Marker Genes Research Articles

Vulnerability of Antioxidant Drug Therapies on Targeting the Nrf2-Trp53-Jdp2 Axis in Controlling Tumorigenesis

Control of oxidation/antioxidation homeostasis is important for cellular protective functions, and disruption of the antioxidation balance by exogenous and endogenous ligands can lead to profound pathological consequences of cancerous commitment within cells. Although cancers are sensitive to antioxidation drugs, these drugs are sometimes associated with problems including tumor resistance or dose-limiting toxicity in host animals and patients. These problems are often caused by the imbalance between the levels of oxidative stress-induced reactive oxygen species (ROS) and the redox efficacy of antioxidants. Increased ROS levels, because of abnormal function, including metabolic abnormality and signaling aberrations, can promote tumorigenesis and the progression of malignancy, which are generated by genome mutations and activation of proto-oncogene signaling. This hypothesis is supported by various experiments showing that the balance of oxidative stress and redox control is important for cancer therapy. Although many antioxidant drugs exhibit therapeutic potential, there is a heterogeneity of antioxidation functions, including cell growth, cell survival, invasion abilities, and tumor formation, as well as the expression of marker genes including tumor suppressor proteins, cell cycle regulators, nuclear factor erythroid 2-related factor 2, and Jun dimerization protein 2; their effectiveness in cancer remains unproven. Here, we summarize the rationale for the use of antioxidative drugs in preclinical and clinical antioxidant therapy of cancer, and recent advances in this area using cancer cells and their organoids, including the targeting of ROS homeostasis.

Reassessment of marker genes in human induced pluripotent stem cells for enhanced quality control

Human induced pluripotent stem cells (iPSCs) have great potential in research, but pluripotency testing faces challenges due to non-standardized methods and ambiguous markers. Here, we use long-read nanopore transcriptome sequencing to discover 172 genes linked to cell states not covered by current guidelines. We validate 12 genes by qPCR as unique markers for specific cell fates: pluripotency (CNMD, NANOG, SPP1), endoderm (CER1, EOMES, GATA6), mesoderm (APLNR, HAND1, HOXB7), and ectoderm (HES5, PAMR1, PAX6). Using these genes, we develop a machine learning-based scoring system, “hiPSCore”, trained on 15 iPSC lines and validated on 10 more. hiPSCore accurately classifies pluripotent and differentiated cells and predicts their potential to become specialized 2D cells and 3D organoids. Our re-evaluation of cell fate marker genes identifies key targets for future studies on cell fate assessment. hiPSCore improves iPSC testing by reducing time, subjectivity, and resource use, thus enhancing iPSC quality for scientific and medical applications.

A-298 A Novel DNA Array Technology to Detect and Discriminate Complex Panels of Microbial Pathogens

