STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

Ecophysiological and transcriptional landscapes of arbuscular mycorrhiza fungi enhancing yield, quality, and stalk rot resistance in Anoectochilus roxburghii

Anoectochilus roxburghii (Wall.) Lindl. (A. roxburghii) is an increasingly popular medicinal herb. Arbuscular mycorrhiza (AM) fungi, known for their symbiotic relationships with plant roots, enhance nutrient uptake and disease resistance in host plants. However, their specific regulatory mechanisms in A. roxburghii are not fully understood. In this study, Fujian A. roxburghii was inoculated with the AM fungus Glomus intraradices, and successful root colonization was observed. Following AM fungal colonization, there was a significant upregulation of photosynthesis-related genes in the stems, accompanied by improved canopy phenotypes and root architecture. Consequently, AM-inoculated plants exhibited increased fresh and dry biomass, as well as elevated levels of polysaccharides and flavonoids. Additionally, the incidence of Fusarium oxysporum-induced stalk rot was reduced in AM-inoculated plants. Analysis of defense-related enzymes indicated that AM-inoculated plants exhibited a rapid and robust response to pathogen infection, mitigating oxidative stress. Transcriptomic analysis revealed significant upregulation of genes associated "Fatty acid degradation", "MAPK signaling pathway-plant", and "Plant-pathogen interaction", suggesting their involvement in enhanced disease resistance. A regulatory network centered on ACX1 and calmodulin, involving multiple transcription factors such as WRKY, bHLH, ERF, NAC, and HSF, was implicated in defense responses. These findings demonstrated the beneficial effects of AM fungi on yield, quality, and disease resistance in A. roxburghii, providing a theoretical foundation for its cultivation and genetic improvement.

Conservation of Putative Liquid-Liquid Phase Separating Proteins in Multiple Drug-Resistant Mycobacterium tuberculosis: Role in Host-Pathogen Interactions?

We observed a high proportion of proteins in pathogenic Mycobacterium species that can potentially undergo liquid-liquid phase separation (LLPS) mediated biomolecular condensate formation, compared to nonpathogenic species. These proteins mainly include the PE-PPE and PE-PGRS families of proteins that have nucleic acid and protein-protein binding functions, typical of LLPS proteins. We also mapped identified LLPS proteins in M. tuberculosis (M.tb) drug-resistant databases PubMLST and TBProfiler, based upon the WHO 2023 catalogue of resistance-associated mutations. High sequence conservation of LLPS-associated proteins in various multiple drug-resistant M.tb isolates points to their potentially important role in virulence and host-pathogen interactions during pathogenic evolution. This analysis provides a perspective on the role of protein phase separation in the evaluation of M.tb pathogenesis and offers avenues for future research aimed at developing innovative strategies to combat M.tb infection.

Paeonol regulates the DDIT4-mTOR signaling pathway in macrophages to promote diabetic wound healing

BACKGROUND

Diabetic foot ulcers are a common complication in people with diabetes, and patients with severe disease are at risk of amputation. Current studies have found that one of the reasons for the difficulty in healing diabetic foot ulcers is the Abnormal polarization of the M1/M2 phenotype of macrophages, which leads to a prolonged inflammatory period of the wound. The aim of this study was to investigate whether paeonol can promote the polarization of macrophages towards the M2 type and whether M2 type macrophages can regulate the DDIT4-mTOR signaling pathway and slow down the inflammatory response of diabetic foot ulcers.

METHODS

C57BL/6 mice were used to establish an animal model of diabetic foot ulcers and the effect of paeonol on wound healing was investigated. The effects of paeonol on wound healing of foot ulcer in diabetic mice were evaluated using histological staining and immunohistochemistry. The molecular mechanism of refractory healing of foot ulcers was speculated through network pharmacology. The effects of Paeonol on phenotypic polarization of macrophages and the mechanism of inhibiting inflammation were studied by q-PCR, ELISA, immunofluorescence and Western.

RESULTS

Paeonol can effectively promote wound healing in diabetic mice. HE staining showed that paeonol could improve the inflammatory infiltration in the ulcer wound of diabetic mice; Masson trichromatic staining showed that paeonol could increase the increase of muscle fibers and collagen in the wound tissue of diabetic mice; immunofluorescence results showed that paeonol could increase the angiogenesis in the wound tissue of diabetic mice. Network pharmacological analysis showed that the molecular mechanism of paeonol in treating diabetic wound healing may be through DDIT4-mTOR signaling pathway. q-PCR, ELISA, immunofluorescence and Western blot showed that paeonol could reduce the expression of the signature protein CD86 and inflammatory factors in M1 macrophages, and promote the phenotypic polarization of M2 macrophages, which is the mechanism of inhibiting inflammation by activating DDIT4-mTOR signaling pathway.

CONCLUSION

Paeonol can promote the polarization of macrophages towards M2 type, reduce inflammatory response and accelerate wound surface healing through DDIT4-mTOR signaling pathway, providing a new therapeutic strategy for the treatment of diabetic foot ulcers.

Identification and validation of hub m7G-related genes and infiltrating immune cells in osteoarthritis based on integrated computational and bioinformatics analysis

BACKGROUND

Osteoarthritis (OA) is a joint disease closely associated with synovial tissue inflammation, with the severity of synovitis impacting disease progression. m7G RNA methylation is critical in RNA processing, metabolism, and function, but its role in OA synovial tissue is not well understood. This study explores the relationship between m7G methylation and immune infiltration in OA.

METHODS

Data were obtained from the GEO database. Hub genes related to m7G were identified using differential expression and LASSO-Cox regression analysis, and a diagnostic model was developed. Functional enrichment, drug target prediction, and target gene-related miRNA prediction were performed for these genes. Immune cell infiltration was analyzed using the CIBERSORT algorithm, and unsupervised clustering analysis was conducted to examine immune infiltration patterns. RT-qPCR was used to validate hub gene expression.

RESULTS

Seven m7G hub genes (SNUPN, RNMT, NUDT1, LSM1, LARP1, CYFIP2, and CYFIP1) were identified and used to develop a nomogram for OA risk prediction. Functional enrichment indicated involvement in mRNA metabolism and RNA transport. Differences in macrophage and T-cell infiltration were observed between OA and normal groups. Two distinct m7G immune infiltration patterns were identified, with significant microenvironment differences between clusters. RT-qPCR confirmed differential hub gene expression.

CONCLUSION

A diagnostic model based on seven m7G hub genes was developed, highlighting these genes as potential biomarkers and significant players in OA pathogenesis.

A large-scale genome-wide study of gene-sleep duration interactions for blood pressure in 811,405 individuals from diverse populations

Although both short and long sleep duration are associated with elevated hypertension risk, our understanding of their interplay with biological pathways governing blood pressure remains limited. To address this, we carried out genome-wide cross-population gene-by-short-sleep and long-sleep duration interaction analyses for three blood pressure traits (systolic, diastolic, and pulse pressure) in 811,405 individuals from diverse population groups. We discovered 22 novel gene-sleep duration interaction loci for blood pressure, mapped to 23 genes. Investigating these genes' functional implications shed light on neurological, thyroidal, bone metabolism, and hematopoietic pathways that necessitate future investigation for blood pressure management that caters to sleep health lifestyle. Non-overlap between short sleep (12) and long sleep (10) interactions underscores the plausible nature of distinct influences of both sleep duration extremes in cardiovascular health. Several of our loci are specific towards a particular population background or sex, emphasizing the importance of addressing heterogeneity entangled in gene-environment interactions, when considering precision medicine design approaches for blood pressure management.

Genome-wide insights into the nomenclature, evolution and expression of tobacco TIFY/JAZ genes

MAIN CONCLUSION

A systematic nomenclature for tobacco TIFY/JAZ proteins was established via genome-wide analysis, and the gene transcription patterns and potential functions of these proteins were analyzed as well. Intensive studies focused on the plant-specific JAZ regulators of jasmonate (JA) signaling in tobacco due to their critical roles in regulating JA-mediated development, secondary metabolism, and stress responses. JAZs comprise a subfamily of the TIFY proteins, yet the reported TIFY/JAZ regulators of tobacco spp. are tangled in naming confusion, which resulted in nomenclature chaos. Here, we identified 32 TIFY/JAZ proteins via genome-wide analysis of tobacco cultivar TN90 and obtained their homologues in Nicotiana sylvestris and Nicotiana tomentosiformis. By bioinformatic analysis, these TIFY/JAZ regulators were classified into 4 subfamilies (i.e., 21 JAZs, 5 ZIM & ZMLs, 2 TIFY8s, and 4 PPDs) based on their phylogenetic relationship to establish a systematic nomenclature, which indicated gene loss or genomic rearrangement during the formation of common tobacco. Analysis of JA-induced expression revealed that these TIFY/JAZ genes displayed distinct expression patterns in the leaves and roots upon JA treatment. Further microarray and metabolomics assays observed that 5 TIFY/JAZ genes were differentially expressed in the plants with dysfunction of COI1, the receptor protein of JA hormone and that the abundance of a series of primary and secondary metabolites was altered as well. A predicted protein interaction network of tobacco TIFY/JAZ proteins was also constructed, and it indicated that 120 proteins may interact with these regulators. Findings of this work provide valuable information about TIFY/JAZ proteins in regulating JA responses and metabolic processes in tobacco and may contribute greatly to future studies on tobacco TIFY/JAZ proteins.

