Protein-Protein Interactions: Co-Immunoprecipitation

Nuclear shuttling of CDC4 mediated broad-spectrum antiviral activity against diverse coronaviruses

Pandemics of coronavirus (CoV)-related infection have been a major issue since the outbreaks of SARS, MERS and COVID-2019 in the past decades, leading a substantial threat to public health. Porcine deltacoronavirus (PDCoV), a new swine coronavirus, causes enteropathogenic disease characterized by acute diarrhoea, vomiting and dehydration in suckling piglets and poses potential risks of cross-species transmission. Here we reveal a novel function of CDC4 protein in restricting PDCoV infection. Ectopic expression of CDC4 suppresses PDCoV replication, whereas knockdown of CDC4 expression enhances PDCoV infection. Importantly, it was revealed that PDCoV encoded nucleocapsid (N) was involved in CDC4 nuclear-cytoplasmic shuttling, which was critical for CDC4 to exert the antiviral activity against PDCoV replication. Mechanistically, PDCoV N protein was detected to specifically interact with RIG-I to antagonize RIG-I-like receptor (RLR)-mediated IFN-β production, leading to disruptions of host innate immune defense. Meanwhile, CDC4 was proved to interact with PDCoV N protein and disrupted the interaction between PDCoV N and RIG-I, resulting in alleviated antagonism of IFN-β production mediated by PDCoV N. Similarly, a broad-spectrum inhibitory effects of CDC4 on N mediated antagonism were confirmed by the shared mechanisms among the different coronaviruses from Coronaviridae family, such as transmissible gastroenteritis virus (TGEV) from Alphacoronavirus (α-CoV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from Betacoronavirus (β-CoV). Therefore, a novel antiviral role of CDC4 was elucidated that CDC4 competes binding with CoVs N proteins to suppress CoVs N mediated antagonism of RLR associated signalling pathway in the context of diverse coronavirus infections.

Expression of poplar sex-determining gene affects plant drought tolerance and the underlying molecular mechanism

It is frequently observed that plant sexes differ in their response to environmental stress. Poplars are dioecious plants, and sex separation of poplars is triggered by the sex-limited expression of the poplar sex-determining gene FERR. In this study, we over-expressed FERR in a male poplar and knocked it out in a female poplar. The over-expression lines exhibited distinct morphological and physiological changes rendering the transformed plants more tolerant to drought stress. By contrast, no obvious change in drought tolerance was observed in the knockout lines. Transcriptome sequencing and molecular interaction analysis demonstrated that the effect of FERR on drought tolerance was conferred by competitive interaction with protein phosphatase 2C and SNF1-related protein kinase 2 (SnRK2). Under drought stress, an FERR-SnRK2s-ARR5 complex forms and activates the ABA signaling pathway. Our results provide direct evidence that the expression of the poplar sex-determining gene pleiotropically affects plant drought tolerance.

FTO Promotes Hepatocellular Carcinoma Progression by Mediating m6A Modification of BUB1 and Targeting TGF-βR1 to Activate the TGF-β Signaling Pathway

Background and Aims

Fat mass and obesity-associated protein (FTO) has been linked to various cancers, though its role in hepatocellular carcinoma (HCC) remains unclear. This study aimed to investigate FTO expression, its clinical relevance, functional role in HCC progression, and the underlying molecular mechanisms.

Methods

Quantitative reverse-transcription polymerase chain reaction and immunohistochemical analysis were used to assess FTO expression in HCC. Functional assays, including proliferation, invasion, and epithelial-mesenchymal transition studies, were conducted using HCC cell lines with FTO knockdown. N6-methyladenosine (m6A) RNA immunoprecipitation and RNA stability assays further elucidated the role of FTO in BUB1 mRNA methylation and stability. Co-immunoprecipitation studies were employed to confirm the interaction between BUB1 and TGF-βR1. In vivo studies in nude mice were conducted to evaluate tumor growth following FTO knockdown.

Results

FTO was significantly upregulated in HCC tissues compared to normal liver tissues, with higher expression observed in advanced tumor-node-metastasis stages and metastatic HCC. Elevated FTO correlated with poor overall survival in patients. Silencing FTO decreased HCC cell proliferation, colony formation, invasion, epithelial-mesenchymal transition, and tumor growth in nude mice. Mechanistically, FTO downregulation led to increased m6A modification of BUB1 mRNA, thereby promoting its degradation via the YTH domain family 2-dependent pathway and reducing BUB1 protein levels. Additionally, BUB1 physically interacted with TGF-βR1, activating downstream TGF-β signaling.

Conclusions

FTO is overexpressed in HCC and is associated with poor clinical outcomes. Mechanistically, FTO promotes HCC progression by stabilizing BUB1 mRNA through an m6A-YTH domain family 2-dependent pathway, which activates TGF-β signaling. Targeting the FTO-BUB1-TGF-βR1 regulatory network may offer a promising therapeutic strategy for HCC.

Novel function of macrophage migration inhibitory factor in regulating post-infarct inflammation and the therapeutic significance

INTRODUCTION

Recent studies indicate that macrophage migration inhibitory factor (MIF) has a dual role in myocardial infarction (MI), with different cellular sources of MIF influencing inflammation and healing differentially.

OBJECTIVES

To investigate the role and underlying mechanism of MIF in MI and interventional efficacy targeting MIF.

METHODS

Wild-type (WT), global MIF gene knockout (KO) and chimeric mice were subjected to coronary artery occlusion. The inflammatory responses and healing processes following MI were studied in both in vivo and in vitro settings. Furthermore, the therapeutic potential of pharmacological MIF inhibition to improve the prognosis of MI was explored.

RESULTS

Globally, MIF enhanced systemic and local inflammatory responses, as well as splenic monocyte mobilization, in mice with MI. MIF promoted monocyte migration through CCR2 and CXCR4 in peripheral blood mononuclear cells (PBMCs) and the infarcted myocardium. Additionally, MIF augmented angiotensin Ⅱ type 1 receptor (AT-1R) expression and interacted with AT-1R to promote the splenic monocyte mobilization following acute MI. MIF derived from bone marrow cells (KOWT mice) had stronger systemic and local inflammatory responses and augmented mobilization of splenic monocytes. In contrast, deficiency of MIF in leukocytes (WTKO mice) increased Ly-6Clow monocyte accumulation, M2 macrophage infiltration, and degree of myocardial fibrosis in infarcted myocardium. In vitro, MIF derived from ischemic heart enhanced M2 but impaired M1 macrophage marker expression in PBMCs. Anti-MIF treatment effectively attenuated splenic monocyte mobilization and both systemic and regional inflammatory responses post-MI without affecting the healing process, thereby improving the long-term prognosis.

CONCLUSION

Deletion of global and inflammatory-cell-derived MIF diminished inflammation following MI by inhibiting monocyte mobilization and downregulating pro-inflammatory mediators, while cardiac-derived MIF exerted anti-inflammatory influence and facilitated healing. Furthermore, MIF antibody therapy protected the heart from severe ischemic injury and improved long-term prognosis.

Cryptochrome-mediated blue light regulates cell lignification via PbbHLH195 activation of the PbNSC in pear fruits

The presence of stone cells in pear fruit, caused by lignified secondary cell walls (SCWs), leads to a grainy texture in the fruit flesh, thereby compromising its overall quality. Lignification is influenced by various environmental signals, including light, however the underlying mechanism are poorly understood. This study reveals that SCW thickening and lignin accumulation in stone cells were regulated by a blue light signal, mediated through the activation of PbNSC by PbbHLH195. The results revealed that the stone cell formation was prompted by supplementary with blue light, with lignin accumulation linked to the upregulation of the NAC STONE CELL PROMOTING FACTOR (PbNSC). PbbHLH195 was identified as a novel molecular hub connecting lignification to blue light signal through its physical interaction with PbCRY1a. The biochemical and functional analysis indicates that PbbHLH195 contributes to stone cell lignification by activating the promoter of PbNSC. Our findings offer novel insights into the mechanisms of lignin biosynthesis in response to blue light, identifying valuable genetic targets for enhancing the fruit quality of pear.