Abstract Background UTI (Urinary Tract Infection) is a prototype for the field of polymicrobial testing. Current testing standards suggest that UTI testing may require the Detection and Discrimination of a panel of at least (@24) bacteria and fungi (@2) along with a panel of antibiotic resistance gene (ARG) markers (>12). Today, such analysis of UTI’s at the DNA level can be obtained with predicates such as large-panel qPCR reactions, e.g. the Thermo OpenArray qPCR assembly, or by NGS based microbiomics. The necessary complexity of such polymicrobial testing pushes the content limits of qPCR and, although NGS has substantial capacity to resolve complex mixtures, NGS remains relatively low throughput and requires a level of data processing that exceeds what is practical in some laboratories. Methods We have developed a new technology for UTI testing, “D3 ArrayTM-UTI”, which obviates most of the present limitations of DNA based polymicrobial testing. The process begins with urine being isolated and purified using standard automated magnetic bead DNA sample prep, already in place in most molecular laboratories, at up to 96 samples in parallel. This is followed by a single multiplex, endpoint PCR reaction on each sample, also at up to 96 samples in parallel, then automated room temperature hybridization of the PCR product in a standard 96 well format, onto a single 21x21 D3 Array at the bottom of each well. Dedicated autonomous software analyzes the hybridization data yielding the complete list of microbial pathogens and ARG’s detected in a urine specimen. The first deployment of the D3 Array-UTI test is now available to support analysis of 96 urine samples in 6hrs. The results of such preliminary testing are presented here. Results aLOD analysis has been performed with purified DNA and found to be in the 0.1-10cp/RXN range among the full set of 24 bacterial species and 12 ARG targets. Concordance analysis for bacterial Species Detection and Discrimination has been performed on 235 clinical isolates obtained from collaborators at Mako Medical laboratories (Thermo Openarray as the comparator) which averaged = 97 +/- 5% for all but two species: A urinae (88%) and M morganii (94%). Concordance analysis for Antibiotic Resistance Gene Detection and Discrimination has been performed on 384 clinical isolates also obtained from Mako Medical laboratories (Thermo Openarray as the comparator) which averaged = 98 +/-5% and was found to be >98% for all but one ARG target: gyrA point mutation (88%). Conclusions The data provided here demonstrates that the D3 Array-UTI platform can perform complex polymicrobial/ARG testing as a high throughput 96 well plate based assay, with Sensitivity and Specificity that matches or exceeds that of qPCR, using standard automation that can be deployed in any molecular laboratory. The resulting performance is unique in that Species and ARG Discrimination are readily scalable to 3-4 dozen Species per test, performed in triplicate in a single well with completely autonomous, cloud enabled data analysis, at a sample-to-answer throughput >96 samples per shift. Beta testing has been initiated among laboratory partners.

Paired Transcriptional Analysis of Periodontitis and Peri-Implantitis within same host: a Pilot study

Background: Peri-implantitis, a plaque-associated pathological condition, has been on the rise with the increasing prevalence of dental implants. Despite its similarities to periodontitis, peri-implantitis is difficult to control completely and has high relapse rates. This has sparked interest in exploring the pathogenic differences between the two conditions. Methods: This cross-sectional study involved 10 participants to concurrently examine periodontitis and peri-implantitis within the same patients, thereby minimizing inter-individual variation. Gingival tissue samples were collected from each participant, comprising 10 periodontitis and 10 peri-implantitis tissues, and RNAs were extracted. Using RNA sequencing and bioinformatics analysis, we investigated complex gene interactions, immune responses, and the role of the extracellular matrix in both conditions. We identified hub genes in each enhanced Protein-Protein Interaction network, providing crucial insights into these diseases’ pathogenesis. Results: Our findings highlighted the potential involvement of activated fibroblasts in the pathogenesis of peri-implantitis, identifying three marker genes (ACTA2, FAP, and PDGFRβ) overexpressed in peri-implantitis, thus highlighting their potential as disease-specific biomarkers. Conclusions: Our study uncovered a novel connection between peri-implantitis and activated fibroblasts, examining specific markers and microbial differences between periodontitis and peri-implantitis. These insights improve our understanding of peri-implantitis pathogenesis, encouraging future research for better management and prevention strategies. Clinical Significance: This study identifies key insights into the pathogenesis of peri-implantitis compared to periodontitis. These findings promise to advance clinical approaches for better managing and preventing peri-implantitis, addressing its complexities and high relapse rates effectively.

Tnfaip8 and Tipe2 Gene Deletion Ameliorates Immediate Proteoglycan Loss and Inflammatory Responses in the Injured Mouse Intervertebral Disc.