Native top-down proteomics enables discovery in endocrine-resistant breast cancer

Oligomerization of proteoforms produces functional protein complexes. Characterization of these assemblies within cells is critical to understanding the molecular mechanisms involved in disease and to designing effective drugs. Here we present a native top-down proteomics (nTDP) strategy to identify protein assemblies (≤70 kDa) in breast cancer cells and in cells that overexpress epidermal growth factor receptor (EGFR), which serves as a resistance model of estrogen receptor-alpha (ER)-targeted therapies. This nTDP approach identified ~104 complexoforms from 17 protein complexes, which revealed several molecular features of the breast cancer proteome, including EGFR-induced dissociation of nuclear transport factor 2 (NUTF2) assemblies that modulate ER activity. We found that the K4 and K55 post-translational modification sites discovered with nTDP differentially impact the effects of NUTF2 on the inhibition of the ER signaling pathway. The characterization of endogenous proteoform-proteoform/ligand interactions revealed the molecular diversity of complexoforms and their role in breast cancer growth.

Behavioral and transcriptomic effects of a novel cannabinoid on a rat valproic acid model of autism

Autism spectrum disorder (ASD) is a complex neurodevelopmental condition characterized by impaired social communication, restricted interests, repetitive behavior and irritability. Exposure to valproic acid (VPA) during pregnancy has been shown to increase the risk of autism in children and has led to the development of the in-utero VPA rat model that elicits neurodevelopmental autistic-like features. Offspring exhibit behavioral and neurobiological alterations modelling ASD symptoms. We performed a behavioral and molecular assessment in a rat in-utero VPA model treated with a novel botanical cannabinoid, JZP541. Male offspring from dams treated with VPA were tested acutely and sub-chronically with JZP541 (10, 30, or 100 mg/kg, intraperitoneally). A behavioral testing battery was performed, and brain frontal cortex and hippocampus used for RNA sequencing. In utero exposure to VPA resulted in progeny showing behavioral phenotypes characteristic of ASD. JZP541 attenuated these deficits in social, stereotypic, hyperactivity and irritability behavior in a dose-dependent fashion. VPA exposure was associated with a substantial transcriptional dysregulation impacting multiple key biological processes in a tissue-dependent manner. The expression profiles were integrated with publicly available datasets of autism-associated genes to support the validity of the model used and to focus on the effects of treatment on known autism-relevant transcriptional targets. This approach indicated a strong and dose-dependent reduction of the autism-associated gene expression signature in brain samples from animals dosed with JZP541. Our findings demonstrate JZP541 was able to ameliorate ASD associated behavioral deficits, and this was supported by improvements in putative transcriptional biomarkers of ASD.

Unlocking the genetic code: a comprehensive Genome-Wide association study and gene set enrichment analysis of cell-mediated immunity in chickens

BACKGROUND

The poultry immune system is essential for protecting against infectious diseases and maintaining health and productivity. Cell-mediated immune responses (CMIs) protect organisms against intracellular pathogens. This study aimed to enrich the findings of genome-wide association studies (GWAS) by including several systematic gene set enrichment analyses (GSEA) related to cell-mediated immune responses in chickens.

METHODS

To investigate the function of the cellular immune system, phenotypic data were collected based on the differences in skin thickness before and after impregnation with dinitrochlorobenzene (DNCB) solution. Additionally, 312 hybrid birds of the F2 generation of Arian broiler chickens and Urmia native chickens were genotyped using the Illumina 60k SNP BeadChip. A general linear model (GLM) with an FDR < 5% was used for the association analysis. Functional enrichment analysis of the identified candidate genes was performed using the Enrichr database. A protein‒protein interaction (PPI) network was constructed using the STRING database. In addition, colocalization analysis was applied to identify QTLs related to the immune system.

RESULTS

GWAS revealed 147 SNPs associated with the CMI trait, which were related to 1363 genes. These genes were significantly enriched in eight KEGG pathways, 22 Reactome pathways, and 18 biological processes. PPI network analysis led to the identification of 26 hub genes. The three hub genes PSMA3, PSMC2 and PSMB4 were enriched in almost all pathways related to cellular immunity, including the proteasome, interleukin-1 signaling, and programmed cell death pathways, which makes them important candidates involved in CMI. In addition, the MAP3K8, NLRC5, UBB, CASP6, DAPK2, TNFRSF6B, TNFSF15, and PIK3CD genes were identified as key genes in several functional pathways. A total of 10 SNPs were found in interferon-gamma QTLs, and two SNPs were found in the cell-mediated immune response QTL region, leading to the identification of 12 cellular immune response-related genes that were reported as important candidates in previous studies.

CONCLUSION

The post-GWAS analysis in this study led to the identification of key genes that regulate the biological processes of cellular immunity in chickens. Therefore, selecting birds that excel in expressing such genes can improve immunity in chickens.

Integrative network analysis reveals novel moderators of Aβ-Tau interaction in Alzheimer's disease

BACKGROUND

Although interactions between amyloid-beta and tau proteins have been implicated in Alzheimer's disease (AD), the precise mechanisms by which these interactions contribute to disease progression are not yet fully understood. Moreover, despite the growing application of deep learning in various biomedical fields, its application in integrating networks to analyze disease mechanisms in AD research remains limited. In this study, we employed BIONIC, a deep learning-based network integration method, to integrate proteomics and protein-protein interaction data, with an aim to uncover factors that moderate the effects of the Aβ-tau interaction on mild cognitive impairment (MCI) and early-stage AD.

METHODS

Proteomic data from the ROSMAP cohort were integrated with protein-protein interaction (PPI) data using a Deep Learning-based model. Linear regression analysis was applied to histopathological and gene expression data, and mutual information was used to detect moderating factors. Statistical significance was determined using the Benjamini-Hochberg correction (p < 0.05).

RESULTS

Our results suggested that astrocytes and GPNMB + microglia moderate the Aβ-tau interaction. Based on linear regression with histopathological and gene expression data, GFAP and IBA1 levels and GPNMB gene expression positively contributed to the interaction of tau with Aβ in non-dementia cases, replicating the results of the network analysis.

CONCLUSIONS

These findings suggest that GPNMB + microglia moderate the Aβ-tau interaction in early AD and therefore are a novel therapeutic target. To facilitate further research, we have made the integrated network available as a visualization tool for the scientific community (URL: https://igcore.cloud/GerOmics/AlzPPMap ).

Uncovering the bioactive constituents and their mechanisms of the Forsythiae Fructus against hyperpigmentation using a combined strategy integrating cell-specific extraction, plasma pharmaceutical chemistry and network pharmacology

Skin hyperpigmentation is a type of difficult-to-treat disease that frequently results from the improper metabolism of facial pigment. The herb Forsythiae Fructus (FF) possesses whitening and freckle-removal properties. Its probable active components and anti-hyperpigmentation mechanism, however, are still unknown. In the current investigation, the active components were initially identified and screened by UHPLC-Q-Orbitrap HRMS/MS employing B16 cell-specific extraction and plasma pharmaceutical chemistry, respectively. Subsequently, the component-target-disease network and protein-protein interaction (PPI) network of FF were built by using a network pharmacology approach. The probable targets and pathways were found using gene ontology (GO) and KEGG enrichment analysis. The essential elements and core genes causing illnesses were identified through molecular docking. Lastly, based on network analysis, cell experiments were carried out to further explore the efficacy of the main active ingredients in the treatment of abnormal melanosis. As a result, 37 ingredients were identified in FF extract, 22 compounds in the decoction had a specific affinity with B16 mouse melanoma cells, and a total of 10 prototype compounds and 11 metabolites were detected in rat plasma. Through in vitro and in vivo screening methods, 16 potential active ingredients were obtained, and 229 biological targets and 1515 disease-related targets were predicted by network pharmacology. In addition, in vitro cell experiments revealed that kaempferol, luteolin, and wogonin all exhibited inhibition of melanin production and tyrosinase activity. The proposed combination method of rapid screening of active ingredients in vivo and integrated network pharmacology in vitro could explore the therapeutic mechanism of FF against hyper-pigmentation, and provide a theoretical evidence for the development and utilization of FF.

Evaluating the Mechanism Underlying Multi-Compound Synergy of Banxia Decoction in the Treatment of Hashimoto's Thyroiditis Based on Network Pharmacology and Molecular Docking

Objective

We aimed to utilize network pharmacological analysis and molecular docking to elucidate the potential mechanisms of Banxia Decoction (BD) action in the treatment of Hashimoto's thyroiditis (HT).

Materials and Methods

Active compounds and HT-related targets were predicted using databases and the intersection of the results was taken. STRING and DAVID 6.8 tools were used to obtain the protein-protein interaction (PPI) network and perform GO and KEGG evaluations, respectively. Discovery Studio 2017 R2 was utilized to perform molecular docking and RT-qPCR was conducted to confirm hub gene expressions in clinical samples.

Results

A total of 136 active compounds in BD were screened, and 74 potential targets related to HT were identified in BD. Further, 17 key targets in the PPI network were identified and HIF1A, EP300, PRKCA, and TERT were included for subnet analysis. Next, a network of "Chinese medicine-active compound-potential target-signal pathway" was obtained and the HIF-1 signaling pathway was identified as the key pathway. Finally, 8 active compounds and their stable binding to target proteins were confirmed by molecular docking; MAPK3, SRC, TERT, and HIF1A were upregulated in HT relative to the goiter samples.

Conclusion

The integration of network pharmacology and molecular docking provides a systematic framework for exploring the multi-component and multi-target characteristics of BD in HT, underscores the therapeutic potential of BD in HT by targeting genes and pathways involved in immune regulation and oxidative stress. These findings not only enhance our understanding of BD's pharmacological mechanisms but also lay the groundwork for the development of novel therapeutic strategies for HT.

