Co-expression of RelA/p65 and ACTN4 induces apoptosis in non-small lung carcinoma cells

Antiproliferative Activity of Piceamycin by Regulating Alpha-Actinin-4 in Gemcitabine-Resistant Pancreatic Cancer Cells

Although gemcitabine-based regimens are widely used as an effective treatment for pancreatic cancer, acquired resistance to gemcitabine has become an increasingly common problem. Therefore, a novel therapeutic strategy to treat gemcitabine-resistant pancreatic cancer is urgently required. Piceamycin has been reported to exhibit antiproliferative activity against various cancer cells; however, its underlying molecular mechanism for anticancer activity in pancreatic cancer cells remains unexplored. Therefore, the present study evaluated the antiproliferation activity of piceamycin in a gemcitabine-resistant pancreatic cancer cell line and patient-derived pancreatic cancer organoids. Piceamycin effectively inhibited the proliferation and suppressed the expression of alpha-actinin-4, a gene that plays a pivotal role in tumorigenesis and metastasis of various cancers, in gemcitabine-resistant cells. Long-term exposure to piceamycin induced cell cycle arrest at the G0/G1 phase and caused apoptosis. Piceamycin also inhibited the invasion and migration of gemcitabine-resistant cells by modulating focal adhesion and epithelial-mesenchymal transition biomarkers. Moreover, the combination of piceamycin and gemcitabine exhibited a synergistic antiproliferative activity in gemcitabine-resistant cells. Piceamycin also effectively inhibited patient-derived pancreatic cancer organoid growth and induced apoptosis in the organoids. Taken together, these findings demonstrate that piceamycin may be an effective agent for overcoming gemcitabine resistance in pancreatic cancer.

Alpha-actnin-4 (ACTN4) selectively affects the DNA double-strand breaks repair in non-small lung carcinoma cells

BACKGROUND

ACTN4 is an actin-binding protein involved in many cellular processes, including cancer development. High ACTN4 expression is often associated with a poor prognosis. However, it has been identified as a positive marker for platinum-based adjuvant chemotherapy for non-small cell lung cancer (NSCLC). The goal of our study was to investigate the involvement of ACTN4 in the NSCLC cells' response to the genotoxic drugs.

RESULTS

We generated H1299 cells with the ACTN4 gene knock-out (ACTN4 KO), using the CRISPR/Cas9 system. The resistance of the cells to the cisplatin and etoposide was analyzed with the MTT assay. We were also able to estimate the efficiency of DNA repair through the DNA comet assay and gamma-H2AX staining. Possible ACTN4 effects on the non-homologous end joining (NHEJ) and homologous recombination (HR) were investigated using pathway-specific reporter plasmids and through the immunostaining of the key proteins. We found that the H1299 cells with the ACTN4 gene knock-out did not show cisplatin-resistance, but did display a higher resistance to the topoisomerase II inhibitors etoposide and doxorubicin, suggesting that ACTN4 might be somehow involved in the repair of DNA strand breaks. Indeed, the H1299 ACTN4 KO cells repaired etoposide- and doxorubicin-induced DNA breaks more effectively than the control cells. Moreover, the ACTN4 gene knock-out enhanced NHEJ and suppressed HR efficiency. Supporting the data, the depletion of ACTN4 resulted in the faster assembly of the 53BP1 foci with a lower number of the phospho-BRCA1 foci after the etoposide treatment.

CONCLUSIONS

Thus, we are the first to demonstrate that ACTN4 may influence the resistance of cancer cells to the topoisomerase II inhibitors, and affect the efficiency of the DNA double strand breaks repair. We hypothesize that ACTN4 interferes with the assembly of the NHEJ and HR complexes, and hence regulates balance between these DNA repair pathways.

Chitinase-3 like-protein-1 promotes glioma progression via the NF-κB signaling pathway and tumor microenvironment reprogramming

Background: Chitinase-3-like protein 1 (CHI3L1) is overexpressed in various types of tumors, especially in glioma, and contributes to tumor progression. However, the definite role of CHI3L1 and involved pathway in glioma progression are not completely understood.

