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The integration of metabolites from Forsythia suspensa and gut microbiota ameliorates drug-induced liver injury: network pharmacology and molecular docking studies

This study integrates metabolites from Forsythia suspensa (FS) and gut microbiota GM to assess combined therapeutic efficacy against drug-induced liver injury (DILI) using network pharmacology and molecular docking. Metabolites of FS and GM were retrieved from the NPASS and gutMGene databases, respectively. Relevant targets for metabolites and DILI-related targets were identified through public databases. The PPI network and KEGG pathway analysis were employed to identify hub targets and key signalling pathways. Furthermore, we performed a molecular docking assay on the active metabolites and targets to verify the network pharmacological concept. The physicochemical properties and toxicity of identified key metabolites were assessed using in silico platforms. 19 final targets were recognized as key proteins responsible for the alleviation of DILI by FS and GM metabolites, with ESR1 emerging as a central target in the PPI network. The estrogen signalling pathway, particularly involving ESR1, ESR2 and JUN genes, was identified as a key mediator in the therapeutic effects. Four GM metabolites (baicalein, luteolin, lunularin and 2,3-bis(3,4-dihydroxybenzyl)butyrolactone) and two FS metabolites (pinoresinol and isolariciresinol) were identified as non-toxic, promising candidates. In conclusion, metabolites from FS and GM may exert a potent synergistic effect on DILI through modulation of the estrogen signalling pathway.

Dissecting the shared molecular mechanisms underlying polycystic ovary syndrome and schizophrenia etiology: a translational integrative approach

Recent evidence suggests that individuals with polycystic ovary syndrome (PCOS) have an increased risk of developing mental health disorders and comorbidities linked to nervous system dysfunction. Interestingly, patients with schizophrenia (SCZ) often exhibit PCOS symptoms, indicating a possible connection between the two conditions. However, the underlying molecular links between these diseases remain poorly understood. We employed a comprehensive in-silico approach, utilizing publicly available datasets to investigate shared biomarkers candidates and key regulators involved in the development of PCOS and SCZ. We retrieved the datasets from the NCBI GEO database and differentially expressed genes (DEGs) were identified for each dataset. Common DEGs (cDEGs) were determined, and transcription factors (TFs) and miRNA targeting cDEGs were examined using the mirDIP portal and TRRUST database, respectively. We also assessed the TF-miRNA interactions by TransmiR database and constructed a regulatory network including TFs-microRNAs-cDEGs. Our analysis identified a total of 15 cDEGs that are regulated by 15 TFs and 8 mRNAs. Among our findings, we prioritized RELA as a potential TF regulator for both diseases, demonstrating synergistic interaction with four cDEGs (EGR1, CXCL8, IL1RN, IL1B) and seven microRNAs (hsa-miR-580, hsa-miR-5695, hsa-miR-936, hsa-miR-3675, hsa-miR-634, hsa-miR-603, hsa-miR-222) that target these genes. Our data highlights potential common biomarkers for PCOS and SCZ, presenting a novel regulatory network that elucidates the molecular mechanisms underlying both conditions. This emphasizes the importance of further research to explore new translational approaches, which may ultimately lead to improved diagnostic and therapeutic strategies for affected individuals.

Pharmacogenomic heterogeneity of N-acetyltransferase 2: a comprehensive analysis of real world data in Indian tuberculosis patients and from literature and database review

BACKGROUND

Isoniazid is primarily metabolized by the arylamine N-acetyltransferase 2 (NAT2) enzyme. Single nucleotide polymorphisms (SNPs) in the NAT2 gene could classify an individual into three distinct phenotypes: rapid, intermediate and slow acetylators. NAT2 SNPs and the slow acetylator phenotype have been implicated as risk factors for the development of antitubercular drug-induced liver injury (AT-DILI) in several tuberculosis (TB) populations.

PATIENTS AND METHODS

We conducted a prospective observational study to characterize and compare the NAT2 SNPs, genotypes and phenotypes among patients with TB and AT-DILI from the Southern and Western regions of India. The NAT2 pharmacogenomic profile of patients from these regions was compared with the reports from several geographically diverse TB populations and participants of different genetic ancestries extracted from literature reviews and the 'All of Us' Research Program database, respectively.

RESULTS

The TB patients of Southern and Western regions of India and several other geographically closer regions exhibited near similar NAT2 MAF characteristics. However significant heterogeneity in NAT2 SNPs was observed within and between countries among AT-DILI populations and the participants of different genetic ancestry from the 'All of Us' Research Program database. The MAF of the NAT2 SNPs rs1041983, rs1801280, rs1799929, rs1799930 and rs1208 of the TB patients from Southern and Western Indian Sites were in near range to that of the South Asian genetic ancestry of 'All of Us' Research Program database. About one-third of the total TB patients from the Southern and Western regions of India were NAT2 slow acetylators, among whom a relatively higher proportion experienced AT-DILI.

CONCLUSION

Further studies exploring the risk of NAT2 SNPs in different AT-DILI patients with larger sample sizes and a population-specific approach are required to establish a policy for NAT2 genotyping as a pre-emptive biomarker for AT-DILI monitoring for personalized isoniazid therapy in clinics.

Mapping the rapid growth of multi-omics in tumor immunotherapy: Bibliometric evidence of technology convergence and paradigm shifts

This study aims to fill the knowledge gap in systematically mapping the evolution of omics-driven tumor immunotherapy research through a bibliometric lens. While omics technologies (genomics, transcriptomics, proteomics, metabolomics)provide multidimensional molecular profiling, their synergistic potential with immunotherapy remains underexplored in large-scale trend analyses. A comprehensive search was conducted using the Web of Science Core Collection for literature related to omics in tumor immunotherapy, up to August 2024. Bibliometric analyses, conducted using R version 4.3.3, VOSviewer 1.6.20, and Citespace 6.2, examined publication trends, country and institutional contributions, journal distributions, keyword co-occurrence, and citation bursts. This analysis of 9,494 publications demonstrates rapid growth in omics-driven tumor immunotherapy research since 2019, with China leading in output (63% of articles) yet exhibiting limited multinational collaboration (7.9% vs. the UK's 61.8%). Keyword co-occurrence and citation burst analyses reveal evolving frontiers: early emphasis on "PD-1/CTLA-4 blockade" has transitioned toward "machine learning," "multi-omics," and "lncRNA," reflecting a shift to predictive modeling and biomarker discovery. Multi-omics integration has facilitated the development of immune infiltration-based prognostic models, such as TIME subtypes, which have been validated across multiple tumor types, which inform clinical trial design (e.g. NCT06833723). Additionally, proteomic analysis of melanoma patients suggests that metabolic biomarkers, particularly oxidative phosphorylation and lipid metabolism, may stratify responders to PD-1 blockade therapy. Moreover, spatial omics has confirmed ENPP1 as a potential novel therapeutic target in Ewing sarcoma. Citation trends underscore clinical translation, particularly mutation-guided therapies. Omics technologies are transforming tumor immunotherapy by enhancing biomarker discovery and improving therapeutic predictions. Future advancements will necessitate longitudinal omics monitoring, AI-driven multi-omics integration, and international collaboration to accelerate clinical translation. This study presents a systematic framework for exploring emerging research frontiers and offers insights for optimizing precision-driven immunotherapy.

Bioprinted high cell density liver model with improved hepatic metabolic functions

In vitro liver tissue models are valuable for studying liver function, understanding liver diseases, and screening candidate drugs for toxicity and efficacy. While three-dimensional (3D) bioprinting shows promise in creating various types of functional tissues, current efforts to engineer a functional liver tissue face challenges in replicating native high cell density (HCD) and maintaining long-term cell viability. HCD is crucial for establishing the cell-cell interactions necessary to mimic the liver's metabolic and detoxification functions. However, HCD bioinks exacerbate light scattering in light-based 3D bioprinting. In this study, we incorporated iodixanol into our bioink formulation to minimize light scattering, enabling the fabrication of hepatic tissue constructs with an HCD of 8 × 107 cells/mL while maintaining high cell viability (∼80 %). The printed dense hepatic tissue constructs showed enhanced cell-cell interactions, as evidenced by increased expression of E-cadherin and ZO-1. Furthermore, these constructs promoted albumin secretion, urea production, and P450 metabolic activity. Additionally, HCD hepatic tissue inactivated the YAP/TAZ pathway via cell-cell interactions, preserving primary hepatocyte functions. Further screening revealed that hepatocytes in the dense model were more sensitive to drug treatments than those in a lower-density hepatic model, highlighting the importance of HCD in recapitulating the physiological drug responses. Overall, our approach represents a significant advancement in liver tissue engineering, providing a promising platform for the development of physiologically relevant in vitro liver models for drug screening and toxicity testing.

Epigenome-wide association study identifies a specific panel of DNA methylation signatures for antenatal and postpartum depressive symptoms

Depression during pregnancy and postpartum poses significant risks to both maternal and child well-being. The underlying biological mechanisms are unclear, but epigenetic variation could be exploited as a plausible candidate for early detection. We investigated whether DNA methylation signatures are associated with antenatal depressive symptoms (ADS) and whether early alterations in methylation patterns could be used to predict postpartum depressive symptoms (PDS). 201 pregnant women in early pregnancy, without a prior history of depressive disorders, from the STratification of Risk of Diabetes in Early Pregnancy study (STRiDE) were recruited. Using the Patient Health Questionnaire-9 (PHQ-9), 92 women were identified with ADS, while 109 served as controls. Edinburgh Postnatal Depression Scale (EPDS) was used to assess PDS during 6-12 weeks after delivery. The dataset was split into 80 % for training and testing and 20 % for validation, to discern potential CpGs for ADS using a support vector machine classifier. Analysis revealed 591 CpGs significantly associated with ADS, from which a panel of 7 CpGs was identified to discriminate between ADS and controls with high sensitivity and specificity (AUC: 0.85 in test, 0.73 in validation). Pathway analysis highlighted involvement in inositol phosphate metabolism, notch, and calcium signaling. The same 7 CpGs predicted PDS with an AUC of 0.76 (95 % CI: 0.66-0.87). Integration of CpG data with patient-reported information significantly enhanced PDS prediction. Our study identified DNA methylation signatures that could potentially differentiate ADS from controls and predict PDS. This suggests potential for developing a CpG panel for diagnostic and preventive strategies for perinatal depression.