An evolutionary dynamics analysis of the plant DEK gene family reveals the role of BnaA02g08940D in drought tolerance

DEK is a chromatin protein that interacts with DNA to influence chromatin formation, thereby affecting plant growth, development, and stress response. This study investigates the molecular evolution of the DEK family in plants, with a particular focus on the Brassica species. A total of 127 DEK genes were identified in 34 plants and classified into seven groups based on the phylogenetic analysis. The distribution of motifs and gene structure is similar within each group, indicating a high degree of conservation. The results of the collinearity analysis indicated that the DEK protein has undergone a certain degree of evolutionary conservation. The expansion of the DEK family is primarily attributable to whole-genome duplication (WGD) or segmental duplication events. The DEK protein has undergone purification during its evolutionary history, and several positively selected sites have been identified. Moreover, the examination of cis-acting elements and expression patterns revealed that the BnDEKs play a significant role in plant growth and stress response. The protein-protein interaction network identified several noteworthy proteins that interact with DEK. These analyses enhance our comprehension of the DEK gene family and establish the foundation for additional validation of its function. Further research demonstrated that the overexpression of one DEK family member, BnaA02g08940D, enhanced the transgenic Arabidopsis tolerance to drought and osmosis. This indicates that the DEK family may respond when plants are subjected to drought stress, thereby strengthening the plant's resilience.

Plasticity of Root System Architecture and Whole Transcriptome Responses Underlying Nitrogen Deficiency Tolerance Conferred by a Wild Emmer Wheat QTL

Our aim was to elucidate mechanisms underlying nitrogen (N)-deficiency tolerance in bread wheat (cultivar Ruta), conferred by a wild emmer wheat QTL (WEW; IL99). We hypothesised that the tolerance in IL99 is driven by enhanced N-uptake through modification of root system architecture (RSA) underscored by transcriptome modifications. Severe N-deficiency (0.1 N for 26 days) triggered significantly higher plasticity in IL99 compared to Ruta by modifying 16 RSA traits; nine of which were IL99-specific. The change in root growth in IL99 was collectively characterised by a transition in root orientation from shallow to steep, increased root number and length, and denser networks, enabling nutrient acquisition from a larger volume and deeper soil layers. Gene ontology and KEGG-enrichment analyses highlighted IL99-specific pathways and candidate genes elevated under N-deficiency. This included Jasmonic acid metabolism, a key hormone mediating RSA plasticity (AOS1, TIFY, MTB2, MYC2), and lignification-mediated root strengthening (CYP73A, 4CL). 'N-metabolism' was identified as a main shared pathway to IL99 and Ruta, with enhanced nitrate uptake predominant in IL99 (NRT2.4), while remobilisation was the main strategy in Ruta (NRT2.3). These findings provide novel insights into wheat plasticity response underlying tolerance to N-deficiency and demonstrate the potential of WEW for improving N-uptake under suboptimal conditions.

Genomic and transcriptomic analyses of chemical hepatocarcinogenesis aggravated by oncoprotein loss

BACKGROUND AND AIMS

The chemical carcinogen diethylnitrosamine (DEN) is often used to induce HCC in mice. Curiously, several labs have reported that the removal of oncoproteins from hepatocytes exacerbated DEN-induced HCC, with mechanisms unknown. This study aimed at deciphering molecular mechanisms underlying the tumor suppressive effect of oncoproteins.

APPROACH AND RESULTS

We generated mutant mouse lines with hepatocyte-specific deletions of Met , Ptpn11 / Shp2 , Ikkβ , or Ctnnb1/β-catenin and assessed DEN-induced tumorigenesis in the wild-type and mutant mice. To systematically examine genetic and molecular signaling alterations, we performed whole exome and RNA-sequencing on liver samples collected at the pre-cancer and established cancer stages. Although the mutational profiles of DEN-induced tumors were barely different in wild-type and mutant mice, oncoprotein ablation increased DEN-induced mutational burdens, especially in Shp2-deficient tumors. RNA-sequencing revealed multiple changes in signaling pathways, in particular, upregulated epithelial-mesenchymal transition, cell migration, and tumor metastasis, as well as downregulated small molecule metabolism that was affected by oncoprotein ablation. We identified key molecules and pathways that are associated with hepatic innate immunity and implicated in liver tumorigenesis. In addition, we unveiled markedly changed expression of a few miRNAs in the human HCC database.

CONCLUSIONS

The aggravation of DEN-induced HCC progression seen on oncoprotein ablation could be caused by common and distinct genomic and signaling alterations. This study reveals a new level of complexity in hepatocarcinogenesis and elucidates molecular mechanisms underlying tumor evolution and recurrence.

Unraveling biomolecular and community grammars of RNA granules via machine learning

Membraneless RNA granules are essential for posttranscriptional gene regulation, influencing cellular functions and contributing to neurodegenerative diseases. However, a comprehensive understanding of their compositions and organization has been challenging due to their complex nature. In this study, we develop robust machine learning models to reliably identify RNA granule proteomes within the human proteome, capturing central RNA granule characteristics despite the heterogeneity across diverse in vitro conditions. Furthermore, we uncover protein-protein interaction (PPI) community grammars within the RNA granule proteome, highlighting PPIs as key stabilizers of RNA granule structure and function. Dense PPI clusters serve as stable "cores," forming key functional subunits across heterogeneous RNA granules. We introduce a state-of-the-art framework for understanding RNA granule biology and underscore the critical role of PPIs in maintaining RNA granule integrity.

The integrated stress response pathway controls cytokine production in tissue-resident memory CD4+ T cells

Tissue-resident memory T (TRM) cells are a specialized T cell population that reside in tissues and provide a rapid protective response upon activation. Here, we showed that human and mouse CD4+ TRM cells existed in a poised state and stored messenger RNAs encoding proinflammatory cytokines without protein production. At steady state, cytokine mRNA translation in TRM cells was suppressed by the integrated stress response (ISR) pathway. Upon activation, the central ISR regulator, eIF2α, was dephosphorylated and stored cytokine mRNA was translated for immediate cytokine production. Genetic or pharmacological activation of the ISR-eIF2α pathway reduced cytokine production and ameliorated autoimmune kidney disease in mice. Consistent with these results, the ISR pathway in CD4+ TRM cells was downregulated in patients with immune-mediated diseases of the kidney and the intestine compared to healthy controls. Our results indicated that stored cytokine mRNA and translational regulation in CD4+ TRM cells facilitate rapid cytokine production during local immune response.

Combined effects of vitamin D3 and dioxopiperidinamide derivative on lipid homeostasis, inflammatory pathways, and redox imbalance in non-alcoholic fatty liver disease in vivo zebrafish model

Liver damage and metabolic dysfunctions, the defining features of non-alcoholic fatty liver disease (NAFLD), are marked by inflammation, oxidative stress, and excessive hepatic fat accumulation. The current therapeutic approaches for NAFLD are limited, necessitating exploring novel treatment strategies. Dioxopiperidinamide derivatives, particularly DOPA-33, have shown effective anti-inflammatory and antioxidant properties, potentially offering therapeutic benefits against NAFLD. This study investigated the combined potential of vitamin D3 (Vit D3) and DOPA-33 in treating NAFLD. The network pharmacology analysis identified key NAFLD targets modulated by Vit D3 and DOPA-33, emphasizing their potential mechanisms of action. In NAFLD-induced zebrafish models, Vit D3 and DOPA-33 significantly reduced hepatic lipid accumulation, oxidative stress, and apoptosis, demonstrating superior efficacy over individual treatments. The treatment also lowered reactive oxygen species (ROS) levels, decreased liver damage, and enhanced antioxidant defense mechanisms. Moreover, behavioral analyses showed improved locomotion and reduced weight gain in treated zebrafish. Biochemical analyses revealed lower triglycerides (TG) and glucose levels with improved oxidative markers. Furthermore, histological analyses indicated reduced hepatic steatosis and inflammation, with decreased expression of lipogenesis-related genes and inflammatory mediators. Finally, high-performance liquid chromatography (HPLC) confirmed a significant reduction in hepatic cholesterol levels, indicating the effectiveness of the combination therapy in addressing key NAFLD-related dyslipidemias. These findings suggest that Vit D3 + DOPA-33 targets pathways involved in lipid metabolism, inflammation, and oxidative stress by offering a promising therapeutic approach for NAFLD.

Quantitative serum proteomic analysis for biomarker discovery in post-COVID-19 postural orthostatic tachycardia syndrome (PC-POTS) patients

Postural orthostatic tachycardia syndrome (POTS) is a chronic, debilitating condition that is characterized by an excessive increase in heart rate upon orthostatic challenge. Before the COVID-19 pandemic, POTS affected 0.5 % to 1 % of the U.S. population. Since the pandemic, the incidence has risen sharply, adding an estimated 6-7 million new cases in the U.S. Despite its importance, there is currently no reliable biomarker for POTS, leading to significant diagnostic delays. A major hurdle in identifying biomarkers is the heterogeneous nature of the syndrome. To address this, we focused on a homogeneous subgroup of post-COVID-19 POTS (PC-POTS) patients. We conducted quantitative proteomics on sera from 9 PC-POTS patients and 9 healthy controls, identifying 31 proteins with significantly different abundances in PC-POTS patients. Most elevated proteins were linked to actin filaments or immune functions/inflammation. Weighted Gene Co-Expression Network Analysis revealed module 7 (M7) correlated strongly with PC-POTS diagnosis and related traits. The key proteins in M7 included MTPN, TAGLN2, ADP-ribosylation factor 1, PDLIM1, PPIA, CNN2, LGALSL, TXN, TLN1, TUBA4A, IL4, TREML1, GP1BA, and, all highly correlated with these traits. Cell-type enrichment analysis revealed that M7 was highly associated with immune and neuronal cells. The main pathways identified in M7 included the integrin signaling pathway, blood coagulation, and glycolysis. These findings suggest that the key proteins in M7 could serve as biomarkers for PC-POTS. This study uses quantitative proteomics to identify potential biomarkers that differentiate PC-POTS patients from healthy controls, establishing a foundation for further research and validation.

