Arl4D-EB1 interaction promotes centrosomal recruitment of EB1 and microtubule growth

Small GTPase ARL4C Associated with Various Cancers Affects Microtubule Nucleation

BACKGROUND/OBJECTIVES

The changes in the level of small GTPase ARL4C are associated with the initiation and progression of many different cancers. The content of ARL4C varies greatly between different tissues, and the induction of ARL4C expression leads to changes in cell morphology and proliferation. Although ARL4C can bind alpha-tubulin and affect intracellular transport, the role of ARL4C in the functioning of the tubulin cytoskeleton remained unclear. The aim of the present work is to study this role; Methods: The cells of the following lines were used for the experiments: HeLa (human cervical carcinoma), MCF7 (human breast cancer), U2OS (human osteosarcoma), Vero, BS-C-1, and COS7 (African green monkey kidney). The receptor activation by agonists followed by the preparation of cell lysates, electrophoresis, and immunoblotting, as well as cell fixation and immunofluorescent staining, were used to assess endogenous ARL4C/ABCA1 levels and the microtubule network morphology. The microtubule regrowth technique was performed to estimate the rate of microtubule nucleation, and the overexpression of different ARL4C constructs was used to affect ARL4C activity in the cells; Results: We showed that the changes in the endogenous ARL4C level or the ARL4C activity alter the microtubule nucleation process in the cells; Conclusions: small GTPase ARL4C may serve as one of the regulators of the microtubule nucleation process both in normal and cancer cells.

Exploring novel drug targets for erectile dysfunction through plasma proteome with genome

Background

Currently, the treatment and prevention of erectile dysfunction (ED) remain highly challenging.

Aim

This study conducted a systematic druggable genome-wide Mendelian randomization (MR) analysis to identify potential therapeutic targets for ED.

Methods

A proteome-wide MR approach was employed to investigate the causal effects of plasma proteins on ED. Subsequently, summary data-based MR (SMR) analysis was performed to identify potential drug targets for ED. Enrichment analysis and protein-protein interaction (PPI) networks revealed the functional characteristics and biological relevance of these potential therapeutic targets. Drug prediction and molecular docking studies were conducted to validate the pharmacological activity of these identified targets. Finally, a systematic MR analysis was conducted to assess upstream intervention factors, such as lifestyles and diseases, associated with these targets, providing insights for the prevention and treatment of ED.

Outcomes

This study identified several potential therapeutic targets for ED.

Results

Proteome-wide MR analysis revealed that 126 genetically predicted plasma proteins were causally associated with ED. SMR analysis indicated that TMEM9 was associated with an increased risk of ED, while MDH1, NQO1, QDPR, ARL4D, TAGLN2, and PPP1R14A were associated with a decreased risk of ED. These potential targets were primarily enriched in metabolic and redox-related biological processes. Molecular docking indicated that the predicted drugs had favorable binding affinities with the proteins, further confirming the pharmacological value of these targets. Finally, 6 plasma proteins (MDH1, NQO1, QDPR, ARL4D, TAGLN2, and TMEM9) could be modulated by lifestyle- and disease-related factors.

Clinical Implications

This study provides new insights into the etiology and potential drug targets of ED and contributes to the development of more effective treatments for ED and reducing the cost of drug development.

Strengths and Limitations

This is a systematic and extensive study exploring the causal relationship between plasma proteins and ED, which helps to provide a comprehensive perspective to understand the role of potential targets in ED. However, we did not conduct this study in different types of ED or different stages of ED progression.

Conclusion

In summary, this study identified 7 plasma proteins causally associated with ED and provided new insights into the etiology and potential drug targets for ED.

Mapping the global interactome of the ARF family reveals spatial organization in cellular signaling pathways

The ADP-ribosylation factors (ARFs) and ARF-like (ARL) GTPases serve as essential molecular switches governing a wide array of cellular processes. In this study, we used proximity-dependent biotin identification (BioID) to comprehensively map the interactome of 28 out of 29 ARF and ARL proteins in two cellular models. Through this approach, we identified ∼3000 high-confidence proximal interactors, enabling us to assign subcellular localizations to the family members. Notably, we uncovered previously undefined localizations for ARL4D and ARL10. Clustering analyses further exposed the distinctiveness of the interactors identified with these two GTPases. We also reveal that the expression of the understudied member ARL14 is confined to the stomach and intestines. We identified phospholipase D1 (PLD1) and the ESCPE-1 complex, more precisely, SNX1, as proximity interactors. Functional assays demonstrated that ARL14 can activate PLD1 in cellulo and is involved in cargo trafficking via the ESCPE-1 complex. Overall, the BioID data generated in this study provide a valuable resource for dissecting the complexities of ARF and ARL spatial organization and signaling.

Mapping the global interactome of the ARF family reveals spatial organization in cellular signaling pathways

The ADP-ribosylation factors (ARFs) and ARF-like (ARLs) GTPases serve as essential molecular switches governing a wide array of cellular processes. In this study, we utilized proximity-dependent biotin identification (BioID) to comprehensively map the interactome of 28 out of 29 ARF and ARL proteins in two cellular models. Through this approach, we identified ~3000 high-confidence proximal interactors, enabling us to assign subcellular localizations to the family members. Notably, we uncovered previously undefined localizations for ARL4D and ARL10. Clustering analyses further exposed the distinctiveness of the interactors identified with these two GTPases. We also reveal that the expression of the understudied member ARL14 is confined to the stomach and intestines. We identified phospholipase D1 (PLD1) and the ESCPE-1 complex, more precisely SNX1, as proximity interactors. Functional assays demonstrated that ARL14 can activate PLD1 in cellulo and is involved in cargo trafficking via the ESCPE-1 complex. Overall, the BioID data generated in this study provide a valuable resource for dissecting the complexities of ARF and ARL spatial organization and signaling.

