Short rib polydactyly syndrome (SRPS), with or without polydactyly, also known as Verma-Naumoff/Saldino-Noonan syndrome, is a type of skeletal ciliopathy. Initially, variants in the IFT80 gene were implicated; however, approximately half of the SRPS cases are associated with variants in the DYNC2H1 gene. Additionally, digenic variants involving DYNC2H1 and NEK1 can contribute to the syndrome.

This case report describes a male patient presenting with characteristic SRPS features, including a constricted thorax and shortened limbs. Exome sequencing was performed to identify causative variants, followed by functional analyses to assess the pathogenicity of the identified variants, including a synonymous variant.

Exome sequencing identified compound heterozygous variants in the DYNC2H1 gene: a novel missense variant c.6439G>T p.(Asp2147Tyr) and a synonymous variant c.6477G>A p.(Gln2159=). Functional analyses confirmed that the synonymous variant triggers nonsense-mediated decay of the affected allele.

This study expands the spectrum of DYNC2H1 variants associated with SRPS and emphasizes the importance of functional analyses in genetic diagnostics. Demonstrating pathogenicity for a synonymous variant highlights the necessity for comprehensive variant assessments to improve diagnostic accuracy and enable early intervention. These findings have significant implications for molecular diagnostics and personalized therapy strategies in skeletal ciliopathies.

The SCN9A gene is primarily expressed in nociceptive pathways within the peripheral nervous system, and pathogenic variants are associated with human pain disorders. In recent years, several studies have proposed SCN9A as a monogenic cause of epilepsy. Our objective was to critically appraise the SCN9A-epilepsy gene-disease relationship.

We assessed "epilepsy-associated" SCN9A variants from four sources: (1) the literature up to December 2023 (n = 27), (2) epilepsy patients referred for genetic testing at a regional service in Glasgow, UK over a 5-year period (n = 30), (3) the Human Genetics Mutation Database (n = 25), and (4) ClinVar (n = 1546). The latter two are genome-wide variant databases, accepting submissions from genetic laboratories and research groups. We checked whether each SCN9A variant is present in the Genome Aggregation Database (gnomAD) V4 (a reference population database for variant interpretation), and classified its pathogenicity based on the American College of Molecular Genetics and Genomics/Association of Molecular Pathologists guidelines.

Only three SCN9A variants were classified as "likely pathogenic," of which two were identified in healthy individuals in gnomAD. A total of 1540 of the 1546 SCN9A variants in ClinVar labeled as being associated with epilepsy were also reported in association with hereditary sensory and autonomic neuropathy. No further clinical data were provided in 1482 of these submissions.

There is no convincing genetic evidence to support SCN9A as a causative epilepsy gene. As such, the inclusion of SCN9A in epilepsy genetic testing panels should be reassessed. Research centers and genetic testing laboratories should be rigorous and consistent in their submissions to variant databases.

Current phenotype-based diagnostic tools often struggle with accurate disease prioritization due to incomplete phenotypic data and the complexity of rare disease presentations. Additionally, they lack the ability to generate patient-centered clinical insights or recommend further symptoms for differential diagnosis.

We developed PhenoDP, a deep learning-based toolkit with three modules: Summarizer, Ranker, and Recommender. The Summarizer fine-tuned a distilled large language model to create clinical summaries from a patient's Human Phenotype Ontology (HPO) terms. The Ranker prioritizes diseases by combining information content-based, phi-based, and semantic-based similarity measures. The Recommender employs contrastive learning to recommend additional HPO terms for enhanced diagnostic accuracy.

PhenoDP's Summarizer produces more clinically coherent and patient-centered summaries than the general-purpose language model FlanT5. The Ranker achieves state-of-the-art diagnostic performance, consistently outperforming existing phenotype-based methods across both simulated and real-world datasets. The Recommender also outperformed GPT-4o and PhenoTips in improving diagnostic accuracy when its suggested terms were incorporated into different ranking pipelines.

PhenoDP enhances Mendelian disease diagnosis through deep learning, offering precise summarization, ranking, and symptom recommendation. Its superior performance and open-source design make it a valuable clinical tool, with potential to accelerate diagnosis and improve patient outcomes. PhenoDP is freely available at https://github.com/TianLab-Bioinfo/PhenoDP .

Percutaneous neoadjuvant therapy has proven effective in diminishing tumor size and the surgical intervention area, which couldeffectively mitigate the risk of tumor recurrence and enhance immunotherapy efficacy. Lenalidomide, an approved medication orally used to treat myeloma, was loaded into nanosuspensions-based hydrogels (Len-NBHs) for transdermal administration as a percutaneous neoadjuvant therapy. This study was designed to investigate the inhibitory effect and mechanism of Len-NBHs on melanoma. Network pharmacology and transcriptomic analyses identified key targets and signaling pathways. The effects of lenalidomide on melanoma were further verified through Western blotting, immunohistochemistry, immunofluorescence, and quantitative real-time polymerase chain reaction，using both in vitro cell experiments and in vivo melanoma mouse models. Lenalidomide could induce melanoma cells apoptosis, disrupt cell cycle progression, impede cell migration and invasion, and modify tumor microenvironment (TME). Mechanistically, lenalidomide reversed the abnormal activation of the PI3K-AKT signaling pathway and the overexpression of CD93, while also recruiting CD8+ T cells, CD4+ T cells, and dendritic cells to infiltrate the tumor site. Transdermal administration of Len-NBHs represents a promising adjuvant therapy for the treatment of malignant melanoma. Preoperative administration of Len-NBHs can inhibit the outward spread of melanoma, reduce tumor size, thereby decreasing the surgical excision area and improving patient survival rates and prognosis.

This study aims to identify new variants and haplotypes associated with monogenic obesity by analyzing known obesity genes in whole exome sequencing (WES) data.

The monogenic obesity-associated genes were identified by using the National Institutes of Health (NIH) Genetic Testing Registry (GTR) monogenic obesity panels. WES was performed on (n = 49) extremely obese (children under 5 with weight-for-height greater than 3 standard deviations (SD) above the World Health Organization (WHO) Child Growth Standards median) and (n = 50) control nonobese (25 > body mass index (BMI) < 30) subjects without a history of childhood obesity, and also Iranome WES data of healthy subjects (n = 800).

Seventy-four genes were included in WES analyses. After Bonferroni correction, the T allele of rs2275155 on SDCCAG8 was significantly associated with the increased risk of obesity for allelic and co-dominant models (p˂0.05). Also, a significant association was observed for the T allele of rs116167439 on CEP19 and the T allele of rs201676524 a rare variant on ADCY3; for allelic, dominant, overdominant, and co-dominant models (p˂0.05). In the haplotype association study, TC (on CEP19), CATA (on SDCCAG8), CAA, CTA, CAAA, and TTGA (on ADCY3) haplotypes showed significant associations with monogenic obesity (p < 0.05).

This study suggested that the T allele of two common variants rs2275155 and rs116167439, also rare variant rs201676524 are associated with an increased risk of monogenic obesity. The significant haplotype associations indicate these variants may be in linkage with causative rare variants and should be considered in future studies.

The online version contains supplementary material available at 10.1007/s40200-024-01507-2.