Highly multiplexed cytokine analysis of bronchoalveolar lavage and plasma reveals age-related dynamics and correlates of inflammation in children

Despite the central role of cytokines in mediating inflammation that underlies a range of childhood diseases, cytokine testing remains primarily limited to research settings and surrogate markers of inflammation are often used to inform clinical diagnostic and treatment decisions. There are currently no reference ranges available for cytokines in healthy children, either systemically (in blood) or at sites of disease (such as the lung). In our study, we aimed to develop an openly accessible dataset of cytokines in the airways and blood of healthy children spanning 1 to 16 years of age. We examined how cytokine concentration changes during childhood and assessed whether a core set of cytokine markers could be used to indirectly evaluate the response of a broad spectrum of inflammatory analytes. To develop our dataset, a total of 65 unique analytes were quantified in cell-free bronchoalveolar lavage (BAL) and plasma from 78 children. We showed that age profoundly impacts soluble immune analyte concentration in both sample types and identified a highly correlative core set of 10 analytes in BAL and 11 analytes in plasma capable of indirectly evaluating the response of up to 44 inflammatory mediators. This study addresses an urgent need to develop reference ranges for cytokines in healthy children to aid in diagnosis of disease, to determine eligibility for, and to monitor the effects of, cytokine-targeted monoclonal antibody therapy.

Integrating network pharmacology and experimental validation to explore the potential mechanism by which resveratrol acts on osimertinib resistance in lung cancer

Globally, osimertinib resistance has been a long-term challenge. Resveratrol, a naturally occurring polyphenolic compound found in various plants, has the potential to modulate multidrug resistance mechanisms. However, the specific role of resveratrol in delaying osimertinib resistance in lung cancer is still unclear. The present study aimed to investigate the therapeutic effects and underlying mechanisms of resveratrol in delaying osimertinib resistance. Accordingly, the corresponding targets of resveratrol were screened through the Traditional Chinese Medicine Systems Pharmacology database. Similarly, the corresponding targets for osimertinib resistance were mined from the GeneCards database. A protein-protein interaction network was subsequently constructed to pinpoint key hub genes that resveratrol may target to delay resistance. Molecular docking analysis was then employed to assess the binding energy between the predicted key targets and resveratrol. Finally, in vitro experiments were performed to validate the results. Ultimately, 13 potential therapeutic targets of resveratrol related to delaying osimertinib resistance were identified. Kyoto Encyclopedia of Genes and Genomes analysis suggested that the effects of resveratrol may be associated with the apoptotic pathway. Molecular docking revealed that resveratrol has good binding affinities with MCL1 and BCL2L11. In vitro experiments confirmed that resveratrol inhibited the proliferation of osimertinib-resistant cells and upregulated the expression of BCL2L11. In conclusion, resveratrol may promote apoptosis by targeting BCL2L11 to delay osimertinib resistance.

Preclinical development of a replication-competent vesicular stomatitis virus-based Lassa virus vaccine candidate advanced into human clinical trials

BACKGROUND

Lassa fever (LF) is a zoonotic haemorrhagic disease caused by Lassa virus (LASV), which is endemic in West African countries. The multimammate rat is the main animal reservoir and its geographic range is expected to expand due to influences like climate change and land usage, and this will place larger parts of Africa at risk. We conducted preclinical development on a promising experimental vaccine that allowed its advancement into human trials.

METHODS

The LF vaccine is based on a vesicular stomatitis virus (VSV) vector in which the VSV glycoprotein (G) was replaced with the LASV glycoprotein complex (GPC). Earlier studies showed that this vaccine (VSVΔG-LASV-GPC) was efficacious in macaques, thus we regenerated VSVΔG-LASV-GPC using laboratory and documentation practices required to support vaccine manufacturing and human trials. The efficacy of the clinical vaccine candidate was assessed in cynomolgus macaques and more extensive immunologic analysis was performed than previously to investigate immune responses associated with protection.

FINDINGS

A single VSVΔG-LASV-GPC vaccination elicited innate, humoural and cellular immune responses, prevented development of substantial LASV viraemia, and protected animals from disease. Vaccinated macaques developed polyfunctional antibodies and serum was shown to neutralize virus expressing GPCs representative of geographically diverse LASV lineages.

INTERPRETATION

The VSVΔG-LASV-GPC clinical candidate elicited immunity that protected 10 of 10 vaccinated macaques from disease supporting its use in a clinical development program, which recently progressed to phase 2 clinical trials. Moreover, immunologic analysis showed that virus-neutralizing serum antibodies likely played a role in preventing LASV disease in vaccinated macaques.

FUNDING

This work was supported by the Coalition for Epidemic Preparedness Innovations (CEPI), The National Institute of Allergy and Infectious Diseases (NIAID)/National Institutes of Health (NIH), The Bill and Melinda Gates Global Vaccine Accelerator Program, the Burroughs Wellcome Fund, and financial gifts and support by Nancy Zimmerman, Mark and Lisa Schwartz, and Terry and Susan Ragon.

[Mechanism of Cnidii Fructus in the treatment of periodontitis with osteoporosis based on network pharmacology, molecular docking, and molecular dynamics simulation]

OBJECTIVES

This study aimed to explore the active components, potential targets, and mechanism of Cnidii Fructus in the treatment of periodontitis with osteoprosis through network pharmacology, molecular docking, and molecular dynamics simulation technology.

METHODS

The main chemical constituents and targets of Cnidii Fructus were screened using the TCMSP and SwissTargetPrediction databases, as well as literature reports. Targets of periodontitis and osteoporosis were predicted using different databases. The intersection targets of Cnidii Fructus, periodontitis, and osteoporosis were obtained using Venny 2.1. The protein-protein interaction network was formed on the STRING platform. Cytoscape 3.9.1 was used to construct the active component-intersection target interaction network, perform the topological analysis, and screen key targets and core active components. Furthermore, the Metascape database was used to perform gene ontology (GO) function and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis on the intersection targets. The top five key targets and core active components were selected as receptor proteins and ligand small molecules. Discovery Studio 2019 was used to dock ligands and receptors and visualize the docking results. Molecular dynamics simulation was conducted using Gromacs2022.3 to assess the stability of the interactions between the core active components and the main targets.

RESULTS

A total of 20 potential active ingredients of Cnidii Fructus were screened, and 116 targets of Cnidii Fructus were obtained for treating periodontitis and osteoporosis. GO and KEGG analyses of the 116 targets showed that Cnidii Fructus may play a therapeutic role through the phosphoinositide 3-kinase-protein kinase B (PI3K-Akt) and advanced glycation end products-receptor for advanced glycation end products (AGE-RAGE) signaling pathways. Molecular docking showed that the core constituents were well bound to the main targets. Molecular dynamics simulations confirmed the stability of the Diosmetin-AKT1 complex system.

CONCLUSIONS

The preliminary discovery of the potential molecular pharmacological mechanism of Cnidii Fructus extract in the targeted treatment of periodontitis with osteoporosis through a multi-component, multitarget, and multi-pathway approach can serve as a theoretical foundation for future drug-development research and clinical application.

Proteomic Insights Into Early Detection and Progression of Knee Osteoarthritis: Unveiling Molecular Signatures

AIM

Osteoarthritis (OA) is the eleventh most disabling condition, with radiographic classification based on the Kellgren-Lawrence (KL) grading system. Early detection is critical to implement interventions to slow disease progression and improve patient outcomes. Proteomics, as a powerful strategy, could contribute to a better understanding of the disease pathophysiology and its early detection.

OBJECTIVES

The study aims to identify and confirm proteins associated with early detection and their role in the progression of knee OA.

METHODOLOGY

Synovial fluid (SF) and serum samples from the Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, were categorized by KL classification and subjected to SWATHTM analysis in the discovery phase. Seven samples of each OA grade were analyzed. A mass dynamics tool was used for data analysis and visualization. Significant protein expression level was defined as -1≤ log2FC ≥1 with p-value < 0.05, and ELISA was used for validation in a greater number of patients.

RESULTS

29 significantly modulated proteins were observed in osteoarthritis grade comparisons. Cathepsin G (CTSG) and angiotensinogen (AGT) were upregulated, whereas fumarylacetoacetase (FAH) and neural cell adhesion molecule 1 (NCAM1) were downregulated with radiographic disease progression, as validated by ELISA. CTSG, AGT, and NCAM1 showed good sensitivity and specificity in discriminating between early and late OA grades. Notably, serum and synovial fluid levels of AGT and NCAM1 exhibited significant correlation.

CONCLUSION

This is one of the first studies to comprehensively analyze proteins associated with OA progression. Additionally, the identified protein signatures have great potential for OA progression and differential diagnosis of early and late-stage OA.

Identification of Ferroptosis-Inflammation Related Hub Genes and the Disease Subtypes in Idiopathic Pulmonary Fibrosis via System Biology Approaches

We aim to screen and analyze the ferroptosis inflammation-related hub genes associated with idiopathic pulmonary fibrosis (IPF). The GSE52463 and GSE110147 datasets were obtained from the GEO database and merged. The DEGs were selected by differential analysis and intersected with inflammation-related genes and ferroptosis-related genes to acquire the ferroptosis-related differentially expressed genes (FRDEGs). GO, KEGG, GSEA, and GSVA were performed to investigate the features of FRDEGs. The key module genes were selected by WGCNA and employed to generate the PPI network using Cytoscape. Subsequently, the hub genes were identified using cytoHubba and validated by ROC curves generated by survivalROC. Finally, the correlations of hub genes were analyzed through Spearman and the subtypes of IPF were constructed using ConsensusClusterPlus. A total of 1814 DEGs were screened out and 18 FRDEGs were acquired from the intersection of DEGs, ferroptosis-related genes, and inflammation-related genes. GO and KEGG analysis revealed that FRDEGs were primarily involved in bacterial-origin molecular, response infectious disease, and iron ion transport. GSEA results suggested a predominant association with autoimmune diseases and GSVA identified ten different pathways between PF and control. Through WGCNA, three highly correlated modules were identified and ten key module genes were obtained by intersecting genes in the three modules with FRDEGs. Finally, employing three algorithms within the cytoHubba led to the identification of eight hub genes: CCND1, TP53, STAT3, CTNNB1 CDH1, ESR1, HSP90AA1, and EP300. Eventually, two distinct subtypes of IPF were identified. The present research successfully identified the hub genes associated with ferroptosis and inflammation and their biological effects on IPF. Furthermore, two disease subtypes of IPF were constructed.