Deubiquitinase dynamics: methodologies for understanding substrate interactions

Deubiquitinases (DUBs) are essential regulators of protein homeostasis that influence cellular signaling, protein stability, and degradation by removing ubiquitin chains from substrate proteins. Understanding DUB-substrate interactions is critical to elucidate their functional roles and therapeutic potential. This review highlights key methodologies to investigate DUB activity and substrate interactions, including biochemical assays, fluorescence-based approaches, and in vitro deubiquitination assays. Biochemical methods, such as those measuring protein degradation rates, ubiquitination dynamics, and protein-protein interactions, provide valuable insights into DUB function and specificity. Fluorescence-based techniques that include photoconvertible reporters, fluorescent timers, and FRET enable the realtime monitoring of DUB dynamics and substrate turnover in live cells. Furthermore, in vitro deubiquitination assays provide direct mechanistic insights into DUB activity on target substrates. While each method provides unique insights, they also present challenges, like limited specificity or sensitivity, technical difficulties, or insufficient physiological relevance. Integrating complementary approaches can enhance accuracy and provide deeper insights into DUB-substrate interactions, facilitating the development of DUB-targeted therapeutic strategies. [BMB Reports 2025; 58(5): 191-202].

IL-17C-Mediated Upregulation of SMURF2 Induces Psoriatic Changes in Keratinocytes by Facilitating PPP6C Ubiquitination

Psoriasis, a persistent inflammatory skin condition, affects approximately 2%-3% of the world's population. Increased IL-17C levels are noted in psoriatic lesions, alongside IL-17's ability to diminish protein phosphatase 6 catalytic subunit (PPP6C) expression in keratinocytes. Additionally, SMAD-specific E3 ubiquitin protein ligase 2 (SMURF2) facilitates the degradation of specific substrates through ubiquitination. However, the precise mechanisms of action involving IL-17C, SMURF2, and PPP6C in psoriasis remain unclear. Therefore, this study aims to delve into how IL-17C, SMURF2, and PPP6C contribute to psoriasis development. A psoriasis mice model was established using 5% imiquimod cream. And the expression of IL-17C, SMURF2, and PPP6C was tested. Further, an investigation was conducted using experimental techniques such as CCK-8, flow cytometry, colony formation assay, ELISA, qRT-PCR, western blot assay, co-immunoprecipitation, and ubiquitination assays. Employing both lentiviral transfection and plasmid transfection methods, an in-depth investigation was conducted into the contributions of IL-17C, SMURF2, and PPP6C to psoriasis. The results showed that the IL-17C, Keratin 17 and SMURF2 were increased, and PPP6C was decreased in psoriasis mice model. Further, IL-17C enhanced the cell viability of human epidermal keratinocytes (HaCaT), induced inflammatory responses, and upregulated SMURF2 and Keratin 17 expression. When SMURF2 was silenced, the effects of IL-17C on HaCaT cells were significantly inhibited. Moreover, SMURF2 interacted with PPP6C, promoting its ubiquitination and degradation. Overexpression of SMURF2 further enhanced the effects of IL-17C on HaCaT cells by targeting PPP6C. In conclusion, our study uncovered the upregulation of SMURF2 mediated by IL-17C, leading to psoriasis-like alterations in keratinocytes through the promotion of PPP6C ubiquitination. This novel finding not only provides crucial insights into the molecular mechanisms of psoriasis but also offers potential avenues for innovative therapeutic strategies targeting this mechanism.

Characterizing host-microbe interactions with bacterial effector proteins using proximity-dependent biotin identification (BioID)

Bacterial pathogens have evolved diverse strategies to manipulate host cells to establish infection. At a molecular level, this is often mediated by virulence factors that are secreted into host cells (herein referred to as effectors), which target host cellular pathways by initiating host-pathogen protein-protein interactions that alter cellular function in the host. By establishing this network of host-pathogen protein-protein interactions, pathogenic bacteria modulate and hijack host cell processes for the benefit of the pathogen, ultimately promoting survival, replication, and cell-to-cell spread within the host. Effector proteins also mediate diverse host-microbe interactions in nature, contributing to symbiotic relationships spanning from mutualism to commensalism to parasitism. While effector proteins play crucial roles in nature, molecular properties such as the transient nature of the underlying protein-protein interactions and their affinity for targeting host biological membranes often presents challenges to elucidating host targets and mechanism of action. Proximity-dependent biotin identification (termed BioID) has proven to be a valuable tool in the field of cell biology to identify candidate protein-protein interactions in eukaryotic cells, yet has remained relatively underexploited by bacterial pathogenesis researchers. Here, we discuss bacterial effector function at a molecular level, and challenges presented by traditional approaches to host target identification. We highlight the BioID approach and its potential strengths in the context of identifying host-pathogen protein-protein interactions, and explore BioID's implementation to study host-microbe interactions mediated by bacteria. Collectively, BioID represents a powerful tool for the study of bacterial effector proteins, providing new insight into our understanding of pathogenesis and other symbiotic relationships, and opportunities to identify new factors that contribute to host response to infection.

The epigenetic landscape of fate decisions in T cells

Specialized T cell subsets mediate adaptive immunity in response to cytokine signaling and specific transcription factor activity. The epigenetic landscape of T cells has an important role in facilitating and establishing T cell fate decisions. Here, we review the interplay between transcription factors, histone modifications, DNA methylation and three-dimensional chromatin organization to define key elements of the epigenetic landscape in T cells. We introduce key technologies in the areas of sequencing, microscopy and proteomics that have enabled the multi-scale profiling of the epigenetic landscape. We highlight the dramatic changes of the epigenetic landscape as multipotent progenitor cells commit to the T cell lineage during development and discuss the epigenetic changes that favor the emergence of CD4+ and CD8+ T cells. Finally, we discuss the inheritance of epigenetic marks and its potential effects on immune responses as well as therapeutic strategies with potential for epigenetic regulation.

N-myc downstream-regulated gene 2, co-regulated by transcription factors c-MYC and SP1, reduces cell proliferation by interacting with mTOR in GBM

NDRG2, a recognized suppressor of tumor cell proliferation, displays downregulation in glioma, yet its specific regulatory mechanisms remain elusive. Our study validated the downregulation of NDRG2 in surgical glioma samples from our center and confirmed its antitumor effects both in vitro and in vivo. Utilizing chromatin immunoprecipitation and dual luciferase reporter assays, we identified MYC and SP1 as negative transcription factors that regulate NDRG2 expression. Furthermore, we identified NDRG2 as a novel binding partner of mTOR, a pivotal regulator of cell growth and proliferation, inhibiting the phosphorylation of mTOR. The downstream signaling pathway of mTOR was then inhibited by overexpression of NDRG2. It suggested a potential mechanism by which NDRG2 exerted its antitumor function. Our findings shed light on the intricate regulatory network involving NDRG2 in glioma development and offer insights into novel therapeutic strategies targeting this pathway.

Glycidol induces necroptosis and inflammation through autophagy-necrosome pathway in renal cell and mice

Glycidol is a common food contaminant, and its main target organ is the kidney. However, the mechanism of nephrotoxicity of glycidol has not been fully elucidated. In this paper, we investigated the mechanism of glycidol toxicity in mice kidneys and NRK-52E cells. We found that glycidol exposure induced necroptosis in renal cells through the RIPK1/RIPK3/MLKL pathway. Mechanistically, it was further found that glycidol blocked renal cell autophagy and induced ectopic aggregation of p62. Accumulated p62 recruited RIPK1 and activated downstream RIPK1/RIPK3/MLKL necrosome production. At the same time, the accumulated p62 could also participate in the activation of intracellular NF-κB nuclear transcription factor by interacting with RIPK1 to form a signalling complex, which promoted the secretion of inflammatory factors TNF-α and IL-1β, and induced inflammation in the kidney. Our present study provided a new understanding of the complex mechanism of glycidol on renal injury.

The mechanism of high mobility group box-1 in the proliferation and macrophage polarization in esophageal squamous cell carcinoma cells

BACKGROUND

Previous studies showed that high mobility group box-1 (HMGB1) facilitates the initiation and progression of esophageal squamous cell carcinoma (ESCC), and the current research investigated the detailed mechanisms implicated.