Non-alcoholic fatty liver disease (NAFLD) and diabetes mellitus (DM) are prevalent metabolic disorders that frequently coexist, yet their shared molecular mechanisms remain poorly understood, and current therapies often yield suboptimal outcomes. Lycium barbarum L. (Lycii fructus, LF), a traditional medicinal herb, has demonstrated clinical efficacy in treating both conditions, but its mechanism of action in comorbidity management remains unclear. Active LF compounds were identified via the TCMSP database, with potential targets predicted using Swiss Target Prediction and PharmMapper. Disease-associated proteins for NAFLD and DM were curated from OMIM, GeneCards, DisGeNET, UniProt, DrugBank, and TTD. A protein-protein interaction (PPI) network was constructed from these targets, and GO and KEGG pathway analyses were performed using the DAVID platform. Key targets were further refined through network module analysis via Metascape. Drug-likeness of bioactive compounds was assessed using SwissADME and ADMETlab 2.0. Molecular docking and dynamics simulations validated interactions between core targets and LF compounds. Mendelian randomization (MR) analysis tested causal relationships between core genes and disease phenotypes. We identified 58 shared therapeutic targets for NAFLD-DM comorbidity, including HSP90AA1, ESR1, MMP9, EGFR, AKT1, and CASP3. GO analysis implicated LF in blood pressure regulation and glucose-stimulated insulin secretion. KEGG pathways highlighted modulation of MAPK, PI3K-Akt, FoxO, and mTOR signaling. 24-methylenelanost-8-enol and cryptoxanthin monoepoxide emerged as core bioactive compounds with favorable drug-likeness. Molecular docking confirmed strong binding of 24-methylenelanost-8-enol to HSP90AA1 and cryptoxanthin monoepoxide to MMP9, further supported by dynamics simulations. MR analysis revealed a significant causal role for CASP3 in both NAFLD and DM, aligning with network pharmacology predictions. LF's therapeutic effects on NAFLD-DM comorbidity likely arise from terpenoid and cryptoxanthin mediated modulation of apoptosis and inflammation pathway. This study identifies shared molecular networks, proposes candidate mechanisms for LF's efficacy, and provides a framework for targeting multifactorial metabolic diseases.

To construct an Alzheimer's Disease Knowledge Graph (ADKG) by extracting and integrating relationships among Alzheimer's disease (AD), genes, variants, chemicals, drugs, and other diseases from biomedical literature, aiming to identify existing treatments, potential targets, and diagnostic methods for AD.

We annotated 800 PubMed abstracts (ADERC corpus) with 20,886 entities and 4935 relationships, augmented via GPT-4. A SpERT model (SciBERT-based) trained on this data extracted relations from PubMed abstracts, supported by biomedical databases and entity linking refined via abbreviation resolution/string matching. The resulting knowledge graph trained embedding models to predict novel relationships. ADKG's utility was validated by integrating it with UK Biobank data for predictive modeling.

The ADKG contained 3,199,276 entity mentions and 633,733 triplets, linking >5K unique entities and capturing complex AD-related interactions. Its graph embedding models produced evidence-supported predictions, enabling testable hypotheses. In UK Biobank predictive modeling, ADKG-enhanced models achieved higher AUROC of 0.928 comparing to 0.903 without ADKG enhancement.

By synthesizing literature-derived insights into a computable framework, ADKG bridges molecular mechanisms to clinical phenotypes, advancing precision medicine in Alzheimer's research. Its structured data and predictive utility underscore its potential to accelerate therapeutic discovery and risk stratification.

Ovarian cancer, often diagnosed at advanced stages, has a 5-year survival rate below 50%, indicating a critical need for innovative treatments. The Zengmian Yiliu (ZMYL) formula, a Traditional Chinese Medicine (TCM) prescription, has shown potential in enhancing chemotherapy efficacy and improving patients' quality of life, PURPOSE: To investigate the effects of the ZMYL formula on ovarian cancer organoids, focusing on its impact on organoid phenotypes and underlying mechanisms, and to explore its potential as an immunotherapeutic agent.

Ovarian cancer organoids were established from surgical tissues and treated with the ZMYL formula at varying concentrations. Network pharmacology was utilized to predict the formula's therapeutic targets and pathways, and molecular docking was conducted to validate ingredient-target interactions. Phenotypic changes were monitored, and RNA sequencing was performed post-treatment to analyze gene expression alterations.

A total of 34 overlapping targets of 10 compounds in the ZMYL formula and ovarian cancer were predicted by Network pharmacology analysis. The ZMYL formula induced dose-dependent morphological changes in organoids, including a reduction in size and structural sparsity at higher concentrations. RNA sequencing revealed significant modulation of cell cycle and immune response pathways, with a particular focus on immunomodulatory effects. The formula's treatment targeted key genes involved in these processes, reshaping the tumor's molecular landscape.

This study establishes ZMYL's capacity to simultaneously target oncogenic drivers (e.g., cell cycle regulators) and immune checkpoints (e.g., CXCL10-mediated T cell recruitment) in ovarian cancer organoids. Unlike conventional monotherapy-focused approaches, ZMYL's multi-component mechanism offers a synergistic framework for integrating TCM with modern immunotherapies. These findings provide a foundation for future clinical evaluation of ZMYL as a precision medicine strategy to enhance treatment efficacy and mitigate chemoresistance in ovarian cancer.

The Portuguese Society of Ophthalmology and the Portuguese Society of Human Genetics developed clinical practice guidelines to streamline genetic testing for inherited retinal dystrophies (IRDs), underlining the critical role of molecular diagnosis in enhancing patient care. Genetic testing is pivotal in diagnosis, genetic counselling, prognosis and access to clinical trials, and new gene-specific therapies. These guidelines recommend genetic testing in all IRD patients and provide a detailed assessment of available testing methods, ensuring that genetic counselling is integrated into ophthalmic care. Essential to this process is the inclusion of at least one genetic counselling session to effectively communicate and discuss implications of test results with patients and families/carers. Key recommendations include cascade testing to identify at-risk family members and standardisation of variant classification according to international criteria to ensure consistency in diagnosis and care. Ophthalmological follow-up is generally prescribed at intervals of 1-2 years for adults and 6 months for paediatric patients, to monitor disease progression and complications. Paediatric considerations are addressed, reflecting the complexities and ethical concerns associated with testing minors. These guidelines aim to elevate diagnostic accuracy, guide therapeutic decisions and ultimately improve patient outcomes, marking a significant advance in the genetic management of IRDs.

Renal cell carcinoma (RCC) is the most common kidney cancer. Despite advances in treatment, current therapeutic strategies are often limited by side effects, drug resistance, and low response rates, necessitating alternatives for RCC treatment. Deoxyelephantopin (DEO), a sesquiterpene lactone from Elephantopi Herba, has demonstrated anticancer properties in multiple cancer models; however, its effects on RCC remain unknown. This study aimed to investigate the anti-RCC effects of DEO and its underlying molecular mechanisms. Human RCC cell lines (786-O, Caki-1, A498) and a murine RCC cell line (RENCA) were used for in vitro assays. Results revealed that DEO dose-dependently inhibited cell viability and colony formation in 786-O, Caki-1, A498, and RENCA cells, while also inducing apoptosis in 786-O and Caki-1 cells. A RENCA allograft mouse model was used for in vivo assays. DEO significantly suppressed tumor growth without causing notable changes in body weight, organ coefficients, or serum biochemical markers (ALT, AST, BUN, Cr). Network pharmacology analysis predicted the PI3K/AKT signaling pathway as a key mediator of DEO's anti-RCC effects. Western blotting showed that DEO downregulated the expression of EGFR, p-EGFR (Tyr1068), PI3K p110α, p-Akt (Ser473), mTOR, p-mTOR (Ser2448), p-p70S6K (Thr389), 4E-BP1, p-4E-BP1 (Thr37/46), HIF-1α, and Bcl-2. Overactivation of AKT attenuated DEO's inhibitory effects on cell viability in 786-O cells. In conclusion, this study is the first to demonstrate that DEO exerts anti-RCC effects in both cellular and animal models, primarily through inhibition of the PI3K/AKT pathway. These findings suggest that DEO holds promise as a lead compound for RCC management.