Pan-Cancer Analysis Identifies BCLAF1 as a Potential Biomarker for Renal Cell Carcinoma

B-cell lymphoma-2-associated transcription factor 1 (BCLAF1) is a versatile protein involved in the regulation of gene transcription and post-transcriptional processing. Although BCLAF1 exerts a broad tumor suppressor effect or tumor promoter effect in many cancer types, the specific roles concerning its expression levels, and its impact on tumorigenesis in Renal cell carcinoma (RCC) remain unclear. Here, we utilized the Cancer Genome Atlas (TCGA) and Genotype Tissue Expression (GTEx) datasets alongside R software and online tools to unravel the specific roles of BCLAF1 in 33 cancer types, including its expression levels, tumor immune and molecular subtypes, and its correlation with prognosis, diagnosis, DNA methylation, and immune microenvironment. Additionally, we carried out cell biology experiments to independently investigate the expression of BCLAF1 in RCC and its effects on tumor progression. BCLAF1 was differentially expressed in tumor tissues compared to normal tissues across various cancer types and was also differentially expressed in different immune and molecular subtypes. In RCC, patients with high BCLAF1 expression had a better prognosis and BCLAF1 was tightly correlated with the stage, gender, and histological grade of patients. Furthermore, BCLAF1 had higher DNA methylation levels and higher immune infiltration levels in tumor tissues. Additionally, cell functional experiments confirmed the low expression of BCLAF1 in RCC and that BCLAF1 significantly inhibited the proliferation, migration, and invasion, while inducing apoptosis and cell cycle arrest in RCC cells in vitro. Our study under-scored the potential of BCLAF1 as an important actor in tumorigenesis, especially concerning RCC where it may serve as an effective prognostic marker.

A genome-wide association meta-analysis links hidradenitis suppurativa to common and rare sequence variants causing disruption of the Notch and Wnt/β-catenin signaling pathways

BACKGROUND

The contributions of genetic and environmental risk factors to hidradenitis suppurativa (HS) are both poorly understood.

OBJECTIVE

To identify sequence variants that associate with HS and determine the contribution of environmental risk factors and inflammatory diseases to HS pathogenesis.

METHODS

A genome-wide association meta-analysis of 4814 HS cases (Denmark: 1977; Iceland: 1266; Finland: 800; UK: 569; and US: 202) and 1.2 million controls, searching for sequence variants associated with HS.

RESULTS

We found 8 independent sequence variants associating with HS, 6 common and 2 rare (frequency <1%). Four associations point to candidate causal genes, NCSTN, PSENEN, WNT10A, and TMED10, that all map to the Notch and Wnt/β-catenin signaling pathways, involved in epidermal keratinization.

LIMITATIONS

Limited racial diversity may prevent identification of sequence variants of particular importance in non-Caucasian populations.

CONCLUSIONS

These findings demonstrate that genes and pathways involved in epidermal keratinization are the genetic backbone of HS pathology.

Plasma extracellular vesicles carry immune system-related peptides that predict human longevity

Extracellular vesicles (EVs) play crucial roles in aging. In this National Institutes on Aging-funded study, we sought to identify circulating extracellular vesicle (EV) biomarkers indicative of longevity. The plasma EV proteome of 48 older adults (mean age 77.2 ± 1.7 years [range 72-80]; 50% female, 50% Black, 50% < 2-year survival, 50% ≥ 10-year survival) was analyzed by high-resolution mass spectrometry and flow cytometry. The ability of EV peptides to predict longevity was evaluated in discovery (n = 32) and validation (n = 16) datasets with areas under receiver operating characteristic curves (AUCs). Longevity-associated large EV (LEV) plasma subpopulations were mainly related to immune cells (HLA-ABC+, CD9+, and CD31+) and muscle cells (MCAD+ and RyR2+). Of 7960 identified plasma EV peptides (519 proteins), 46.4% were related to the immune system and 10.1% to muscle. Compared with short-lived older adults, 756 EV peptides (131 proteins) had a higher abundance, and 130 EV peptides (78 proteins) had a lower abundance in long-lived adults. Among longevity-associated peptides, 437 (58 proteins) were immune system related, and 12 (2 proteins) were muscle related. Using just three to five plasma EV peptides (mainly complement components C2-C6), we achieved high predictive accuracy for longevity (AUC range 0.91-1 in a hold-out validation dataset). Our findings suggest that immune cells produce longevity-associated plasma EVs and elucidate fundamental mechanisms regulating aging and longevity. EV longevity predictors suggest there may be merit in targeting complement pathways to extend lifespan, for instance, with any one of the multiple complement inhibitors currently available or in clinical development.

Proteomic profiling identifies classic Hodgkin lymphoma patients at risk of bleomycin pulmonary toxicity

Advances in treating classic Hodgkin lymphoma (cHL) have improved cure rates, with overall survival exceeding 80%, resulting in a growing population of survivors at risk of long-term complications, particularly cardiac and pulmonary toxicity. Bleomycin, a key component of combination chemotherapy, is associated with bleomycin-induced pulmonary toxicity (BPT). Using label-free quantification nano liquid chromatography-tandem mass spectrometry, protein expression in diagnostic lymphoma samples from patients with and without BPT was compared. Results showed differential protein expression and disrupted cellular pathways, suggesting biological differences in BPT risk. Immunohistochemical analysis revealed higher expression of JAK3, BID, and MMP9, and lower expression of CD20, TPD52, and PIK3R4 in patients with BPT. High BID and low CD20 expression were associated with inferior overall survival, while high BID and low JAK3 and CD20 expression were linked to poorer progression-free survival. These findings highlight altered protein profiles in pretreatment cHL biopsies associated with BPT development.

Mechanism of β‑sitosterol in treating keloids: Network pharmacology, molecular docking and experimental verification

β‑sitosterol (SIT) has anti‑inflammatory, anti‑tumor and anti‑fibrotic effects. However, the precise mechanisms underlying its efficacy in keloid treatment remain elusive. The present study aimed to elucidate the therapeutic effect of SIT on keloids. The active components of Fructus arctii, target molecules of these components and disease‑associated target molecules were identified and retrieved from various databases. Molecular docking was employed to evaluate the binding affinity of the active compounds for key targets. Cell viability and proliferation were evaluated via CCK‑8 and EdU assays, while cell migration capacity was assessed via wound healing assays and cell migration and invasion abilities were determined via Transwell assays. A rescue study involving YS‑49 was conducted. Western blot analysis was performed to assess the expression levels of proteins associated with EMT and proteins involved in the PI3K/AKT signaling pathway. A subcutaneous keloid fibroproliferative model was established in nude mice and immunohistochemical staining was performed on tissue sections. By intersecting the keloid targets, 29 targets were identified, with 10 core targets revealed by protein-protein interaction analysis. Molecular docking revealed a robust binding affinity between SIT and PTEN. In addition to inhibiting cell viability, invasion and migration, SIT significantly decreased the levels of phosphorylated (p‑)PI3K and p‑AKT, downregulated the protein expression of Vimentin and Snail proteins and increased the protein expression of Zonula Occludens‑1 and E‑cadherin. YS‑49 reversed the inhibitory effect of SIT on keloid in SIT‑treated cells. In vivo experiments demonstrated that SIT suppressed the growth of a keloid model in nude mice and increased PTEN expression. The present study provided the first evidence that SIT inhibits keloid proliferation, migration and invasion by modulating the PTEN/PI3K/AKT signaling pathway, suggesting its potential as a novel therapeutic approach for keloid treatment.

Modulation of host gene expression by the zinc finger antiviral protein

The zinc finger antiviral protein (ZAP) depletes nonself RNAs through recognition of their elevated CpG dinucleotide content. CpG dinucleotides are sparse in most endogenous mammalian mRNAs, but a subset might potentially be modulated by ZAP. While CpG frequency alone is insufficient to predict ZAP-regulation, we developed an algorithm using experimentally determined compositional features to predict which endogenous mRNAs may be ZAP-regulated. Using ZAP-knockout mice, we demonstrate that levels of many host mRNAs that are algorithmically predicted ZAP targets are indeed increased when ZAP is absent. ZAP is interferon-inducible, and we also identify genes that are downregulated by ZAP during an innate immune response. Many ZAP-regulated gene products are extracellular matrix or of nucleosome components, whose ZAP-mediated control is conserved in human cells. Overall, we provide a tool for the prediction of ZAP target genes and reveal host mRNAs that are ZAP-regulated.

TPPP3, a Good Prognostic Indicator, Suppresses Cell Proliferation and Migration in OSCC

INTRODUCTION AND AIMS

Oral squamous cell carcinoma (OSCC) is one of the most prevalent malignancy of the head and neck. Early diagnosis of OSCC is difficult and the prognosis has not improved significantly. This study aims to explore the role of tubulin polymerisation promoting protein 3 (TPPP3) in the occurrence and development of OSCC and discover new diagnostic and prognostic markers for OSCC.