TNFAIP8 and TIPE2 belong to TNFa-induced protein 8 (TNFAIP8/TIPE) family. They control apoptosis and direct leukocyte migration. Nucleus pulposus cell loss is a hallmark of intervertebral disc degeneration in response to injury, and inflammation may cause pain. Here, we examined the effects of TNFAIP8/TIPE2 deficiency on the intervertebral discs in mice with these genes deleted. Tail intervertebral discs in Tnfaip8 or Tipe2 single and double knockout mice ( Tnfaip8 -/- , Tipe2 -/- , and Tnfaip8/Tipe2 dko) , and wild-type controls were injured. The spine motion segments were stained with safranin O to reveal proteoglycans. Macrophages were identified by immunostaining, and selected inflammatory marker and collagen gene expression was examined by Real Time PCR. The injured tail intervertebral discs of Tnfaip -/- , Tipe2 -/- , and Tnfaip8/Tipe2 dko mice all displayed higher levels of proteoglycans than wild-type controls. Fewer macrophages were found in the injured intervertebral discs of Tipe2 -/- and Tnfaip8/Tipe2 dko mice than wild type. Il6 , Adam8 , and Col1 gene expression was downregulated in the injured intervertebral discs of Tnfip8/Tipe2 dko mice. TNFAIP8 and TIPE2 loss of function ameliorated proteoglycan loss and inflammation in the injured intervertebral discs. They may serve as molecular targets to preserve disc structure and reduce inflammation.

Protective Effects of Hydroalcoholic Leaf Extract of Origanum Vulgare against Paraquat-induced Lung Toxicity in Rats: The Role of the Inflammation-related Markers and Oxidative Stress

Background:: The pesticide paraquat is hazardous to both humans and animals. Lung damage is a common complication of paraquat poisoning. Objective:: This research analyzes the preventive properties of Origanum vulgare leaf extract against paraquat-induced acute pulmonary toxicity and oxidative stress. Methods:: In this experiment, the rats were assigned to five distinct groups. Group 1 served as the control, group 2 got only 25 mg/kg bw paraquat, and groups 3, 4, and 5 received paraquat and Origanum vulgare leaf extract at dosages of 200, 400, and 800 mg/kg bw, respectively. In rats, inflammation- related indicators and oxidative stress were analyzed after therapy. Results:: Compared with the control group, the levels of the serum PC, MDA, and inflammatory markers such as TNF-α, IL-6, and IL-1β remarkably rose (p < 0.05) and the pulmonary contents of the SOD, CAT, and vitamin C greatly decreased (p < 0.05) in the paraquat-only group. Origanum vulgare leaf extract administration after paraquat exposure resulted in a substantial increase in lung SOD, CAT, and vitamin C levels as well as a significant reduction in MDA, PC, and lung inflammatory markers (TNF-α, IL-6, and IL-1β) gene expression relative to the paraquat-only group. Conclusion:: Origanum vulgare leaf extract might be supplied to lessen the toxicity of paraquat, based on the findings of this research, which indicated that Origanum vulgare leaf extract has antioxidant- enhancing properties and can improve the antioxidant defense system. other: Ethic number: IR. SKUMS. REC. 1395. 151.

Enhancing osteoblast differentiation and bone repair: The priming effect of photobiomodulation on adipose stromal cells

Cellular therapy using adipose tissue–derived mesenchymal stromal cells (at-MSCs) has garnered attention for the treatment of bone defects. Therefore, preconditioning strategies to enhance the osteogenic potential of at-MSCs could optimize cell therapy outcomes, and photobiomodulation (PBM) therapy has emerged as an effective, noninvasive, and low-cost alternative. This study explored the impacts of PBM on at-MSCs differentiation and the subsequent repair of bone defects treated with cell injection. Rat at-MSCs were cultured and irradiated (at-MSCsPBM) following the PBM protocol (660 nm; 20 mW; 0.714 W/cm2; 0.14 J; 5 J/cm2). Cellular differentiation was assessed based on the expression of gene and protein markers. Reactive oxygen species (ROS) were detected using fluorescence. At-MSCsPBM were injected into 5-mm calvarial lesions, and bone formation was analyzed using micro-CT and histological evaluations. At-MSCs were used as control. Data were analyzed using the ANOVA or t-test. At-MSCsPBM exhibited high levels of gene and protein runt-related transcription factor-2 (Runx2) and alkaline phosphatase (Alp) expression. PBM increased ALP activity and significantly reduced ROS levels. In addition, PBM increased the expression of Wnt pathway–associated genes. In vivo, there was an increase in the morphometric parameters, including bone volume, percentage of bone volume, bone surface area, and trabecular number, in at-MSCsPBM-treated defects compared with those in the control. These findings suggest that PBM enhances the osteogenic potential of at-MSCs, thereby supporting the advancement of improved cellular therapies for bone regeneration.