Progressive Myoclonic Epilepsies (PMEs) are a rare and heterogeneous group of epileptic disorders often with progressive neurologic deterioration. The intensity of the clinical features varies depending on the underlying genetic etiology. This study aims to identify the genetic mutation associated with PME in a family belonging to the Iranian-Azeri-Turkish ethnic population. A 5-year-old boy and his 8-year-old sister, presenting with PME-related electroclinical features such as myoclonic seizures and progressive cognitive and motor decline, underwent comprehensive clinical evaluations, including pedigree analysis, laboratory tests, and EEG assessments, followed by Whole-Exome Sequencing (WES) to identify potential disease-causing mutations. We identified a novel homozygous mutation (c.14C > T) in the KCTD7 gene in both siblings, confirmed through Sanger sequencing. This mutation was not observed in a cohort of 430 healthy individuals from the same Iranian-Azeri-Turkish ethnic background, providing strong evidence for its pathogenic role. This finding advances our understanding of the genetic basis and phenotypic diversity of PMEs, but further research is needed to elucidate how KCTD7 mutations contribute to epilepsy and neurodegeneration.

This study aims to investigate the material basis and underlying mechanisms of action of the Dan Zhi Qing'e Formula in the treatment of menopausal hot flashes. The composition analysis of the Dan Zhi Qing'e Formula was conducted using UHPLC-Q-TOF MS, facilitated by MassLynx V4.1 software. Subsequently, Cytoscape 3.10.1 was employed to merge the data with information from Swiss, GeneCards, and OMIM databases to identify the active components and primary targets. GO and KEGG analyses were performed to elucidate the potential mechanisms of action. Finally, the molecular docking technique was applied to validate the results. A total of 118 components, 73 blood-absorbed components, and 89 potential targets were identified. Seven key targets were obtained, which were aldose reductase (AKR1B1, UniProtKB: P15121), carbonic anhydrase 4 (CA4, UniProtKB: P22748), carbonic anhydrase 2 (CA2, UniProtKB: P00918), acetylcholinesterase (ACHE, UniProtKB: P22303), estrogen receptor beta (ESR2, UniProtKB: Q92731), cytochrome P450 19A1 (CYP19A1, UniProtKB: P11511), and matrix metalloproteinase-2 (MMP2, UniProtKB: P08253). Molecular docking studies indicate that these core components exhibit strong affinity for the identified targets. These targets contribute to the tonic function of the liver and kidneys through hormone response. The findings provide a scientific foundation for further in-depth research into the therapeutic mechanisms of Dan Zhi Qing'e Formula for menopausal hot flashes.

Depression is a chronic and recurrent neuropsychiatric disorder with complex pathophysiology. Dihydromyricetin (DMY), a bioactive flavonoid compound isolated from Ampelopsis grossedentata (commonly known as rattan tea), has demonstrated multiple pharmacological properties including anti-inflammatory, antioxidant, antitumor, and antimicrobial activities. In the present study, a well-established rodent model of depression was generated through chronic unpredictable mild stress (CUMS) paradigm combined with social isolation. Following eight weeks of DMY intervention, comprehensive behavioral assessments were conducted to validate both the successful establishment of the depression model and the therapeutic efficacy of DMY treatment. We employed network pharmacology approaches to systematically predict potential antidepressant targets of DMY. Further mechanistic investigations were performed to elucidate the underlying molecular pathways, providing novel perspectives for developing innovative antidepressant therapeutics.Integrating network pharmacology prediction with molecular biology validation, our findings revealed that DMY exerts significant antidepressant-like effects through suppression of the advanced glycosylation end products (AGEs)-RAGE signaling pathway, activation of the nuclear factor E2-related factor 2 (NRF2)-mediated antioxidant defense system, and upregulation of synaptic plasticity-related proteins including postsynaptic density protein 95 (PSD95) and synaptophysin (SYP). These results suggest that DMY may represent a promising natural therapeutic candidate for depression treatment.

Tightly controlled duplication of centrosomes, the primary microtubule-organizing centers of animal cells, ensures bipolarity of the mitotic spindle and accurate chromosome segregation. The RING-B-box-coiled coil ubiquitin ligase tripartite motif-containing protein 37 (TRIM37), whose loss is associated with elevated chromosome missegregation and the tumor-prone human developmental disorder Mulibrey nanism, prevents the formation of ectopic spindle poles assembling around structured condensates that contain the centrosomal protein centrobin. Here, we show that TRIM37's tumor necrosis factor receptor-associated factor (TRAF) domain, which is unique in the extended TRIM family, engages peptide motifs in centrobin to suppress condensate formation. TRIM family proteins form antiparallel coiled-coil dimers with RING-B-box domains at each end. Oligomerization resulting from RING-RING interactions and conformational regulation through B-box 2-B-box 2 interfaces are essential for TRIM37 to suppress centrobin condensate formation. These results indicate that, similar to antiviral TRIM ligases, TRIM37 activation is coupled to detection of oligomerized substrates, facilitated by recognition of specific motifs in the substrate, to enforce ubiquitination-mediated clearance of ectopic centrosomal protein assemblies.

Mycotoxins are potent triggers of hepatocellular carcinoma (HCC) due to their intricate interplay with cellular macromolecules and signaling pathways. This study integrates machine learning and biomolecular analyses to elucidate the mechanisms underlying mycotoxin-induced hepatocarcinogenesis. Using a data set of 1767 mycotoxins and 1706 non-mycotoxin fungal metabolites, we evaluated 51 machine learning models. The KPGT model achieved optimal performance with an ROC-AUC of 0.979 and balanced accuracy of 0.930. Clustering analysis identified six distinct mycotoxin clusters with unique structural features. Network toxicology analysis revealed distinct protein-protein interaction patterns across different mycotoxin clusters, identifying key regulatory proteins including EGFR, SRC, and ESR1. GO enrichment analysis uncovered cluster-specific effects on protein complexes and macromolecular assemblies, particularly in membrane organization and vesicular transport. KEGG pathway analysis demonstrated systematic perturbation of major signaling cascades, with each mycotoxin cluster distinctly modulating protein kinase networks and receptor tyrosine kinase pathways. Molecular docking analyses validated these interactions, with binding affinities ranging from -9.6 to -4.7 kcal/mol. Notably, cluster 5 showed strong binding to SRC (-9.6 kcal/mol), EGFR (-9.5 kcal/mol), and ESR1 (-7.8 kcal/mol), providing structural insights into toxin-macromolecule recognition. These findings enhance our understanding of mycotoxin-protein interactions in HCC development and suggest potential therapeutic strategies targeting these macromolecular interfaces.

Chronic pancreatitis (CP) is a progressive inflammatory condition of the pancreas that leads to irreversible changes in pancreatic structure. The pancreatic α and β cells secrete hormones such as insulin and glucagon into the bloodstream. The pancreatic acinar cells secrete digestive enzymes that break down macromolecules. When these digestive enzymes do not function properly, maldigestion, malabsorption, and malnutrition may result. Presented here is a case study of an individual newly diagnosed with chronic pancreatitis, along with a genetic analysis of his son and an in-silico analysis of two of the variant proteins.