Serum metabolic signatures and MetalnFF diagnostic score for mild and moderate metabolic dysfunction-associated steatotic liver disease

To explore serum metabolic changes in metabolic dysfunction-associated steatotic liver disease (MASLD) with mild or moderate steatosis and develop a diagnostic index based on liver fat content to differentiate these stages. A total of 149 participants were enrolled from the Nutrition Health Atlas Project in 2019 (Stage 1, n = 92) and 2022 (Stage 2, n = 57). Serum levels of amino acids, free fatty acids (FFAs) and other organic acids were quantified using liquid or gas chromatography-mass spectrometry. The relationships between serum metabolites and magnetic resonance imaging proton density hepatic fat fraction were analyzed and a predictive model fitting fat fraction was constructed in Stage 1 and validated in Stage 2. Patients with moderate MASLD had significantly higher pyruvic acid, 2-ketoglutaric acid, malic acid, 2-hydroxyisocaproic acid and FFA(C14:0) than mild MASLD. Pathway analysis indicated that liver fat accumulation is associated with alterations in amino acid, FFA metabolism and tricarboxylic acid cycle (TCA). The MetalnFF score was developed to discriminate among three groups, achieving an area under the curve (AUC) of 0.956 (95 %CI:0.905, 1.00) for MASLD and 0.857 (95 %CI:0.745, 0.968) for moderate MASLD in Stage 1, and was further validated in Stage 2 with an AUC of 0.986 (95 %CI: 0.951, 1.00) and 0.759 (95 %CI:0.607, 0.921), respectively. In the early stages of MASLD, disrupted amino acid, FFAs metabolism and TCA cycle have occurred. As the disease progresses, metabolic disturbances in pyruvate metabolism become more severe. These findings enhance a deeper understanding of pathogenesis and propose MetalnFF score as a potential diagnostic tool.

Reducing the allergenicity of whey proteins while improving their functional properties and bioactivity using combined enzymes

The aim of this study was to investigate the changes in functional properties, bioactivity and allergenicity of whey protein hydrolysates (WPH) prepared by combinations of endopeptidases and exopeptidases. The immunoglobulin E-binding capacity of WPH made by combining pineapple protease and papain with the exopeptidase ProteAXH was reduced by 47.62 % and 51.91 %, respectively, and the emulsification performance was improved by about 40 % in both cases. Multispectral results indicated that the addition of ProteAXH increased the disruption of protein conformation. Liquid chromatography coupled with tandem mass spectrometry analysis revealed that the exopeptidase altered the hydrolysis sites of the protein. Further combination with bioinformatics revealed that increased conformational disruption and altered linear epitope hydrolysis sites decreased the allergenicity of WPH. Meanwhile, the structural changes also increased the release of emulsifying peptides and bioactive peptides, thus improving the functional properties. In conclusion, these two WPHs combine hypoallergenicity with excellent functional properties and bioactivity.

Probing the antibacterial mechanism of Aloe vera based on network pharmacology and computational analysis

Bacterial resistance has emerged as a major clinical challenge globally. Natural products, such as Aloe vera, offer promising antimicrobial potential due to their diverse active components. However, the explicit molecular mechanisms remain unknown. In this study, we employed a multidisciplinary approach integrating network pharmacology, molecular docking, and molecular dynamics simulation to explore the antibacterial mechanism of Aloe vera. We screened the eight major active components of Aloe vera and their targets using multi-source bioinformatics platforms, identifying 55 targets closely associated with the antibacterial effects of Aloe vera. Protein-protein interaction network analysis, revealed potential crucial targets, including cysteine-aspartic acid protease-3 (CASP3) and matrix metalloproteinase-9 (MMP-9). Gene ontology functional enrichment analysis revealed that these targets play critical roles in several essential biological processes, such as "response to xenobiotic stimulus", "positive regulation of gene expression", and "collagen catabolism". The Kyoto Encyclopedia of Genes and Genomes signal pathway analysis indicated that these targets are primarily involved in pathways associated with cancer, lipid metabolism, atherosclerosis, and the AGE/RAGE signaling pathway in diabetes. This finding suggests that Aloe vera may exert its antibacterial effects by regulating the host's immune response and metabolism. Molecular docking and molecular dynamics simulations demonstrated that active ingredients of Aloe vera, such as quercetin and aloe-emodin, can form stable complexes with CASP3 and MMP-9, exhibiting vigorous binding affinity to the active sites of the target. Further antibacterial activity assays and reverse transcription quantitative polymerase chain reaction (RT-qPCR) analysis demonstrated that aloe-emodin exerts antibacterial effects against gram-positive bacteria and inhibits the expression of the MMP-9 gene. This study provided insight into the antibacterial mechanisms of Aloe vera, highlighting MMP-9 as a key target. These findings lay a foundation for further studies on natural antibacterial agents.

Protein to biomaterials: Unraveling the antiviral and proangiogenic activities of Ac-Tβ1-17 peptide, a thymosin β4 metabolite, and its implications in peptide-scaffold preparation

Peptide metabolites are emerging biomolecules with numerous possibilities in biomaterial-based regenerative medicine due to their inherent bioactivities. These small, naturally occurring compounds are intermediates or byproducts of larger proteins and peptides, and they can have profound effects, such as antiviral therapeutics, proangiogenic agents, and regenerative medicinal applications. This study is among the first to focus on using thymosin β4 protein-derived metabolites to pioneer novel applications for peptide metabolites in biomaterials. This study found that the novel peptide metabolite acetyl-thymosin β4 (amino acid 1-17) (Ac-Tβ1-17) exhibited significant protease inhibition activity against SARS-CoV-2, surpassing its precursor protein. Additionally, Ac-Tβ1-17 demonstrated beneficial effects, such as cell proliferation, wound healing, and scavenging of reactive oxygen species (ROS) in human umbilical vein endothelial cells (HUVEC). Integrating Ac-Tβ1-17 into a peptide-based scaffold facilitated cell growth and angiogenesis inside the scaffold and through gradual release into the surrounding environment. The Ac-Tβ1-17 peptide treatment induced significant biochemical responses in HUVEC, increasing Akt, ERK, PI3K, MEK, and Bcl-2 gene expression and proangiogenic proteins. Ac-Tβ1-17 peptide treatment showed similar results in ex vivo by enhancing mouse fetal metatarsal growth and angiogenesis. These findings highlight the potential of natural protein metabolites to generate biologically active peptides, offering a novel strategy for enhancing biomaterial compatibility. This approach holds promise for developing therapeutic biomaterials using peptide metabolites, presenting exciting prospects for future research and applications.

Short-chain chlorinated paraffins induce hippocampal damage and glycerophospholipids disruption contributing to neurobehavioral deficits in mice

Short-chain chlorinated paraffins (SCCPs), a class of widely used industrial chemicals, have raised significant health concerns due to their persistence, bioaccumulation, and potential neurotoxicity. This study investigated the neurotoxic effects of SCCPs on the hippocampus and their impact on brain glycerophospholipid metabolism in mice. Behavioral tests revealed that 50 mg/kg SCCPs exposure significantly reduced spontaneous activity and impaired learning and memory. Pathological examination showed neuronal damage, including nuclear pyknosis and cytoplasmic vacuolization, in the hippocampus. Biochemical analyses indicated elevated oxidative stress markers (reactive oxygen species, malondialdehyde) and decreased antioxidant levels (glutathione, superoxide dismutase), alongside reduced levels of neurotransmitters (5-Hydroxytryptamine, dopamine, brain-derived neurotrophic factor). Lipidomics analysis identified significant alterations in glycerophospholipid metabolites, such as decreased levels of phosphatidylcholine and phosphatidylserine. Immunohistochemistry demonstrated downregulation of tight junction proteins (Claudin-1, ZO-1), suggesting blood-brain barrier disruption. These findings highlight SCCPs' potential to induce hippocampal oxidative stress, neurotransmitter dysregulation, decreased claudin-1 expression and glycerophospholipid metabolism disruption, contributing to neurobehavioral deficits. This study provides insights into the mechanisms of SCCPs-induced neurotoxicity and emphasizes their potential implications for brain health.

A SlRBP1-SlFBA7/SlGPIMT module regulates fruit size in tomato

Fleshy fruits are vital to the human diet, providing essential nutrients, such as sugars, organic acids, and dietary fibers. RNA-binding proteins play critical functions in plant development and environment adaption, but their specific contributions to fruit development remain largely unexplored. In this study, we centered on the function of SlRBP1 in tomato fruit and reported an unexpected finding that SlRBP1 controls fruit size by regulating its targets SlFBA7 and SlGPIMT. Here, the fruit-specific silencing of SlRBP1 was achieved by artificial miRNA which subsequently led to a marked reduction of fruit size. Cytological analysis suggested that SlRBP1 silencing decreased cell division and expansion of fruit pericarp. Those key genes involved in cell development were significantly repressed in SlRBP1 knock-down mutants. Furthermore, native RNA immunoprecipitation sequencing deciphered 83 SlRBP1-binding target RNAs in fruit, including two targets that are highly expressed in fruit: SlFBA7 and SlGPIMT, which are involved in developing fruit. Indeed, silencing either SlFBA7 or SlGPIMT resulted in fruit size reduction identical to that seen with SlRBP1 silencing. These results suggest that SlRBP1 modulates fruit size through its targets SlFBA7 and SlGPIMT. Our findings provide novel perspectives on the molecular mechanisms though which RNA-binding proteins control fruit size.