Methods: CHI3L1 expression in human gliomas and its association with patient survival was determined using enzyme-linked immunosorbent assay, western blot, immunohistochemistry, and public databases. Single-cell RNA-seq was used to characterize the landscape of tumor and myeloid cells. Human proteome microarray assay was applied to identify the binding partners of CHI3L1. Protein-protein interactions were analyzed by co-immunoprecipitation and cellular co-localization. The roles of CHI3L1 in glioma proliferation and invasion were investigated in tumor cell lines by gain- and loss- of function, as well as in vivo animal experiments.

Results: CHI3L1 was up-regulated in all disease stages of glioma, which was closely related with tumor survival, growth, and invasion. CHI3L1 was primarily expressed in glioma cells, followed by neutrophils. Moreover, glioma cells with high expression of CHI3L1 were significantly enriched in NF-κB pathway. Pseudo-time trajectory analysis revealed a gradual transition from CHI3L1^low to CHI3L1^high glioma cells, along with the NF-κB pathway gradually reversed from inhibition to activation. Intriguingly, CHI3L1 binds to actinin alpha 4 (ACTN4) and NFKB1, and enhances the NF-κB signaling pathway by promoting the NF-κB subunit nuclear translocation in glioma cells. Further, CHI3L1 were released into the tumor microenvironment (TME) and interacted with CD44 expressed on tumor-associated macrophages to activate AKT pathway, thereby contributing to M2 macrophage polarization. In addition, CHI3L1 positively correlated to the expression of immune checkpoints, such as CD274 (PD-L1) and HAVCR2 (LAG3), which then remodeled the TME to an immunosuppressive phenotype.

Conclusion: Our research revealed that CHI3L1 facilitated NF-κB pathway activation within glioma cells and reprogramed the TME, thereby serving as a promising therapeutic target for glioma.

Gene model-related m6A expression levels predict the risk of preeclampsia

Background

This is the first study to explore the potential functions and expression patterns of RNA N6-methyladenosine (m6A) and potential related genes in preeclampsia.

Methods

We identified two m6A modification patterns through unsupervised cluster analysis and validated them by principal component analysis. We quantified the relative abundance of specific infiltrating immunocytes using single-sample gene set enrichment analysis (ssGSEA) and the Wilcoxon test. To screen hub genes related to m6A regulators, we performed weighted gene coexpression network analysis. Functional enrichment analysis was conducted for differential signalling pathways and cellular processes. Preeclampsia patients were grouped by consensus clustering based on differentially expressed hub genes and the relationship between different gene-mediated classifications and clinical features.

Results

Two m6A clusters in preeclampsia, cluster A and cluster B, were determined based on the expression of 17 m6A modification regulators; ssGSEA revealed seven significantly different immune cell subtypes between the two clusters. A total of 1393 DEGs and nine potential m6A-modified hub genes were screened. We divided the patients into two groups based on the expression of these nine genes. We found that almost all the patients in m6A cluster A were classified into hub gene cluster 1 and that a lower gestational age may be associated with more m6A-associated events.

Conclusions

This study revealed that hub gene-mediated classification is consistent with m6A modification clusters for predicting the clinical characteristics of patients with preeclampsia. Our results provide new insights into the molecular mechanisms of preeclampsia.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12920-022-01254-4.

Comprehensive network analysis of different subtypes of molecular disorders in lung cancer

Lung cancer is the leading cause of cancer-related death worldwide. In this study, we attempted to identify the common pathogenesis of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) based on a modular and comprehensive analysis method. Data were downloaded and the differences analyzed in LUAD samples, LUSC samples, and normal samples, respectively. Co-expression analysis, enrichment analysis, and hypergeometric testing were used to predict transcription factors (TFs) and ncRNAs, as well as target genes. We obtained 4,596 differentially expressed genes which were clustered into 14 modules dysfunction. The 14 clustered genes (including DOK2, COL5A1, and TSPAN8) were identified as the core genes of the module. Module genes are substantially involved in biological processes, such as extracellular matrix, carbohydrate binding and renal system development, and signal transduction as well, including PPAR signal transduction, cGMP-PKG signal transduction, PI3K-Akt signal transduction, and Apelin signal transduction. We identified ncRNA (miR-335-5p, ANCR, TUG1) and transcription factors (RELA, SP1) to regulate dysfunction module genes essentially. The analysis showed that comprehensive co-expression analysis contributes to understanding the TF ncRNA. Moreover, it assisted in further understanding of the molecular pathogenesis of co-expression of modular genes that regulate LUAD and LUSC. It provided a precious resource and theoretical basis for further experiments.