This study was conducted using human subjects, namely, the proband (father) and his son. Medical genetic testing of the proband (father) identified the presence of two variants in the cystic fibrosis transmembrane receptor gene (CFTR): variant rs213950, resulting in a single amino acid change (p. Val470Met), and variant rs74767530, a nonsense variant (Arg1162Ter) with known pathogenicity for cystic fibrosis. Medical testing also revealed an additional missense variant, rs515726209 (Ala73Thr), in the CTRC gene. Cheek cell DNA was collected from both the proband and his son to determine the inheritance pattern and identify any additional variants. A variant in the human leukocyte antigen (rs7454108), which results in the HLA-DQ8 haplotype, was examined in both the proband and his son due to its known association with autoimmune disease, a condition also linked to chronic pancreatitis. In silico tools were subsequently used to examine the impact of the identified variants on protein function.

Heterozygosity for all variants originally identified through medical genetic testing was confirmed in the proband and was absent in the son. Both the proband and his son were found to have the DRB1*0301 (common) haplotype for the HLA locus. However, the proband was also found to carry a linked noncoding variant, rs2647088, which was absent in the son. In silico analysis of variant rs213950 (Val470Met) in CFTR and rs515726209 (Ala73Thr) in CTRC revealed distinct changes in predicted ligand binding for both proteins, which may affect protein function and contribute to the development of CP.

This case study of a proband and his son provides additional evidence for a polygenic inheritance pattern in CP. The results also highlight new information on the role of the variants on protein function, suggesting additional testing of ligand binding for these variants should be done to confirm the functional impairments.

Alzheimer's disease (AD) is a neurodegenerative disease characterized by amyloid beta (Aβ) deposition, phosphorylated Tau protein aggregation, inflammation, and neuronal damage. Neuronal autophagy plays an important role in ameliorating central nervous system diseases such as AD. As an emerging form of iron-dependent cell death, ferroptosis has attracted great attention in the field of neurodegenerative diseases. Berberine (BBR), a natural alkaloid, has demonstrated excellent in inflammation reduction, inhibition of Aβ production, and neuroprotection, making it a potential candidate for AD treatment. However, the mechanisms of autophagy and ferroptosis in BBR treatment of AD have not been elucidated.

This study aimed to investigate the potential of BBR in alleviating AD and evaluate its molecular mechanism through a combination of network pharmacology and biological experiments.

We assessed alterations in Aβ plaques, neurons, neuroinflammation, and autophagy-related markers in the mice brain using immunofluorescence staining. Network pharmacology and molecular docking were used to analyze the potential targets and signaling pathways of BBR in the treatment of AD. Morris Water Maze (MWM) and new object recognition (NOR) experiments were used to test the spatial memory ability of mice. In addition, we validated the relationship between JNK-P38MAPK, autophagy, ferroptosis, and BBR treatment in 5xFAD mice and A β-induced SH-SY5Y cell models.

The results of immunofluorescence staining showed that BBR effectively mitigated Aβ plaque deposition, ameliorated neuronal damage and neuroinflammation. The autophagy-related markers Beclin1 and LC3B were upregulated and P62 was downregulated after BBR treatment. The expression levels of ROS and lipid peroxide MDA decreased significantly after BBR treatment. qPCR results showed that the expression levels of ferroptosis-related genes TFR1, ASCL4, DMT1, and IREB2 were decreased, while the expression levels of FTH1 and SLC7A11 increased after BBR treatment. Behavioral experiments showed that BBR treatment enhanced spatial memory impairment in 5xFAD mice. Network pharmacological and in vitro analyses demonstrated that BBR activated autophagy and inhibited ferroptosis by inhibiting the JNK-P38MAPK signaling pathway. Following treatment with an autophagy inhibitor on SH-SY5Y cells, autophagy was markedly suppressed, and ferroptosis was induced.

In summary, we found that BBR alleviates AD by inhibiting the JNK-P38MAPK pathway to enhance autophagy and inhibit ferroptosis, further reducing Aβ plaque deposition, inhibiting inflammatory response, and improving neuronal damage.

This study predicted and verified the effects of Jujuboside A (JuA) on the proliferation and migration ability of glioma cells to developing new therapies for glioma treatment.

The druggability of JuA was determined by using cheminformatics. Network pharmacology was used to analyse common targets, biological function and metabolic pathways of JuA against glioma. The core targets of JuA against glioma were validated by using molecular docking. The biological functions of JuA were verified by in vitro experiments.

Cheminformatics results showed that JuA is possible to be a drug. Network pharmacology revealed 294 shared targets between JuA and glioma, which were associated with proliferation, migration, and multiple signalling pathways. A total of 16 core targets related to the signalling pathways were verified by molecular docking. The in vitro experiments showed that JuA could inhibit cell proliferation and migration, decrease cell numbers and alter cell morphology.

The results of network pharmacology and in vitro experiments indicate that JuA has significant toxic effects on glioma cells, and can play a therapeutic role in treating glioma by inhibiting the proliferation and migration of glioma cells.

Diabetes cardiomyopathy (DCM) is a prevalent complication of diabetes, characterized by a multifaceted pathogenesis. Zhilong Huoxue Tongyu Capsule (ZL), a traditional Chinese medicine, is extensively employed for the treatment of cardiovascular diseases. Thus, this study aimed to comprehensively explore the mechanism of action of ZL on DCM.

Network pharmacology approaches were applied to predict the potential pathways and targets of ZL on DCM. Then, a DCM model mouse was constructed and divided into a control group, DCM group, DCM + ZL group, SB203580 group, and DCM + R group. The DCM + ZL group was administered 6.24g/kg/d ZL via gavage, the SB203580 group was given 1 mg/kg/d SB203580 (p38MAPK inhibitor) via intraperitoneal injection, the DCM + R group received 4 mg/kg/d rosiglitazone via gavage, and the control group and DCM group were given equal volume of physiological saline by gavage. The intervention period lasted for 6 weeks to verify these key targets.

Network pharmacology analyses identified 45 active ingredients in ZL linked to 719 potential targets, forming an herbal compound-target network. Screening of databases revealed 1032 DCM-related targets, with MAPK14, TNF, FOS, AKT1, and IL-10 emerging as key hub genes from PPI network analysis. Additionally, enrichment analysis indicated that the candidate targets were enriched in response to the MAPK signaling pathway. Finally, in vivo studies in DCM mice demonstrated that ZL significantly mitigated myocardial fibrosis and down-regulated the expression of p-P38MAPK, TNF-α, α-SMA, and Collagen-I proteins in myocardial tissue.

Our results collectively indicated that ZL can effectively ameliorate diabetes cardiomyopathy, possibly by modulating the P38MAPK signaling pathway.

Evidence has shown that ibuprofen and celecoxib are effective in improving depressive symptoms, but their mechanisms of action are unclear. In this study, we aimed to determine the relationship between these two drugs and depressive disorder (DD) and elucidate potential mechanisms of action.

Relevant targets for ibuprofen, celecoxib, and DD were obtained and screened from multiple online drug and disease public databases. A protein-protein interaction network was obtained. The Centiscape and CytoHubba plug-ins were applied to screen for core targets. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed. Molecular docking was performed to predict the binding of ibuprofen and celecoxib to core targets. Examined the differences in core target protein expression between DD patients (DDs, n = 18) and healthy controls (HCs, n = 16) as a further experimental validation of the network pharmacology results.

