Probable Molecular Mechanisms Research Articles

System biology-based assessment of the molecular mechanism of IMPHY000797 in Parkinson’s disease: a network pharmacology and in-silico evaluation

IMPHY000797 derivatives have been well known for their efficacy in various diseases. Moreover, IMPHY000797 derivatives have been found to modulate such genes involved in multiple neurological disorders. Hence, this study seeks to identify such genes and the probable molecular mechanism that could be involved in the pathogenesis of Parkinson’s disease. The study utilized various biological tools such as DisGeNET, STRING, Swiss target predictor, Cytoscape, AutoDock 4.2, Schrodinger suite, ClueGo, and GUSAR. All the reported genes were obtained using DisGeNET, and further, the common genes were incorporated into the STRING to get the KEGG pathway, and all the data was converted to a protein/pathway network via Cytoscape. The clustering of the genes was performed for the gene-enriched data using two-sided hypergeometrics (p-value). The binding affinity of the IMPHY000797 was verified with the highest regulated 25 proteins via utilizing the “Monte Carlo iterated search technique” and the “Emodel and Glide score” function. Three thousand five hundred eighty-three genes were identified for Parkinson’s disease and 31 genes for IMPHY000797 compound, among which 25 common genes were identified. Further, the “FOXO-signaling pathway” was identified to be a modulated pathway. Among the 25 proteins, the highest modulated genes and highest binding affinity were exhibited by SIRT3, FOXO1, and PPARGC1A with the compound IMPHY000797. Further, rat toxicity analysis provided the efficacy and safety of the compound. The study was required to identify the probable molecular mechanism, which needs more confirmation from other studies, which is still a significant hit-back.

Understanding the molecular basis of anti-fibrotic potential of intranasal curcumin and its association with mitochondrial homeostasis in silica-exposed mice

Silicosis is an occupational disease of the lungs brought in by repeated silica dust exposures. Inhalation of crystalline silica leads to persistent lung inflammation characterized by lung lesions due to granuloma formation. The specific molecular mechanism has not yet been identified, though. The Present study investigated the impact of silica-exposed lung fibrosis and probable molecular mechanisms. Here, Curcumin, derived from Curcuma longa shown to be an effective anti-inflammatory and anti-fibrotic molecule has been taken to investigate its therapeutic efficacy in silica-induced lung fibrosis. An experimental model of silicosis was established in mice where curcumin was administered an hour before intranasal silica exposure every alternate day for 35 days. Intranasal Curcumin treatment reduced silica-induced oxidative stress, inflammation marked by inflammatory cell recruitment, and prominent granuloma nodules along with aberrant collagen repair. Its protective benefits were confirmed by reduced MMP9 activities along with EMT markers (Vimentin and α-SMA). It has restored autophagy and suppressed the deposition of damaged mitochondria after silica exposure. Intranasal Curcumin also inhibited oxidative stress by boosting antioxidant enzyme activities and enhanced Nrf2-Keap1 expressions. Higher levels of PINK1, PARKIN, Cyt-c, P62/SQSTM, and damaged mitochondria in the silicosis group were significantly lowered after curcumin and dexamethasone treatments. Curcumin-induced autophagy resulted in reduced silica-induced mitochondria-dependent apoptosis. We report that intranasal curcumin treatment showed protective properties on pathological features prompted by silica particles, suggesting that the compound may constitute a promising strategy for the treatment of silicosis in the near future.

Sequence of Molecular Events in the Development of Alzheimer's Disease: Cascade Interactions from Beta-Amyloid to Other Involved Proteins.

Alzheimer's disease is the primary neurodegenerative disease affecting the elderly population. Despite the first description of its pathology over a century ago, its precise cause and molecular mechanism remain unknown. Numerous factors, including beta-amyloid, tau protein, the APOEε4 gene, and different metals, have been extensively investigated in relation to this disease. However, none of them have been proven to have a decisive causal relationship. Furthermore, no single theory has successfully integrated these puzzle pieces thus far. In this review article, we propose the most probable molecular mechanism for AD, which clearly shows the relationship between the main aspects of the disease, and addresses fundamental questions such as: Why is aging the major risk factor for the disease? Are amyloid plaques and tau tangles the causes or consequences of AD? Why are the distributions of senile plaques and tau tangles in the brain different and independent of each other? Why is the APOEε4 gene a risk factor for AD? Finally, why is the disease more prevalent in women?