METHODS

Using UALCAN, GEPIA, western blot, and quantitative real-time polymerase chain reaction, we studied TPPP3 expression and its relationship with tumour stage. Then, we detected the effect of TPPP3 on OSCC biological functions by CCK-8 and cell scratch assays, as well as correlations between TPPP3 expression and survival of different kinds of head and neck squamous cell carcinoma (HNSC) patients through Kaplan-Meier plotter. Besides, we explored coexpressed genes associated with TPPP3 in HNSC using LinkedOmics and protein-protein interaction networks of TPPP3 using STRING and Cytoscape. Furthermore, we explored possible molecular mechanisms that TPPP3 functions in HNSC using UALCAN, Kaplan-Meier plotter, and TIMER. Finally, we analysed promoter methylation level by UALCAN and mutation by cBioPortal of TPPP3 in HNSC.

RESULTS

TPPP3 was less expressed in OSCC. The TPPP3 expression level was negatively correlated with tumour stage. Furthermore, TPPP3 significantly inhibited OSCC proliferation and migration. Besides, TPPP3 high expression was significantly associated with good prognosis in different kinds of HNSC patients. Additionally, TPPP3 may regulate the occurrence and development of OSCC through the PALMD/PI3K pathway. TPPP3 methylation level in HNSC decreased. Finally, we found that TPPP3 genetic alteration was involved in TPPP3 mRNA expression change in HNSC.

CONCLUSION

TPPP3 functions as a tumour suppressor in OSCC and is associated with good prognosis in HNSC patients. TPPP3 can be used as a potential biomarker for prognosis and diagnosis of OSCC.

CLINICAL RELEVANCE

TPPP3 can be used as a potential biomarker for prognosis and diagnosis of OSCC in clinical practice.

Network pharmacology, molecular docking and molecular dynamics simulation of chalcone scaffold-based compounds targeting breast cancer receptors

Compounds with a chalcone scaffold-based structure have demonstrated promising anticancer biological activity. However, the molecular interactions between chalcone scaffold-based compounds and breast cancer-associated proteins remain unclear. Through network pharmacology, molecular docking, and molecular dynamics (MD) simulation analyses, compounds with a chalcone scaffold-based structure were evaluated for their interaction with potential breast cancer targets. The compounds were retrieved from the ASINEX database, resulting in 575,302 compounds. A total of 342 compounds with chalcone scaffold-based structures were discovered. From the 342 compounds that was analysed, ten were chosen due to their adherence to Lipinski's rule, having an appropriate range of lipophilicity (LOGP), and topological polar surface area (TPSA), and absence of any toxicity. Based on target intersection, 50 target genes were found and subjected to protein-protein interaction (PPI), gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Four target genes were found to be involved in the breast cancer pathway. Consequently, molecular docking was utilised to analyse the molecular interactions between the compounds and four target protein receptors. Compound 211 exhibited the highest binding affinities for the epidermal growth factor receptor (EGFR), fibroblast growth factor receptor 1 (FGFR1), oestrogen receptor (ESR1), and cyclin dependent kinase 6 (CDK6) with values of -8.95 kcal/mol, -8.60 kcal/mol, -10.33 kcal/mol, and -9.90 kcal/mol, respectively. During MD simulation, compound 211 and its respective proteins were stable, compact, and had minimal flexibility. The findings provide foundations for future studies into the interaction underlying the anti-breast cancer potential of compounds with chalcone-based scaffold structures.

GLKs directly regulate carotenoid biosynthesis via interacting with GBFs in plants

Carotenoids are vital photosynthetic pigments for plants. Golden2-like transcription factors (GLKs) are widely recognized as major regulators of Chl biosynthesis and chloroplast development. However, despite GLKs being subjected to intensive investigations, whether GLKs directly regulate carotenoid biosynthesis and the molecular mechanisms by which GLKs transcriptionally activate their target genes remain unclear. Here, we report that GLKs directly regulate carotenoid biosynthesis and activate their target genes in a G-box binding factor (GBF)-dependent manner in Arabidopsis. Both in vitro and in vivo studies reveal that GLKs physically interact with GBFs to activate transcription of phytoene synthase (PSY), the gene encoding a rate-limiting enzyme for carotenoid biosynthesis. While GLKs possess transactivation activity, they depend on GBFs to directly bind to the G-box motif to modulate PSY expression. Loss of GBFs impairs GLK function in regulating carotenoid and Chl biosynthesis. Since the G-box motif is an enriched motif in the promoters of GLK-regulated genes, the GLK-GBF regulatory module likely serves as a common mechanism underlying GLK-regulated photosynthetic pigment biosynthesis and chloroplast development. Our findings uncover a novel regulatory machinery of carotenoid biosynthesis, discover a molecular mechanism of transcriptional regulation by GLKs, and divulge GLKs as important regulators to coordinate photosynthetic pigment synthesis in plants.

Genome-wide identification of CA genes in cotton and the functional analysis of GhαCA4-D, GhβCA6-D and GhγCA2-D in response to drought and salt stresses

Carbonic anhydrases (CAs) are critical metalloenzymes, widely exist in organisms, which involve in many physiological processes, including response to adverse environmental conditions. Although CA genes have been comprehensive identified and analyzed in numerous plants, there are a few of reports in cotton. Therefore, we conducted an exhaustive research for CA genes from two tetraploid cotton species and their ancestral species. A total of 138 CA genes were found, and 45 of them belonged to Gossypium hirsutum. Phylogenetic relationships and sequences analysis showed that CA genes were categorized into three distinct subtypes: α-type, β-type and γ-type. The exon numbers of β-type members were highly variable. Various types of cis-elements, including drought inducibility, were identified in CA genes, suggesting that CA genes might be involved in the regulation of drought stress response. qRT-PCR was applied to assess the gene expression level in various tissues under drought stress. The results indicated that the expression levels of GhαCA4-D, GhβCA1-A, GhβCA1-D, GhβCA3-D and GhβCA6-D were significantly higher in leaves than that in stems and roots. The expression of GhαCA4-A, GhαCA8-A, GhαCA4-D, GhβCA3-D, GhβCA6-D and GhγCAL1-D was significantly upregulated in roots at severe drought treatment. The functions of GhαCA4-D, GhβCA6-D and GhγCA2-D were analyzed using virus-induced gene silencing (VIGS) technology. Compared to the controls, GhγCA2-D-silenced upland cotton seedlings were more sensitive to salt stress. However, the drought tolerance of GhαCA4-D and GhβCA6-D silenced plants was significantly decreased. Stomatal density, width and area were significantly higher in TRV:GhβCA6-D compared to TRV:00 inoculated plants. GhαCA4-D silenced plants were susceptible to oxidative stress, and silencing GhαCA4-D induced leave cell death. Our results will assist to make clear the regulatory mechanism of CA genes under abiotic stress.

Pannexin 1 crosstalk with the Hippo pathway in malignant melanoma

In this study, we explored the intricate relationship between Pannexin 1 (PANX1) and the Hippo signaling pathway effector, Yes-associated protein (YAP). Analysis of The Cancer Genome Atlas (TCGA) data revealed a significant positive correlation between PANX1 mRNA and core Hippo components, Yes-associated protein 1 [YAP], Transcriptional coactivator with PDZ-binding motif [TAZ], and Hippo scaffold, Ras GTPase-activating-like protein IQGAP1 [IQGAP1], in invasive cutaneous melanoma and breast carcinoma. Furthermore, we demonstrated that PANX1 expression is upregulated in invasive melanoma cell lines and is associated with increased YAP protein levels. Notably, our investigations uncovered a previously unrecognized interaction between endogenous PANX1 and the Hippo scaffold protein IQGAP1 in melanoma cells. Moreover, our findings revealed that IQGAP1 exhibits differential expression in melanoma cells and plays a regulatory role in cellular morphology. Functional studies involving PANX1 knockdown provided compelling evidence that PANX1 modulates YAP protein levels and its cotranscriptional activity in melanoma and breast carcinoma cells. Importantly, our study highlights the potential therapeutic significance of targeting PANX1. Pharmacological inhibition of PANX1 using selective FDA-approved inhibitors or PANX1 knockdown reduced YAP levels in melanoma cells. Furthermore, our Clariom™ S analysis unveiled key genes implicated in cell proliferation, such as neuroglin1 (NRG1), β-galactoside binding protein and galectin-3 (LGALS3), that are affected in PANX1-deficient cells. In summary, our investigation delves into the intricate interplay between PANX1 and YAP in the context of invasive melanoma, offering valuable insights into potential therapeutic strategies for effective treatment.

Beyond traditional medications: exploring novel and potential inhibitors of trypanothione reductase (LmTr) of Leishmania parasites

The trypanothione reductase enzyme, which neutralizes the reactive oxygen species produced inside the macrophages to kill the parasites, is one of the evasion strategies Leishmania uses to survive inside the cells. The vitality of the parasite depends on Leishmania major trypanothione reductase (LmTr), a NADPH-dependent flavoprotein oxidoreductase essential for thiol metabolism. Since this enzyme is distinct and lacking in humans, we focused on it in our study to screen for new inhibitors to combat leishmaniasis. Using the I-TASSER server, a three-dimensional model of LmTr was generated. The Autodock vina program was used in high-throughput virtual screening of the ZINC database. The top seven molecules were ranked according to their binding affinity. The compounds with the highest binding affinities and the right number of hydrogen bonds were chosen. These compounds may be effective at inhibiting the target enzyme's (LmTr) activity, making them new leishmaniasis treatments. These compounds may serve as a useful starting point for a hit-to-lead approach in the quest for new anti-Leishmania drugs that are more efficient and less cytotoxic. The average node degree is 5.09, the average local clustering coefficient is 0.868, and the PPI enrichment p-value is 8.9e-06, indicating that it is sufficiently connected to regulate the network. TRYR (LmTr protein) also interacts physically with ten additional proteins in the pathogenesis network. The findings of the study indicated that successfully suppressing the LmTr protein in vitro and in vivo may finally result in regulating the L. major pathogenesis.