Inhibition of mitochondrial genome-encoded mitomiR-3 contributes to ZEB1 mediated GPX4 downregulation and pro-ferroptotic lipid metabolism to induce ferroptosis in breast cancer cells

Ferroptosis, an iron-dependent form of regulated cell death driven by lipid peroxidation, represents a unique vulnerability in cancer cells. However, current ferroptosis-inducing therapies face clinical limitations due to poor cancer cell specificity, systemic toxicity, and off-target effects. Therefore, a deeper understanding of molecular regulators of ferroptosis sensitivity is critical for developing targeted therapies. The metabolic plasticity of cancer cells determines their sensitivity to ferroptosis. While mitochondrial dysfunction contributes to metabolic reprogramming in cancer, its role in modulating ferroptosis remains poorly characterized. Previously, studies have identified that mitochondrial genome also encodes several non-coding RNAs. We identified 13 novel mitochondrial genome-encoded miRNAs (mitomiRs) that are aberrantly overexpressed in triple-negative breast cancer (TNBC) cell lines and patient tumors. We observed higher levels of mitomiRs in basal-like triple-negative breast cancer (TNBC) cells compared to mesenchymal stem-like TNBC cells. Strikingly, 11 of these mitomiRs directly target the 3'UTR of ZEB1, a master regulator of epithelial-to-mesenchymal transition (EMT). Using mitomiR-3 mimic, inhibitor and sponges, we demonstrated its role as a key regulator of ZEB1 expression in TNBC cells. Inhibition of mitomiR-3 via sponge construct in basal-like TNBC, MDA-MB-468 cells, promoted ZEB1 upregulation and induced a mesenchymal phenotype. Further, mitomiR-3 inhibition in TNBC cells contributed to reduced cancer cell proliferation, migration, and invasion. Mechanistically, mitomiR-3 inhibition in TNBC cells promote metabolic reprogramming toward pro-ferroptotic pathways, including iron accumulation, increased polyunsaturated fatty acid (PUFA) metabolites, and lipid peroxidation, contributing to ferroptotic cell death via ZEB1-mediated downregulation of GPX4, a critical ferroptosis defense enzyme. We observed that mitomiR-3 inhibition significantly suppressed tumor growth in vivo. Our identified mitomiR-3 has low expression in normal breast cells, minimizing potential off-target toxicity, making them a promising target for pro-ferroptotic cancer therapy. Our study reveals a novel link between mitochondrial miRNAs and ferroptosis sensitivity in TNBC paving a way for miRNA-based therapeutics.

Coupling proteomics and lipidomics for insights into regulation of oat (Avena sativa) grain lipid synthesis

Breeding is a feasible strategy to develop low-oil oat (Avena sativa) varieties, which aligns with specific processing needs and dietary preferences. To identify factors contributing to a low-oil phenotype, we optimised a sequential extraction workflow for proteomics and lipidomics analyses on five Australian oat varieties with different oil contents. Oat oil content positively correlated with abundances of several proteins in lipid synthesis pathways, suggesting their key lipid regulatory roles. Lipidomics was used to complement proteomics data and revealed a negative correlation between triacylglycerols and other lipid classes such as diacylglycerols and phospholipids. Spatial regulation of lipids was also investigated using matrix-assisted laser desorption and ionisation mass spectrometry imaging (MALDI-MSI) and proteomics analysis of tissue-enriched fractions, providing further insights into distinct physiological functions of the endosperm and embryo. Pathway enrichment analysis indicated different nutrient-synthesising capacity in high- vs low-oil varieties. Findings from this study may support future breeding for low-oil oats.

Direct hybridization and bioinformatics analysis of circulating microRNAs in patients with Alzheimer's disease under intravenous trehalose treatment

Trehalose has been proposed as a possible therapeutic option for attenuating the neuropathological changes associated with neurodegeneration, including Alzheimer's disease (AD). The administration of trehalose in human and murine models was linked to restoring antioxidant status, decreasing lipoperoxidation, and alleviating neuroinflammation. This latter biochemical mechanism was associated with the upregulation of specific brain-enriched microRNAs (miRNA). Herein, using a direct hybridization approach, we evaluate trehalose intravenous treatment in AD patients, conducting a phase two clinical trial (IRCT20130829014521N15) examining the alteration of microRNA profiles before and after the treatment. Twenty patients were recruited and randomly assigned to two groups: the intervention group received 15 g/week of intravenous trehalose. The control group received placebo in the form of normal saline. The period chosen was 12 weeks. Blood samples were obtained at the beginning and end of the study. Circulating microRNAs expression data between the placebo and treatment groups were assessed using microarray analysis. Subsequently, differentially expressed (DE) miRNAs specific to the trehalose-treated group were identified, and their gene targets were determined by bioinformatics-based approaches. The analysis of DE miRNAs pointed out modulation in unique miRNAs between treatment and placebo groups. Specifically, hsa-miR-1268a, -3605-3p, -555, and -6511a-3p were significantly downregulated, while hsa-miR-324-3p and -539-5p showed significant upregulation. Of the 147 overlapped validated genes identified in the bioinformatics analysis, several are related to autophagy, protein aggregation, oxidative stress, and inflammation. KEGG enrichment pathways reveal regulation of actin cytoskeleton, axon guidance, and neurotrophin signaling pathways. The results identify significant modulation in unique miRNAs in AD patients under trehalose. These findings suggest the potential utility of these microRNAs as biomarkers for trehalose pharmacological monitoring in AD.

Basil chilling injury: Oxidative stress or energy depletion?

Basil (Ocimum basilicum L.) is susceptible to chilling injury (CI), leading to significant postharvest quality loss. This research aimed to identify key metabolites involved in CI of basil during cold storage to better understand the underlying mechanisms. Metabolite profiles of basil leaves stored at 4 and 12 °C for up to 12 days were quantified by 1H NMR and GC-MS. At 4 °C shelf life was reduced due to CI. At 4 °C, several osmoprotectants, including proline, gamma-aminobutyric acid, trehalose and myo-inositol increased, whereas antioxidants like ascorbic acid and rosmarinic acid decreased; the latter likely due to scavenging reactive oxygen species. During chilling stress, antioxidant defence pathways were upregulated and carbohydrate related energy pathways were downregulated. We suggest that CI in basil associates with redirection of carbohydrate flux towards antioxidant defence systems, leading to energy depletion. This energy depletion is hypothesized as a primary trigger for CI in postharvest basil.

Potential mechanism of Camellia luteoflora against colon adenocarcinoma: An integration of network pharmacology and molecular docking

BACKGROUND

Camellia luteoflora is a unique variety of Camellia in China which is only distributes in Chishui City, Guizhou Province and Luzhou City, Sichuan Province. Its dried leaves are used by local residents as tea to drink with light yellow and special aroma for health care. It has high potential economic medicinal value. Colon adenocarcinoma (COAD) is the third most frequent malignancy and its incidence and mortality is increasing. However, the current common treatments for COAD bring great side effects. In recent years, natural products and their various derivatives have shown significant potential to supplement conventional therapies and to reduce associated toxicity while improving efficacy. In order to overcome the limitations of traditional treatment methods, the global demand and development of natural anti-COAD drugs were increasingly hindered.

AIM

To investigate the potential targets and mechanisms of Camellia luteoflora anti-COAD.

METHODS

Nuclear magnetic resonance and mass spectrometry was used to identified the compounds of Camellia luteoflora. Network pharmacology analysis and survival analysis was used in this study to investigate the anti-COAD effect and mechanism of Camellia luteoflora.

RESULTS

Firstly, a total of 13 compounds were identified. Secondly, 10 active ingredients for 204 potential targets were screened and protein-protein interaction analysis showed that TP53, STAT3, ESR1, MAPK8, AKR1C3, RELA, CYP19A1, CYP1A1, JUN and CYP17A1 were hub targets. GO and KEGG enrichment analyses revealed that Camellia luteoflora exerted anti-COAD effect through multiple functions and pathways. Then, the analysis of survival and stage indicated that TP53 was highly expressed in COAD and the overall survival of high-TP53 and high-CYP19A1 COAD patients was significantly shorter than the low group and there was significant difference in MAPK and RELA expression between different stages. Finally, the molecular docking results demonstrated the binding affinities and sites between active ingredients and TP53, STAT3, ESR1.

CONCLUSION

Our study systematically demonstrated the potential anti-COAD mechanism of Camellia luteoflora and provided a theoretical basis for its further application in the COAD treatment.

Resting Ca2+ fluxes protect cells from fast mitochondrial fragmentation, cell stress responses, and immediate transcriptional reprogramming

Homeostatic calcium ion (Ca2+) fluxes between the endoplasmic reticulum, cytosol, and extracellular space occur not only in response to cell stimulation but also in unstimulated cells. Using murine astrocytes as a model, we asked whether there is a signaling function of these resting Ca2+ fluxes. The data showed that endoplasmic reticulum (ER) Ca²⁺ depletion, induced by sarcoplasmic/endoplasmic reticulum Ca²⁺-ATPase (SERCA) inhibition, resulted to prolonged Ca²⁺ influx and mitochondrial fragmentation within 10 to 30 min. This mitochondrial fragmentation could be prevented in Ca2+-free medium or by inhibiting store-operated Ca2+ entry (SOCE). Similarly, attenuation of STIM proteins, which are vital ER Ca2+ sensors, protected mitochondrial morphology. On the molecular level, ER Ca2+ depletion, achieved either by removing extracellular Ca2+ or through acute SERCA inhibition, led to changes in gene expression of about 13% and 41% of the transcriptome within an hour, respectively. Transcriptome changes were associated with universal biological processes such as transcription, differentiation, or cell stress. Strong increase in expression was observed for the transcription factor ATF4, which is under control of the kinase PERK (EIF2AK3), a key protein involved in ER stress. Corroborating these findings, PERK was rapidly phosphorylated in Ca2+-free medium or after acute pharmacological inhibition of SOCE. In summary, resting, homeostatic Ca2+ fluxes prevent immediate-early cell stress and transcriptional reprogramming.