METHODS

The impact of HMGB1 and IGFBP3 levels on the survival of ESCC was examined by plotting Kaplan-Meier (KM) curves based on the data collected from The Cancer Genome Atlas (TCGA). Quantitative real-time PCR (qRT-PCR) was performed to detect the expressions of HMGB1 in both human esophageal epithelial cells (HEEC) and ESCC cells. After cell transfection, the proliferation of ESCC cells was measured, and the cell metastasis was determined based on the levels of cadherins (CDHs) and Vimentin (VIM). Macrophage polarization was determined by calculating the mean fluorescence intensity (MFI) of CD206 and CD86. In addition, co-immunoprecipitation and immunoblotting were applied to evaluate the interaction between insulin-like growth factor binding protein 3 (IGFBP3)/DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and HMGB1.

RESULTS

A high level of HMGB1 was predictive of an unfavorable prognosis of ESCC (p < 0.05). HMGB1 showed a higher expression in ESCC cells (p < 0.05), while knockdown of HMGB1 inhibited ESCC cell proliferation, downregulated the levels of CDH2 and VIM and upregulated the level of CDH1 (p < 0.05). In contrast, overexpressed HMGB1 showed the opposite effects (p < 0.05), suggesting the role of HMGB1 in the epithelial-mesenchymal transition (EMT) of ESCC. After the knockout of HMGB1, the MFI of CD86 was increased but that of CD206 was reduced, indicating the polarization towards M1 macrophages (p < 0.05). However, the results were reversed when HMGB1 was overexpressed (p < 0.05). Meanwhile, HMGB1 could interact with the IGFBP3/DNA-PKcs complex (p < 0.05). Low-expressed IGFBP3 was predictive of an unfavorable prognosis of ESCC, and IGFBP3 silencing promoted the proliferation of ESCC cells (p < 0.05). Besides, HMGB1 and IGFBP3 could act antagonistically in influencing the proliferation of ESCC cells and macrophage polarization.

CONCLUSIONS

Through in vitro experiments, this study found that HMGB1 was linked to the proliferation and polarization of macrophages in ESCC, providing novel evidence for the role of HMGB1 in ESCC development.

Peptide design to control protein-protein interactions

Targeting of protein-protein interactions has become of huge interest in every aspect of medicinal and biological sciences. The control of protein interactions selectively offers the opportunity to control biological processes while limiting off target effects. This interest has massively increased with the development of cryo-EM and protein structure prediction with tools such as RosettaFold and AlphaFold. When designing molecules to control protein interactions, either inhibition or stabilisation, a starting point is commonly peptide design. This tutorial review describes that process, highlighting the selection of an initial sequence with and without structural information. Subsequently, methods for how the sequence can be analysed for key residues and how this information can be used to optimise the ligand efficiency are highlighted. Finally a discussion on how peptides can be further modified to increase their affinity and cell permeability, improving their drug-like properties, is presented.

Ginkgolic acid inhibits Ebola virus transcription and replication by disrupting the interaction between nucleoprotein and VP30 protein

The Ebola virus, a filovirus, has been responsible for significant human fatalities since its discovery. Despite extensive research, effective small-molecule drugs remain elusive due to its complex pathogenesis. Inhibition of RNA synthesis is a promising therapeutic target, and the VP30 protein plays a critical role in this process. The interaction between VP30 and the nucleoprotein (NP) is essential for viral replication. We identified ginkgolic acid as a small molecule with strong affinity for VP30, which was validated through multiple assays, including thermal shift, surface plasmon resonance, fluorescence polarization, pull-down, and co-immunoprecipitation. The antiviral efficacy of ginkgolic acid was demonstrated in the EBOV transcription- and replication-competent virus-like particle (trVLP) system. Furthermore, we resolved the crystal structure of the VP30-ginkgolic acid complex, revealing two ginkgolic acid molecules located at the VP30/NP interaction interface. This structural information provides insight into the molecular basis of ginkgolic acid's antiviral activity and suggests a novel therapeutic strategy targeting the VP30/NP interaction.

Decursinol angelate relieves inflammatory bowel disease by inhibiting the ROS/TXNIP/NLRP3 pathway and pyroptosis

Introduction

Despite evidence of the efficacy of decursinol angelate (DA), a prescription medication derived farom traditional Chinese medicine, in alleviating inflammatory bowel disease (IBD), the precise mechanisms behind its action remain unclear.

Methods

Lipopolysaccharides (LPS) and dextran sodium sulfate (DSS) induction were used as in vitro and in vivo models of IBD, respectively, to assess the role of DA in alleviating IBD. Enzyme-linked immunosorbent assay (ELISA) was performed to detect the expression levels of pro-inflammatory cytokines in mouse serum, Western blot was performed to detect the expression of TXNIP/NLRP3 pathway tight junction (TJ) proteins in colon tissues and cells, and immunohistochemistry, immunofluorescence and immunohistochemistry, immunofluorescence and qRT-PCR were used to validate the proteins related to this signaling pathway. Molecular docking technique and co-immunoprecipitation (Co-IP) method assay were applied to evaluate the targeting effect of DA on NLRP3 proteins, and MCC950, a specific inhibitor of NLRP3, was used as a positive control for validation.

Results

Our research indicates that DA's distinctive molecular mechanism could entail binding to the NLRP3 protein, thereby suppressing the activation of the NLRP3 pathway and diminishing the assembly and activation of the NLRP3 inflammasome, thus functioning as an anti-inflammatory agent.

Conclusion

DA may play a role in improving BD by inhibiting the activation of the ROS/TXNIP/NLRP3 signaling pathway and the release of inflammatory mediators, and by repairing the intestinal barrier function.

Identifying a Ubiquitinated Adaptor Protein by a Viral E3 Ligase Through Co-immunoprecipitation

Co-immunoprecipitation is a technique widely utilized to isolate protein complexes and study protein-protein interactions. Ubiquitinated proteins could be identified by combining co-immunoprecipitation with SDS-PAGE followed by immunoblotting. In this chapter, we use Herpes Simplex Virus 1 immediate-early protein ICP0-mediated polyubiquitination of p50 as an example to describe the method to identify a ubiquitinated adaptor protein by a viral E3 ligase by co-immunoprecipitation.

Identifying an Abnormal Phosphorylated Adaptor by Viral Kinase Using Mass Spectrometry

Mass spectrometers are widely used to identify protein phosphorylation sites. The process usually involves selective isolation of phosphoproteins and subsequent fragmentation to identify both the peptide sequence and phosphorylation site. Immunoprecipitation could capture and purify the protein of interest, greatly reducing sample complexity before submitting it for mass spectrometry analysis. This chapter describes a method to identify an abnormal phosphorylated site of the adaptor protein by a viral kinase through immunoprecipitation followed by LC-MS/MS.

Galangin promotes apoptosis by upregulating the pro-apoptotic gene BAX in triple-negative breast cancer

BACKGROUND

Triple-negative breast cancer (TNBC) is one of the most aggressive and formidable subtypes of breast cancer, devoid of targeted therapy and frequently leading to unfavorable prognoses and significant side effects. The demand for creative and effective treatment options has prompted the current study to investigate the potential of natural chemicals as therapeutic agents. This study intends to examine the efficacy of Galangin, a naturally occurring flavonoid, in treating triple-negative breast cancer.

METHODS

The research utilizes a dual methodology, combining in silico network pharmacology with in vitro experimental methods. The in silico research proved crucial in finding significant gene targets and cellular signaling pathways influenced by Galangin in triple-negative breast cancer. To corroborate these computational predictions, a variety of in vitro studies were conducted, including the MTT assay, wound scratch assay, apoptosis assay, reactive oxygen species assay, mitochondrial membrane potential assessment, and RT-PCR.

RESULTS

Fifteen prevalent genes were identified, demonstrating involvement in cellular proliferation, apoptosis regulation, cell migration, MAPK cascade regulation, and cell cycle regulation. The predominant genes implicated in the ten principal pathways were MAPK1, MAPK8, MAPK14, and IL6, which were observed to be linked to the MAPK signaling pathway, perhaps serving as the critical channel through which Galangin may facilitate the treatment of oral cancer. In vitro experiments demonstrated anti-proliferative effects, late-stage apoptosis, anti-migratory characteristics, antioxidant activity, and upregulation of the pro-apoptotic BAX gene.

CONCLUSION

This study's results demonstrate that Galangin possesses considerable anti-proliferative effects on TNBC cells, underscoring its potential as a viable therapeutic drug. These findings facilitate the development of more effective and precisely focused therapy approaches for TNBC, providing optimism for enhanced treatment outcomes for patients suffering from this challenging disease.