Temporal resolved multi-proteomic analysis enabled the systematic characterization of N-glycosylation pattern changes during Jurkat T cell activation

Protein glycosylation plays essential roles in regulating innate and adaptive immune response. Previous studies only focused on individual protein-glycan interactions or specific glycoform changes during T cell activation, yet the systematic characterization of protein glycosylation alterations remains insufficiently elucidated. To address these limitations, we conducted temporally resolved quantitative analysis of glycoforms, site-specific glycans, glycoproteins, and glycosylation enzymes in activated Jurkat T cells, and successfully portrayed the dynamic landscape of protein glycosylation during Jurkat T cell activation. We found the heterogeneity and number of significantly upregulated glycopeptides increased along with activation. For most glycopeptides, their alteration patterns did not correlate with the abundance of their glycoprotein substrates. However, functional molecules including CD69, CD28, and PTPRC demonstrated co-upregulation at both the protein and glycosylation levels. Correlation analysis between glycopeptides and glycotransferases indicated that sialylated or fucosylated peptides were well correlated with enzymes involved in glycan branching and capping. Comparative analysis of global peptides, glycopeptides, and phosphopeptides revealed their distinctive changing patterns along Jurkat T cell activation, and only glycosylation demonstrated a steady increase trend with a large proportion of upregulated glycopeptides. Collectively, this integrated multi-proteomics characterization of activated Jurkat T cells provided insights for the development of novel therapeutic strategy targeting glycosylation.

Search for germline gene variants in colorectal cancer families presenting with multiple primary colorectal cancers

A double primary colorectal cancer (CRC) in a familial setting signals a high risk of CRC. In order to identify novel CRC susceptibility genes, we whole-exome sequenced germline DNA from nine persons with a double primary CRC and a family history of CRC. The detected variants were processed by bioinformatics filtering and prioritization, including STRING protein-protein interaction and pathway analysis. A total of 150 missense, 19 stop-gain, 22 frameshift and 13 canonical splice site variants fulfilled our filtering criteria. The STRING analysis identified 20 DNA repair/cell cycle proteins as the main cluster, related to genes CHEK2, EXO1, FAAP24, FANCI, MCPH1, POLL, PRC1, RECQL, RECQL5, RRM2, SHCBP1, SMC2, XRCC1, in addition to CDK18, ENDOV, ZW10 and the known mismatch repair genes. Another STRING network included extracellular matrix genes and TGFβ signaling genes. In the nine whole-exome sequenced patients, eight harbored at least two candidate DNA repair/cell cycle/TGFβ signaling gene variants. The number of families is too small to provide evidence for individual variants but, considering the known role of DNA repair/cell cycle genes in CRC, the clustering of multiple deleterious variants in the present families suggests that these, perhaps jointly, contributed to CRC development in these families.

Polysaccharides from Scrophularia ningpoensis Hemsl. improve reserpine-induced depression-like behavior by inhibiting HTR2A/HTR2C mediated AKT/GSK3β/β-catenin/CBP/BDNF signalling

Scrophularia ningpoensis Hemsl. is a traditional Chinese medicine used to regulate blood sugar levels, immunity, etc. We previously isolated polysaccharides from S. ningpoensis Hemsl. (SNPS) and innovatively observed that SNPS exhibit antidepressant properties; however, the underlying mechanism is still unclear. Here, we employed network pharmacology to predict the potential targets and antidepressant mechanism of SNPS. Accordingly, we detected the effects of SNPS on monoamine neurotransmitter synthesis, metabolism, receptor expression and signal transduction in reserpine (RES)-treated mice using ELISA, HPLC-electrochemistry, metabonomics, Golgi-Cox staining and Western blotting. Finally, the mechanism of SNPS on key targets (HTR2A and HTR2C) was verified in vivo and in vitro. Results showed that SNPS ameliorated depression by restoring monoamine neurotransmitter homeostasis and hippocampal neurogenesis. SNPS reversed the depletion of 5-HT, NE and DA by activating the tryptophan (Trp)/5-HT and tyrosine (Tyr)/DA/NE metabolic pathways. SNPS decreased HTR2A and HTR2C contents, leading to the phosphorylation of AKT and GSK3β, followed by increases in β-catenin, CBP and BDNF levels. Mechanistically, SNPS reduced the levels of HTR2A and HTR2C proteins by inhibiting their mRNA transcription, rather than inducing protein degradation. In conclusion, by inhibiting the transcription of HTR2A and HTR2C, SNPS activated the AKT/GSK3β/β-catenin/CBP/BDNF pathway, thereby exerting dose-dependent antidepressant effects.

Genetic Dissection of Cyclic di-GMP Signalling in Pseudomonas aeruginosa via Systematic Diguanylate Cyclase Disruption

The second messenger bis-(3' → 5')-cyclic dimeric guanosine monophosphate (c-di-GMP) governs adaptive responses in the opportunistic pathogen Pseudomonas aeruginosa, including biofilm formation and the transition from acute to chronic infections. Understanding the intricate c-di-GMP signalling network remains challenging due to the overlapping activities of numerous diguanylate cyclases (DGCs). In this study, we employed a CRISPR-based multiplex genome-editing tool to disrupt all 32 GGDEF domain-containing proteins (GCPs) implicated in c-di-GMP signalling in P. aeruginosa PA14. Phenotypic and physiological analyses revealed that the resulting mutant was unable to form biofilms and had attenuated virulence. Residual c-di-GMP levels were still detected despite the extensive GCP disruption, underscoring the robustness of this regulatory network. Taken together, these findings provide insights into the complex c-di-GMP metabolism and showcase the importance of functional overlapping in bacterial signalling. Moreover, our approach overcomes the native redundancy in c-di-GMP synthesis, providing a framework to dissect individual DGC functions and paving the way for targeted strategies to address bacterial adaptation and pathogenesis.

Natural Antisense Transcript-Mediated Regulation of HOXA10-AS in Oral Squamous Cell Carcinoma

BACKGROUND

The oncogenic role of HOXA10-AS and HOXA10 in cancer has been well documented. However, the epigenetic role of HOXA10 and the natural antisense-mediated regulation of HOXA10-AS in oral squamous cell carcinoma progression is not understood.

METHODS

A total of 35 oral squamous cell carcinoma specimens and 35 adjacent normal clinical specimens were collected and categorized on the basis of their lymph node status. HOXA10-AS and HOXA10 expression were analyzed using RT-qPCR. Methyl-capture sequencing was performed using lymph node-negative (n = 6) and lymph node-positive (n = 5) matched cases. The promoter activity of HOXA10 was determined using a luciferase assay. ChIP-qPCR was performed to determine histone mark localization in the distal promoter region of HOXA10. A protein-protein interaction network of genome-wide antisense targets was constructed using StringDB, and functional enrichment was performed using the R package ClusterProfiler. Transient siRNA-mediated transfection was performed to target specific exons of the HOXA10-AS gene, followed by subsequent cell proliferation, cell cycle, and cell migration assays and validation of cancer signaling pathways through western blotting.

RESULTS

HOXA10-AS and its antisense target HOXA10 were significantly overexpressed in the lymph node-positive samples. The transcriptionally active distal promoter of HOXA10 consists of a constitutively unmethylated CpG island region (CUR). H3K4me3, H3K27ac, and H3K27me3 histone mark deposition at the adjacent methylated loci of the distal promoter suggest the nature of euchromatin-driven regulation. Genome-wide mapping revealed 11 potential targets of HOXA10-AS. Targeted specific knockdown of HOXA10-AS exons significantly reduced the expression of HOXA10 and deregulated its downstream targets, contributing to decreased cell cycle progression and epithelial-to-mesenchymal transition.

CONCLUSION

HOXA10-AS regulates the expression of HOXA10 through a natural antisense-mediated mechanism and is epigenetically regulated by constitutively unmethylated marks in the distally enhancing promoter of HOXA10.

Network pharmacology and in silico study of quercetin and structurally similar flavonoids as osteogenesis inducers that interact with oestrogen receptors

Background: Osteoporosis poses a global health challenge, particularly with an ageing population. Quercetin, isorhamnetin, avicularin, isoquercetin, quercitrin, and taxifolin are natural flavonoids with similar structure that induce ontogenesis.

Methods: In the present study, proteins in oestrogen signalling and bone morphogenesis were analysed, and hub genes were identified with Cytoscape, followed by pathway analysis. Then, molecular targets of flavonoids and osteoporosis-related targets were identified, and overlaps were detected. Molecular docking and dynamics simulations assessed flavonoid interactions with ERs.

Results: The study identified 14 gene products linked to osteoporosis, including ESR1 and ESR2. Enrichment analyses confirmed ESR involvement in various biological processes. SwissTargetPrediction highlighted quercetin and isorhamnetin as favourable targets for ESR1 and ESR2. Molecular docking and dynamics revealed favourable and stable binding of flavonoids to ERα and ERβ.

Conclusion: These interactions suggest therapeutic potential of natural flavonoids for osteoporosis treatment by targeting ERs, laying a foundation for future research in preclinical and clinical settings.