Ankem M, Damodaran C. Interaction between NF-κB and PLAC8 impairs autophagy providing a survival advantage to prostate cells transformed by cadmium

Prostate cancer risk is influenced by various factors, including exposure to heavy metals like cadmium (Cd). The study reveals that the autophagy-regulating gene PLAC8 (placenta-specific 8) is significantly involved in Cd-induced prostate carcinogenesis, and NF-κB acts as the upstream transcriptional activator of PLAC8, which then selectively up-regulates BCL-xL, providing a survival advantage to Cd-transformed cells. NF-κB activation stabilizes PLAC8 in the cytosol, disrupting autophagy by allowing PLAC8 to colocalize with LC3B instead of LAMP1. Silencing NF-κB down-regulates PLAC8 and its survival function while inhibiting NF-κB or PLAC8, which restores autophagy and decreases tumor growth in xenograft models. In addition, targeting BCL-xL confirmed this signaling pathway. The findings suggest that sustained NF-κB activation regulates PLAC8 and highlights the NF-κB-PLAC8-BCL-xL axis as a potential target for early detection and therapies in metal-induced prostate cancer.

Proteomic Data and Drug Implications for Cerebral Microvascular Endothelial Cells Under Varying Oxygen Levels

Hyperoxia in standard cell cultures (18 kPa O2) imposes cellular oxidative stress, potentially skewing research and drug screening outcomes. Cerebral microvascular endothelial cells (hCMEC/D3) experience no more than 7 kPa O2 in vivo. In this study, hCMEC/D3 cells were adapted to 5 kPa O2 for 5 days to optimize an in vitro physiological cell culture model. Using a SYNAPT G2-Si mass spectrometer, we compared the proteomic profiles of cells cultured under 5 kPa versus 18 kPa O2. A substantial proteomic shift under hyperoxia highlighted the strong impact of oxygen levels on protein expression. We further investigated the effect of oxygen levels on drug screening using sulforaphane (SFN), an inducer of NRF2-regulated antioxidant defense genes. SFN induced more pronounced changes in proteomic profiles under 18 kPa O2 compared to 5 kPa, indicating oxygen-dependent cellular drug responses. This dataset offers a valuable resource for analyzing oxygen-sensitive proteomic changes. Comparative studies using different drugs or cell types could further elucidate oxygen-dependent signaling and inform the development of therapies aligned with physiological oxygen levels.

Analysis of Genomic-Transcriptomic Dynamics Delineates Key Molecular Signatures Modulating Seed Size and Weight in Lentil

Delineating key genetic determinants associated with seed size/weight is crucial for increasing productivity. In this study, the advantages of an integrated approach combining QTL mapping, GWAS and transcriptomics to identify robust candidates governing seed size and weight were demonstrated in lentil, an important grain legume. QTL mapping identified three stable QTLs harbouring 5113 genes. GWAS identified 42 MTAs (5 consistent) containing 192 underlying genes. Comparative transcriptome analysis identified 1202 differentially expressed transcripts. Integrated analysis of the results obtained from QTL mapping and GWAS revealed nine SNPs located in the three robust QTLs harbouring 32 candidate genes. Upon integration with transcriptome data, only one (LcWDL1) was identified as the most promising candidate. LcWDL1 (a member of TPX2 family involved in microtubule organisation and cell expansion) and its predicted interacting partners that is, LcGLIPs are known to function as regulators of seed size. Candidate gene-based association analysis identified a SNP on second exon of LcWDL1 to be significantly associated with seed size and weight of lentil. The genomic loci/candidate gene identified in the study will serve to expedite the molecular breeding and gene editing programs for enhancing seed size and seed weight in lentils.

Single-cell RNA sequencing reveals tissue-specific transcriptomic changes induced by perfluorooctanesulfonic acid (PFOS) in larval zebrafish (Danio rerio)

Perfluorooctanesulfonic acid (PFOS) elicits adverse effects on numerous organs and developmental processes but the mechanisms underlying these effects are not well understood. Here, we use single-cell RNA-sequencing to assess tissue-specific transcriptomic changes in zebrafish (Danio rerio) larvae exposed to 16 µM PFOS or dimethylsulfoxide (0.01 %) from 3-72 h post fertilization (hpf). Data analysis was multi-pronged and included pseudo-bulk, untargeted clustering, informed pathway queries, and a cluster curated for hepatocyte biomarkers (fabp10a, and apoa2). Overall, 8.63 % (2390/27698) genes were significantly differentially expressed. Results from untargeted analysis revealed 22 distinct clusters that were manually annotated to specific tissues using a weight-of-evidence approach. The clusters with the highest number of significant differentially expressed genes (DEGs) were digestive organs, muscle, and otolith. Additionally, we assessed the distribution of pathway-specific genes known to be involved in PFOS toxicity: the PPAR pathway, β-oxidation of fatty acids, the Nfe2l2 pathway, and epigenetic modifications by DNA methylation, across clusters and identified the blood-related tissue to be the most sensitive. The curated hepatocyte cluster showed 220 significant DEGs and was enriched for the Notch signaling pathway. These findings provide insights into both established and novel sensitive target tissues and molecular mechanisms of developmental toxicity of PFOS.

Cytochrome c oxidase inactivation in Physcomitrium patens reveals that respiration coordinates plant metabolism

Photosynthetic organisms use sunlight as an energy source but rely on respiration during the night and in nonphotosynthetic tissues. Respiration also occurs in photosynthetically active cells, where its role is still unclear due to the lack of viable mutants. Mutations abolishing cytochrome c oxidase (Complex IV) activity are generally lethal. In this study, we generated cytochrome c oxidase assembly protein 11 (cox11) knockout lines through vegetative propagation in the moss Physcomitrium patens. These mutants showed severely impaired growth, with an altered composition of the respiratory apparatus and increased electron transfer through alternative oxidase. The light phase of photosynthesis remained largely unaffected in cox11 plants, while the efficiency of carbon fixation was reduced. Transcriptomic and metabolomic analyses showed that disrupting the cytochrome pathway had broad consequences for carbon and nitrogen metabolism. A major alteration in nitrogen assimilation was observed, with a general reduction in amino acid abundance. Partial growth rescue was achieved by externally supplying plants with amino acids but not with sugars, demonstrating that respiration in photosynthetic plant cells plays an essential role at the interface between carbon and nitrogen metabolism and a key role in providing carbon skeletons for amino acid biosynthesis.

Diverse effects of Bacillus sp. NYG5-emitted volatile organic compounds on plant growth, rhizosphere microbiome, and soil chemistry

Bacterial strains in the rhizosphere secrete volatile organic compounds (VOCs) that play critical roles in inter- and intra-kingdom signaling, influencing both microbe-microbe and microbe-plant interactions. In this study we evaluated the plant growth-promoting effects of VOCs emitted by Bacillus sp. NYG5 on Arabidopsis thaliana, Nicotiana tabacum, and Cucumis sativus, focusing on VOC-induced alterations in plant metabolic pathways, rhizosphere microbial communities, and soil chemical properties. NYG5 VOCs enhanced plant biomass across all tested species and induced significant shifts in rhizosphere microbial community composition, specifically increasing relative abundance of Gammaproteobacteria and reducing Deltaproteobacteria (Linear discriminant analysis Effect Size, p < 0.05). Soil analysis revealed a considerable reduction in humic substance concentrations following VOCs exposure, as detected by fluorescent spectral analysis. Using SPME-GC-MS, several novel VOCs were identified, some of which directly promoted plant growth. Transcriptomic analysis of N. tabacum exposed to NYG5 VOCs demonstrated activation of pathways related to phenylpropanoid biosynthesis, sugar metabolism, and hormone signal transduction. Within the phenylpropanoid biosynthesis pathway, a significant upregulation (p adj = 1.16e-14) of caffeic acid 3-O-methyltransferase was observed, a key enzyme leading to lignin and suberin monomer biosynthesis. These results highlight the complex mechanisms through which bacterial VOCs influence plant growth, including metabolic modulation, rhizosphere microbiome restructuring, and soil chemical changes. Collectively, this study highlights the pivotal role of bacterial VOCs in shaping plant-microbe-soil interactions.

Identification of the potential role of PANoptosis-related genes in burns via bioinformatic analyses and experimental validation

BACKGROUND

The treatment of burns is highly challenging due to their complex pathophysiological mechanisms. PANoptosis, as an important form of cell death, is suggested to play a crucial role in the inflammatory response and tissue damage following burns. However, the role of PANoptosis-related biomarkers in the pathophysiological processes of burns remains unclear. In this study, we aim to identify PANoptosis-related signature genes and validate them as biomarkers in burns METHODS: Burn-related datasets were obtained from the Gene Expression Omnibus（GEO） database. GSE37069 was used for bioinformatic analysis and machine learning, while GSE19743 was used specifically for external validation. A set of PANoptosis-associated genes was obtained from the GeneCards database. Three machine learning models (LASSO, RF, and SVM-RFE) and WGCNA were utilized to screen for signature genes. The diagnostic efficacy of the identified genes was assessed through receiver operating characteristic (ROC) curves. Gene Set Enrichment Analysis (GSEA) was performed to identify pathways associated with the signature genes, while single-sample gene set enrichment analysis (ssGSEA) was employed to investigate the immune landscape. Finally, Western blotting and RT-qPCR were employed to validate the signature genes.

RESULTS

BCL-2, CCAR1, CERK, TRIAP1, S100A8, and SNHG1 were identified as signature genes. The biological processes involving these genes mainly include endocytosis, apoptosis, and ECM receptor interaction. Immune infiltration analysis revealed that neutrophils, eosinophils, M0 macrophages, and monocytes are significantly elevated in burn samples. Additionally, these signature genes showed significant correlations with multiple immune cell types. Finally, Western blotting and RT-qPCR analysis revealed that the expression levels of BCL2, CCAR1, CERK, and TRIAP1 were significantly down-regulated in the burn groups compared to the normal groups, with the exception of S100A8.