Exploring the mechanism of aidi injection for lung cancer by network pharmacology approach and molecular docking validation

Background. Aidi injection (ADI) is an effective Traditional Chinese medicine preparation widely used for lung cancer. However, the pharmacological mechanisms of ADI on lung cancer remain to be elucidated. Methods. A network pharmacology (NP)-based approach and the molecular docking validation were conducted to explore underlying mechanisms of ADI on lung cancer. The compounds and target genes were screened by Traditional Chinese Medicine Systems Pharmacology (TCMSP) database and Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine (Batman-TCM) database. The STRING database was utilized for protein interaction network construction. The R package clusterProfiler was used for bioinformatics annotation of hub target genes. The gene expression analysis and survival analysis were performed based on The Cancer Genome Atlas (TCGA) database. The Autodock Vina was used for molecular docking validation. Results. A total of five key compounds with 324 putative target genes were screened out, and 14 hub target genes were identified for treating lung cancer. Six hub genes could influence the survival of non-small cell lung cancer (NSCLC) patients. Of these hub genes, the expression pattern of EGFR, MYC, PIK3CA, and SMAD3 were significantly higher in the LUSC, while PIK3CA and RELA expressed lower in the LUAD group and LUSC group, respectively. These six hub genes had good docking affinity with the key compounds of ADI. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that ADI may exert therapeutic effects on lung cancer by regulating critical pathways including the thyroid hormone signaling pathway, MAPK signaling pathway, and PI3K-Akt signaling pathway. Conclusions. The present study explored the potential pharmacological mechanisms of ADI on lung cancer, promoting the clinical application of ADI in treating lung cancer, and providing references for advanced researches.

Binding of alpha-ACTN4 to EGF receptor enables its rapid phosphorylation

Alpha-ACTN4, a member of alpha-actinin family is critical for cell motility through its regulated binding of actin filaments. We previously found that EGF exposure of cells triggers the tyrosyl-phosphorylation of ACTN4 in fibroblasts that dramatically downregulates its binding to actin filaments. However, the exact kinase remained uncertain. In the present study, we report that the phosphorylation of ACTN4 occurs within seconds upon EGF treatments and is accomplished via direct interaction of ACTN4 with the EGF receptor. The major binding domain of ACTN4 for EGF receptor is mapped to the N-terminal 32 amino acids. A second domain minimizes the interaction, as truncation of the C-terminal tail enhances ACTN4 binding to EGF receptor. A mimetic phosphorylated ACTN4, Y4/31E, presents low binding to EGF receptor. Overexpression of EGF receptor in melanoma cell lines, also accomplishes the phosphorylation of ACTN4 in the presence of EGF. These findings suggest that the binding of ACTN4 to EGFR enables its direct and rapid phosphorylation resulting in dissociation from EGFR and decreased binding to actin filaments.

Ceramide Pathway Regulators Predict Clinical Prognostic Risk and Affect the Tumor Immune Microenvironment in Lung Adenocarcinoma

Purpose

The ceramide pathway is strongly associated with the regulation of tumor proliferation, differentiation, senescence, and apoptosis. This study aimed to explore the gene signatures, prognostic value, and immune-related effects of ceramide-regulated genes in lung adenocarcinoma (LUAD).

Methods

Public datasets of LUAD from The Cancer Genome Atlas and Gene Expression Omnibus were selected. Consensus clustering was adopted to classify LUAD patients, and a least absolute shrinkage and selection operator (LASSO) regression model was employed to develop a prognostic risk signature. CIBERSORT algorithm was used to estimate the association between the risk signature and the tumor immune microenvironment.

