained for transcriptome sequencing and real-time quantitative polymerase chain reaction (qRT-PCR) 6 months later. Screening differentially expressed genes (DEGs), Cluster analysis, gene ontology (GO) functional annotation analysis and Kyoto Encyclopedia of Genes and Gnomes (KEGG) functional annotation and enrichment analysis were performed for DEGs. Six DEGs related to apoptosis were selected for qTR-PCR verification.

RESULTS

Transcriptomic analysis showed that there were 1016 DEGs between the gastrocnemius muscle of T2DM and normal rats, among which 665 DEGs were up-regulated and 351 DEGs were down-regulated. GO analysis showed that the extracellular matrix organization was the most enriched in biological processes, with 26 DEGs. The extracellular matrix with 35 DEGs was the most abundant cellular component. The extracellular matrix structural constituent, with 26 DEGs, was the most enriched in molecular functions. The highest number of DEGs enriched in biological processes, cellular components and molecular functions were positive regulation of transcription by RNA polymerase II, nucleus and metal ion binding, respectively. There were 78, 230 and 89 DEGs respectively. KEGG pathway enrichment analysis showed that ECM-receptor interaction, PI3K-Akt signaling pathway and TGF-β signaling pathway(p < 0.001) had higher enrichment degree and number of DEGs. qRT-PCR results showed that the fold change of Map3k14, Atf4, Pik3r1, Il3ra, Gadd45b and Bid were 1.95, 3.25, 2.97, 2.38, 0.43 and 3.6, respectively. The fold change of transcriptome sequencing were 3.45, 2.21, 2.59, 5.39, 0.49 and 2.78, respectively. The transcriptional trends obtained by qRT-PCR were consistent with those obtained by transcriptome sequencing.

CONCLUSIONS

Transcriptomic analysis was used to obtain the "gene profiles" of gastrocnemius muscle of T2DM and normal rats. qRT-PCR verification showed that the genes related to apoptosis were differentially expressed. These DEGs and enrichment pathways may provide new ideas for exploring the pathogenesis of diabetic sarcopenia.

Role of MARK2 in the nervous system and cancer

Microtubule-Affinity Regulating Kinase 2 (MARK2), a member of the serine/threonine protein kinase family, phosphorylates microtubule-associated proteins, playing a crucial role in cancer and neurodegenerative diseases. This kinase regulates multiple signaling pathways, including the WNT, PI3K/AKT/mTOR (PAM), and NF-κB pathways, potentially linking it to cancer and the nervous system. As a crucial regulator of the PI3K/AKT/mTOR pathway, the loss of MARK2 inhibits the growth and metastasis of cancer cells. MARK2 is involved in the excessive phosphorylation of tau, thus influencing neurodegeneration. Therefore, MARK2 emerges as a promising drug target for the treatment of cancer and neurodegenerative diseases. Despite its significance, the development of inhibitors for MARK2 remains limited. In this review, we aim to present detailed information on the structural features of MARK2 and its role in various signaling pathways associated with cancer and neurodegenerative diseases. Additionally, we further characterize the therapeutic potential of MARK2 in neurodegenerative diseases and cancer, and hope to facilitate basic research on MARK2 and the development of inhibitors targeting MARK2.

A review and analysis of key biomarkers in Alzheimer's disease

Alzheimer's disease (AD) is a progressive neurodegenerative disorder that affects over 50 million elderly individuals worldwide. Although the pathogenesis of AD is not fully understood, based on current research, researchers are able to identify potential biomarker genes and proteins that may serve as effective targets against AD. This article aims to present a comprehensive overview of recent advances in AD biomarker identification, with highlights on the use of various algorithms, the exploration of relevant biological processes, and the investigation of shared biomarkers with co-occurring diseases. Additionally, this article includes a statistical analysis of key genes reported in the research literature, and identifies the intersection with AD-related gene sets from databases such as AlzGen, GeneCard, and DisGeNet. For these gene sets, besides enrichment analysis, protein-protein interaction (PPI) networks utilized to identify central genes among the overlapping genes. Enrichment analysis, protein interaction network analysis, and tissue-specific connectedness analysis based on GTEx database performed on multiple groups of overlapping genes. Our work has laid the foundation for a better understanding of the molecular mechanisms of AD and more accurate identification of key AD markers.