CONCLUSION

Our study has identified BCL-2, CCAR1, CERK, and TRIAP1 as reliable potential biomarkers for burn injuries. These genes play crucial roles in immune response, wound healing, and anti-apoptotic mechanisms, which are key pathological processes involved in the progression of burn injuries. Specifically, BCL-2, CCAR1, CERK, and TRIAP1 have been shown to significantly impact the regulation of inflammation, the efficiency of wound repair, and the prevention of cell apoptosis during burn injury.

Hematopoietic MyD88 orchestrates the control of gut colonization by segmented filamentous bacteria

Host-microbiota cooperation is critical for successful intestinal homeostasis. The commensal segmented filamentous bacteria (SFB) are crucial for orchestrating the post-natal maturation of the host gut immune system and establishing a healthy state of physiological inflammation, which largely depends on their intimate attachment to the ileal mucosa. However, the signaling pathways used by SFB to induce gut immune responses and how such responses ultimately control SFB colonization remain controversial. Using gnotobiotic approaches, we showed that SFB load is controlled by complex interactions involving the gut microbiota and the host immune system. Therefore, to clearly determine the role of host immune responses induced by SFB in directly controlling their growth, immunodeficient mice monocolonized with SFB were used. Here, we show that in the absence of a complex microbiota, the humoral immune response is dispensable to control SFB growth in the jejunum and ileum, shortly and later after colonization. In contrast, MyD88 signaling in myeloid cells is critical for licensing interleukin (IL)-22 production by type 3 innate lymphoid cells (ILC3) and CD4+ T cells, which ultimately limits SFB expansion. Thus, by revisiting the hierarchy of immune mechanisms that directly control SFB growth, our results emphasize the necessary and sufficient role of a hematopoietic MyD88/IL-22 axis.

A mitochondria-interfering nanocomplex cooperates with photodynamic therapy to boost antitumor immunity

Immunotherapeutics against triple-negative breast cancer (TNBC) hold great promise. In this work, we provide a combination therapy for simultaneous increasing tumor immunogenicity and down-regulating programmed cell death ligand 1 (PD-L1) to boost antitumor immunity in TNBC. We prepare bis (diethyldithiocarbamate)-copper/indocyanine green nanoparticles (CuET/ICG NPs) simply in aqueous with one-pot method. CuET/ICG NPs interfere mitochondria, reduce oxygen consumption, and alleviate tumor hypoxia to potentiate photodynamic therapy (PDT) for amplifying immunogenic cell death (ICD). Meanwhile, mitochondria dysfunction leads to energy stress and activates AMPK pathway. As a result, CuET/ICG NPs downregulates membrane PD-L1 (mPD-L1) on both 4T1 cancer cells and cancer stem cells (CSCs) through AMP-activated protein kinase (AMPK)-mediated pathway in hypoxia. Cooperatively, the combinational therapy activates antitumor immunity and triggers long lasting immune memory response to resist tumor re-challenge. Our study represents an attempt that conquers tumor immunosuppressive microenvironment with simple biomedical materials and multimodality treatments.

Ref-1 redox activity modulates canonical Wnt signaling in endothelial cells

Ischemic retinopathies, including proliferative diabetic retinopathy (PDR) and retinopathy of prematurity (ROP), are characterized by abnormal retinal neovascularization and can lead to blindness in children and adults. Current treatments, such as intravitreal anti-VEGF injections, face limitations due to high treatment burden and variable efficacy, as multiple signaling pathways, beyond VEGF, contribute to retinal neovascularization. Previous studies demonstrate that targeting the redox-mediated transcriptional regulatory function of APE1/Ref-1 reduces pathological neovascularization. We aimed to identify novel signaling pathways regulated by Ref-1 redox activity utilizing RNA sequencing of human retinal endothelial cells (HRECs) treated with a Ref-1 redox inhibitor. We found that Wnt/β-catenin signaling was significantly downregulated after Ref-1 inhibition. Given the role of Wnt signaling in vascular pathologies, we investigated how Ref-1 regulates Wnt/β-catenin signaling. Ref-1 inhibition downregulated Wnt co-receptors LRP5/6 at both the mRNA and protein levels in endothelial cells, suggesting transcriptional regulation. Ref-1 redox inhibitors APX3330 and APX2009 reduced Wnt3a-induced nuclear β-catenin levels, decreased Wnt transcriptional activity by TOPFlash luciferase assay, and blocked hypoxia-induced Wnt/β-catenin activation in HRECs. In the oxygen-induced retinopathy mouse model of retinal neovascularization, Ref-1 specific inhibitor APX2009 reduced the expression of Wnt-related genes at sites of neovascularization. These findings reveal a novel role for Ref-1 redox activity in modulating Wnt/β-catenin signaling in endothelial cells and highlight the potential of Ref-1 redox activity targeted inhibitors as a novel therapeutic approach for retinal neovascular diseases by modulating multiple disease-relevant pathways.

The ABC transporters and their epigenetic regulation under drought stress in chickpea

Chickpea (Cicer arietinum L.) is a globally essential pulse crop, providing dietary protein for millions. However, it suffers significant yield losses due to drought stress, therefore, identification of genes that confer drought tolerance is crucial. The ATP-binding cassette (ABC) transporters are vital proteins in plant growth and development, facilitating the transport of phytohormones like abscisic acid (ABA) that helps plants adapt to drought conditions. In this study, we identified 121 ABC transporter genes in chickpea, categorized into eight subfamilies. Consistent with other crops, the CaABCG family was the largest, with 48 members, while the CaABCE family had only one protein. Structural analysis revealed a conserved domain organization, including Walker A and B motifs and the ABC signature motif. Both segmental and tandem duplications were observed, with the highest duplication in the CaABCG and CaABCC subfamilies. Using RNA-seq and Whole Genome Bisulfite Sequencing (WGBS) data from the root tissues of two chickpea genotypes contrasting in drought tolerance, we found that DNA methylation at cytosine residues might regulate these genes under drought stress. Notably, the CaABCG41 gene was identified as drought-responsive, showing significant upregulation (p < 0.05) and hypermethylation (q < 0.01) in the drought tolerant genotype compared to the drought sensitive genotype under drought stress. CaABCG41 thus holds potential for developing drought-tolerant chickpea cultivars.

Abscisic acid, stress and ripening (ASR) proteins play a role in iron homeostasis in rice (Oryza sativa L.)

Iron (Fe) is essential for plant growth, playing a key role in photosynthesis, respiration, and nitrogen fixation. Despite its abundance, Fe is not easily available for uptake by roots, making Fe deficiency a common issue that reduces crop yields. The ASR (Abscisic acid/Stress/Ripening) proteins are known to be responsive to different abiotic stresses. Two ASR proteins from rice (Oryza sativa L.), OsASR1 and OsASR5, were described as transcription factors involved in aluminum (Al) toxicity response, and were shown to be partially redundant in their function. Here we explored a possible role of ASR proteins in Fe deficiency in rice plants. We showed that rice plants silenced for ASR genes (named OsASR5-RNAi) had increased sensitivity to Fe deficiency, with early and more severe chlorosis, as well as reduced photosynthesis, stunted growth, reduced seed set and altered ionome in roots, leaves and seeds. Transcriptomic analysis indicated that roots of OsASR5-RNAi plants had similar expression of Fe uptake genes, such as OsIRT1 and OsYSL15. However, long distance phloem transporter OsYSL2 was up-regulated in OsASR5-RNAi roots to a larger extent compared to WT, suggesting ASR proteins negatively regulate OsYSL2 expression. We also identified other interesting candidate genes, such as OsZIFL2 and Thionins, that are dependent on ASR proteins for regulation under Fe deficiency. Our work demonstrated that OsASR proteins are important for proper Fe deficiency response in rice.

In silico drug repurposing for potential HPV-induced skin wart treatment - A comparative transcriptome analysis

INTRODUCTION

Warts are dermal disorders resulting from HPV infection and can be transmitted by direct contact. Existing treatment approaches, such as topical treatment with salicylate, have low efficiency and demonstrate side effects. Thus, the discovery of potent drug treatments for skin warts is necessary. Here we propose the use of alternative medications for the possible treatment of skin warts with the help of comparative transcriptome analysis and drug repurposing approaches.

METHODS

Gene expression datasets related to HPV-induced warts and cervical cancer were extracted from the GEO database. Differentially expressed genes (DEGs) were identified using DESeq2 in the Galaxy database. Upregulated DEGs were assessed for druggability using the DGIdb tool. Gene ontology and enrichment analysis were performed to investigate the characteristics of druggable DEGs. A molecular docking virtual screening was conducted using PyRx software to identify potential therapeutic targets for skin warts. The interactions between selected drug candidates and the target protein were analyzed using the BIOVIA Discovery Studio. The physicochemical characteristics of potential pharmaceuticals were evaluated using the SwissADME database. Finally, the molecular dynamics (MD) simulation was performed to validate the stability and dynamic behavior of drug-protein interactions.

RESULTS

Based on the findings from gene expression profiling, Integrin Alpha-X (ITGAX, CD11c) has been identified as a candidate protein that is significantly upregulated in individuals afflicted with skin warts. Integrin Alpha-X plays a crucial role in mediating intercellular interactions during inflammatory processes and notably enhances the adhesion and chemotactic activity of monocytes. Through molecular docking, MD, and physicochemical analyses, it has been demonstrated that dihydroergotamine effectively inhibits the ITGAX protein, suggesting its potential as a therapeutic agent for the management of skin warts.

CONCLUSION

Dihydroergotamine can be repurposed as a potential drug in the treatment of skin warts by targeting Integrin Alpha-X protein.