Vaping/e-cigarette-induced pulmonary extracellular vesicles contribute to exacerbated cardiomyocyte impairment through the translocation of ERK5

AIMS

The impact of e-cigarettes/vaping on cardiac function remains contradictory owing to insufficient direct evidence of interorgan communication. Extracellular vesicles (EVs) have protective or detrimental effects depending on pathological conditions, making it crucial to understand their role in lung-cardiac cell interactions mediated by vaping inhalation.

METHODS AND KEY FINDINGS

Pulmonary EVs were characterized from animals that underwent 12 weeks of nicotine inhalation (vaping component) (EVsNicotine) or vehicle control (EVsVehicle). EVsNicotine significantly increased in size and abundance compared with EVsVehicle. The direct effect of EVs Nicotine and EVs Vehicle on cardiomyocytes was then assessed in vitro and in vivo. EVs Nicotine led to a decrease in cardiac function as manifested by reduced cardiac contractility and impaired relaxation. EVs Nicotine induced increased levels of cleaved caspase-1 and cleaved caspase-11 in cardiomyocytes, indicating the promotion of pyroptosis. Meanwhile, EVsNicotine stimulated the secretion of fibrotic factors. Further analysis revealed that nicotine inhalation stimulated EVs Nicotine enriched with high levels of ERK5 (EVs Nicotine-ERK5). It was discovered that these EVs derived from pulmonary epithelial cells. Furthermore, inhibiting cardiac ERK5 blunted the EVs Nicotine-induced pyroptosis and fibrotic factor secretion. We further identified GATA4, a pro-pyroptosis transcription factor, as being activated through ERK5-dependent phosphorylation.

SIGNIFICANCE

Our research demonstrates that nicotine inhalation exacerbates cardiac injury through the activation of EVs derived from the lungs during e-cigarettes/vaping. Specifically, the EVs containing ERK5 play a crucial role in mediating the detrimental effects on cardiac function. This research provides new insights into the cardiac toxicity of vaping and highlights the role of EVs Nicotine-ERK5 in this process.

Studying protein-protein interactions: Latest and most popular approaches

PPIs, or protein-protein interactions, are essential for many biological processes. According to the findings, abnormal PPIs have been linked to several diseases, such as cancer and infectious and neurological disorders. Consequently, focusing on PPIs is a path toward disease treatment and a crucial tool for producing novel medications. Many methods exist to investigate PPIs, including low- and high-throughput studies. Since many PPIs have been discovered using in vitro and in vivo experimental approaches, the use of computational methods to predict PPIs has grown due to the expanding scale of PPI data and the intrinsic complexity of interacting mechanisms. Recognizing PPI networks offers a systematic means of predicting protein functions, and pathways that are included. These investigations can help uncover the underlying molecular mechanisms of complex phenotypes and clarify the biological processes related to health and diseases. Therefore, our goal in this study is to provide an overview of the latest and most popular approaches for investigating PPIs. We also overview some important clinical approaches based on the PPIs and how these interactions can be targeted.

Integration of molecular coarse-grained model into geometric representation learning framework for protein-protein complex property prediction

Structure-based machine learning algorithms have been utilized to predict the properties of protein-protein interaction (PPI) complexes, such as binding affinity, which is critical for understanding biological mechanisms and disease treatments. While most existing algorithms represent PPI complex graph structures at the atom-scale or residue-scale, these representations can be computationally expensive or may not sufficiently integrate finer chemical-plausible interaction details for improving predictions. Here, we introduce MCGLPPI, a geometric representation learning framework that combines graph neural networks (GNNs) with MARTINI molecular coarse-grained (CG) models to predict PPI overall properties accurately and efficiently. Extensive experiments on three types of downstream PPI property prediction tasks demonstrate that at the CG-scale, MCGLPPI achieves competitive performance compared with the counterparts at the atom- and residue-scale, but with only a third of computational resource consumption. Furthermore, CG-scale pre-training on protein domain-domain interaction structures enhances its predictive capabilities for PPI tasks. MCGLPPI offers an effective and efficient solution for PPI overall property predictions, serving as a promising tool for the large-scale analysis of biomolecular interactions.

Potential Biomarkers in Myocardial Fibrosis: A Bioinformatic Analysis

BACKGROUND

Myocardial fibrosis (MF) occurs throughout the onset and progression of cardiovascular disease, and early diagnosis of MF is beneficial for improving cardiac function, but there is a lack of research on early biomarkers of MF.

OBJECTIVES

Utilizing bioinformatics techniques, we identified potential biomarkers for MF.

METHODS

Datasets related to MF were sourced from the GEO database. After processing the data, differentially expressed genes were screened. Differentially expressed genes were enriched, and subsequently, protein-protein interaction (PPI) was performed to analyze the differential genes. The associated miRNAs and transcription factors were predicted for these core genes. Finally, ROC validation was performed on the core genes to determine their specificity and sensitivity as potential biomarkers. The level of significance adopted was 5% (p < 0.05).

RESULTS

A total of 91 differentially expressed genes were identified, and PPI analysis yielded 31 central genes. Enrichment analysis showed that apoptosis, collagen, extracellular matrix, cell adhesion, and inflammation were involved in MF. One hundred and forty-two potential miRNAs were identified. the transcription factors JUN, NF-κB1, SP1, RELA, serum response factor (SRF), and STAT3 were enriched in most of the core targets. Ultimately, IL11, GADD45B, GDF5, NOX4, IGFBP3, ACTC1, MYOZ2, and ITGB8 had higher diagnostic accuracy and sensitivity in predicting MF based on ROC curve analysis.

CONCLUSION

Eight genes, IL11, GADD45B, GDF5, NOX4, IGFBP3, ACTC1, MYOZ2, and ITGB8, can serve as candidate biomarkers for MF. Processes such as cellular apoptosis, collagen protein synthesis, extracellular matrix formation, cellular adhesion, and inflammation are implicated in the development of MF.

Regulation of the SOS response and homologous recombination by an integrative and conjugative element

Integrative and conjugative elements (ICEs) are mobile genetic elements that transfer between bacteria and influence host physiology and promote evolution. ICEBs1 of Bacillus subtilis modulates the host DNA damage response by reducing RecA filament formation. We found that the two ICEBs1-encoded proteins, RamT and RamA that modulate the SOS response in donors also function in recipient cells to inhibit both the SOS response and homologous recombination following transfer of the element. Expression of RamT and RamA caused a decrease in binding of the host single strand binding protein SsbA to ssDNA. We found that RamA interacted with PcrA, the host DNA translocase that functions to remove RecA from DNA, likely functioning to modulate the SOS response and recombination by stimulating PcrA activity. These findings reveal how ICEBs1 can modulate key host processes, including the SOS response and homologous recombination, highlighting the complex interplay between mobile genetic elements and their bacterial hosts in adaptation and evolution.

Progress in mass spectrometry approaches to profiling protein-protein interactions in the studies of the innate immune system

Understanding protein-protein interactions (PPIs) is pivotal for deciphering the intricacies of biological processes. Dysregulation of PPIs underlies a spectrum of diseases, including cancer, neurodegenerative disorders, and autoimmune conditions, highlighting the imperative of investigating these interactions for therapeutic advancements. This review delves into the realm of mass spectrometry-based techniques for elucidating PPIs and their profound implications in biological research. Mass spectrometry in the PPI research field not only facilitates the evaluation of protein-protein interaction modulators but also discovers unclear molecular mechanisms and sheds light on both on- and off-target effects, thus aiding in drug development. Our discussion navigates through six pivotal techniques: affinity purification mass spectrometry (AP-MS), proximity labeling mass spectrometry (PL-MS), cross-linking mass spectrometry (XL-MS), size exclusion chromatography coupled with mass spectrometry (SEC-MS), limited proteolysis-coupled mass spectrometry (LiP-MS), and thermal proteome profiling (TPP).