Sercocephalous latifolius fruit attenuates aluminum chloride-induced oxidative stress and neurotoxicity in Drosophila melanogaster via Drn1 regulation of the IMD signaling pathway

IntroductionAlzheimer disease (AD) is a form of dementia that is a heterogeneous dysfunction of various pathophysiological features. Its morphological characteristics consist of tau aggregates and amyloid plaques. The need for novel therapy in the treatment of AD is required. Hence use of antioxidant, natural products are widely employed for the management and treatment of AD and other neurodegenerative diseases. However, there are still a lot of limitations. Sercocephalous latifolius fruit (SLF) is also known as the African peach and has numerous well-being-endorsing advantages. The Chinese name of SLF is Feizhou hong tao, while the Nigeria (Yoruba) name is Eso Gberesi. It can be grown all over the world. SLF has anti-neurodegenerative properties, however, there is a lack of evidence on their probable molecular mechanism for novel therapeutic properties. Investigations have been conducted on the SFL which shows its medicinal capability, but its ability to attenuate neurodegenerative diseases such as AD is yet to be fully elucidated, and the molecular signally pathways whichmay serve as a therapeutic target. MethodsThe modulatory effect of SLF on aluminum chloride-induced neurotoxicity and oxidative stress in Drosophila melanogaster via Defense repressor-1 (Drn1) regulation of immune deficiency (Imd) signaling pathway which may be a useful therapeutic target. D. melanogaster was divided into nine groups. Group 1 served as the basal control as they were fed with a normal basal diet, group 2 served as the negative control as they were fed with Basal Diet and 0.5 ml of aluminum/100 ml distilled water, group 3 served as the positive control as they were fed with basal diet 0.5 ml aluminum chloride/100 ml distilled water and Garlic acid, group 4 and 5 were fed with basal diet and 0.1 and 1 % SLF respectively, group 6 and 7 were fed with basal diet, aluminum chloride and 0.1 and 1.0 % respectively, group 8 and 9 were fed with basal diet, garlic acid, aluminum chloride and 0.1 and 1.0 % SLF respectively. All the groups were left for seven days. The experiment was conducted for 3 months, and the fruit flies were changed every 5 days. ResultsSuperoxide dismutase, catalase, malondialdehyde, and nitric oxide enzymatic enzymes were assayed. However, the relative expression of Defense repressor-1 was also determined both in vitro and on aluminum-induced neurodegenerative D. melanogaster tissue. A significant increase was observed in the catalase when 0.1 % and 1 % were compared, it could be inferred that the extract proved effective at low concentrations, since its highest antioxidant potential was observed at low concentrations. The results revealed decrease in the activity of malondialdehyde, superoxide dismutase, and nitric oxide biological enzymes in the test groups. There was upregulation of Defense repressor -1 in groups 3, 4, 5, and 6, when compared with the positive and negative control, respectively. DiscussionThe result provides evidence that SLF has the potential of upregulating defense repressor genes and modulating biological antioxidant enzymes, which could be further exploited to fully understand the underlying molecular mechanisms responsible for the attenuation of neurotoxicity, oxidative stress, and neurodegenerative diseases such as AD. The results suggest that SLF may be useful as a therapeutic target in AD and other neurodegenerative diseases

Mechanisms of low nighttime temperature promote oil accumulation in Brassica napus L. based on in-depth transcriptome analysis.