Results

Most of the 22 ceramide-regulated genes were differentially expressed between LUAD and normal samples. LUAD patients were classified into two subgroups (cluster 1 and 2) and cluster 2 was associated with a poor prognosis. Furthermore, a prognostic risk signature was developed based on the three ceramide-regulated genes, Cytochrome C (CYCS), V-rel reticuloendotheliosis viral oncogene homolog A (RELA) and Fas-associated via death domain (FADD). LUAD patients with low- and high-risk scores differed concerning the subtypes of tumor-infiltrating immune cells. A moderate to weak correlation was observed between the risk score and tumor-infiltrating immune cells.

Conclusions

Ceramide-regulated genes could predict clinical prognostic risk and affect the tumor immune microenvironment in LUAD.

A Novel Risk Model Based on Autophagy Pathway Related Genes for Survival Prediction in Lung Adenocarcinoma

Background

Autophagy has a principal role in mediating tumor cell metabolism. However, the role of autophagy-pathway-related genes (APRGs) as prognostic markers remains obscure in lung adenocarcinoma (LUAD). More potential prognostic biomarkers are needed to deepen our understanding to explore the prognostic role of APRGs in LUAD.

Material/Methods

We used The Cancer Genome Atlas (TCGA) database to identify differentially expressed APRGs. Cox proportional hazard regression was used to identify prognostic APRGs, and then a risk model was constructed. The efficacy of the risk model was confirmed using a testing group. Lastly, we explored mutational signatures of prognostic of APRGs. T-tests were used to analyze all the expression patterns of genes by SPSS 19.0.

Results

Using TCGA database, 5 differently expressed APRGs were identified in LUAD patients, and functional enrichment analyze of the genes that were closely associated with the survival status in LUAD patients. Cox proportional hazard regression was facilitated to identify 9 APRGs (CCR2, LAMP1, RELA, ATG12, ATG9A, NCKAP1, ATG10, DNAJB9, and MBTPS2). Multivariate Cox proportional hazards regression analyses further identified 5 key prognostic APRGs (CCR2, LAMP1, RELA, ATG12, and MBTPS2) that were closely related to the survival status in LUAD. Then the prognostic scores based on the 5 genes as independent prognostic indicators were constructed for overall survival (OS) of LUAD patients; area under the curve (AUC) values >0.70 (all P<0.05). The efficacy of prognostic scores was confirmed by data from the testing group and showed significant differences between the low-risk and the high-risk groups for OS (P<0.05).

Conclusions

The risk model based on the construction of 5 APRGs can predict the prognosis of patients with LUAD, which may potentially predict prognostic signatures for LUAD.

DriverDBv3: a multi-omics database for cancer driver gene research

An integrative multi-omics database is needed urgently, because focusing only on analysis of one-dimensional data falls far short of providing an understanding of cancer. Previously, we presented DriverDB, a cancer driver gene database that applies published bioinformatics algorithms to identify driver genes/mutations. The updated DriverDBv3 database (http://ngs.ym.edu.tw/driverdb) is designed to interpret cancer omics’ sophisticated information with concise data visualization. To offer diverse insights into molecular dysregulation/dysfunction events, we incorporated computational tools to define CNV and methylation drivers. Further, four new features, CNV, Methylation, Survival, and miRNA, allow users to explore the relations from two perspectives in the ‘Cancer’ and ‘Gene’ sections. The ‘Survival’ panel offers not only significant survival genes, but gene pairs synergistic effects determine. A fresh function, ‘Survival Analysis’ in ‘Customized-analysis,’ allows users to investigate the co-occurring events in user-defined gene(s) by mutation status or by expression in a specific patient group. Moreover, we redesigned the web interface and provided interactive figures to interpret cancer omics’ sophisticated information, and also constructed a Summary panel in the ‘Cancer’ and ‘Gene’ sections to visualize the features on multi-omics levels concisely. DriverDBv3 seeks to improve the study of integrative cancer omics data by identifying driver genes and contributes to cancer biology.