In total, 220 potential targets for ibuprofen and 316 potential targets for celecoxib were identified and associated with DD. The antidepressant effects of both drugs involve many key targets in pathways such as "pathways in cancer" and "neuroactive ligand-receptor interaction," including ALB, BCL2, MAPK3, SRC, STAT3, EGFR, and PPARG. The binding affinity of ALB with ibuprofen is the strongest, and it is connected only by hydrophobic interactions. Celecoxib exhibits higher affinity at multiple targets such as SRC, EGFR, and PPARG, with stronger and more specific intermolecular interactions, including salt bridges and halogen bonds. Clinical trials have found that serum ALB expression in DDs is significantly lower than that in HCs (t = 6.653, p < 0.001), further confirming the potential role of ibuprofen in DD.

Ibuprofen and celecoxib primarily exert their antidepressant effects through targets and pathways related to inflammation, neural signaling, and cancer, with celecoxib showing a stronger potential antidepressant effect. The expression difference of the core target ALB between depression and healthy individuals further supports the potential effect of the drug on DD. Our findings propose new treatment strategies, support the link between inflammation and depression, and encourage reassessing existing medications for depression.

Congenital heart disease (CHD) exhibits a marked male predominance in birth prevalence, yet the genetic mechanisms underlying this sex disparity remain poorly understood. This study investigates the contribution of rare damaging variants on autosomes and the X chromosome to sex differences in foetal CHD.

Parents of foetuses with CHD were recruited for the study. Rare damaging variants were identified by analysing whole-exome sequencing data from foetus-parental trios, and their contributions to sex differences were estimated through case-control studies. Functional enrichment analysis was conducted to assess functional differences in genetic variants between sexes.

820 foetal probands with CHD were recruited, including 487 males and 333 females. We identified a significant enrichment of X-linked rare damaging variants, primarily driven by maternally inherited hemizygous variants (MIHVs) in male probands (OR = 1·84, P < 0·05), which accounted for 7·2% of male cases in our cohort. These variants were not found to be enriched in female probands. Additionally, X-linked rare damaging de novo variants (DNVs) were not enriched in either male or female probands (female probands: 1·8% versus female controls: 0·7%, P = 0·6789; no DNVs observed in males). Gene-level variant burden analysis revealed three X-linked CHD candidate genes: DCX, CACNA1F, and MAP3K15. Autosomal rare variants did not show significant differences in variant burdens between sexes. Notably, male probands showed specific functional enrichments in cilia-related pathways for autosomal recessive variants, as well as in chromatin remodelling and nervous system development pathways for autosomal DNVs.

Male and female foetal CHD have significantly different genetic landscapes. The enrichment of X-linked rare damaging MIHVs in males provides a genetic explanation for the higher prevalence of CHD in males. This finding highlights the importance of incorporating sex-stratified approaches in clinical diagnostics and research.

Natural Science Foundation of China and Key research and development project of Hebei Province.

Genetic diagnostics is driven by technological advances, forming a tight interface between research, clinic and industry, which enables rapid implementation of new technologies. Short-read genome and exome sequencing, the current state of the art in clinical genetics, can detect a broad spectrum of genetic variants across the genome. However, despite these advancements, more than half of individuals with rare diseases remain undiagnosed after genomic investigations. Long-read whole-genome sequencing (LR-WGS) is a promising technology that identifies previously difficult-to-detect variants while also enabling phasing and methylation analysis and has the potential of generating complete personal assemblies. To pave the way for clinical use of LR-WGS, the clinical genomic community must establish standardized protocols and quality parameters while also developing innovative tools for data analysis and interpretation. In this Perspective, we explore the key challenges and benefits in integrating LR-WGS into routine clinical diagnostics.

We aim to determine whether epilepsy can be considered part of the arginine:glycine amidinotransferase (AGAT) deficiency syndrome phenotype and to identify its associated electroclinical signatures. We reviewed clinical data from our center, identifying individuals with AGAT deficiency. Each individual underwent a dedicated epilepsy assessment with electroencephalography and 3-T brain magnetic resonance imaging (MRI). Additionally, 30 age- and sex-matched healthy controls (18 females, 28.2 ± 3.7 years old) were recruited for advanced MRI analysis. A family with four affected members carrying homozygous AGAT c.446>A:p.Trp149* variant was identified. Two individuals had focal epilepsy with sensory seizures characterized by a prominent "tingling" sensation. Three experienced febrile seizures plus and marked temperature sensitivity. Corpus callosum dysmorphisms were observed in three cases. Despite creatine supplementation, cortical thickness was significantly reduced across multiple brain regions compared to controls, as indicated by Z-scores. A brain map of AGAT mRNA expression revealed lower expression in the parieto-occipital areas. Our findings suggest that focal epilepsy with sensory seizures and temperature-related seizures may be part of the AGAT deficiency spectrum. Furthermore, significant brain atrophy was demonstrated, despite creatine supplementation. The sensory-predominant epilepsy phenotype aligns with observed atrophy and AGAT-mRNA regional expression patterns, supporting its biological plausibility.

In recent years, pneumonia caused by multiple viruses has posed a significant threat to public health, particularly affecting vulnerable populations such as the elderly and immunocompromised individuals. Current treatments primarily focused on antiviral medications, lacking "miracle cure" and innovative approaches for the pathological damage caused by viruses. Since 2019, Traditional Chinese Medicine (TCM) has shown remarkable efficacy in treating coronavirus disease 2019 (COVID-19). However, the application is hindered by intricate mechanisms, variable quality, and slow onset. Clinically, Ge-Gen Decoction (GGD) effectively reduced the severity in patients with viral infections. Taking COVID-19 as a case, the bioactive ingredients from GGD: glabridin (GLA) and puerarin (PUE) are identified. Interestingly, it was discovered that PUE can self-assemble into a 3D hydrogel structure upon heating and cooling, namely PUE@gel. This process mirrored the formation of gel-like precipitates in GGD post-decoction. Motivated by this phenomenon, a decoction-mimicking drug delivery system, glabridin─puerarin self-assembled hydrogel (GLA-PUE@gel) was constructed, which exhibits strong anti-inflammatory and antioxidant properties, comparable to GGD at the same dosage. Additionally, PUE that has a high biosafety threshold can competitively bind to angiotensin converting enzyme 2 (ACE2) on host cells, preventing SARS-CoV-2 from invading. This study offered a promising approach for treating virus-induced lung injury.

Stomach cancer has become one of the most common types of cancer, with its mortality rate ranking third in the world. Currently, the main treatments for gastric cancer are surgery, radiation therapy, and chemotherapy. Although current treatments can effectively prevent postoperative metastasis and recurrence of gastric cancer, they may also bring various adverse reactions in the gastrointestinal tract and side effects such as bone marrow suppression. Years of research have confirmed that traditional Chinese medicine treatment for gastric and other cancers has distinct characteristics and advantages. Combined treatment can increase the tumor inhibition rate, reduce the side effects of radiation and chemotherapy, improve patients' quality of life, and prolong the survival prognosis.

This study explores the anti-tumor effect and specific molecular mechanism of Hairyvein Agrimonia Herb on gastric cancer.

The combination of network pharmacology technology and various experimental techniques, including in vitro cell verification, was carried out throughout the whole study. The results show that five active components in the Hairyvein Agrimonia Herb can act on 160 carcinogenic targets in gastric cancer. String correlation analysis, Cytoscape network topology analysis, core target screening, protein molecule docking, immunohistochemical expression levels, and survival immune correlation analysis revealed that the carcinogenic genes JUN, HIF1A, and PTGS2 may be the primary drug targets for Hairyvein Agrimonia Herb in treating gastric cancer. The active component quercetin shows the best inhibitory effect on the docking of the PTGS2 protein. Furthermore, the prognostic models constructed by the carcinogenic genes JUN, HIF1A, and PTGS2 are significantly correlated with the survival time of gastric cancer patients.