A novel peptide TCL6148 induces ferroptosis via the GOT1/GPX4 pathway to enhance sunitinib sensitivity in renal cell carcinoma

Renal cell carcinoma (RCC) represents a deadly type of genitourinary cancer, noted for its strong tendency to metastasize and its unfavorable outlook for patients. Despite significant advancements in targeted therapies and immunotherapies, tumor heterogeneity and therapeutic resistance remain formidable challenges, underscoring the urgent need for novel treatment strategies. Long non-coding RNAs (lncRNAs), once thought to be non-translatable, have recently been discovered to encode functional peptides that are crucial in the progression of tumors. In this study, we employed peptidomics to screen RCC tissues for lncRNA-encoded peptides and identified a novel peptide, TCL6148, encoded by TCL6. Through detailed bioinformatics assessments, laboratory experiments, and studies conducted in living organisms, we established that TCL6148 exerts anti-tumor effects by triggering ferroptosis in RCC cells through the GOT1/GPX4 signaling pathway. Mechanistically, TCL6148 facilitated the accumulation of Fe2+, increased levels of reactive oxygen species (ROS), and boosted lipid peroxidation, thus rendering RCC cells more susceptible to ferroptosis. Importantly, TCL6148 significantly enhanced the therapeutic effectiveness of sunitinib, indicating a promising combined approach for addressing drug resistance. In vivo experiments further validated the safety and efficacy of TCL6148 in suppressing RCC tumor growth. Collectively, our findings identify TCL6148 as a promising candidate for RCC treatment and provide novel insights into peptide-based therapeutic approaches, offering a potential avenue for improving RCC management.

Phylogenomic and morphological evidence supports the reinstatement of the bamboo genus Clavinodum from Oligostachyum (Poaceae: Bambusoideae)

One of the most intractable problems in bamboo systematics concerns the three-branched bamboos of tribe Arundinarieae (Poaceae: Bambusoideae), which are collectively characterized by having three branches per mid-culm node. Previous phylogenetic studies based on double-digest restriction-site associated DNA sequencing (ddRAD-seq) data confirmed that Oligostachyum, a member of this group, is non-monophyletic, and in particular that Oligostachyum oedogonatum is a problematic species deserving further attention, as it appears to be morphologically and phylogenetically distinct from the other three-branched bamboos. Here we aim to define and confirm the phylogenetic position of O. oedogonatum, by including representatives from across its geographic range. We also provide new insights into the overall phylogeny of the three-branched bamboos and closely related genera, using multiple phylogenomic datasets. While a plastid genome-based tree is very poorly supported, phylogenies inferred using two sets of conserved nuclear genes and single nucleotide polymorphism (SNP) data yield generally well-supported and congruent topologies using coalescent-based approaches. The tree inferred from the largest concatenated gene set is the most dissimilar to other inferences. The nuclear-based data sets all recover a major clade that includes all of the three-branched bamboos and four other genera, which can be distinguished from related taxa due to their possession of three stigmas per floret and leptomorph rhizomes. Notably, eight O. oedogonatum samples form a clade that is distantly related to other members of Oligostachyum, including the type species of the genus (Oligostachyum sulcatum). Population genetic approaches and multi-species coalescent-based analysis of the nuclear data sets imply that seven of these populations can be treated as a single species, O. oedogonatum, but that one population from Jinggangshan is likely an intergeneric hybrid between O. oedogonatum and Pleioblastus. Morphologically, O. oedogonatum differs from all other three-branched bamboos, in having strongly asymmetrically swollen supra-nodal ridges, a laterally compressed spikelet, and rachilla segments that disarticulate readily below fertile florets. Because of its morphological distinctiveness and molecular phylogenetic position, we propose that this taxon should be reinstated as Clavinodum oedogonatum. We provide a new description for this monotypic genus here.

Exosomes derived let-7f-5p is a potential biomarker of SLE with anti-inflammatory function

This study found that in patients with SLE (n = 5), lethal (let)-7f-5p expression was significantly downregulated in peripheral blood mononuclear cells. Further, high-throughput RNA sequencing was used to mine the differential transcriptome expression in renal tissue exosomes of systemic lupus erythematosus (SLE)-prone mice, and bioinformatics was utilized to analyze non-coding RNAs and coding RNAs in exosomes for their possible roles in SLE. In renal tissues of MRL/lpr SLE-prone mice with exosomes and Pristane-induced SLE mice, we also demonstrated aberrant expression levels of microRNA (miRNA) let-7f-5p. Meanwhile, in the macrophage inflammation model, the expression levels of let-7f-5p were downregulated, that of guanylate binding protein (Gbp2 and Gbp7) were upregulated, and the inflammatory state of macrophages was alleviated following transfection with the let-7f-5p mimic. Co-culturing mesenchymal stem cells with a macrophage model of inflammation resulted in increased let-7f-5p expression and downregulated inflammatory factors, Gbp2 and Gbp7 expression in macrophages. Dual luciferase reporter gene assays confirmed that let-7f-5p directly binds to the 3' UTR of Gbp7 to regulate its expression. Let-7f-5p regulation of the Gbp family is involved in SLE pathogenesis and is a biomarker associated with the inflammatory response with potential clinical applications.

Molecular Mechanisms of Biochanin A in AML Cells: Apoptosis Induction and Pathway-Specific Regulation in U937 and THP-1

Biochanin A, a naturally occurring isoflavone derived from legumes, possesses anti-inflammatory, estrogenic, and anticancer activities. In this study, we investigated the cytotoxic effects and underlying molecular mechanisms of Biochanin A in acute myeloid leukemia (AML) cell lines, U937 and THP-1, using in vitro cytotoxicity assays, RNA sequencing, and bioinformatic analyses. Biochanin A induced dose-dependent apoptosis, as evidenced by caspase-7 activation and PARP1 cleavage. Over-representation analysis (ORA) revealed that differentially expressed genes (DEGs) were significantly enriched in pathways related to inflammatory responses, DNA replication, and cell cycle regulation. Gene set enrichment analysis (GSEA) further confirmed the upregulation of apoptosis- and inflammation-related pathways and the downregulation of MYC targets, cholesterol biosynthesis, and G2/M checkpoint gene sets. RT-qPCR analysis demonstrated that Biochanin A downregulated oncogenes such as RUNX1, BCL2, and MYC while upregulating CHOP (GADD153), CDKN1A (p21), and SQSTM1 (p62), contributing to apoptosis and cell cycle arrest across both cell lines. Notably, Biochanin A downregulated PLK1 and UHRF1 in THP-1 cells, indicating a disruption of mitotic progression and epigenetic regulation. In contrast, in U937 cells, Biochanin A upregulated TXNIP and downregulated CCND2, highlighting the involvement of oxidative stress and G1/S cell cycle arrest. These findings support the potential of Biochanin A as a promising therapeutic candidate for AML through both shared and distinct regulatory pathways.

In Search of Healthy Ageing: A Microbiome-Based Precision Nutrition Approach for Type 2 Diabetes Prevention

Background/Objectives: Type 2 diabetes (T2D) is a leading cause of morbidity and mortality worldwide and in Spain, particularly in the elderly population, affecting healthy ageing. Nutritional strategies are key to its prevention. The gut microbiota is also implicated in T2D and can be modulated by nutrition. We hypothesize that precision nutrition through microbiota modulation may help prevent T2D. This article aims to (1) describe a gut microbiota bacterial profile associated with T2D prevention, (2) provide precision nutrition tools to optimize this profile, (3) analyze how overweight influences the microbiota composition and precision nutrition response, and (4) address the technical challenges of microbiome-based precision nutrition clinical implementation to prevent T2D. Methods: A review of gut microbiota associated with T2D prevention was conducted. 13 healthy Spanish participants over 62 with optimal blood glucose levels (7 normal weight and 6 overweight) underwent a 3-month precision nutrition intervention to optimize T2D-preventive gut microbiota using a bioinformatics food recommendation system, Phymofood (EP22382095). Fecal microbiota was analyzed pre- and post-intervention using full-length 16S rRNA gene amplification, MinION sequencing, and NCBI taxonomic classification. Results: 31 potentially preventive bacteria against T2D were selected. The intervention increased the relative abundance of beneficial genera (Butyrivibrio and Faecalibacterium) and species (Eshraghiella crossota, and Faecalibacterium prausnitzii). The overweight influenced microbiota composition and intervention response. Conclusions: A gut microbiota profile associated with T2D prevention was identified, and precision nutrition could increase the relative abundance of beneficial bacteria. Confounding factors such as overweight should be considered when designing microbiome-based precision nutrition interventions. These results contribute to a better understanding of the microbiota associated with T2D prevention and address technical challenges for clinical implementation in future healthy ageing strategies.

Deciphering the Overlapping Immune Mechanism Between Depression and Breast Cancer

Depression and breast cancer (BC) demonstrate significant clinical comorbidity, yet their shared molecular mechanisms remain unclear, particularly regarding immune pathway regulation. This study systematically analyzed Depression-associated gene expression profiles (Gene Expression Omnibus (GEO) database) and BC transcriptomic data (The Cancer Genome Atlas (TCGA) database), identifying overlapping differentially expressed genes (DEGs). Functional enrichment (Gene Ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG)) and protein-protein interaction (PPI) network analyses (STRING/Cytoscape) were employed to elucidate biological processes, followed by least absolute shrinkage and selection operator (LASSO) regression and receiver operating characteristic (ROC) curve validation to prioritize key genes. Immune infiltration patterns were assessed via the xCell algorithm, with Spearman correlation linking genes to immune subsets, and single-gene Gene Set Enrichment Analysis (GSEA) evaluating pathway activity. In total, 93 overlapping genes were identified, with predominant involvement in immune-related pathways being revealed by functional enrichment analysis. BHLHE41, EpCAM, and GSTM2 were prioritized as mechanism-associated genes through integrated LASSO regression and ROC analyses. Significant correlations were observed between these genes and specific immune cell populations. GSEA further linked these genes to immune response pathways, suggesting their regulatory roles. These findings highlight immune dysregulation as a shared mechanism underlying Depression-BC comorbidity, providing a foundation for developing early diagnostic strategies and therapeutic strategies targeting both conditions.

