Phosphorylation of Arl4A/D promotes their binding by the HYPK chaperone for their stable recruitment to the plasma membrane

The underlying molecular mechanisms and biomarkers of Hip fracture combined with deep vein thrombosis based on self sequencing bioinformatics analysis

BACKGROUND

Thrombus formation is a severe complication in orthopedic surgery, significantly increasing mortality in patients with fractures. Therefore, identifying feature genes to determine thrombus presence in fracture surgeries is critical.

METHODS

Whole blood samples were collected from 18 patients with fractures with thrombosis (YES_thrombus) and 18 patients with fractures without thrombosis (NO_thrombus) from the Second Hospital of Shanxi Medical University, China, and used for transcriptome sequencing and quality control to generate the YES_thrombus dataset. Candidate genes were identified by overlapping differentially expressed genes (DEGs) with key module genes from weighted gene co-expression network analysis (WGCNA). Functional enrichment analysis was then performed to explore the roles of the candidate genes. Feature genes were further refined by intersecting results from three machine learning algorithms and constructing an artificial neural network (ANN). Diagnostic performance was assessed using receiver operating characteristic (ROC) curves. Additionally, single-gene gene set enrichment analysis (GSEA) was conducted, and correlations between feature genes and differential immune cells were analyzed. The competing endogenouse RNA (ceRNA) regulatory network for feature genes was also constructed. Finally, quantitative reverse transcriptase PCR (qRT-PCR) was used to validate gene expression.

RESULTS

Seven candidate genes were selected, with functional enrichment analysis linking them to the autophagosome and PPAR signaling pathways. Five feature genes with excellent diagnostic performance were identified. Single-gene GSEA enrichment showed that the feature genes were primarily associated with the cytosolic ribosome and oxidative phosphorylation. The correlation analysis revealed that aDC exhibited the strongest negative correlation with WDR81 and the strongest positive correlation with RGS1. The ceRNA regulatory network encompassed three feature genes, five miRNAs, and 236 lncRNAs. Expression analysis indicated that, with the exception of WDR81, other genes were significantly upregulated in the NO_thrombus group. qRT-PCR validation confirmed that the expression of AAED1, ARL4A, and WDR81 matched sequencing results.

CONCLUSIONS

In conclusion, five feature genes (RGS1, HSF2, ARL4A, AAED1, and WDR81) were identified, and functional enrichment analyses were conducted, providing a foundation for predicting the diagnosis of fractures associated with thrombosis.

The phosphorylation of Pak1 by Erk1/2 to drive cell migration requires Arl4D acting as a scaffolding protein

Activation of extracellular signal-regulated kinases 1 and 2 (Erk1/2; also known as MAPK3 and MAPK1, respectively) at the plasma membrane usually leads to their translocation to various intracellular sites, where scaffolding proteins mediate substrate targeting. However, in platelet-derived growth factor (PDGF)-induced signaling, Erk1/2 phosphorylate Pak1 to drive cell migration while remaining at the plasma membrane, raising the question of whether scaffolding proteins are required. Similarly, the small GTPase Arf-like protein 4D (Arl4D) promotes cell migration by recruiting Pak1 to the plasma membrane and facilitating its phosphorylation, although the mechanism linking recruitment to phosphorylation remains unclear. To address these questions, we show that Arl4D functions as a scaffolding protein by recruiting Erk1/2 and Pak1 to the plasma membrane, assembling them into a functional complex. This complex allows Erk1/2 to phosphorylate Pak1, supporting the role of the latter in cell migration. Our findings identify Arl4D as a novel regulator of Erk1/2, reveal a conserved role of scaffolding proteins in Erk1/2 substrate targeting, and uncover an unrecognized interplay among Arl4D, Erk1/2 and Pak1. These insights provide a deeper understanding of the molecular coordination underlying Pak1-mediated cell migration and its regulation by Erk1/2 and Arl4D.

A combination of transcriptomics and epigenomics identifies genes and regulatory elements involved in embryonic tail development in the mouse

BACKGROUND

The post-anal tail is a common physical feature of vertebrates including mammals. Although it exhibits rich phenotypic diversity, its development has been evolutionarily conserved as early as the embryonic period. Genes participating in embryonic tail morphogenesis have hitherto been widely explored on the basis of experimental discovery, whereas the associated cis-regulatory elements (CREs) have not yet been systematically investigated for vertebrate/mammalian tail development.

RESULTS

Here, utilizing high-throughput sequencing schemes pioneered in mice, we profiled the dynamic transcriptome and CREs marked by active histone modifications during embryonic tail morphogenesis. Temporal and spatial disparity analyses revealed the genes specific to tail development and their putative CREs, which facilitated the identification of novel molecular expression features and potential regulatory influence of non-coding loci including long non-coding RNA (lncRNA) genes and CREs. Moreover, these identified sets of multi-omics data supply genetic clues for understanding the regulatory effects of relevant signaling pathways (such as Fgf, Wnt) dominating embryonic tail morphogenesis.