Low frequency‑pulsed electromagnetic fields promote osteogenic differentiation of bone marrow‑derived mesenchymal stem cells by regulating connexin 43 expression.

The present study investigated the effect of connexin 43 (Cx43) on the regulation of osteogenic differentiation of rat bone marrow-derived mesenchymal stem cells (BMSCs) using low-frequency-pulsed electromagnetic fields (LPEMF). The BMSCs were isolated and cultured in vitro using adherent whole-bone marrow cultures. CCK-8 assay was used to detect the effects of LPEMF on the proliferation ability of BMSCs and alkaline phosphatase (ALP) activity and the levels of osteogenic marker genes were detected to evaluate the osteogenic ability change following LPEMF treatment. Lentiviral vector-mediated RNA interference was transfected into BMSCs to inhibit the expression of Cx43 and western blotting was used to detect Cx43 expression. The BMSCs showed the highest proliferation following LPEMF treatment at 80 Hz for 1 h. The results of ALP activity, osteogenic marker genes and Alizarin Red S staining showed that the osteogenic ability was notably increased following LPEMF treatment at 80 Hz for 1 h. Cx43 expression increased during the osteogenic differentiation of BMSCs following LPEMF treatment at 80 Hz. The enhanced osteogenic differentiation of the LPEMF-treated BMSCs were partially reversed when Cx43 expression was inhibited. LPEMF may promote the osteogenic differentiation of BMSCs by regulating Cx43 expression and enhancing osteogenic ability.

SpotGF: Denoising spatially resolved transcriptomics data using an optimal transport-based gene filtering algorithm.

Spatially resolved transcriptomics (SRT) combines gene expression profiles with the physical locations of cells in their native states but suffers from unpredictable spatial noise due to cell damage during cryosectioning and exposure to reagents for staining and mRNA release. To address this noise, we developed SpotGF, an algorithm for denoising SRT data using optimal transport-based gene filtering. SpotGF quantifies diffusion patterns numerically, distinguishing widespread expression genes from aggregated expression genes and filtering out the former as noise. Unlike conventional denoising methods, SpotGF preserves raw sequencing data, thereby avoiding false positives that can arise from imputation. Additionally, SpotGF demonstrates superior performance in cell clustering, identifying potential marker genes, and annotating cell types. Overall, SpotGF has the potential to become a crucial preprocessing step in the downstream analysis of SRT data. The SpotGF software is freely available at GitHub. A record of this paper's transparent peer review process is included in the supplemental information.

Effects of rumen metabolite butyric acid on bovine skeletal muscle satellite cells proliferation, apoptosis and transcriptional states during myogenic differentiation

Butyric acid, a pivotal short-chain fatty acid in rumen digestion, profoundly influences animal digestive and locomotor systems. Extensive research indicates its direct or indirect involvement in the growth and development of muscle and fat cells. However, the impact of butyric acid on the proliferation and differentiation of bovine skeletal muscle satellite cells (SMSCs) remains unclear. This study aimed to elucidate the effects of butyrate on SMSCs proliferation and differentiation. After isolating, SMSCs were subjected to varying concentrations of sodium butyrate (NaB) during the proliferation and differentiation stages. Optimal treatment conditions (1 mM NaB for 2 days) were determined based on proliferative force, cell viability, and mRNA expression of proliferation and differentiation marker genes. Transcriptome sequencing was employed to screen for differential gene expression between 1 mM NaB-treated and untreated groups during SMSCs differentiation. Results indicated that lower NaB concentrations (≤1.0 mM) inhibited proliferation while promoting differentiation and apoptosis after a 2-day treatment. Conversely, higher NaB concentrations (≥2.0 mM) suppressed proliferation and differentiation and induced apoptosis. Transcriptome sequencing revealed differential expression of genes(ND1, ND3, CYTB, COX2, ATP6, MYOZ2, MYOZ3, MYBPC1 and ATP6V0A4,etc.) were associated with SMSCs differentiation and energy metabolism, enriching pathways such as Oxidative phosphorylation, MAPK, and Wnt signaling. These findings offer valuable insights into the molecular mechanisms underlying butyrate regulation of bovine SMSCs proliferation and differentiation, as well as muscle fiber type conversion in the future study.