Protein-Protein Interaction Prediction Model Based on ProtBert-BiGRU-Attention

The physiological activities within cells are mainly regulated through protein-protein interactions (PPI). Therefore, studying protein interactions has become an essential part of researching protein function and mechanisms. Traditional biological experiments required for PPI prediction are expensive and time consuming. For this reason, many methods based on predicting PPI from protein sequences have been proposed in recent years. However, existing computational methods usually require the combination of evolutionary feature information of proteins to predict PPI docking situations. Because different relevant features of selected proteins are chosen, there may be differences in the predicted results for PPI. This article proposes a PPI prediction method based on the pretrained protein sequence model ProtBert, combined with the Bidirectional Gated Recurrent Unit (BiGRU) and attention mechanism. Only using protein sequence information and leveraging ProtBert's powerful ability to capture amino acid feature information, BiGRU is used for further feature extraction of the amino acid vectors output by ProtBert. The attention mechanism is then applied to enhance the focus on different amino acid features and improve the expression ability of protein sequence features, ultimately obtaining binary classification results for protein interactions. Experimental results show that our proposed ProtBert-BiGRU-Attention model has good predictive performance for PPI. Through relevant comparative experiments, it has been proven that our model performs well in protein binary prediction. Furthermore, through the ablation experiment of the model, different deep learning modules' contributions to the prediction have been demonstrated.

Comparative time-series multi-omics analyses suggest H1.2 involvement in anoxic adaptation and cancer resistance

The naked mole rat (NMR), Heterocephalus glaber, is known as the longest-lived rodent and is extraordinarily resistant to hypoxia and cancer. Here, both NMR embryonic fibroblasts (NEFs) and their mouse counterparts (MEFs) were subjected to anoxic conditions (0% O2, 5% CO2). A combination of comparative transcriptomics and proteomics was then employed to identify differentially expressed genes (DEGs). Notably, we observed distinct levels of histone H1.2 (encoded by HIST1H1C) accumulation between NEFs and MEFs. Subsequent mechanistic analyses showed that higher H1.2 expression in NEFs was associated with the lower expression of its inhibitor, PARP1. Additionally, we discovered that H1.2 can directly interact with HIF-1α PAS domains, thereby promoting the expression of HIF-1α through facilitating the dimerization with HIF-1β. The overexpression of H1.2 was also found to trigger autophagy and to suppress the migration of cancer cells, as well as the formation of xenograft tumors, via the NRF2/P62 signaling pathway. Moreover, an engineered H1.2 knock-in mouse model exhibited significantly extended survival in hypoxic conditions (4% O2) and showed a reduced rate of tumor formation. Collectively, our results indicate a potential mechanistic link between H1.2 and the dual phenomena of anoxic adaptation and cancer resistance.

Exploring ABHD5 as a Lipid-Related Biomarker in Idiopathic Pulmonary Fibrosis: Integrating Machine Learning, Bioinformatics, and In Vitro Experiments

Recent studies increasingly suggest a connection between lipids and idiopathic pulmonary fibrosis (IPF). This study was aimed at exploring potential lipid-related biomarkers for IPF and uncovering the mechanisms underlying pulmonary fibrosis. IPF-related datasets were retrieved from the GEO database, and the ComBat algorithm was used to merge multiple datasets and eliminate batch effects. Weighted gene co-expression network analysis (WGCNA) was utilized to identify modules and genes associated with IPF. Potential hub genes were determined by intersecting these genes with lipid-related genes from the GeneCards database. A machine learning-based integrative approach was developed to construct diagnostic and prognostic signatures, which were validated across several datasets. Additionally, single-cell sequencing data was used to validate the expression differences of core IPF-related genes across various cell types. The effect of ABHD5 on fibroblasts was assessed using the cell counting kit-8, 5-ethynyl-2'-deoxyuridine, and cell scratch assays. The expression levels of fibrotic factors were measured using real-time quantitative polymerase chain reaction and western blot analysis. WGCNA identified a red module potentially related to IPF, and the intersection with lipid-related genes yielded 51 hub genes. These genes were used to build diagnostic and prognostic models that demonstrated robust validation capabilities across multiple datasets. Single-cell sequencing analysis revealed low expression of ABHD5 in the lung tissues of IPF patients, with a higher proportion of fibroblasts exhibiting low ABHD5 expression. Cell experiments showed that under the influence of TGF-β1, knockdown of ABHD5 slightly promoted fibroblast proliferation. Additionally, fibroblasts with low ABHD5 expression exhibited enhanced migratory capabilities and secreted more fibrotic factors. Lipid-related diagnostic and prognostic models for IPF were developed, and ABHD5 may serve as a potential biomarker. Low ABHD5 expression could potentially accelerate the progression of pulmonary fibrosis.

Current understanding of functional peptides encoded by lncRNA in cancer

Dysregulated gene expression and imbalance of transcriptional regulation are typical features of cancer. RNA always plays a key role in these processes. Human transcripts contain many RNAs without long open reading frames (ORF, > 100 aa) and that are more than 200 bp in length. They are usually regarded as long non-coding RNA (lncRNA) which play an important role in cancer regulation, including chromatin remodeling, transcriptional regulation, translational regulation and as miRNA sponges. With the advancement of ribosome profiling and sequencing technologies, increasing research evidence revealed that some ORFs in lncRNA can also encode peptides and participate in the regulation of multiple organ tumors, which undoubtedly opens a new chapter in the field of lncRNA and oncology research. In this review, we discuss the biological function of lncRNA in tumors, the current methods to evaluate their coding potential and the role of functional small peptides encoded by lncRNA in cancers. Investigating the small peptides encoded by lncRNA and understanding the regulatory mechanisms of these functional peptides may contribute to a deeper understanding of cancer and the development of new targeted anticancer therapies.

Cell Biology Techniques for Studying Drosophila Peripheral Glial Cells

Glial cells are essential for the proper development and functioning of the peripheral nervous system (PNS). The ability to study the biology of glial cells is therefore critical for our ability to understand PNS biology and address PNS maladies. The genetic and proteomic pathways underlying vertebrate peripheral glial biology are understandably complex, with many layers of redundancy making it sometimes difficult to study certain facets of PNS biology. Fortunately, many aspects of vertebrate peripheral glial biology are conserved with those of the fruit fly, Drosophila melanogaster With simple and powerful genetic tools and fast generation times, Drosophila presents an accessible and versatile model for studying the biology of peripheral glia. We introduce here three techniques for studying the cell biology of peripheral glia of Drosophila third-instar larvae. With fine dissection tools and common laboratory reagents, third-instar larvae can be dissected, with extraneous tissues removed, revealing the central nervous system (CNS) and PNS to be processed using a standard immunolabeling protocol. To improve the resolution of peripheral nerves in the z-plane, we describe a cryosectioning method to achieve 10- to 20-µm thick coronal sections of whole larvae, which can then be immunolabeled using a modified version of standard immunolabeling techniques. Finally, we describe a proximity ligation assay (PLA) for detecting close proximity between two proteins-thus inferring protein interaction-in vivo in third-instar larvae. These methods, further described in our associated protocols, can be used to improve our understanding of Drosophila peripheral glia biology, and thus our understanding of PNS biology.

METTL3 promotes the progression of osteosarcoma through the N6-methyladenosine modification of MCAM via IGF2BP1

BACKGROUND

The molecular mechanisms of osteosarcoma (OS) are complex. In this study, we focused on the functions of melanoma cell adhesion molecule (MCAM), methyltransferase 3 (METTL3) and insulin like growth factor 2 mRNA binding protein 1 (IGF2BP1) in OS development.

METHODS

qRT-PCR assay and western blot assay were performed to determine mRNA and protein expression of MCAM, METTL3, IGF2BP1 and YY1. MTT assay and colony formation assay were conducted to assess cell proliferation. Cell apoptosis, invasion and migration were evaluated by flow cytometry analysis, transwell assay and wound-healing assay, respectively. Methylated RNA Immunoprecipitation (MeRIP), dual-luciferase reporter, Co-IP, RIP and ChIP assays were performed to analyze the relationships of MCAM, METTL3, IGF2BP1 and YY1. The functions of METTL3 and MCAM in tumor growth were explored through in vivo experiments.

RESULTS

MCAM was upregulated in OS, and MCAM overexpression promoted OS cell growth, invasion and migration and inhibited apoptosis. METTL3 and IGF2BP1 were demonstrated to mediate the m6A methylation of MCAM. Functionally, METTL3 or IGF2BP1 silencing inhibited OS cell progression, while MCAM overexpression ameliorated the effects. Transcription factor YY1 promoted the transcription level of METTL3 and regulated METTL3 expression in OS cells. Additionally, METTL3 deficiency suppressed tumor growth in vivo, while MCAM overexpression abated the effect.