Proteomic profiling of small extracellular vesicles from bovine nucleus pulposus cells

Small extracellular vesicles (small EV) are a conserved means of communication across the domains of life and lately gained more interest in mammalian non-cancerous work as non-cellular, biological therapeutic with encouraging results in recent studies of chronic degenerative diseases. The nucleus pulposus (NP) is the avascular and aneural center of an intervertebral disc (IVD), home to unique niche conditions and affected in IVD degeneration. We investigated autologous and mesenchymal stem cell (MSC) small EVs for their potential to contribute to cell and tissue homeostasis in the NP niche via mass spectrometric proteome and functional enrichment analysis using adult and fetal donors. We compared these findings to published small EV databases and MSC small EV data. We propose several mechanisms associated with NP small EVs: Membrane receptor trafficking to modify signal responses promoting niche homeostasis; Redox and energy homeostasis via metabolic enzymes delivery; Cell homeostasis via proteasome delivery and immunomodulation beyond an association with a serum protein corona. The proteome signature of small EVs generated by NP parent cells is similar to previously published small EV data, yet with a focus on supplementing anaerobic metabolism and redox balance while contributing to the maintenance of an aneural and avascular microniche.

A testis-specific heat shock protein gene plays a critical role in male fertility in the fall armyworm

Heat shock proteins (Hsps) are critical for stress responses and multiple physiological processes, yet their function in insect reproduction remains underexplored. In this study, we identified 36 Hsp genes in the fall armyworm (Spodoptera frugiperda), of which LOC118269601 (designated as SfHsp68A) exhibited robust testis-specific expression, peaking during pupal testis development. CRISPR/Cas9-mediated knockout of SfHsp68A resulted in recessive male sterility, significantly reduced testis size, sperm counts, and egg hatch rates. Transcriptomic analysis of mutant testes revealed substantial downregulation of genes linked to mitochondrial function, oxidative phosphorylation, energy metabolism, and reactive oxygen species (ROS) metabolism. These results demonstrate that SfHsp68A is essential for male fertility in S. frugiperda, likely by maintaining mitochondrial integrity and metabolic homeostasis during spermatogenesis. These studies reveal that testis-specific Hsps function in male fertility and highlight SfHsp68A as a potential genetic target for developing sterile insect technology, offering an environmentally sustainable strategy for controlling this globally invasive pest.

VCPIP1 facilitates pancreatic adenocarcinoma progression via Hippo/YAP signaling

Dysregulation of Hippo signaling is observed in pancreatic adenocarcinoma (PAAD). Moreover, overactivation of YAP is crucial for tumor progression. Although the inhibitory phospho-cascade is functional, the reason for YAP hyperactivation in PAAD remains unclear. Recent studies have revealed that the ubiquitin modification of YAP also plays an important role in the Hippo/YAP axis and cancer progression. To gain a better understanding of the potential mechanisms underlying the ubiquitination and deubiquitination of YAP, we carried out siRNA screening for critical deubiquitinases in PAAD. By using a deubiquitinase (DUB) library, we identified valosin-containing protein-interacting protein 1 (VCPIP1) as an important effector of YAP function and PAAD progression. Inhibition of VCPIP1 hampered PAAD progression via Hippo signaling. Clinical data revealed that VCPIP1 was elevated in PAAD and correlated with poor survival in PAAD patients. Biochemical assays demonstrated that VCPIP1 interacted with YAP, inhibiting K48-linked polyubiquitination and thereby increasing YAP stability. YAP directly binds to the VCPIP1 promoter region, enhancing its transcription in PAAD. Our study revealed a forward feedback loop between VCPIP1 and Hippo signaling in PAAD, indicating that VCPIP1 is a potential therapeutic drug target in PAAD.

Breed-specific differences of gut microbiota and metabolomic insights into fat deposition and meat quality in Chinese Songliao Black Pig and Large White × Landrace Pig Breeds

BACKGROUND

Gut microbiota ferment non-digestible substances to produce metabolites that accumulate in muscle and influence host metabolism. However, the regulatory mechanisms connecting gut microbiota, metabolites, and fat deposition across pig breeds remain unclear. This study explores the gut-muscle axis regulating fat deposition and meat quality in Chinese Songliao Black Pig (SBP) and Large White × Landrace Pigs (LWLDP). Digesta samples from the ileum, cecum, and rectum of both breeds were analyzed using 16 S rRNA sequencing for microbiome profiling and ultra-high-performance liquid chromatography (UHPLC) for metabolomics. Multi-omics data, including microbiota and metabolite profiles were integrated with our previously published data of transcriptomics and metabolomics insights into fat deposition in the longissimus dorsi (LD) muscle using the MixOmics DIABLO method.

RESULTS

Microbiome analysis revealed that Fibrobacter, Unidentified_Peptostreptococcaceae, Sutterella, and Unidentifed_Rickettsiales were enriched in SBP, while Ruminococcus, Corynebacterium, and Streptococcaceae in LWLDP. Metabolomic analysis indicated that SBP was enriched in fatty acid biosynthesis pathways, including linoleic acid, α-linolenic acid, and arachidonic acid, whereas LWLDP was associated with insulin signaling, starch and sucrose metabolism. Integrated analysis identified Peptostreptococcaceae and Rickettsiales in SBP, along with metabolites phosphatidylcholine (PC(22:4)), N-acylethanolamine (NAE(20:4)), and lysophosphatidylcholine (LysoPC(24:1)) were correlated with key genes (EIF4E, MSTN, PPARGC1A, NR4A3, and SOCS1) regulating fat deposition. In LWLDP, Corynebacterium and Streptococcaceae were linked to the PPP1R3B gene, which is involved in glycogen metabolism, as well as metabolites 2-methyl-3-hydroxybutyric acid and 5-keto-gluconic acid, suggesting a shift toward glycolysis over lipolysis.

CONCLUSION

This study concluded that cecum-associated microbes in LWLDP may enhance carbohydrate metabolism, leading to reduced fat deposition, whereas rectum-associated microbes in SBP contribute to docosahexaenoic acid (DHA) biosynthesis, thereby improving meat quality. These findings highlight gut microbiota-derived metabolites as potential biomarkers for optimizing meat production and livestock breeding strategies.

Essential oil-derived compounds target core fatigue-related genes: A network pharmacology and molecular Docking approach

Fatigue is a widespread condition associated with various health issues, yet identifying specific bioactive compounds for its management remains challenging. This study integrates network pharmacology and molecular docking to uncover essential oil-derived compounds with potential antifatigue properties by targeting key genes and molecular pathways. A comprehensive analysis of 872 essential oil compounds was conducted using PubChem, with target prediction via SwissTargetPrediction. The protein-protein interaction (PPI) network and KEGG pathway analysis identified core fatigue-related targets, including ALB, BCL2, EGFR, IL-6, and STAT3, in metabolic dysregulation and inflammatory responses linked to fatigue. Molecular docking exhibits strong binding affinity between key compounds such as Calamenene, T-cadinol, and Bornyl acetate and core targets, suggesting their potential antifatigue effects. However, ADMET analysis confirmed T-cadinol's drug-likeness, suggesting good bioavailability and minimal toxicity risks. Thus, molecular docking revealed high binding affinity, which was further validated through a 100 ns MD simulation and demonstrated stable interactions with low root mean square deviation (RMSD). Additionally, hydrogen bond analysis confirmed that T-cadinol maintained consistent interactions with key residues such as Thr-790 in EGFR, Arg-222 in ALB, and Arg-104 in IL-6, indicating strong binding stability. While this study provides valuable computational insights, further in vitro and in vivo validation is necessary to confirm these findings and explore potential therapeutic applications.

Integrative in silico and in vivo Drosophila model studies reveal the anti-inflammatory, antioxidant, and anticancer properties of red radish microgreen extract

Red radish microgreens (RRM) have gained considerable attention for their promising therapeutic potential. However, the molecular mechanisms underlying their bioactivity remain inadequately characterized. This study explores the anti-inflammatory, antioxidant, and anticancer properties of RRM extract using in silico and in vivo Drosophila model analyses. The metabolite profile of the RRM extract was characterized using comprehensive metabolomics techniques, including Gas Chromatography-Mass Spectrometry (GC-MS) and Liquid Chromatography High-Resolution Mass Spectrometry (LC-HRMS). Furthermore, in silico analysis utilizing network pharmacology identified target proteins of RRM compounds associated with cancer, inflammation, and oxidative stress. Concurrently, in vivo experiments with Drosophila melanogaster PGRP-LBΔ (Dm PGRP-LBΔ) larvae was conducted to assess the extract's impact on immune and oxidative stress pathways. In silico analysis revealed that RRM compounds interacted with key proteins (AKT1, ESR1, MAPK1, SRC, TP53), modulating pathways related to cancer, inflammation, and oxidative stress. Molecular dynamics simulations reinforced the docking results by confirming robust binding of kaempferitrin to AKT1. In vivo studies showed that RRM extract suppressed immune-related genes (dptA, totA) through the NFκB and JAK-STAT pathways, reduced ROS levels, and selectively regulated antioxidant gene expression by enhancing sod1 while decreasing sod2 and cat. These results suggest RRM extract as a functional food for managing oxidative stress, inflammation, and cancer. Further research in higher organisms and clinical settings is needed.