Bone quality relies on hyaluronan synthesis – Insights from mice with complete knockout of hyaluronan synthase expression

Bone consists of a complex mineralised matrix that is maintained by a controlled equilibrium of synthesis and resorption by different cell types. Hyaluronan (HA) is an important glycosaminoglycan in many tissues including bone.Previously, the importance of HA synthesis for bone development during embryogenesis has been shown. We therefore investigated whether HA synthesis is involved in adult bone turnover and whether abrogation of HA synthesis in adult mice would alter bone quality.To achieve complete abrogation of HA synthesis in adult mice, we generated a novel Has-total knockout (Has-tKO) mouse model in which a constitutive knockout of Has1 and Has3 was combined with an inducible, Ubc-Cre-driven Has2 knockout.By comparing bone tissue from wild-type, Has1,3 double knockout and Has-tKO mice, we demonstrate that Has2-derived HA mainly contributes to the HA content in bone. Furthermore, Has-tKO mice show a significant decrease of bone integrity in trabecular and cortical bone, as shown by µ-CT analysis. These effects are detectable as early as five weeks after induced Has2 deletion, irrespective of sex and progress with age.Mesenchymal stem cells (MSC) during osteogenic differentiation in vitro showed that Has2 expression is increased while Has3 expression is decreased during differentiation. Furthermore, the complete abrogation of HA synthesis results in significantly reduced osteogenic differentiation as indicated by reduced marker gene expression (Runx-2, Tnalp, Osterix) as well as alizarin red staining. RNAseq analysis revealed that MSC from Has-tKO are characterised by decreased expression of genes annotated for bone and organ development, whereas expression of genes associated with chemokine related interactions and cytokine signalling is increased.Taken together, we present a novel mouse model with complete deletion of HA synthases in adult mice which has the potential to study HA function in different organs and during age-related HA reduction. With respect to bone, HA synthesis is important for maintaining bone integrity, presumably based on the strong effect of HA on osteogenic differentiation.

The phyllosphere of Nigerian medicinal plants, Euphorbia lateriflora and Ficus thonningii is inhabited by a specific microbiota

The microbiota of medicinal plants is known to be highly specific and can contribute to medicinal activity. However, the majority of plant species have not yet been studied. Here, we investigated the phyllosphere composition of two common Nigerian medicinal plants, Euphorbia lateriflora and Ficus thonningii, by a polyphasic approach combining analyses of metagenomic DNA and isolates. Microbial abundance estimated via qPCR using specific marker gene primers showed that all leaf samples were densely colonized, with up to 108 per gram of leaf, with higher bacterial and fungal abundance than Archaea. While no statistically significant differences between both plant species were found for abundance, amplicon sequencing of 16S rRNA and ITS genes revealed distinct microbiota compositions. Only seven of the 27 genera isolated were represented on both plants, e.g. dominant Sphingomonas spp., and numerous members of Xanthomonadaceae and Enterobacteriaceae. The most dominant fungal families on both plants were Cladosporiaceae, Mycosphaerellaceae and Trichosphaeriaceae. In addition, 225 plant-specific isolates were identified, with Pseudomonadota and Enterobacteriaceae being dominant. Interestingly, 29 isolates are likely species previously unknown, and 14 of these belong to Burkholderiales. However, a high proportion, 56% and 40% of the isolates from E. lateriflora and F. thonningii, respectively, were characterized as various Escherichia coli. The growth of most of the bacterial isolates was not influenced by extractable secondary metabolites of plants. Our results suggest that a specific and diverse microbial community inhabits the leaves of both E. lateriflora and F. thonningii, including potentially new species and producers of antimicrobials.