CONCLUSION

YY1/METTL3/IGF2BP1/MCAM axis aggravated OS development, which might provide novel therapy targets for OS.

P62 promotes FSH-induced antral follicle formation by directing degradation of ubiquitinated WT1

In females, the pathophysiological mechanism of poor ovarian response (POR) is not fully understood. Considering the expression level of p62 was significantly reduced in the granulosa cells (GCs) of POR patients, this study focused on identifying the role of the selective autophagy receptor p62 in conducting the effect of follicle-stimulating hormone (FSH) on antral follicles (AFs) formation in female mice. The results showed that p62 in GCs was FSH responsive and that its level increased to a peak and then decreased time-dependently either in ovaries or in GCs after gonadotropin induction in vivo. GC-specific deletion of p62 resulted in subfertility, a significantly reduced number of AFs and irregular estrous cycles, which were same as pathophysiological symptom of POR. By conducting mass spectrum analysis, we found the ubiquitination of proteins was decreased, and autophagic flux was blocked in GCs. Specifically, the level of nonubiquitinated Wilms tumor 1 homolog (WT1), a transcription factor and negative controller of GC differentiation, increased steadily. Co-IP results showed that p62 deletion increased the level of ubiquitin-specific peptidase 5 (USP5), which blocked the ubiquitination of WT1. Furthermore, a joint analysis of RNA-seq and the spatial transcriptome sequencing data showed the expression of steroid metabolic genes and FSH receptors pivotal for GCs differentiation decreased unanimously. Accordingly, the accumulation of WT1 in GCs deficient of p62 decreased steroid hormone levels and reduced FSH responsiveness, while the availability of p62 in GCs simultaneously ensured the degradation of WT1 through the ubiquitin‒proteasome system and autophagolysosomal system. Therefore, p62 in GCs participates in GC differentiation and AF formation in FSH induction by dynamically controlling the degradation of WT1. The findings of the study contributes to further study the pathology of POR.

Co-immunoprecipitation for identifying protein-protein interaction on lipid droplets

The lipid droplet (LD) is a conserved organelle that exists in almost all organisms, ranging from bacteria to mammals. Dysfunctions in LDs are linked to a range of human metabolic syndromes. The formation of protein complexes on LDs is crucial for maintaining their function. Investigating how proteins interact on LDs is essential for understanding the role of LDs. We have developed an effective method to uncover protein-protein interactions and protein complexes specifically on LDs. In this method, we conduct co-immunoprecipitation (co-IP) experiments using LD proteins extracted directly from isolated LDs, rather than utilizing proteins from cell lysates. To elaborate, we begin by purifying LDs with high-quality and extracting LD-associated proteins. Subsequently, the co-IP experiment is performed on these LD-associated proteins directly, which would enhance the co-IP experiment specificity of LD-associated proteins. This method enables researchers to directly unveil protein complexes on LDs and gain deeper insights into the functional roles of proteins associated with LDs.

Transcription Factor McHB7 Improves Ice Plant Drought Tolerance through ABA Signaling Pathway

As global climate change continues, drought episodes have become increasingly frequent. Studying plant stress tolerance is urgently needed to ensure food security. The common ice plant is one of the model halophyte plants for plant stress biology research. This study aimed to investigate the functions of a newly discovered transcription factor, Homeobox 7 (HB7), from the ice plant in response to drought stress. An efficient Agrobacterium-mediated transformation method was established in the ice plant, where ectopic McHB7 expression may be sustained for four weeks. The McHB7 overexpression (OE) plants displayed drought tolerance, and the activities of redox enzymes and chlorophyll content in the OE plants were higher than the wild type. Quantitative proteomics revealed 1910 and 495 proteins significantly changed in the OE leaves compared to the wild type under the control and drought conditions, respectively. Most increased proteins were involved in the tricarboxylic acid cycle, photosynthesis, glycolysis, pyruvate metabolism, and oxidative phosphorylation pathways. Some were found to participate in abscisic acid signaling or response. Furthermore, the abscisic acid levels increased in the OE compared with the wild type. McHB7 was revealed to bind to the promoter motifs of Early Responsive to Dehydration genes and abscisic acid-responsive genes, and protein-protein interaction analysis revealed candidate proteins responsive to stresses and hormones (e.g., abscisic acid). To conclude, McHB7 may contribute to enhance plant drought tolerance through abscisic acid signaling.

Climbing into their Skin to Understand Contextual Protein-Protein Associations and Localizations: Functional Investigations in Transgenic Live Model Organisms

Borrowing some quotes from Harper Lee's novel "To Kill A Mockingbird" to help frame our manuscript, we discuss methods to profile local proteomes. We initially focus on chemical biology regimens that function in live organisms and use reactive biotin species for this purpose. We then consider ways to add new dimensions to these experimental regimens, principally by releasing less reactive (i. e., more selective) (preter)natural electrophiles. Although electrophile release methods may have lower resolution and label fewer proteins than biotinylation methods, their ability to probe simultaneously protein function and locale raises new and interesting possibilities for the field.

Identification of a robust biomarker LAPTM4A for glioma based on comprehensive computational biology and experimental verification

BACKGROUND

Glioma, a highly invasive and deadly form of human neoplasm, presents a pressing need for the exploration of potential therapeutic targets. While the lysosomal protein transmembrane 4A (LATPM4A) has been identified as a risk factor in pancreatic cancer patients, its role in glioma remains unexplored.

METHODS

The analysis of differentially expressed genes (DEG) was conducted from The Cancer Genome Atlas (TCGA) glioma dataset and the Genotype Tissue Expression (GTEx) dataset. Through weighted gene co-expression network analysis (WGCNA), the key glioma-related genes were identified. Among these, by using Kaplan-Meier (KM) analysis and univariate/multivariate COX methods, LAPTM4A emerged as the most influential gene. Moreover, the bioinformatics methods and experimental verification were employed to analyze its relationships with diagnosis, clinical parameters, epithelial-mesenchymal transition (EMT), metastasis, immune cell infiltration, immunotherapy, drug sensitivity, and ceRNA network.

RESULTS

Our findings revealed that LAPTM4A was up-regulated in gliomas and was associated with clinicopathological features, leading to poor prognosis. Furthermore, functional enrichment analysis demonstrated that LATPM4A played a role in the immune system and cancer progression. In vitro experiments indicated that LAPTM4A may influence metastasis through the EMT pathway in glioma. Additionally, we found that LAPTM4A was associated with the tumor microenvironment (TME) and immunotherapy. Notably, drug sensitivity analysis revealed that patients with high LAPTM4A expression were sensitive to doxorubicin, which contributed to a reduction in LAPTM4A expression. Finally, we uncovered the FGD5-AS1-hsa-miR-103a-3p-LAPTM4A axis as a facilitator of glioma progression.

CONCLUSIONS

In conclusion, our study identifies LATPM4A as a promising biomarker for prognosis and immune characteristics in glioma.

Generation and Characterization of Engineered Ubiquitin Variants to Modulate the Ubiquitin Signaling Cascade

The ubiquitin signaling cascade plays a crucial role in human cells. Consistent with this, malfunction of ubiquitination and deubiquitination is implicated in the initiation and progression of numerous human diseases, including cancer. Therefore, the development of potent and specific modulators of ubiquitin signal transduction has been at the forefront of drug development. In the past decade, a structure-based combinatorial protein-engineering approach has been used to generate ubiquitin variants (UbVs) as protein-based modulators of multiple components in the ubiquitin-proteasome system. Here, we review the design and generation of phage-displayed UbV libraries, including the processes of binder selection and library improvement. We also provide a comprehensive overview of the general in vitro and cellular methodologies involved in characterizing UbV binders. Finally, we describe two recent applications of UbVs for developing molecules with therapeutic potential.

VDR regulates mitochondrial function as a protective mechanism against renal tubular cell injury in diabetic rats

PURPOSE

To investigate the regulatory effect and mechanism of Vitamin D receptor (VDR) on mitochondrial function in renal tubular epithelial cell under diabetic status.