Identification of key genes in immune-response post-endurance run in horses

Intense physical activity in endurance horses triggers complex immune and inflammatory responses, yet the molecular mechanisms underlying these adaptations remain unclear. This study investigated immune-related transcriptomic changes following a 160 km endurance ride, focusing on sex-based differences. Using a bioinformatics approach, differentially expressed genes (DEGs), pathways, microRNAs (miRNAs), and transcription factors (TFs) were analyzed before (T0) and after (T1) the ride. A protein-protein interaction (PPI) analysis was conducted to identify key regulatory genes. Pathway enrichment analysis revealed significant activation of immune-regulatory and ribosomal pathways. Notably, TLR4, CXCL8, and CCL5 were identified as key hub genes involved in immune modulation post-exercise. Comparisons between female (FT1 vs FT0) and gelding (GT1 vs GT0) horses revealed distinct molecular responses. Female horses exhibited upregulation of ribosomal protein genes, suggesting enhanced protein synthesis and muscle recovery. In contrast, geldings showed increased expression of inflammatory and stress-related genes, indicating a heightened immune response. Notably, sex-based differences were observed, with FT1 vs FT0 and GT1 vs GT0 comparisons revealing distinct KEGG pathway enrichments. Additionally, miRNA and TF analyses revealed regulatory elements influencing endurance-related immune responses. Our findings demonstrated sex-specific molecular mechanisms underlying endurance exercise adaptation, with females prioritizing protein synthesis and recovery, while geldings exhibit stronger inflammatory responses and stress-related pathways. This study provides critical insights into how sex influences exercise physiology at the transcriptomic level, with potential applications in training and recovery strategies for endurance horses.

Structural and Functional Characterization of a Putative Type VI Secretion System Protein in Cronobacter sakazakii as a Potential Therapeutic Target: A Computational Study

Background

Cronobacter sakazakii, a foodborne pathogen with a fatality rate of 33%, is a rod-shaped, Gram-negative, non-spore-forming bacterium responsible for causing meningitis, bacteremia, and necrotizing enterocolitis. Despite many unknown functions of hypothetical proteins in bacterial genomes, bioinformatic techniques have successfully annotated their roles in various pathogens.

Objectives

The aim of this investigation is to identify and annotate the structural and functional properties of a hypothetical protein (HP) from Cronobacter sakazakii 7G strain (accession no. WP_004386962.1, 277 residues) using computational tools.

Methods

Multiple bioinformatic tools were used to identify the homologous protein and to construct and validate its 3D structure. A 3D model was generated using SWISS-MODEL and validated using tools, developing a reliable 3D structure. The STRING and CASTp servers provided information on protein-protein interactions and active sites, identifying functional partners.

Results

The putative protein was soluble, stable, and localized in the cytoplasmic membranes, indicating its biological activity. Functional annotation identified TagJ (HsiE1) within the protein, a member of the ImpE superfamily involved in the transport of toxins and a part of the bacterial type VI secretion system (T6SS). The 3-dimensional structure of this protein was validated through molecular docking involving 6 different compounds. Among these, ceforanide demonstrated the strongest binding scores, -7.5 kcal/mol for the hypothetical protein and -7.2 kcal/mol for its main template protein (PDB ID: 4UQX.1).

Conclusion

Comparative genomics study suggests that the protein found in C. sakazakii may be a viable therapeutic target because it seems distinctive and different from human proteins. The results of multiple sequence alignment (MSA) and molecular docking supported HP's potential involvement as a T6SS. These in silico results represent that the examined HP could be valuable for studying C. sakazakii infections and creating medicines to treat C. sakazakii-mediated disorders.

Genomic Dissection of Chinese Yangtze River Delta White Goat Based on Whole Genome Sequencing

The conservation and utilization of livestock genetic resources is essential for the maintenance of biodiversity and breed innovation. Whole genome sequencing (WGS) was performed on 90 samples from Chinese Yangtze River Delta White goats (YRD), sourced from two populations of Chongming island white goats and Haimen white goats, aiming to dissect their genomic characteristics. In addition, 262 WGS data from nine other breeds of goats were downloaded from the NCBI database. These WGS data obtained were used to identify and analyze genetic variation with the goat reference genome, and the genetic structure of goat populations was analyzed. Through selective sweep analysis, the selection-signature genes and their polymorphic features were identified. It was found that the most significant genomic selection region in YRD goats was in the region of 62.9-64.6 Mb on chromosome 13, which contained genes related to the coat color and muscle growth of the goats. Nucleotide diversity of MYH7B, a gene related to the development of the goat's skeletal muscle, within the Yangtze River Delta white goat population was significantly lower than in other domestic and foreign goat breeds, suggesting that the gene was subject to selection. In addition, the IGF2BP2 gene, reported to be associated with litter size in goats, showed clear selection-signature characteristics in the Boer goats compared to the YRD goats.

Proteogenomic discovery of RB1-defective phenocopy in cancer predicts disease outcome, response to treatment, and therapeutic targets

Genomic defects caused by truncating mutations or deletions in the Retinoblastoma tumor suppressor gene (RB1) are frequently observed in many cancer types leading to dysregulation of the RB pathway. Here, we propose an integrative proteogenomic approach that predicts cancers with dysregulation in the RB pathway. A subset of these cancers, which we term as "RBness," lack RB1 genomic defects and yet phenocopy the transcriptional profile of RB1-defective cancers. We report RBness as a pan-cancer phenomenon, associated with patient outcome and chemotherapy response in multiple cancer types, and predictive of CDK4/6 inhibitor response in estrogen-positive breast cancer. Using RNA interference and a CRISPR-Cas9 screen in isogenic models, we find that RBness cancers also phenocopy synthetic lethal vulnerabilities of cells with RB1 genomic defects. In summary, our findings suggest that dysregulation of the RB pathway in cancers lacking RB1 genomic defects provides a molecular rationale for how these cancers could be treated.

Bioinformatic analysis of glycolysis and lactate metabolism genes in head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous cancer with significant global incidence. This study investigates glycolysis- and lactate metabolism-related genes (GALMRGs) in HNSCC, focusing on their impact on prognosis, the tumor immune microenvironment, and their potential as therapeutic biomarkers. Analysis of data from the Cancer Genome Atlas and Gene Expression Omnibus identified 16 GALMRGs that were differentially expressed in HNSCC compared to normal tissues. Functional analysis revealed the involvement of lactate and pyruvate metabolism and HIF-1 signaling pathways. Weighted gene co-expression network analysis identified two module genes, CDKN3 and SLC2A1. Five key genes (CAV1, CDKN3, LDHA, MB, and PER2) were identified through univariate, multivariate, and LASSO regression analyses and used to construct a prognostic model. This model demonstrated strong predictive accuracy for overall survival, stratifying patients into high- and low-risk groups. Immune cell infiltration analysis showed a negative correlation between resting and activated mast cells, and low-risk patients had higher tumor mutational burden, suggesting a better response to immunotherapy. Consensus clustering classified HNSCC into two distinct molecular subtypes with differing expression of the key genes. This GALMRG-based prognostic model is a promising biomarker for predicting HNSCC outcomes and immunotherapy responses, providing valuable insights for personalized treatment strategies.

Comprehensive analysis of GDFs as therapeutic targets and prognosis biomarkers in gastric cancer

Growth/differentiation factors (GDFs, GDF1-3, GDF5-7, GDF9-11, and GDF15) belong to a subfamily of the transforming growth factor-β. GDFs play an important role in morphogenetic and developmental activities in many tissues. And many GDFs family numbers have been observed to be correlated with various types of tumors. However, the diverse expression patterns and prognostic values of ten GDFs in gastric cancer (GC) have yet to be analyzed. Herein we investigated the transcriptional and survival data of GDFs in patients with GC from the Gene Expression Profiling Interactive Analysis, The Cancer Genome Atlas, cBioPortal, Tumor Immune Estimation Resource, Tumor Immune Syngeneic Mouse, UALCAN, Human Protein Atlas Gene Expression Omnibus and The Database for Annotation, Visualization and Integrated Discovery databases. We found that multiple GDF family members are highly expressed in GC, which can prompt diagnosis and evaluate prognosis, and can be used as target points for GC immunotherapy.

Connexin46 in the nucleus of cancer cells: a possible role as transcription modulator

BACKGROUND

Oncogenes drive cancer progression, but few are active exclusively in tumor cells. Connexins (Cxs), traditionally recognized as ion channel proteins, can localize to the nucleus and regulate gene expression, playing key roles in both physiological and pathological processes. Cx46, once thought to be restricted to the eye lens, has been implicated in tumor growth, though its underlying mechanisms remain unclear. This study investigates the nuclear presence of Cx46 in cancer cells and its potential role as a transcriptional modulator.

METHODS

We employed ChIP-Seq, confocal immunofluorescence, and nuclear protein purification to assess Cx46 localization and DNA interactions. Functional assays were conducted to evaluate its effects on invasion, division, spheroid formation, and mesenchymal marker expression. Single-point mutations and molecular dynamics simulations were used to explore potential Cx46-DNA interactions.

RESULTS

Cx46 mRNA upregulation was found in a variety of tumors compared to adjacent healthy tissue. In HeLa cells, which do not express Cx46, its transfection promoted proliferation, invasion and self-renewal capacity, cancer stem cell traits and mesenchymal features. Consistently, in Sk-Mel-2, which naturally express Cx46, reduced Cx46 expression led to a decrease in the similar parameters. In HeLa cells, nuclear Cx46 was detected in two forms, full length 46 kDa and a 30 kDa fragment (GJA3-30 k), ChIP-Seq experiments revealed that Cx46 binds to the DNA at intergenic and promoter regions, leading to the activation of oncogenic pathways. Molecular dynamics simulations suggest that GJA3-30 k dimerizes in a RAD50-like structure, forming stable DNA complexes. Cx46 and in some cases GJA3-30 k were detected in the nuclei of multiple cancer cell lines, including prostate, breast and skin cancers.

CONCLUSIONS

Our findings reveal a novel nuclear role for Cx46 in cancer, demonstrating its function as a transcriptional regulator and its potential as a therapeutic target.