Development of a TBXT-EGFP iPS Cell Model for Screening the Early Developmental Toxicity of Typical Environmental Pollutants

In our daily lives, we are inevitably exposed to a variety of environmental pollutants in numerous ways. Fortunately, recent years have witnessed significant advancements in the field of stem cell toxicology, which have provided new opportunities for research in environmental toxicology. Applying stem cell technology to environmental toxicology, overcomes some of the limitations of traditional screening methods and we can more accurately predict the toxicity of environmental pollutants. However, there are still several aspects of stem cell toxicology models that require improvement, such as increasing the throughput of detection and simplifying detection methods. Consequently, we developed an environmental pollutant toxicity detection model based on TBXT-EGFP iPS cells and screened the developmental toxicity of 38 typical environmental pollutants. Our results indicate that TBBPA-BDBPE, TBBPA-BHEE, DG, and AO2246 may interfere with the expression of TBXT, a critical marker gene for early human embryo development, implying that these environmental pollutants could lead to developmental abnormalities.

Arabidopsis WRKY55 Transcription Factor Enhances Soft Rot Disease Resistance with ORA59

<i>Pectobacterium</i> is a major bacterial causal agent leading to soft rot disease in host plants. With the <i>Arabidopsis-Pectobacterium</i> pathosystem, we investigated the function of an <i>Arabidopsis thaliana WRKY55</i> during defense responses to <i>Pectobacterium carotovorum</i> ssp. <i>carotovorum</i> (<i>Pcc</i>). <i>Pcc</i>-infection specifically induced WRKY55 gene expression. The overexpression of <i>WRKY55</i> was resistant to the </i>Pcc</i> infection, while <i>wrky55</i> knockout plants compromised the defense responses against <i>Pcc</i>. <i>WRKY55</i> expression was mediated via <i>Arabidopsis</i> COI1-dependent signaling pathway showing that WRKY55 can contribute to the gene expression of jasmonic acid-mediated defense marker genes such as <i>PDF1.2</i> and <i>LOX2</i>. WRKY55 physically interacts with <i>Arabidopsis</i> ORA59 facilitating the expression of <i>PDF1.2</i. Our results suggest that WRKY55 can function as a positive regulator for resistance against <i>Pcc</i> in <i>Arabidopsis</i>.

Black phosphorus quantum dots induced neurotoxicity, intestinal microbiome and metabolome dysbiosis in zebrafish (Danio rerio)

The potential toxicity of BPQDs has received considerable attention due to their increasing use in biomedical applications. In this study, the toxicity of BPQDs at concentrations of 5 μg/mL, 50 μg/mL, and 500 μg/mL on the brain-gut axis was assessed in zebrafish. Following 35 days of exposure, the neurotransmitter, locomotor behavior, gut barrier (physical barrier, chemical barrier, and microbial barrier), and gut content metabolism in zebrafish were evaluated. The results indicated that BPQDs induced the locomotor behavior abnormalities, inhibited acetylcholinesterase activity, induced dopaminase activity, and promoted apoptosis in zebrafish brain tissue. Meanwhile, BPQDs caused damage to the physical and chemical barriers in zebrafish intestinal tissue, which increased the permeability of the intestinal mucosa, and induced oxidative stress and apoptosis. The gut microbiota was analyzed by 16S rRNA gene sequencing. The results showed that BPQDs caused dysbiosis of the gut microbiota, resulting in decreased diversity. Specifically, the relative abundance of Firmicutes, Bacteroidetes, and Actinobacteria decreased, while the relative abundance of Proteobacteria and Clostriobacteria increased. At the genus level, the high concentration BPQDs showed a significant increase in Cetobacterium, Pleisionomas, Aeromonas, and other bacteria. Bioinformatic analysis revealed a correlation between the relative abundance of the gut microbiota and antioxidant levels, immune response, and apoptosis. Statistical analysis of the metabolomic revealed significant perturbations in several metabolic pathways, including amino acid, lipid, nucleotide, and energy metabolism. In addition, correlation analysis between microbiota and metabolism confirmed that gut microbiota dysbiosis was closely associated with metabolic dysfunction. The histopathologic injury supported the changes in biomarkers and the expression of related marker genes in the gut-brain axis, indicating the communication between the gut peripheral nerves and the CNS. The results indicate that BPQDs induce gut microbiota dysbiosis, disrupt metabolic function, and induce neurotoxicity, probably by disrupting the homeostasis of the microbiota-gut-brain axis. In summary, this study demonstrates the effects of BPQDs on physiological changes within the zebrafish brain-gut axis and provides valuable data for assessing the toxicological risks of BPQDs in aquatic ecosystems.