Rape (Brassica napus L.; AACC) is an important oil-bearing crop worldwide. Temperature significantly affects the production of oil crops; however, the mechanisms underlying temperature-promoted oil biosynthesis remain largely unknown. In this study, we found that a temperature-sensitive cultivar (O) could accumulate higher seed oil content under low nighttime temperatures (LNT,13°C) compared with a temperature-insensitive cultivar (S). We performed an in-depth transcriptome analysis of seeds from both cultivars grown under different nighttime temperatures. We found that low nighttime temperatures induced significant changes in the transcription patterns in the seeds of both cultivars. In contrast, the expression of genes associated with fatty acid and lipid pathways was higher in the O cultivar than in the S cultivar under low nighttime temperatures. Among these genes, we identified 14 genes associated with oil production, especially BnLPP and ACAA1, which were remarkably upregulated in the O cultivar in response to low nighttime temperatures compared to S. Further, a WGCNA analysis and qRT-PCR verification revealed that these genes were mainly regulated by five transcription factors, WRKY20, MYB86, bHLH144, bHLH95, and NAC12, whose expression was also increased in O compared to S under LNT. These results allowed the elucidation of the probable molecular mechanism of oil accumulation under LNT conditions in the O cultivar. Subsequent biochemical assays verified that BnMYB86 transcriptionally activated BnLPP expression, contributing to oil accumulation. Meanwhile, at LNT, the expression levels of these genes in the O plants were higher than at high nighttime temperatures, DEGs (SUT, PGK, PK, GPDH, ACCase, SAD, KAS II, LACS, FAD2, FAD3, KCS, KAR, ECR, GPAT, LPAAT, PAP, DGAT, STERO) related to lipid biosynthesis were also upregulated, most of which are used in oil accumulation.

Akkermansia muciniphila - A Potential Next-generation Probiotic for Non-alcoholic Fatty Liver Disease.

Nonalcoholic fatty liver disease (NAFLD) is a spectrum of liver conditions, and its growing prevalence is a serious concern worldwide, especially in Western countries. Researchers have pointed out several genetic mutations associated with NAFLD; however, the imbalance of the gut microbial community also plays a critical role in the progression of NAFLD. Due to the lack of approved medicine, probiotics gain special attention in controlling metabolic disorders like NAFLD. Among these probiotics, Akkermansia muciniphila (a member of natural gut microflora) is considered one of the most efficient and important bacterium in maintaining gut health, energy homeostasis, and lipid metabolism. In this perspective, we discussed the probable molecular mechanism of A. muciniphila in controlling the progression of NAFLD and restoring liver health. The therapeutic potential of A. muciniphila in NAFLD has been tested primarily on animal models, and thus, more randomized human trials should be conducted to prove its efficacy.

CPLX2 is a novel tumor suppressor and improves the prognosis in glioma.

Glioma is a type of malignant cancer that affect the central nervous system. New predictive biomarkers have been investigated in recent years, but the clinical prognosis for glioma remains poor. The function of CPLX2 in glioma and the probable molecular mechanism of tumor suppression were the focus of this investigation. The glioma transcriptome profile was downloaded from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) databases for analysis of CPLX2 expression in glioma. RT-qPCR was performed to detect the expression of CPLX2 in 68 glioma subjects who have been followed up. Kaplan-Meier survival analyses were conducted to assess the effect of CPLX2 on the prognosis of glioma patients. The knockdown and overexpressed cell lines of CPLX2 were constructed to investigate the impact of CPLX2 on glioma. The cell growth, colony formation, and tumor formation in xenograft were performed. The expression of CPLX2 was downregulated in glioma and was negatively correlated with the grade of glioma. The higher expression of CPLX2 predicted a longer survival, as indicated by the analysis of Kaplan-Meier survival curves. Overexpressed CPLX2 impaired tumorigenesis in glioma progression both in vivo and in vitro. Knocking down CPLX2 promoted the proliferation of glioma cells. The analysis of GSEA and co-expression analysis revealed that CPLX2 may affect the malignancy of glioma by regulating the hypoxia and inflammation pathways. Our data indicated that CPLX2 functions as a tumor suppressor and could be used as a potential prognostic marker in glioma.

System biology mediated assessment of molecular mechanism for sinapic acid against breast cancer: via network pharmacology and molecular dynamic simulation