Replicative senescence in MSCWJ-1 human umbilical cord mesenchymal stem cells is marked by characteristic changes in motility, cytoskeletal organization, and RhoA localization

Here, we document changes in cell motility and organization of the contractile apparatus of human umbilical cord Wharton's jelly mesenchymal stem cells (MSCWJ-1) in the process of replicative senescence. Colocalization dynamics of F-actin and actin-binding proteins (myosin-9, α-actinin-4, RhoA) were examined in the MSCWJ-1 cell line. The results show that nuclear-cytoplasmic redistribution of RhoA occurs during replicative senescence, with maximal RhoA/nucleus colocalization evident at passage 15. At that time point, decreases in colocalization, namely myosin-9/F-actin and α-actinin-4/F-actin, were seen and myosin-9 was found in cytosolic extracts in the assembly-incompetent form. Using an automated intravital confocal cytometry system and quantitative analysis of MSCWJ-1 movements, we found that changes in cytoskeletal organization correlate with cell motility characteristics over a time period from passages 9 to 38. The factors examined (cytoskeleton structure, cell motility) indicate that the process by which cells transition to replicative senescence is best represented as three stages. The first stage lasts from cell culture isolation to passage 15 and is characterized by: accumulation of actin-binding proteins in assembly-incompetent forms; nuclear RhoA accumulation; and an increase in movement tortuosity. The second stage extends from passages 15 to 28 and is characterized by: an increase in the structural integrity of the actin cytoskeleton; exit of RhoA and alpha-actinin-4 from the nucleus; and a decrease in path tortuosity. The third stage extends from passage 28 to 38 and is marked by: a plateau in actin cytoskeleton structural integrity; significant decreases in nuclear RhoA levels; and decreases in cell speed.

Role of ACTN4 in Tumorigenesis, Metastasis, and EMT

The actin-binding protein ACTN4 belongs to a family of actin-binding proteins and is a non-muscle alpha-actinin that has long been associated with cancer development. Numerous clinical studies showed that changes in ACTN4 gene expression are correlated with aggressiveness, invasion, and metastasis in certain tumors. Amplification of the 19q chromosomal region where the gene is located has also been reported. Experimental manipulations with ACTN4 expression further confirmed its involvement in cell proliferation, motility, and epithelial-mesenchymal transition (EMT). However, both clinical and experimental data suggest that the effects of ACTN4 up- or down-regulation may vary a lot between different types of tumors. Functional studies demonstrated its engagement in a number of cytoplasmic and nuclear processes, ranging from cytoskeleton reorganization to regulation of different signaling pathways. Such a variety of functions may be the reason behind cell type and cell line specific responses. Herein, we will review research progress and controversies regarding the prognostic and functional significance of ACTN4 for tumorigenesis.

ACTN4 Promotes the Proliferation, Migration, Metastasis of Osteosarcoma and Enhances its Invasive Ability through the NF-κB Pathway

Alpha-actinin-4 (ACTN4) is associated with different types of tumors, but its role in osteosarcoma (OS) is not known. We aimed to investigate the effect of ACTN4 on the growth, migration, invasion and metastasis of OS. We further explored the possible mechanism of how ACTN4 affects the development of OS. First, the expression of ACTN4 in OS tissues and OS cell lines was analyzed by PCR. Second, the role of ACTN4 in the development of OS was explored by the proliferation, scratch, and invasion assays. We further explored the effect of ACTN4 on OS growth in an orthotopic xenograft model of nude mice. In addition, we used hematoxylin and eosin (HE) staining of lung tissues in nude mice to observe the effect of ACTN4 on lung metastasis of OS. Finally, rescue experiments further investigated the role of NF-κB on ACTN4 in the development of OS. ACTN4 was highly expressed in OS tissues and OS cell lines. In vitro experiments demonstrated that reducing ACTN4 expression inhibited the proliferation, migration, and invasion of OS. In contrast, overexpression of ACTN4 promotes these effects. In vivo experiments further validated that ACTN4 promoted the growth of OS. The HE staining of lungs in nude mice revealed that ACTN4 promoted lung metastasis of OS. In addition, we found that ACTN4 enhanced the ability of OS to invade, through the NF-κB pathway. ACTN4 promotes the proliferation, migration, metastasis of OS and enhances its invasion ability through the NF-κB pathway.