METHODS

The diabetic rats induced by streptozotocin (STZ) and HK-2 cells under high glocose(HG)/transforming growth factor beta (TGF-β) stimulation were used in this study. Calcitriol was administered for 24 weeks. Renal tubulointerstitial injury and some parameters of mitochondrial function including mitophagy, mitochondrial fission, mitochondrial ROS, mitochondrial membrane potential (MMP), mitochondrial ATP, Complex V activity and mitochondria-associated ER membranes (MAMs) integrity were examined. Additionally, paricalcitol, 3-MA (an autophagy inhibitor), VDR over-expression plasmid, VDR siRNA and Mfn2 siRNA were applied in vitro.

RESULTS

The expression of VDR, Pink1, Parkin, Fundc1, LC3II, Atg5, Mfn2, Mfn1 in renal tubular cell of diabetic rats were decreased significantly. Calcitriol treatment reduced the levels of urinary albumin, serum creatinine and attenuated renal tubulointerstitial fibrosis in STZ induced diabetic rats. In addition, VDR agonist relieved mitophagy dysfunction, MAMs integrity, and inhibited mitochondrial fission, mitochondrial ROS. Co-immunoprecipitation analysis demonstrated that VDR interacted directly with Mfn2. Mitochondrial function including mitophagy, mitochondrial membrane potential (MMP), mitochondrial Ca2+, mitochondrial ATP and Complex V activity were decreased dramatically in HK-2 cells under HG/TGF-β ambience. In vitro pretreatment of HK-2 cells with autophagy inhibitor 3-MA, VDR siRNA or Mfn2 siRNA negated the activating effects of paricalcitol on mitochondrial function. Pricalcitol and VDR over-expression plasmid activated Mfn2 and then partially restored the MAMs integrity. Additionally, VDR restored mitophagy was partially associated with MAMs integrity through Fundc1.

CONCLUSION

Activated VDR could contribute to restore mitophagy through Mfn2-MAMs-Fundc1 pathway in renal tubular cell. VDR could recover mitochondrial ATP, complex V activity and MAMs integrity, inhibit mitochondrial fission and mitochondrial ROS. It indicating that VDR agonists ameliorate renal tubulointerstitial fibrosis in diabetic rats partially via regulation of mitochondrial function.

Cell surface β-lactamase recruitment: A facile selection to identify protein-protein interactions

Protein-protein interactions (PPIs) are central to many cellular processes, and the identification of novel PPIs is a critical step in the discovery of protein therapeutics. Simple methods to identify naturally existing or laboratory evolved PPIs are therefore valuable research tools. We have developed a facile selection that links PPI-dependent β-lactamase recruitment on the surface of Escherichia coli with resistance to ampicillin. Bacteria displaying a protein that forms a complex with a specific protein-β-lactamase fusion are protected from ampicillin-dependent cell death. In contrast, bacteria that do not recruit β-lactamase to the cell surface are killed by ampicillin. Given its simplicity and tunability, we anticipate this selection will be a valuable addition to the palette of methods for illuminating and interrogating PPIs.

The assessment of the mechanism of action of lauric acid in the context of oral cancer through integrative approach combining network pharmacology and molecular docking technology

OBJECTIVES

Lauric acid has been investigated for its effects on various human cancer cell types, although limited research has been dedicated to its impact on oral cancer. In light of this, the objective of our study was to comprehensively assess the anticancer properties of lauric acid specifically in the context of oral cancer. This evaluation was achieved through an in-silico approach, leveraging network analysis techniques. By employing this methodology, we aimed to gain valuable insights into the potential therapeutic benefits of lauric acid for treating oral cancer.

METHODS

The in-silico analysis involved determination of drug-likeness prediction, prediction of common targets between oral cancer and LA, protein-protein interactions (PPI), hub genes, top 10 associated pathways by gene ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway, molecular docking experiments.

RESULTS

Our study pinpointed 23 common genes involved in critical cellular processes, including proliferation, apoptosis regulation, PI3K AKT cascade, and cell cycle control. Among them, CXCL8, MMP9, PPARA, MAPK1, and AR stood out in the top 10 pathways, particularly in the PI3K/AKT signaling pathway. This highlights the potential role of lauric acid in oral cancer treatment through the PI3K/AKT pathway and calls for further exploration of this mechanism.

CONCLUSIONS

Our study highlights lauric acid's promising anticancer properties through computational analysis, offering a foundation for future research in cancer treatment development. This approach combines molecular insights with in-silico methods, paving the way for identifying therapeutic compounds and understanding their mechanisms. Lauric acid holds potential as a chemotherapeutic agent, opening up new avenues for cancer therapy exploration.

Non-electrophysiological techniques targeting transient receptor potential (TRP) gene of gastrointestinal tract

Transient receptor potential (TRP) channels are cation channels related to a wide range of physical and chemical stimuli, they are expressed all along the gastrointestinal system, and a myriad of diseases are often associated with aberrant expression or mutation of the TRP gene, suggesting that TRPs are promising targets for drug therapy. Therefore, a better understanding of the information of TRPs in health and disease could facilitate the development of effective drugs for the treatment of gastrointestinal diseases like IBD. But there are very few generalizations about the experimental techniques studied in this field. In view of the promise of TRP as a therapeutic target, we discuss experimental methods that can be used for TRPs including their distribution, function and interaction with other proteins, as well as some promising emerging technologies to provide experimental methods for future studies.

TRIM59-mediated ferroptosis enhances neuroblastoma development and chemosensitivity through p53 ubiquitination and degradation

Neuroblastoma, predominantly afflicting young individuals, is characterized as an embryonal tumor, with poor prognosis primarily attributed to chemoresistance. This study delved into the impact of tripartite motif (TRIM) 59, an E3 ligase, on neuroblastoma development and chemosensitivity through mediating ferroptosis and the involvement of the tumor suppressor p53. Clinical samples were assessed for TRIM59 and p53 levels to explore their correlation with neuroblastoma differentiation. In neuroblastoma cells, modulation of TRIM59 expression, either through overexpression or knockdown, was coupled with doxorubicin hydrochloride (DOX) or ferrostatin-1 (Fer-1) therapy. In vivo assessments examined the influence of TRIM59 knockdown on neuroblastoma chemosensitivity to DOX. Co-immunoprecipitation and ubiquitination assays investigated the association between TRIM59 and p53. Proliferation was gauged with Cell Counting Kit-8, lipid reactive oxygen species (ROS) were assessed via flow cytometry, and protein levels were determined by Western blotting. TRIM59 expression was inversely correlated with neuroblastoma differentiation and positively linked to cell proliferation in response to DOX. Moreover, TRIM59 impeded lipid ROS generation and ferroptosis by directly interacting with p53, promoting its ubiquitination and degradation in DOX-exposed neuroblastoma cells. Fer-1 countered the impact of TRIM59 knockdown on neuroblastoma, while TRIM59 knockdown enhanced the therapeutic efficacy of DOX in xenograph mice. This study underscores TRIM59 as an oncogene in neuroblastoma, fostering growth and chemoresistance by suppressing ferroptosis through p53 ubiquitination and degradation. TRIM59 emerges as a potential strategy for neuroblastoma therapy.

Searching for EGF Fragments Recreating the Outer Sphere of the Growth Factor Involved in Receptor Interactions

The aims of this study were to determine whether it is possible to use peptide microarrays obtained using the SPOT technique (immobilized on cellulose) and specific polyclonal antibodies to select fragments that reconstruct the outer sphere of proteins and to ascertain whether the selected peptide fragments can be useful in the study of their protein-protein and/or peptide-protein interactions. Using this approach, epidermal growth factor (EGF) fragments responsible for the interaction with the EGF receptor were searched. A library of EGF fragments immobilized on cellulose was obtained using triazine condensing reagents. Experiments on the interactions with EGFR confirmed the high affinity of the selected peptide fragments. Biological tests on cells showed the lack of cytotoxicity of the EGF fragments. Selected EGF fragments can be used in various areas of medicine.

Seq-InSite: sequence supersedes structure for protein interaction site prediction

MOTIVATION

Proteins accomplish cellular functions by interacting with each other, which makes the prediction of interaction sites a fundamental problem. As experimental methods are expensive and time consuming, computational prediction of the interaction sites has been studied extensively. Structure-based programs are the most accurate, while the sequence-based ones are much more widely applicable, as the sequences available outnumber the structures by two orders of magnitude. Ideally, we would like a tool that has the quality of the former and the applicability of the latter.