Sinapic acid is a hydroxycinnamic acid widespread in the plant kingdom, known to be a potent anti-oxidant used for the treatment of cancer, infections, oxidative stress, and inflammation. However, the mode of action for its chemotherapeutic properties has yet not been unleashed. Hence, we aimed to identify potential targets to propose a possible molecular mechanism for sinapic acid against breast cancer. We utilized multiple system biology tools and databases like DisGeNET, DIGEP-Pred, Cytoscape, STRING, AutoDock 4.2, AutoDock vina, Schrodinger, and gromacs to predict a probable molecular mechanism for sinapic acid against breast cancer. Targets for the disease breast cancer, were identified via DisGeNET database which were further matched with proteins predicted to be modulated by sinapic acid. In addition, KEGG pathway analysis was used to identify pathways; a protein-pathway network was constructed via Cytoscape. Molecular docking was performed using three different algorithms followed by molecular dynamic simulations and MMPBSA analysis. Moreover, cluster analysis and gene ontology (GO) analysis were performed. A total of 6776 targets were identified for breast cancer; 95.38% of genes predicted to be modulated by sinapic acid were common with genes of breast cancer. The ‘Pathways in cancer’ was predicted to be modulated by most umber of proteins. Further, PRKCA, CASP8, and CTNNB1 were predicted to be the top 3 hub genes. In addition, molecular docking studies revealed CYP3A4, CYP1A1, and SIRT1 to be the lead proteins identified from AutoDock 4.2, AutoDock Vina, and Schrodinger suite Glide respectively. Molecular dynamic simulation and MMPBSA were performed for the complex of sinapic acid with above mentioned proteins which revealed a stable complex throughout simulation. The predictions revealed that the mechanism of sinapic acid in breast cancer may be due to regulation of multiple proteins like CTNNB1, PRKCA, CASP8, SIRT1, and cytochrome enzymes (CYP1A1 & CYP3A4); the majorly regulated pathway was predicted to be ‘Pathways in cancer’. This indicates the rationale for sinapic acid to be used in the treatment of breast cancer. However, these are predictions and need to be validated and looked upon in-depth to confirm the exact mechanism of sinapic acid in the treatment of breast cancer; this is future scope as well as a drawback of the current study.

Exploratory research on the probable shared molecular mechanism and transcription factors between chronic periodontitis and chronic obstructive pulmonary disease.

To investigate possible cross-talk genes, associated pathways, and transcription factors between chronic periodontitis (CP) and chronic obstructive pulmonary disease (COPD). The gene expression profiles of CP (GSE10334 and GSE16134) and COPD (GSE76925) were downloaded from the GEO database. Differential expression and functional clustering analyses were performed. The protein‑protein interaction (PPI) network was constructed. The core cross-talk genes were filtered using four topological analysis algorithms and modular segmentation. Then, functional clustering analysis was performed again. GSE10334 detected 164 differentially expressed genes (DEGs) (119 upregulated and 45 downregulated). GSE16134 identified 208 DEGs (154 upregulated and 54 downregulated). GSE76925 identified 1 408 DEGs (557 upregulated and 851 downregulated). The PPI network included 21 nodes and 20 edges. The final screening included seven cross-talk genes: CD79A, FCRLA, CD19, IRF4, CD27, SELL, and CXCL13. Relevant pathways included primary immunodeficiency, the B-cell receptor signaling pathway, and cytokine-cytokine receptor interaction. This study indicates the probability of shared pathophysiology between CP and COPD, and their cross-talk genes, associated pathways, and transcription factors may offer novel concepts for future mechanistic investigations.

Multivalent Dynamic Colocalization of Avian Influenza Polymerase and Nucleoprotein by Intrinsically Disordered ANP32A Reveals the Molecular Basis of Human Adaptation.

Adaptation of avian influenza RNA polymerase (FluPol) to human cells requires mutations on the 627-NLS domains of the PB2 subunit. The E627K adaptive mutation compensates a 33-amino-acid deletion in the acidic intrinsically disordered domain of the host transcription regulator ANP32A, a deletion that restricts FluPol activity in mammalian cells. The function of ANP32A in the replication transcription complex and in particular its role in host restriction remains poorly understood. Here we characterize ternary complexes formed between ANP32A, FluPol, and the viral nucleoprotein, NP, supporting the putative role of ANP32A in shuttling NP to the replicase complex. We demonstrate that while FluPol and NP can simultaneously bind distinct linear motifs on avian ANP32A, the deletion in the shorter human ANP32A blocks this mode of colocalization. NMR reveals that NP and human-adapted FluPol, containing the E627 K mutation, simultaneously bind the identical extended linear motif on human ANP32A in an electrostatically driven, highly dynamic and multivalent ternary complex. This study reveals a probable molecular mechanism underlying host adaptation, whereby E627K, which enhances the basic surface of the 627 domain, is selected to confer the necessary multivalent properties to allow ANP32A to colocalize NP and FluPol in human cells.