Analysis of the pluripotent and germline marker gene expression, and the state of X chromosome reactivation of primordial germ cells in pig gonads

Analysis of the pluripotent and germline marker gene expression, and the state of X chromosome reactivation of primordial germ cells in pig gonads

The expression and function of Gpnmb in lymphatic endothelial cells.

The lymphatic system functions in fluid homeostasis, lipid absorption and the modulation of the immune response. The role of Gpnmb (osteoactivin), an established osteoinductive molecule with newly identified anti-inflammatory properties, has not been studied in lymphangiogenesis. Here, we demonstrate that Gpnmb increases lymphatic endothelial cell (LEC) migration and lymphangiogenesis marker gene expression in vitro by enhancing pro-autophagic gene expression, while no changes were observed in cell proliferation or viability. In addition, cellular spreading and cytoskeletal reorganization was not altered following Gpnmb treatment. We show that systemic Gpnmb overexpression in vivo leads to increases in lymphatic tubule number per area. Overall, data presented in this study suggest Gpnmb is a positive modulator of lymphangiogenesis.

Advanced machine learning unveils CD8 + T cell genetic markers enhancing prognosis and immunotherapy efficacy in breast cancer

BackgroundBreast cancer (BC) is the most common cancer in women and poses a significant health burden, especially in China. Despite advances in diagnosis and treatment, patient variability and limited early detection contribute to poor outcomes. This study examines the role of CD8 + T cells in the tumor microenvironment to identify new biomarkers that improve prognosis and guide treatment strategies.MethodsCD8 + T-cell marker genes were identified using single-cell RNA sequencing (scRNA-seq), and a CD8 + T cell-related gene prognostic signature (CTRGPS) was developed using 10 machine-learning algorithms. The model was validated across seven independent public datasets from the GEO database. Clinical features and previously published signatures were also analyzed for comparison. The clinical applications of CTRGPS in biological function, immune microenvironment, and drug selection were explored, and the role of hub genes in BC progression was further investigated.ResultsWe identified 71 CD8 + T cell-related genes and developed the CTRGPS, which demonstrated significant prognostic value, with higher risk scores linked to poorer overall survival (OS). The model’s accuracy and robustness were confirmed through Kaplan-Meier and ROC curve analyses across multiple datasets. CTRGPS outperformed existing prognostic signatures and served as an independent prognostic factor. The role of the hub gene TTK in promoting malignant proliferation and migration of BC cells was validated.ConclusionThe CTRGPS enhances early diagnosis and treatment precision in BC, improving clinical outcomes. TTK, a key gene in the signature, shows promise as a therapeutic target, supporting the CTRGPS’s potential clinical utility.