This study provides a new ethical basis and research direction for understanding the mechanism of action of Hairyvein Agrimonia Herb in treating gastric cancer.

Single amino acid substitutions in protein sequences are generally harmless, but a certain number of these changes can lead to disease. Accurately predicting the effect of genetic variants is crucial for clinicians as it accelerates the diagnosis of patients with missense variants associated with health problems. Many computational tools have been developed to predict the pathogenicity of genetic variants with various approaches. Analysing the performance of these different computational tools is crucial to provide guidance to both future users and especially clinicians. In this study, a large-scale investigation of 65 tools was conducted. Variants from both clinical and functional contexts were used, incorporating data from the ClinVar database and bibliographic sources. The analysis showed that AlphaMissense often performed very well and was in fact one of the best options among the existing tools. In addition, as expected, meta-predictors perform well on average. Tools using evolutionary information showed the best performance for functional variants. These results also highlighted some heterogeneity in the difficulty of predicting some specific variants while others are always well categorized. Strikingly, the majority of variants from the ClinVar database appear to be easy to predict, while variants from other sources of data are more challenging. This raises questions about the use of ClinVar and the dataset used to validate tools accuracy. In addition, these results show that this variant predictability can be divided into three distinct classes: easy, moderate and hard to predict. We analyzed the parameters leading to these differences and showed that the classes are related to structural and functional information.

The etiology of spina bifida is multifactorial; the phenotype is the end result of both genetic and environmental influences. While whole exome sequencing has identified several pathogenic variants in Indian cohorts, the role of chromosomal imbalances and long contiguous stretches of homozygosity (LCSHs) remains largely unexplored in this population. Chromosomal microarray analysis (CMA) is an important tool that provides insights into such genetic aberrations, making it significant for evaluating patients with spina bifida.

To identify LCSHs and chromosomal imbalances in three spina bifida patients through CMA analysis as a pilot investigation.

Genomic DNA was isolated from three spina bifida patients (P1: 10-year-old female, P2: 1-year-old male, and P3: 2.8-year-old male) and subjected to CMA using the Affymetrix 750K high-density array platform. The submicroscopic chromosomal imbalances and LCSHs were cross-referenced with public databases (Database of Genomic Variants, ClinVar, and OMIM) to evaluate their clinical significance. Functional annotations of the affected genes were performed to understand their role in neural tube development.

CMA revealed significant LCSH on chromosomes 2, 3, and 7 involving the genes SOX11, WNT7A, FZD9, SEMA3A, and VHL, all of which are involved in neural tube closure. Mosaic Klinefelter syndrome (25.9% mosaicism) was identified in the second patient while the third patient had a normal genetic profile. The detection of significant genetic variations in two of three cases underscores the potential utility of CMA in spina bifida patients.

This study has generated valuable insights into the complex genetic landscape underlying the multifactorial etiopathogenesis of spina bifida. The findings not only underscore the importance of an integrated approach but also support the cause of a platform for large-scale investigations in the Indian population.

SuoquanYishen formula (SQYSF), a traditional Chinese herbal prescription for treating diabetic kidney disease (DKD), has demonstrated clinical efficacy in lowering blood glucose and alleviating renal damage. Emerging evidence implicates cellular senescence as a critical contributor to DKD progression. This study aimed to elucidate the mechanism by which SQYSF improves renal cellular senescence using both in vivo (db/db mice) and in vitro (high glucose-induced HK-2 cells) DKD models, with interventions involving SQYSF aqueous extract and SQYSF-containing serum. We screened 59 chemical compounds by UHPLC-QTOF-MS and used network pharmacology approach to discover that autophagy and cellular senescence are important pathways for pharmacological treatment of disease. Experimental validation demonstrated that senescence and damage occurred in the kidneys of db/db mice and HK-2 cells under high glucose environment, and SQYSF ameliorated these abnormal changes. Then, we also found that SQYSF enhanced autophagy in renal tissues and cells, whereas co-treatment with the autophagy inhibitor Bafilomycin A1 abolished SQYSF's anti-senescence effects. Notably, DKD progression was associated with elevated Rubicon expression at mRNA and protein levels, accompanied by increased m6A modification. While SQYSF effectively downregulated Rubicon mRNA and protein expression, it did not influence m6A modification levels. Further investigation identified that SQYSF was able to target to reduce YTHDF1 expression level. Overexpression of YTHDF1 in HK-2 cells increased Rubicon mRNA stability and protein expression, while concurrently reversing SQYSF-induced autophagy enhancement and senescence amelioration. These results suggest that SQYSF exerts its role in ameliorating renal cellular senescence in DKD by targeting to reduce the expression level of YTHDF1, which inhibits the level of Rubicon mRNA and protein translation, and thus promotes autophagy. Our results reveal the active components and mechanisms of SQYSF for the treatment of DKD, which may provide useful information to guide the clinical application of SQYSF as well as the therapeutic pathway for DKD.

The clinical consequences of the co-infection with novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and respiratory syncytial virus (RSV) are not optimistic. Nevertheless, there is currently no approved therapeutic regimen specifically targeting SARS-CoV-2/RSV co-infection, with existing monotherapies showing limited efficacy. According to recent studies, probenecid has both anti-SARS-CoV-2 and anti-RSV effects. Therefore, as one probable molecular candidate for the co-infection with SARS-CoV-2 and RSV, probenecid was researched in this exploration.

Using systems pharmacology and bioinformatics, we characterized the targets associated with probenecid for the treatment of SARS-CoV-2/RSV co-infection, focusing on their biological functions, mechanisms and binding activities. To further validate these findings, we conducted molecular docking, MD simulations, electrostatic potential mapping, and SAR analysis to explore the binding interactions between probenecid and the identified core targets.

We identified 141 targets that overlapped with the co-infection and probenecid, and used these shared targets to construct a protein-protein interaction (PPI) network. Subsequently, we obtained the top 16 hub targets of probenecid for SARS-CoV-2/RSV co-infection, namely, AKT1, ALB, EGFR, CASP3, CTNNB1, SRC, HSP90AA1, and so on. According to the enrichment analysis, probenecid might affect inflammation, immunity, oxidative stress, and virus defenses; Toll-like receptor, TNF, IL-17, NOD-like receptor, cytokine-cytokine receptor, among others. Additionally, based on molecular docking analysis, probenecid is effectively bound to the targets related to the SARS-CoV-2/RSV co-infection. Meanwhile, according to molecular dynamics (MD) simulations and structure-activity relationship (SAR) analysis, we speculated that SRC and HSP90AA1 are more likely to be the target proteins of probenecid than the other proteins.

Our findings from systems pharmacology and bioinformatics analysis indicate that immune and inflammatory responses play a pivotal role in the therapeutic effects of probenecid. Infectious disease-related pathways also contribute significantly to its effectiveness in treating SARS-CoV-2/RSV co-infection. Further validation was conducted through molecular docking, MD simulations, electrostatic potential mapping, and SAR analysis. These analyses suggest that SRC and HSP90AA1 are the potential binding targets of probenecid. This study provides valuable preliminary insights into the molecular mechanisms of probenecid. It establishes a strong foundation for future research to explore its potential as a therapeutic strategy for SARS-CoV-2/RSV co-infection.