PAK4 inhibition significantly potentiates Gemcitabine activity in PDAC cells via inhibition of Wnt/β-catenin, p-ERK/MAPK and p-AKT/PI3K pathways

Pancreatic Ductal Adenocarcinoma (PDAC) remains one of the most difficult to treat cancers. Gemcitabine is still the standard of care treatment for PDAC but with modest survival benefit and well reported resistance. Here we explored potential of inhibiting p21 activated kinase 4 (PAK4), a downstream protein of KRAS oncogenic pathway, in combination with Gemcitabine in PDAC cells. PAK4 inhibition by KPT-9274 led to significant potentiation of Gemcitabine activity in PDAC cells, with an increase in apoptosis, DNA damage and cell cycle arrest. At molecular level, PAK4 inhibition dose dependently inhibited Gemcitabine-induced β-catenin, c-JUN and Ribonucleotide Reductase subunit 2 (RRM2) levels. PAK4 inhibition further inhibited levels of phosphorylated ERK (p-ERK); Gemcitabine-induced phosphorylated AKT (p-AKT), phosphorylated and total c-Myc. These results suggest possible role of β-catenin, p-ERK and p-AKT, key effector proteins of Wnt/β-catenin, MAPK and PI3K pathways respectively, in sensitisation of Gemcitabine activity with PAK4 inhibition. Our data unravel probable molecular mechanisms behind combination of PAK4 inhibition with Gemcitabine to counter PDAC, which may be unequivocally proved further with knock down of PAK4. Our findings provide a strong rationale to exploit the combination therapy of Gemcitabine and PAK4 inhibitor for PDAC at pre-clinical and clinical levels.

Bioinformatics Research and qRT-PCR Verify Hub Genes and a Transcription Factor-MicroRNA Feedback Network in Intervertebral Disc Degeneration.

The present study explores the potentials of bioinformatics analysis to identify hub genes linked to intervertebral disc degeneration (IDD) and explored the potential molecular mechanism of transcription factor-microRNA regulatory network. Furthermore, the hub genes were identified through quantitative reverse transcriptase PCR (qRT-PCR). GEO database expression profile datasets for candidate genes (GSE124272) were downloaded. Genes that were differentially expressed (DEGs) were detected utilizing limma technique in the R programming language. Search Tool for the Retrieval of Interacting Genes/Proteins and NetworkAnalyst software identified hub genes. The Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis as well as Gene Ontology annotation of the DEGs were performed using Metascape. Using Bioinformatics data from the TRRUST, StarBase, and TransmiR databases, a TF-miRNA-hub genes network was constructed. qRT-PCR was utilized to confirm the result. As compared to healthy persons, 521 DEGs, comprising 203 down-regulated and 318 up-regulated genes, as well as 7 core genes, were found in people with IDD. Analysis revealed that all seven essential genes were under-expressed. qRT-PCR further confirmed the low expression of these seven important genes. Based on the TRRUST database, 16 TFs that could target five junction genes were then predicted. According to the StarBase database, four miRNAs were linked to crucial genes, while the TransmiR database predicted regulatory connections between four miRNAs and five TFs. The expression of the TP53-(hsa-miR-183-5p)-CCNB1 TF-miRNA-mRNA interaction network was discovered to be correlated with IDD. Throughout this investigation, a network of TF-miRNA-mRNA connections was built for investigation of the probable molecular mechanisms responsible for IDD. The identification of hub genes associated with IDD may reveal promising IDD treatment strategies.

Polystyrene microplastics disrupt female reproductive health and fertility via sirt1 modulation in zebrafish (Danio rerio)