Estrogenic Post-Menopausal Anti-Osteoporotic Mechanism of Achyranthes aspera L.: Phytochemicals and Network Pharmacology Approaches

Hormone replacement therapy is used to treat postmenopausal syndrome caused by estrogen deficiency, but it has been linked to an increased risk of breast cancer. In India, Achyranthes aspera L. is traditionally used to treat menstrual problems; however, there is a lack of mechanistic evidence of its phytoestrogenicity. Therefore, this study investigated the estrogenic activity of A. aspera on estrogen-responsive MCF-7 breast cancer cells. In a cell proliferation assay, the MeOH fraction (100 μg/mL) exhibited the highest proliferation effect (PE) of 138% (p<0.001) and relative proliferation effect (RPE) of 96.5%, compared to 17β-estradiol (0.01 μM: 143% PE, p<0.001; 100% RPE). The MeOH fraction was shown to upregulate the oestrogen marker genes trefoil factor 1 and progesterone receptor by 20.14-23.94 folds and 10.83-14.83 folds, respectively. Twelve phenolics were identified by LC-MS/MS in the active MeOH fraction, i.e. quinic acid, kaempferol hexoside, kaempferol 3-O-(2''-O-galloyl)-glucoside)-β-D-glucoside, geniposide, 3-O-(6'-O-(9Z,12Z-octadecadienoyl)-β-D-glucopyranosyl)-stigmast-5,22E-dien-3β-ol, kaempferol-3-O-glucoside (astragalin), 3,30-di-O-methylellagic acid isomer, procyanidin, naringin, propapyriogenin A2, (3β,22E,24R)-23-methylergosta-5,7,22-trien-3-ol and 6-prenylapigenin. Through network pharmacology, the potential effects, and mechanisms of these compounds in osteoporosis were revealed. About 55 target genes were linked to osteoporosis. GO and KEGG enrichment suggest regulation of female reproductive hormone related signaling pathways, which are also associated with estrogen dependent osteoporosis. Molecular docking analysis of the compounds revealed potential interactions with hERα receptor for 3-O-(6'-O-(9Z,12Z-octadecadienoyl)-β-D-glucopyranosyl)-stigmast-5,22E-dien-3β-ol and kaempferol-3-O-glucoside (astragalin) (docking scores of -9.3 and -10.1 kcal/mol, respectively) as compared to 17β-estradiol (-9.3 kcal/mol). These results suggest the estrogenicity of A. aspera via an ERα-associated mechanism and support its traditional usage in the management of menopausal-related problems.

Integrated metagenomics and metabolomics analyses revealed biomarkers in β-casein A2A2-type cows

In Holstein cows, β-casein, one of the most critical proteins in milk, exists in two main genotypes, A1 and A2. Herein, 45 Holstein cows [categorized into three groups based on β-casein A1A1, A1A2, and A2A2 genotypes (N = 15)] with the same feeding management and litter size were enrolled to explore differences in rumen microflora and metabolites across various β-casein genotypes. Rumen fluids were collected for metagenomics and metabolomics analyses. Metabolomics and weighted gene co-expression network analysis (WGCNA) revealed that arachidonic acid (AA), adrenic acid (AdA), glycocholic acid (GCA), and taurocholic acid (TCA) were significantly and positively correlated with milk fat % in dairy cows (p &amp;lt; 0.05). Furthermore, macro-genomics and Spearman’s correlation analysis revealed significant positive correlations (p &amp;lt; 0.05) between the characteristic flora (g_Acetobacter, g_Pseudoxanthomonas, g_Streptococcus, and g_Pediococcus) and the five characteristic metabolites in the rumen of A2A2 dairy cows. Moreover, functional enrichment analysis revealed more genes enriched to the TRP channel’s inflammatory mediator-regulated pathway and the mTOR signaling pathway in A2A2 genotyped cows. Additionally, the regulatory effects of AA on bovine mammary epithelial cells (BMECs) were examined using CCK-8, EdU, and qRT-PCR assays, revealing that AA promoted triglyceride (TG) synthesis and upregulated the milk fat marker genes including SREBF1, ACSS2, AGPAT6, and FASN. Overall, we identified characteristic microorganisms and metabolites in A2A2 Holstein cows and established that AA could be a biomarker for higher milk fat %.