RESULTS

We provide here the first solution that achieves these two goals. Our new sequence-based program, Seq-InSite, greatly surpasses the performance of sequence-based models, matching the quality of state-of-the-art structure-based predictors, thus effectively superseding the need for models requiring structure. The predictive power of Seq-InSite is illustrated using an analysis of evolutionary conservation for four protein sequences.

AVAILABILITY AND IMPLEMENTATION

Seq-InSite is freely available as a web server at http://seq-insite.csd.uwo.ca/ and as free source code, including trained models and all datasets used for training and testing, at https://github.com/lucian-ilie/Seq-InSite.

Antibody Design for the Quantification of Photosynthetic Proteins and Their Isoforms

Antibodies are a valuable research tool, with uses including detection and quantification of specific proteins. By using peptide fragments to raise antibodies, they can be designed to differentiate between structurally similar proteins, or to bind conserved motifs in divergent proteins. Peptide sequence selection and antibody validation are crucial to ensure reliable results from antibody-based experiments. This chapter describes the steps for the identification of peptide sequences to produce protein- or isoform-specific antibodies using recombinant technologies as well as the subsequent validation of such antibodies. The photosynthetic protein Rubisco activase is used as a case study to explain the various steps involved and key aspects to take into consideration.

Co-immunoprecipitation Assays to Detect Protein-Protein Interactions

Proteins usually do not function as monomers but rather perform their functions by interacting with themselves or other proteins. Co-immunoprecipitation is an essential assay for detecting protein interactions in vivo. In this chapter, we describe how to use co-immunoprecipitation to detect protein interactions in Arabidopsis protoplasts, seedlings, and Nicotiana benthamiana leaves. When using co-immunoprecipitation assays to detect protein interactions, it is necessary to pay attention to the design of the experimental and control groups.

Cristae shaping and dynamics in mitochondrial function

Mitochondria are multifunctional organelles of key importance for cell homeostasis. The outer mitochondrial membrane (OMM) envelops the organelle, and the inner mitochondrial membrane (IMM) is folded into invaginations called cristae. As cristae composition and functions depend on the cell type and stress conditions, they recently started to be considered as a dynamic compartment. A number of proteins are known to play a role in cristae architecture, such as OPA1, MIC60, LETM1, the prohibitin (PHB) complex and the F1FO ATP synthase. Furthermore, phospholipids are involved in the maintenance of cristae ultrastructure and dynamics. The use of new technologies, including super-resolution microscopy to visualize cristae dynamics with superior spatiotemporal resolution, as well as high-content techniques and datasets have not only allowed the identification of new cristae proteins but also helped to explore cristae plasticity. However, a number of open questions remain in the field, such as whether cristae-resident proteins are capable of changing localization within mitochondria, or whether mitochondrial proteins can exit mitochondria through export. In this Review, we present the current view on cristae morphology, stability and composition, and address important outstanding issues that might pave the way to future discoveries.

BioID Analysis of Actin-Binding Proteins

Proteins often exist and function as part of higher-order complexes or networks. A challenge is to identify the universe of proximal and interacting partners for a given protein. We describe how the high-activity promiscuous biotin ligase called TurboID is fused to the actin-binding peptide LifeAct to label by biotinylation proteins that bind, or are in close proximity, to actin. The rapid enzyme kinetics of TurboID allows the profiles of actin-binding proteins to be compared under different conditions, such as acute disruption of filamentous actin structures with cytochalasin D.

Analysis of Protein Interactions in Patient-Derived Xenografts Using Immunoprecipitation

Proteins are large, complex molecules that regulate multiple functions within the cell. The protein rarely functions as a single molecule, but rather interacts with one or more other proteins forming a dynamic network. Protein-protein interactions are critical for regulating the cell's response toward various stimuli from outside and inside the cell. Identification of protein-protein interactions enhanced our understanding of various biological processes in the living cell. Immunoprecipitation (IP) has been one of the standard and most commonly used biochemical methods to identify and confirm protein-protein interactions. IP uses a target protein-specific antibody conjugated with protein A/G affinity beads to identify molecules interacting with the target protein. Here, we describe the principle, procedure and challenges of the IP assay.

Thermal proteome profiling unveils protein targets of deoxycholic acid in living neuronal cells

Bile acids, synthesized in the liver and modified by the gut microbiota, play vital roles in various physiological processes. The dysregulation of bile acids has been extensively documented in patients with neurodegenerative diseases. However, limited attention has been given to the protein targets associated with microbiota-derived bile acids in neurological diseases. To address this knowledge gap, we conducted comprehensive thermal proteomic analyses to elucidate and comprehend the protein targets affected by microbiota-derived bile acids. Our investigation identified sixty-five unique proteins in SH-SY5Y neuronal cells as potential targets of deoxycholic acid (DCA), a primary component of the bile acid pool originating from the gut microbiota. Notably, Nicastrin and Casein kinase 1 epsilon stood out among these proteins. We found that DCA, through its interaction with the Nicastrin subunit of γ-secretase, significantly contributed to the formation of amyloid beta, a key hallmark in the pathology of neurodegenerative diseases. In summary, our findings provide crucial insights into the intricate interplay between microbiota-derived bile acids and the pathogenesis of neurodegenerative diseases, thereby shedding light on potential therapeutic targets for neurodegenerative diseases.

D-allose Inhibits TLR4/PI3K/AKT Signaling to Attenuate Neuroinflammation and Neuronal Apoptosis by Inhibiting Gal-3 Following Ischemic Stroke

BACKGROUND

Ischemic stroke (IS) occurs when a blood vessel supplying the brain becomes obstructed, resulting in cerebral ischemia. This type of stroke accounts for approximately 87% of all strokes. Globally, IS leads to high mortality and poor prognosis and is associated with neuroinflammation and neuronal apoptosis. D-allose is a bio-substrate of glucose that is widely expressed in many plants. Our previous study showed that D-allose exerted neuroprotective effects against acute cerebral ischemic/reperfusion (I/R) injury by reducing neuroinflammation. Here, we aimed to clarify the beneficial effects D-allose in suppressing IS-induced neuroinflammation damage, cytotoxicity, neuronal apoptosis and neurological deficits and the underlying mechanism in vitro and in vivo.

METHODS

In vivo, an I/R model was induced by middle cerebral artery occlusion and reperfusion (MCAO/R) in C57BL/6 N mice, and D-allose was given by intraperitoneal injection within 5 min after reperfusion. In vitro, mouse hippocampal neuronal cells (HT-22) with oxygen-glucose deprivation and reperfusion (OGD/R) were established as a cell model of IS. Neurological scores, some cytokines, cytotoxicity and apoptosis in the brain and cell lines were measured. Moreover, Gal-3 short hairpin RNAs, lentiviruses and adeno-associated viruses were used to modulate Gal-3 expression in neurons in vitro and in vivo to reveal the molecular mechanism.

RESULTS

D-allose alleviated cytotoxicity, including cell viability, LDH release and apoptosis, in HT-22 cells after OGD/R, which also alleviated brain injury, as indicated by lesion volume, brain edema, neuronal apoptosis, and neurological functional deficits, in a mouse model of I/R. Moreover, D-allose decreased the release of inflammatory factors, such as IL-1β, IL-6 and TNF-α. Furthermore, the expression of Gal-3 was increased by I/R in wild-type mice and HT-22 cells, and this factor further bound to TLR4, as confirmed by three-dimensional structure prediction and Co-IP. Silencing the Gal-3 gene with shRNAs decreased the activation of TLR4 signaling and alleviated IS-induced neuroinflammation, apoptosis and brain injury. Importantly, the loss of Gal-3 enhanced the D-allose-mediated protection against I/R-induced HT-22 cell injury, inflammatory insults and apoptosis, whereas activation of TLR4 by the selective agonist LPS increased the degree of neuronal injury and abolished the protective effects of D-allose.

CONCLUSIONS

In summary, D-allose plays a crucial role in inhibiting inflammation after IS by suppressing Gal-3/TLR4/PI3K/AKT signaling pathway in vitro and in vivo.