Microplastics (MPs) pollution poses an emerging threat to aquatic biota, which could hinder their physiological processes. Recently various evidence has demonstrated the toxic impacts of MPs on cellular and organismal levels, but still, the underlying molecular mechanism behind their toxicity remains ambiguous. The hypothalamic-pituitary-gonadal (HPG) axis regulates the synthesis and release of sex steroid hormones, and SIRT1 plays a vital role in this process. The current study aimed to elucidate the harmful effects of MPs on female reproduction via SIRT1 modulation. Healthy female zebrafish were exposed to different concentrations (50 and 500 µg/L) of polystyrene microplastics (PS-MPs). The results revealed a significant change in the gonadosomatic index (GSI) after exposure to PS-MPs. In addition, the decreased fecundity rate displayed an evident dosage effect, indicating that exposure to PS-MPs causes deleterious effects on fertilization. Furthermore, significantly enhanced levels of reactive oxygen species (ROS) and apoptotic signals through the TUNEL assay were evaluated in different treated groups. Moreover, morphological alterations in the gonads of zebrafish exposed to MPs were also observed through H&E staining. The subsequent change in plasma steroid hormone levels (E2/T ratio) showed an imbalance in hormonal homeostasis. Meanwhile, to follow PS-MPs’ effects on the HPG axis via SIRT1 modulation and gene expression related to steroidogenesis, SIRT1/p53 pathway was evaluated through qPCR. The altered transcription levels of genes indicated the plausible interference of PS-MPs on the HPG axis function. Our in-silico molecular docking study proves that PS-MPs efficiently bind and inhibit endocrine receptors and SIRT1. Thus, these findings add to our understanding of the probable molecular mechanisms of reproductive impairment caused by PS-MPs in zebrafish.

Construction of the Interaction Network of Hub Genes in the Progression of Barrett's Esophagus to Esophageal Adenocarcinoma.

Esophageal adenocarcinoma (EAC) is one of the histologic types of esophageal cancer with a poor prognosis. The majority of EAC originate from Barrett's esophagus (BE). There are few studies focusing on the dynamic progression of BE to EAC. R software was used to analyze differentially expressed genes (DEGs) based on RNA-seq data of 94 normal esophageal squamous epithelial (NE) tissues, 113 BE tissues and 147 EAC tissues. The overlapping genes of DEGs between BE and EAC were analyzed by Venn diagram tool. The hub genes were selected by Cytoscape software based on the protein-protein interaction network of the overlapping genes using STRING database. The functional analysis of hub genes was performed by R software and the protein expression was identified by immunohistochemistry. In the present study, we found a large degree of genetic similarity between BE and EAC, and further identified seven hub genes (including COL1A1, TGFBI, MMP1, COL4A1, NID2, MMP12, CXCL1) which were all progressively upregulated in the progression of NE-BE-EAC. We have preliminarily uncovered the probable molecular mechanisms of these hub genes in disease development and constructed the ceRNA regulatory network of hub genes. More importantly, we explored the possibility of hub genes as biomarkers in the disease progression of NE-BE-EAC. For example, TGFBI can be used as biomarkers to predict the prognosis of EAC patients. COL1A1, NID2 and COL4A1 can be used as biomarkers to predict the response to immune checkpoint blockade (ICB) therapy. We also constructed a disease progression risk model for NE-BE-EAC based on CXCL1, MMP1 and TGFBI. Finally, the results of drug sensitivity analysis based on hub genes showed that drugs such as PI3K inhibitor TGX221, bleomycin, PKC inhibitor Midostaurin, Bcr-Abl inhibitor Dasatinib, HSP90 inhibitor 17-AAG, and Docetaxel may be potential candidates to inhibit the progression of BE to EAC. This study is based on a large number of clinical samples with high credibility, which is useful for revealing the probable carcinogenic mechanism of BE to EAC and developing new clinical treatment strategies.

Network pharmacology and molecular modelling study of Enhydra fluctuans for the prediction of the molecular mechanisms involved in the amelioration of nephrolithiasis

In view of the ethno medicinal use of Enhydra fluctuans for the treatment of kidney stones; the present study aimed to elucidate the molecular mechanisms involved in the amelioration of nephrolithiasis through a network pharmacology approach. The phytoconstituents were queried in DIGEP-Pred to identify the regulated proteins. The modulated proteins were then enriched in the STRING to predict the protein-protein interactions and the probably regulated pathways were traced in the Kyoto Encyclopedia of Genes and Genomes. Further, the network was constructed using Cytoscape ver 3.5.1. Results showed that β-carotene was found to be regulating maximum targets i.e. 26. In addition, 63 proteins were triggered by the components in which the vitamin D receptor was targeted by the maximum phytoconstituents i.e. 16. The enrichment analysis identified the regulation of 67 pathways in which fluid shear stress and atherosclerosis-associated pathways (KEGG entry hsa05418) regulated ten genes. Further, protein kinase C-α was traced in 23 different pathways. In addition, the majority of the regulated genes were identified from the extracellular space via the modulation of 43 genes. Also, nuclear receptor activity had the maximum molecular function via the regulation of 7 genes. Likewise, the response to organic substance was predicted to trigger the top genes i.e. 43. In contrast, Stigmasterol, Baicalein-7-o-glucoside, and Kauran-16-ol were found to have a high affinity to bind with the VDR receptor confirmed by the molecular modelling and the dynamics. Hence, the study elucidated the probable molecular mechanisms of E. fluctuans in managing nephrolithiasis and identified the lead molecules, their targets, and possible pathways. Communicated by Ramaswamy H. Sarma