Diet plays a significant role in mitigating inflammation, with lettuce and its polyphenols showing potential for improving inflammatory conditions. However, research on the material basis and mechanisms of action remains unclear.

This study investigated the primary components and anti-inflammatory effects of the new lettuce cultivar Binfen-1, which is rich in polyphenols and may offer enhanced health benefits. There were 65 metabolites with significant changes in Binfen-1 by metabolomics, comprising mainly polyphenols. Meanwhile, the high-polyphenol lettuce extract (HPLE) from Binfen-1 demonstrated superior antioxidant and anti-inflammatory effects in vitro. Moreover, HPLE showed a significant improvement in mice with dextran sodium sulfate-induced ulcerative colitis. By integrating network pharmacology with high-performance liquid chromatographic quantitative results, isoquercitrin and chlorogenic acid were identified as the core active substances in HPLE, and the PI3K-Akt, MAPK, and JAK-STAT pathways were the key anti-inflammatory pathways for HPLE, supported by mRNA validation and molecular docking predictions.

The core anti-inflammatory substances in HPLE were isoquercitrin and chlorogenic acid, with the key anti-inflammatory pathways being the PI3K-Akt, MAPK, and JAK-STAT pathways. These findings substantially propel the understanding of the therapeutic potential of lettuce in the treatment of inflammatory diseases. © 2025 Society of Chemical Industry.

Cisplatin is an important chemotherapeutic agent is widely used to treat breast cancer and olaparib is the most studied PARP inhibitor to date. To explore the combinational anti-cancer potential and synergistic mechanism of Olaparib and cisplatin in breast cancer using network pharmacology. Drugs targets were drawn from PharmMapper, DrugBank, BATMAN-TCM, DrugCentral, STITCH, Swiss Institude of Bioinformatics and Comparative Toxigenomics Database (CTD). Breast cancer targets were extracted from OMIM, KEGG, GeneCards and DrugBank. The protein-protein interaction (PPI) network was created using the STRING database. Core targets were selected by incorporating PPI networks using Cytoscape 3.9.1. GO and KEGG analyses were performed to investigate common targets of Olaparib and cisplatin in breast cancer. The drug-disease-target network contained 82 nodes and 901 edges. The common targets obtained from Olaparib, cisplatin and breast cancer were identified, including ATK, p53, caspase-3, HSP90AA1, IL-6, IL-1β, ANXA5, SIRT1, caspase-9 and PARP. Core targets were primarily related to response to reactive oxygen species, regulation of apoptotic signaling pathway, regulation of DNA metabolic process, and regulation of cell activation. The KEGG pathway analysis revealed that Olaparib and cisplatin may affect breast cancer through platinum drug resistance and longevity regulating pathway. Furthermore, Olaparib combined with cisplatin downregulated the expression of caspase-3 and caspase-9 proteins and upregulated p53, PARP, and SIRT1 protein levels in MCF-7 cells. Functionally, the cooperative effect of Olaparib and cisplatin reduced the applied concentration of cisplatin and enhanced the anticancer effect, emphasizing the importance of combination therapy to overcome side effects and significantly improve the anticancer efficacy of cisplatin.

The risk of PCOS is significantly increased in obese women, and studies have shown that weight loss can improve symptoms of PCOS. Coffee has been shown to be effective in reducing body weight. In this study, we focused on the SLC16A6 gene using bioinformatics and searched for coffee and its monomers using reverse network pharmacology. The gene expression omnibus (GEO) database was searched to screen for differentially expressed genes (DEGs) in PCOS patients. Gene ontology (GO) functional enrichment analysis and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis were then performed. The effects of caffeine on body weight, estrous cycle, ovarian pathology, serum insulin concentration and insulin resistance index, and SLC16A6 transporter gene expression in ovarian tissue of obese PCOS rats were monitored. The common differentially expressed gene SLC16A6 was identified in this study, and animal experiments confirmed the efficacy of caffeine in the treatment of obese PCOS rats. Caffeine can effectively improve the symptoms of obese PCOS rats. The mechanism by which caffeine can treat obese patients with PCOS is related to increasing the expression of the SLC16A6 gene.

Rheumatoid arthritis (RA) is a chronic inflammatory disorder characterized by joint swelling, cartilage degradation, and joint deformity. The traditional Chinese herb Cynanchum paniculatum (Bunge) Kitag has been utilized in the management of RA, but the underlying mechanisms are unknown. This study utilized network pharmacology analysis to identify 26 active compounds associated with RA treatment and elucidate their interactions with 23 critical targets linked to RA. Subsequently, molecular docking studies revealed eight compounds with the capacity to bind to multiple key targets, with butyl isobutyl phthalate and geranyl acetone emerging as the most promising candidates based on their drug-likeness properties. To validate these findings, a rat model of adjuvant-induced arthritis was employed. Oral administration of geranyl acetone led to a significant reduction in paw swelling and pro-inflammatory markers, including TNF-α, IL-6, IL-1β, and MPO. Furthermore, it resulted in histological improvements in ankle tissues, all without adverse effects on weight or immune organs. Mechanistically, geranyl acetone was found to impede the progression of RA by modulating the TLR4/MyD88/NF-κB signaling pathway. In conclusion, C. paniculatum demonstrates substantial therapeutic potential for RA due to its multi-target and multi-pathway activities. Moreover, geranyl acetone, when used as a standalone agent, exhibits significant promise in alleviating RA symptoms, offering a compelling avenue for further research and potential clinical applications.

As an important self-protection response mechanism of the body, inflammation can not only remove the necrotic or even malignant cells in the body, but also take a series of targeted measures to eliminate the pathogen of foreign invasion and block the foreign substances that may affect the life and health of the body. Flavonoids have known anti-inflammatory, anti-oxidation, anti-cancer and other effects, including glycyrrhizin molecules is one of the representatives. Licochalcone D has known anti-inflammatory and antioxidant properties and is effective in the treatment of a variety of inflammatory diseases. However, the underlying mechanism for the treatment of sepsis remains unclear. In this study, the therapeutic potential of Licochalcone D for sepsis was studied by analyzing network pharmacology and molecular dynamics simulation methods. Sepsis-related genes were collected from the database to construct PPI network maps and drug-targeting network profiles. The potential mechanism of Licochalcone D in sepsis was predicted by gene ontology, KEGG and molecular dynamics simulation. Sixty drug-disease genes were subsequently validated. Go analysis showed that monomeric small molecule Licochalcone D could regulate the process of intracellular enzyme system. The KEGG pathway analysis showed that the signal pathway of the main effect was related to the calcium pathway. The results of intersections with iron death-related target genes showed that ALOX5, ALOX15B and other nine targets all had the effect of possibly improving sepsis, while GSE 54,514, GSE 95,233 and GSE 69,528 were used to analyze the survival rate and ROC curve. Five genes were screened, including ALOX5, ALOX15B, NFE2L2 and NR4A1, HIF1A. The results of molecular docking showed that ALOX5 and Licochalcone D had strong binding activity. Finally, the results of molecular dynamics simulation showed that there was good binding power between drug and target. In the present study, we utilized molecular dynamics simulation techniques to assess the binding affinity between the small-molecule ligand and the protein receptor. The simulation outcomes demonstrate that the binding interface between the ligand and receptor remains stable, with a calculated binding free energy (ΔG) of -32.47 kJ/mol. This signifies a high-affinity interaction between the ligand and receptor, suggesting the long-term stability of the small molecule under physiological conditions. These findings provide critical insights for drug development efforts. This study elucidates the therapeutic potential of Licochalcone D, a traditional Chinese medicine monomer, in improving sepsis through the regulation of ferroptosis, thereby providing a new direction and option for subsequent clinical drug development in the treatment of sepsis.