The white lupin CCR1 receptor-like kinase controls systemic Autoregulation of Cluster Root and Nodule Development

Root development is tightly regulated in plants to optimize nutrient acquisition and interactions with soil microorganisms. In legumes, the Autoregulation of Nodulation (AoN) pathway systemically controls the proliferation of root nodules, which are energy-intensive organs. Mutations affecting the AoN pathway result in a hypernodulation phenotype accompanied by altered root development. However, it remains unclear whether this modification of root development is also systemic and coordinated with nodulation. In this study, we report the identification of the constitutive cluster root 1 (ccr1) mutant in white lupin (Lupinus albus), which exhibits constitutive production of an excessive number of cluster roots. We demonstrate that CCR1 is an ortholog of HAR1/SUNN/NARK leucin-rich repeat-receptor like kinases (LRR-RLKs), which are key regulators of the AoN pathway. Furthermore, we show that CCR1 negatively regulates both nodule and cluster root development. Interspecific grafting experiments between white and narrow-leaved lupin (Lupinus angustifolius), a species incapable of producing cluster roots, show that ccr1 shoots can induce the formation of cluster-like roots in narrow-leaved lupin rootstocks. This highlights the conservation of a CCR1-dependent signaling cascade. Transcriptome analyses reveal that CCR1 targets the conserved NIN/LBD16-NFYA regulatory module, which connects nodule and lateral root development through a shared inhibitory systemic pathway. We propose that this pathway represents a broader developmental control mechanism of root organogenesis, termed Autoregulation of Cluster Root and Nodule Development (AoDev).

Evolutionary unique N-glycan-dependent protein quality control system plays pivotal roles in cellular fitness and extracellular vesicle transport in Cryptococcus neoformans

A conserved N-glycan-dependent endoplasmic reticulum protein quality control (ERQC) system has evolved in eukaryotes to ensure accuracy during glycoprotein folding. The human pathogen Cryptococcus neoformans possesses a unique N-glycosylation pathway that affects microbial physiology and interactions with the infected host. To investigate the molecular features and functions of the ERQC system in C. neoformans, we characterized a set of mutants with deletion of genes coding for the ERQC sensor UDP-glucose:glycoprotein glucosyltransferase (UGG1) and putative α1,2-mannose-trimming enzymes (MNS1, MNS101, MNL1, and MNL2). The ugg1Δ, mns1Δ, mns101Δ, and mns1Δ101Δ mutants showed alterations in N-glycan profiles, defective cell surface organization, decreased survival in host cells, and varying degrees of reduced in vivo virulence. The ugg1Δ strain exhibited severely impaired extracellular secretion of capsular polysaccharides and virulence-related enzymes. Comparative transcriptome analysis showed the upregulation of protein folding, proteolysis, and cell wall remodeling genes, indicative of induced endoplasmic reticulum stress. However, no apparent changes were observed in the expression of genes involved in protein secretion or capsule biosynthesis. Additionally, extracellular vesicle (EV) analysis combined with proteomic analysis showed significant alterations in the number, size distribution, and cargo composition of EVs in ugg1Δ. These findings highlight the essential role of the functional ERQC system for cellular fitness under adverse conditions and proper EV-mediated transport of virulence factors, which are crucial for the full fungal pathogenicity of C. neoformans.

An integrated approach of transcriptomics, network pharmacology and molecular docking uncovers the mechanisms of 5,6,7,4'-tetramethoxyflavone in treating cervical cancer

5,6,7,4'-tetramethoxyflavone (TMF), a dietary polymethoxyflavone (PMF) with multifaceted health-promoting benefits, has recently been identified as a potential chemotherapeutic agent for cervical cancer (CCA) in our previous study. Nevertheless, its mechanisms of action involved remain unclear. To address this knowledge gap, we employed an integrative strategy combining transcriptomic profiling, network pharmacology, and molecular docking to systematically investigate TMF's inhibitory effects on HeLa cells. Transcriptomic analysis revealed 1,127 differentially expressed genes (DEGs) in TMF-treated HeLa cells, comprising 765 down-regulated and 362 up-regulated genes. Protein-protein interaction (PPI) network analysis identified 12 hub targets ranked by connectivity: JUN, FN1, VEGFA, FOS, ITGB3, NOTCH1, ESR1, EGF, APP, DLG4, EGR1 and ITGB2. Gene Ontology (GO) enrichment analysis demonstrated significant associations with biological processes including signal transduction, cytoplasm, protein binding, positive regulation of apoptotic cell clearance, t-tubules and extracellular matrix structural constituent conferring tensile strength. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed enrichment in 38 signaling pathways. Molecular docking simulations comfirmed good affinities between TMF and all 12 targets, exhibiting binding energies below -5.0 kcal/mol. Our findings suggest that TMF exerts antitumor activity against HeLa cells through multi-target modulation of critical pathways including Pathway in cancer, FoxO, PI3K-Akt, mTOR, AMPK and apoptosis signaling pathway. While these bioinformatics predictions provide mechanistic insights, experimental validation through q-PCR, western blotting, and surface plasmon resonance remains essential to confirm these findings. This study establishes a foundation for further exploration of TMF's therapeutic potential in CCA management.

Triptolide Ameliorates Collagen-Induced Arthritis and Bleomycin-Induced Pulmonary Fibrosis in Rats by Suppressing IGF1-Mediated Epithelial Mesenchymal Transition

OBJECTIVE

To investigate the common mechanisms among collagen-induced arthritis (CIA), bleomycin (BLM)-induced pulmonary fibrosis, and CIA+BLM to evaluate the therapeutic effect of triptolide (TP) on CIA+BLM.

METHODS

Thirty-six male Sprague-Dawley rats were randomly assigned to 6 groups according to a random number table (n=6 per group): normal control (NC), CIA, BLM, combined CIA+BLM model, TP low-dose (TP-L, 0.0931 mg/kg), and TP high-dose (TP-H, 0.1862 mg/kg) groups. The CIA model was induced by intradermal injection at the base of the tail with emulsion of bovine type II collagen and incomplete Freund's adjuvant (1:1), with 200 µL administered on day 0 and a booster of 100 µL on day 7. Pulmonary fibrosis was induced via a single intratracheal injection of BLM (5 mg/kg). The CIA+BLM model combined both protocols, and TP was administered orally from day 14 to 35. After successful modeling, arthritis scores were recorded every 3 days, and pulmonary function was assessed once at the end of the treatment period. Lung tissues were collected for histological analysis (hematoxylin eosin and Masson staining), immunohistochemistry, measurement of hydroxyproline (HYP) content, and calculation of lung coefficient. In addition, HE staining was performed on the ankle joint. Total RNA was extracted from lung tissues for transcriptomic analysis. Differentially expressed genes (DEGs) were compared with those from the RA-associated interstitial lung diseases patient dataset GSE199152 to identify overlapping genes, which were then used to construct a protein-protein interaction network. Hub genes were identified using multiple topological algorithms.

RESULTS

The successfully established CIA+BLM rat model exhibited significantly increased arthritis scores and severe pulmonary fibrosis (P<0.01). By intersecting the DEGs obtained from transcriptomic analysis of lung tissues in CIA, BLM, and CIA+BLM rats with DEGs from rheumatoid arthritis-interstitial lung disease patients (GSE199152 dataset), 50 upregulated and 44 downregulated genes were identified. Through integrated PPI network analysis using multiple topological algorithms, IGF1 was identified as a central hub gene. TP intervention significantly improved pulmonary function by increasing peak inspiratory flow (P<0.01), and reduced lung index and HYP content (P<0.01). Histopathological analysis showed that TP alleviated alveolar collapse, interstitial thickening, and collagen deposition in the lung tissues (P<0.01). Moreover, TP treatment reduced the expression of collagen type I and α-SMA and increased E-cadherin levels (P<0.01). TP also significantly reduced arthritis scores and ameliorated synovial inflammation (P<0.05). Both transcriptomic and immunohistochemical analyses confirmed that IGF1 expression was elevated in the CIA+BLM group and downregulated following TP treatment (P<0.05).

CONCLUSION

TP exerts protective effects in the CIA+BLM model by alleviating arthritis and pulmonary fibrosis through the inhibition of IGF1-mediated EMT.

Transcriptomic profiling and bioinformatics-driven statistical prioritization of CRC biomarkers: A step toward precision oncology

Colorectal adenocarcinoma (COAD) is among the most common causes of cancer-related death globally. Early detection and targeted therapy depend on identifying key molecular biomarkers that drive tumor progression. The molecular heterogeneity of COAD demands robust computational strategies to improve the accuracy of biomarker discovery.

METHODS

We developed and implemented a comprehensive, multi-step bioinformatics and statistical pipeline to systematically prioritize clinically relevant biomarkers in COAD. This pipeline integrated differential gene expression analysis, protein-protein interaction (PPI) network construction, and functional enrichment analysis to identify key hub genes associated with tumor progression. We subsequently applied principal component analysis (PCA) and overall survival modeling to evaluate the diagnostic and prognostic relevance of these candidates. Receiver operating characteristic (ROC) curve analysis was used to assess their sensitivity and specificity. Finally, experimental validation of the prioritized hub genes was conducted via qPCR across three CRC cell lines (LoVo, HCT-116, and HT-29), confirming their upregulation and supporting their clinical potential.

RESULTS

Our integrative pipeline prioritized five key hub genes (CDH3, CXCL1, MMP1, MMP3, and TGFBI) as significantly upregulated in COAD tissues compared to normal controls. Functional enrichment analysis linked these genes to extracellular matrix degradation, epithelial-mesenchymal transition (EMT), inflammatory signaling, and tumor invasion, underscoring their roles in key oncogenic processes. Survival analysis revealed varying degrees of association with patient prognosis, most notably for CXCL1. Diagnostic performance, assessed by ROC analysis, yielded moderate AUC values (0.669-0.692), supporting their potential as biomarkers. Finally, qPCR validation across three CRC cell lines confirmed robust upregulation of all five genes, reinforcing their biological relevance in COAD progression.

CONCLUSION

Our study establishes a reproducible, integrative bioinformatics and statistical framework for the systematic identification of clinically actionable biomarkers in CRC. The five hub genes prioritized (CDH3, CXCL1, MMP1, MMP3, and TGFBI) demonstrated consistent diagnostic and prognostic value, offering a solid basis for the development of non-invasive molecular diagnostics and contributing to precision oncology.