Identification of m6A methylation-related genes in cerebral ischaemia‒reperfusion of Breviscapus therapy based on bioinformatics methods

BACKGROUND

Cerebral ischaemia‒reperfusion (I/R) frequently causes late-onset neuronal damage. Breviscapine promotes autophagy in microvascular endothelial cells in I/R and can inhibit oxidative damage and apoptosis. However, the mediation mechanism of breviscapine on neuronal cell death is unclear.

METHODS

First, transcriptome sequencing was performed on three groups of mice: the neuronal normal group (Control group), the oxygen-glucose deprivation/ reoxygenation group (OGD/R group) and the breviscapine administration group (Therapy group). Differentially expressed genes (DEGs) between the OGD/R and control groups and between the Therapy and OGD/R groups were obtained by the limma package. N6-methyladenosine (m6A) methylation-related DEGs were selected by Pearson correlation analysis. Then, prediction and confirmation of drug targets were performed by Swiss Target Prediction and UniProt Knowledgebase (UniProtKB) database, and key genes were obtained by Pearson correlation analysis between m6A-related DEGs and drug target genes. Next, gene set enrichment analysis (GSEA) and Ingenuity pathway analysis (IPA) were used to obtain the pathways of key genes. Finally, a circRNA-miRNA‒mRNA network was constructed based on the mRNAs, circRNAs and miRNAs.

RESULTS

A total of 2250 DEGs between the OGD/R and control groups and 757 DEGs between the Therapy and OGD/R groups were selected by differential analysis. A total of 7 m6A-related DEGs, including Arl4d, Gm10653, Gm1113, Kcns3, Olfml2a, Stk26 and Tfcp2l1, were obtained by Pearson correlation analysis. Four key genes (Tfcp2l1, Kcns3, Olfml2a and Arl4d) were acquired, and GSEA showed that these key genes significantly participated in DNA repair, e2f targets and the g2m checkpoint. IPA revealed that Tfcp2l1 played a significant role in human embryonic stem cell pluripotency. The circRNA-miRNA‒mRNA network showed that mmu_circ_0001258 regulated Tfcp2l1 by mmu-miR-301b-3p.

CONCLUSIONS

In conclusion, four key genes, Tfcp2l1, Kcns3, Olfml2a and Arl4d, significantly associated with the treatment of OGD/R by breviscapine were identified, which provides a theoretical basis for clinical trials.

The ADP-Ribosylation Factor 4d Restricts Regulatory T-Cell Induction via Control of IL-2 Availability

Interleukin-2 is central to the induction and maintenance of both natural (nT_reg) and induced Foxp3-expressing regulatory T cells (iT_reg). Thus, signals that modulate IL-2 availability may, in turn, also influence T_reg homeostasis. Using global knockout and cell-specific knockout mouse models, we evaluated the role of the small GTPase ADP-ribosylation factor 4d (Arl4d) in regulatory T-cell biology. We show that the expression of Arl4d in T cells restricts both IL-2 production and responsiveness to IL-2, as measured by the phosphorylation of STAT5. Arl4d-deficient CD4 T cells converted more efficiently into Foxp3⁺ iT_reg in vitro in the presence of αCD3ε and TGFβ, which was associated with their enhanced IL-2 secretion. As such, Arl4d^−/− CD4 T cells induced significantly less colonic inflammation and lymphocytic infiltration in a model of transfer colitis. Thus, our data reveal a negative regulatory role for Arl4d in CD4 T-cell biology, limiting iT_reg conversion via the restriction of IL-2 production, leading to reduced induction of T_reg from conventional CD4 T cells.

Identification and validation of seven RNA binding protein genes as a prognostic signature in oral cavity squamous cell carcinoma

RNA binding proteins (RBPs) play a pivotal role in various biological processes, and aberrant expression of RBPs is closely associated with tumorigenesis and progression. However, the role of RBPs in oral cavity squamous cell carcinoma (OCSCC) is yet unveiled. In this study, RNA sequences and clinical information of OCSCC samples were acquired from The Cancer Genome Atlas (TCGA) database. A total of 650 RBPs, with significantly different expression between healthy and OCSCC samples, were identified using the limma package. A prognostic model was constructed by Lasso-Cox analysis, resulting in the determination of 7 prognosis-related RBPs: ERMP1, RNASE3, ARL4D, CSRP2, ULK1, ZC3H12D, and RPS28. Based on the prognostic model, the risk scores of the OCSCC samples were calculated. The capability of the prognostic model was further evaluated using the receiver operating characteristic curve (ROC). The areas under ROC were 0.764, 0.771, and 0.809 at 1, 3 and 5-year respectively in the TCGA dataset. Internal and external validation showed satisfactory predictive capability for prognosis in OCSCC. In addition, a nomogram was created to graphically present the model. To further validate the analytical data, qRT-PCR was performed on normal and OCSCC cell lines. The mRNA expression of the 7 prognostic genes was in accordance with the analytical results. Functional analysis and gene connection networks were used to describe the biological functions and underlying interactions among the 7 prognostic genes Overall, 7 prognosis-related RBPs were identified, which could be used to predict clinical prognosis and to identify potential therapeutic targets for OCSCC.