Mongolian Medicine Areca Thirteen Pill (GY-13), a traditional Mongolian medicine, is esteemed for its efficacy in treating Heyi disease. Studies indicate its antidepressant effects on depression model rats induced by chronic stress, but the specific plant extracts (PEs) and their targets remain undetermined. Network pharmacology was applied to identify the key target SLC6A4 and crucial PEs in GY-13 for treating major depressive disorder (MDD). Molecular docking techniques were used to validate the binding capabilities between GY-13 components and SLC6A4. Mendelian randomization was employed to confirm SLC6A4 as a genetically predisposed gene to depression. Molecular dynamics simulations supported the binding affinity between SLC6A4 and PEs Kaempferol and Quercetin. Immunohistochemical techniques were used to confirm the down-regulatory effect of GY-13 on SLC6A4 in an animal model. The key target SLC6A4 and critical PEs Kaempferol and Quercetin in GY-13 were identified for MDD treatment. Strong binding affinity between these PEs and SLC6A4 was demonstrated, and the genetic predisposition of SLC6A4 to depression was confirmed. This study elucidates the molecular mechanisms of GY-13 in treating MDD, highlighting the importance of SLC6A4 and specific PEs Kaempferol and Quercetin in its therapeutic effects.

Non-alcoholic fatty liver disease (NAFLD) is prevalent worldwide and lacks effective treatments. Arctiin (AR), a natural product, has shown promise for NAFLD therapy, due to its antioxidant, anti-inflammatory, and inhibition adipogenesis properties. However, its therapeutic efficacy is hindered by low water solubility, poor bioavailability, and inadequate liver targeting. In this study, selenium-based antioxidant nanoparticles were developed to load and deliver AR to the liver for synergistic AR and selenium effective treatment of NAFLD.

The therapeutic potential of AR was analyzed by network pharmacology. GA-MSe@AR was synthesized by encapsulating AR within galactose-modified mesoporous selenium nanoparticles (GA-MSe) for liver-specific targeting. The nanoparticle size, chemical structure, and elemental composition were explored. The toxicity, cellular uptake, lysosomal escape, and AR release efficiency of GA-MSe@AR were investigated by in vitro experiments. The liver targeting ability of GA-MSe@AR was evaluated through live imaging. The lipid-lowering and antioxidant activities of GA-MSe@AR were assessed in both in vitro and in vivo NAFLD models. Additionally, its effects on inflammation and pancreatic function were analyzed in vivo.

Network pharmacology analysis revealed AR may against NAFLD through regulating metabolism, inflammation, and oxidative stress. GA-MSe@AR exhibited low toxicity, efficient cellular uptake, remarkable lysosomal escape ability, and high AR release efficiency in vitro. In both in vitro and in vivo NAFLD models, GA-MSe@AR demonstrated more pronounced lipid-lowering and antioxidant properties than AR and GA-MSe. Additionally, GA-MSe@AR effectively targeted the liver, resulting in a greater decrease in blood glucose, lipids, ALT, AST levels, and reduction liver inflammation, as well as improved pancreatic function in high-fat diet (HFD)-fed mice compared to AR alone.

The GA-specific modification enhanced liver-targeted accumulation of the selenium-based nanoparticles, enabling precise targeted delivery of AR. GA-MSe@AR demonstrated superior lipid-lowering efficacy and antioxidant activity in a NAFLD mice model. These findings collectively establish GA-MSe@AR as a promising therapeutic candidate for NAFLD treatment.

This study aims to identify core Traditional Chinese Medicine compound prescriptions (TCM CPs) for Primary Liver Cancer (PLC) and their underlying mechanisms. A comprehensive search was conducted using China National Knowledge Infrastructure (CNKI) and the Chinese Medical Code V5.0, identifying 151 TCM CPs. Medication frequency and association rules were analyzed with TCMICS V3.0, while active compounds were identified via TCMSP and TCMIP V2.0. Targets were predicted using Swiss Target Prediction, and disease targets from DisGeNET, OMIM, and GeneCards were cross-referenced. A protein-protein interaction (PPI) network was constructed, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis using DAVID. In the process of studying active compounds, an orthogonal experiment was carried out on the extraction process of relevant herbs. The results of the orthogonal experiment and range analysis showed that for the extraction rate of the extract and the content of paeoniflorin, the decoction cycles had the most significant impact, followed by soaking time and water volume. The optimal extraction conditions were determined as soaking time of 30 min, water volume of tenfold, and 3 decoction cycles. Under these conditions, the extract yield reached 42.49%, and the paeoniflorin content was 73.60 mg/25.02 g crude herb (equivalent to 2.94 mg/g). ANOVA analysis further confirmed the significance of these factors. The results revealed 109 common targets between TCM component targets and disease targets, with key targets including STAT3, SRC, AKT1, HRAS, and PIK3CA. Molecular docking showed strong binding affinities of paeoniflorin and 3,5,6,7-tetramethoxy-2-(3,4,5-trimethoxyphenyl) chromone to PLC targets, with ADME predictions favoring paeoniflorin. Furthermore, Molecular Dynamics (MD) simulations revealed that paeoniflorin maintains stable binding to the target proteins, demonstrating promising conformational stability. The CCK-8 assay demonstrated that the core TCM CP exerted a dose-dependent inhibitory effect on HepG2 cells. After 24 h of intervention, the IC50 values of paeoniflorin and the TCM CP on HepG2 cells were 17.58 μg/mL and 120.5 μg/mL, respectively, which confirmed their anti-proliferative activity against PLC. This study identifies key active compounds and investigates their roles in modulating the Ras/Raf/MEK/ERK, AKT/NF-κB, and JAK-STAT signaling pathways, offering valuable insights into the therapeutic potential of TCM for PLC treatment.

The online version contains supplementary material available at 10.1007/s40203-025-00352-2.

In humans, PHARC (polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, and cataract) is an early onset autosomal recessive neurological disorder caused by deleterious mutations to ABHD12 (α/β-hydrolase domain protein # 12). Biochemically, ABHD12 functions as a lipase and catalyzes the hydrolysis of lysophosphatidylserine (lyso-PS) (lyso-PS lipase). By doing so, it controls the concentrations and signaling pathways regulated by this potent signaling lysophospholipid in the mammalian brain. While genetic mapping efforts have identified over 30 mutations in ABHD12 from human PHARC subjects, the biochemical activity of these pathogenic mutants remains unknown. To understand this, here, we performed an exhaustive bioinformatics survey and collated ABHD12 protein sequences from various organisms across evolution. Next, based on sequence alignments and structural modeling, we identified functionally relevant conserved residues in the ABHD12 protein sequence that are potentially important for its enzymatic activity. To validate these in silico findings, we generated numerous mutants of murine ABHD12, including those associated with human PHARC subjects, and assayed them for their enzymatic activity. Taken together, these complementary in silico and biochemical studies provide the first thorough sequence-function relationship for mammalian ABHD12, especially relevant in the context of PHARC. Finally, our evolutionary analysis identified CG15111 as an ABHD12 ortholog in the fruit fly (Drosophila melanogaster), and enzymatic assays indeed confirmed that recombinant CG15111 has robust lyso-PS lipase activity. Flies serve as an excellent animal system to model various human neurological diseases, and the identification of CG15111 as a Drosophila melanogaster ABHD12 ortholog opens new avenues to study PHARC in fly models.