MicroRNA-210-3p mediates trabecular meshwork extracellular matrix accumulation and ocular hypertension – Implication for novel glaucoma therapy

Elevation of intraocular pressure (IOP) is a major, controllable risk factor of primary open-angle glaucoma (POAG). Transforming growth factor-β2 (TGF-β2)-induced excessive accumulation of extracellular matrix (ECM) in the trabecular meshwork (TM) has been demonstrated to contribute significantly to the development of high IOP. We previously showed that treatment with salidroside (Sal), a plant-derived glucoside, can ameliorate the TGF-β2-induced ECM expression in cultured human TM cells and reduce TGF-β2-induced ocular hypertension in mice. In the current study, its underlying molecular mechanism associated with microRNA-210–3p (miR-210–3p) was characterized. We discovered that, in TM tissues of POAG patients, there was an increase in miR-210–3p. And miR-210–3p mediated a portion of the pathological effects of TGF-β2 in vitro (excessive accumulation of ECM in cultured human TM cells) and in vivo (mouse ocular hypertension and ECM accumulation in the TM). Most interestingly, miR-210–3p was down-regulated by Sal, which appeared to mediate a significant portion of its IOP-lowering effect. Thus, these results shed light on the probable molecular mechanisms of TGF-β2 and Sal and indicate that manipulation of miR-210–3p level/activity represents a potential new therapeutic strategy for POAG.

SLC22A3 methylation-mediated gene silencing predicts adverse prognosis in acute myeloid leukemia

BackgroundWe screened out several hypermethylated solute carrier (SLC) family genes in acute myeloid leukemia by reduced representation bisulfite sequencing. SLC22A3 encodes an organic cation transport protein, which is critical for drug transportation and cellular detoxification. SLC22A3 is significantly downregulated and associated with tumor progression and worse prognosis in a variety of solid tumors. However, there are no data available regarding the role of SLC22 in AML. This study aimed to explore the regulatory mechanism of DNA methylation on SLC22A3 expression, as well as its clinical significance in AML prognosis.ResultsSLC22A3 was identified as the sole prognosis-associated gene among SLCs based on TCGA and Beat AML databases. Bone marrow mononuclear cells (BMMNCs) from AML, MDS patients, and healthy donors were enrolled in this study. SLC22A3 methylation was significantly increased in AML compared with controls and MDS patients; meanwhile, the expression level of SLC22A3 was decreased. SLC22A3 hypermethylation presented an obvious association with some specific clinical characteristics and affected the survival time of AML patients as an independent risk indicator. SLC22A3 expression changed regularly as the disease complete remissions and relapses. Demethylation drug 5-aza-2′-deoxycytidine (DAC) activated transcription and increased mRNA expression of SLC22A3 in leukemia cell lines and AML fresh BMMNCs. Knockdown of SLC22A3 in leukemia cells enhanced cell proliferation and suppressed cell apoptosis. Data from public programs were used for auxiliary screening of probable molecular mechanisms of SLC22A3 in the antileukemia effect.ConclusionsOur results showed that increased methylation and decreased expression of SLC22A3 may be indicators of poor prognosis in AML. Methylation-silenced SLC22A3 expression may have potential guiding significance on antileukemia effect of DAC.

Photobiomodulation activates the PI3K/AKT pathway in diabetic fibroblast cells in vitro.