CONCLUSIONS

Our work brings new insights and provides exploitable fundamental datasets for the elucidation of the complex genetic mechanisms responsible for the formation of the vertebrate/mammalian tail.

DUSP6 protein action and related hub genes prevention of sepsis-induced lung injury were screened by WGCNA and Venn

During a sepsis infection, the lung is extremely susceptible to damage. A condition known as acute respiratory distress syndrome (ARDS) may develop in extreme circumstances. The primary objective of this research is to identify important genes that are related with both sepsis and lung injury. These genes have the potential to act as novel biomarkers in the investigation of sepsis-induced lung injury prevention strategies. It was possible to download from GEO data both the sepsis-related dataset (GSE64457) and the lung injury-related dataset (GSE40839). In the GSE64457 dataset, using the "limma" package in R revealed 429 differentially expressed genes (DEGs) with logFC values more than or equal to -1 and p values <0.05. There were 266 genes that were up-regulated and 163 genes that were down-regulated. Through the use of Gene Ontology (GO), it was discovered that the majority of the DEGs were associated with the inflammatory response (BP terms), a particular granule lumen (CC terms), and protein binding (MF terms). By doing a pathway enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG), researchers were able to identify DEGs that were mostly associated with the NOD-like receptor signalling pathway, the TNF signalling pathway, and Epstein-Barr virus infection. Within the GSE40839 dataset, Weighted Gene Co-Expression Network Analysis (WGCNA) yielded a total of 7 modules, from which it was possible to screen out 2 critical modules and 693 key genes. The important genes and DEGs were both subjected to a Venn analysis. Finally, 14 genes that overlapped (ARL4A, LAIR1, MTHFD2, TSPAN13, DUSP6, PECR, CBS, TES, ASNS, SYNE1, FGF13, LCN2, KLF10, BCAT1) were closely associated to the incidence and development of sepsis-induced lung injury. This indicates that these genes are the essential genes to avoid the occurrence of sepsis-induced lung injury. This study provides novel strategies for preventing lung harm brought on by sepsis.

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.

HYPK controls stability and catalytic activity of the N-terminal acetyltransferase A in Arabidopsis thaliana

The ribosome-tethered N-terminal acetyltransferase A (NatA) acetylates 52% of soluble proteins in Arabidopsis thaliana. This co-translational modification of the N terminus stabilizes diverse cytosolic plant proteins. The evolutionary conserved Huntingtin yeast partner K (HYPK) facilitates NatA activity in planta, but in vitro, its N-terminal helix α1 inhibits human NatA activity. To dissect the regulatory function of HYPK protein domains in vivo, we genetically engineer CRISPR-Cas9 mutants expressing a HYPK fragment lacking all functional domains (hypk-cr1) or an internally deleted HYPK variant truncating helix α1 but retaining the C-terminal ubiquitin-associated (UBA) domain (hypk-cr2). We find that the UBA domain of HYPK is vital for stabilizing the NatA complex in an organ-specific manner. The N terminus of HYPK, including helix α1, is critical for promoting NatA activity on substrates starting with various amino acids. Consequently, deleting only 42 amino acids inside the HYPK N terminus causes substantial destabilization of the plant proteome and higher tolerance toward drought stress.

An evolutionary perspective on Arf family GTPases

The Arf family GTPases are regulators of eukaryotic cellular organization, functioning in the secretory and endocytic pathways, in cilia and flagella, in cytoskeleton dynamics, and in lipid metabolism. We describe the evolution of this protein family and its well-studied regulators. The last eukaryotic common ancestor had fifteen members, and the current complement of Arf GTPases has been sculpted by gene loss and gene duplications since that point. Some Arf family GTPases (such as those that recruit vesicle coats in the secretory pathway) are present in virtually all eukaryotes, whereas others (such as those functioning in cilia/flagella) have a more limited distribution. A challenge for the future is understanding the full spectrum of Arf family functions throughout eukaryotes.

BAG6 supports stress fiber formation by preventing the ubiquitin-mediated degradation of RhoA

The Rho family of small GTPases is a key regulator of cytoskeletal actin polymerization. Although the ubiquitination of Rho proteins is reported to control their activity, the mechanisms by which the ubiquitination of Rho family proteins is controlled by ubiquitin ligases have yet to be elucidated. In this study, we identified BAG6 as the first factor needed to prevent the ubiquitination of RhoA, a critical Rho family protein in F-actin polymerization. We found that BAG6 is necessary for stress fiber formation by stabilizing endogenous RhoA. BAG6 deficiency enhanced the association between RhoA and Cullin-3-based ubiquitin ligases, thus promoting its polyubiquitination and subsequent degradation, leading to the abrogation of actin polymerization. In contrast, the restoration of RhoA expression through transient overexpression rescued the stress fiber formation defects induced by BAG6 depletion. BAG6 was also necessary for the appropriate assembly of focal adhesions as well as cell migration events. These findings reveal a novel role for BAG6 in maintaining the integrity of actin fiber polymerization and establish BAG6 as a RhoA-stabilizing holdase, which binds to and supports the function of RhoA.