Photobiomodulation (PBM) has been known to facilitate the healing of numerous ailments including diabetic wounds. PBM is not broadly acknowledged largely due to scepticism regarding its mechanism of action, including the specific molecular targets and the effects rendered at a tissue, cellular and molecular level. Diabetes mellitus (DM) reduces cellular signalling, including the phosphatidylinositol 3 kinase/protein kinase B (PI3K/AKT) signalling pathway that is critical during wound healing. In DM, wound chronicity is common and may lead to non-traumatic limb amputation. This study investigated the hypothesis that PBM at 660nm activates PI3K/AKT and downstream signalling proteins in fibroblast cells in vitro. Cells were incubated for 24 and 48h after PBM (660nm and 5J/cm2), followed by evaluation of activated PI3K/AKT and downstream mammalian target of rapamycin (mTOR) and glycogen synthase kinase-3 beta (GSK3β) signalling proteins using western blotting and ELISA. Irradiated cell models displayed increased activation of PI3K/AKT and downstream mTOR and GSK3β signalling proteins. Our findings suggest that the therapeutic effects of PBM in stressed cells are through activation of the PI3K/AKT cell signalling pathway and downstream GSK3β and mTOR signalling proteins. This study provides a novel understanding into one of the probable molecular mechanisms in which PBM at a wavelength of 660nm (5J/cm2) enhances therapeutic activities in diabetic wound healing.

Dissection of transcriptome dysregulation and immune characterization in women with germline BRCA1 mutation at single-cell resolution

BackgroundHigh-grade serous carcinoma (HGSC) is the most frequent and lethal type of ovarian cancer. It has been proposed that tubal secretory cells are the origin of ovarian HGSC in women with familial BRCA1/2 mutations. However, the molecular changes underlying malignant transformation remain unknown.MethodWe performed single-cell RNA and T cell receptor sequencing of tubal fimbriated ends from 3 BRCA1 germline mutation carriers (BRCA1 carriers) and 3 normal controls with no high-risk history (non-BRCA1 carriers).ResultsExploring the transcriptomes of 19,008 cells, predominantly from BRCA1+ samples, we identified 5 major cell populations in the fallopian tubal mucosae. The secretory cells of BRCA1+ samples had differentially expressed genes involved in tumor growth and regulation, chemokine signaling, and antigen presentation compared to the wild-type BRCA1 controls. There are several novel findings in this study. First, a subset of the fallopian tubal secretory cells from one BRCA1 carrier exhibited an epithelial-to-mesenchymal transition (EMT) phenotype, which was also present in the mucosal fibroblasts. Second, we identified a previously unreported phenotypic split of the EMT secretory cells with distinct evolutionary endpoints. Third, we observed increased clonal expansion among the CD8+ T cell population from BRCA1+ carriers. Among those clonally expanded CD8+ T cells, PD-1 was significantly increased in tubal mucosae of BRCA1+ patients compared with that of normal controls, indicating that T cell exhaustion may occur before the development of any premalignant or malignant lesions.ConclusionThese results indicate that EMT and immune evasion in normal-looking tubal mucosae may represent early events leading to the development of HGSC in women with BRCA1 germline mutation. Our findings provide a probable molecular mechanism explaining why some, but not all, women with BRCA1 germline mutation present with early development and rapid dissemination of HGSC.

DEHP induces ferroptosis in testes via p38α-lipid ROS circulation and destroys the BTB integrity

Exposure to Di (2-ethylhexyl) phthalate (DEHP) has been associated with toxic effects of the reproductive system. However, the exact mechanism remains to be elucidated. In this study we explored the testicular toxicity induced by DEHP, and the probable molecular mechanism in the process. In vivo, the results demonstrated that DEHP affected testosterone levels and blood-testosterone barrier (BTB) integrity and caused ferroptosis. We further demonstrated that DEHP up-regulated the expression of p38α, p-p38α, p53, p-p53, SAT1, ALOX15. This view has also been confirmed in TM4 cells. After pre-treatment with fer-1 or si-MAPK14, the expression of either p53, p-p53, SAT1 and ALOX15 up-regulated by MEHP was inhibited in vitro. Interestingly, p38α can prevent the accumulation of lipid ROS, and the production of lipid ROS in turn promoted the expression of p38α, thus forming a feedback loop during the ferroptosis. In this process, a vicious cycle consisting of p38α, p53, SAT1, ALOX15, lipid ROS was involved. This study provides new mechanistic insights into DEHP-induced toxicity of the reproductive system.