Silencing lncRNA LOC101928963 Inhibits Proliferation and Promotes Apoptosis in Spinal Cord Glioma Cells by Binding to PMAIP1

Inhibition of ATG5-mediated autophagy maintains PMAIP1 stability to promote cell apoptosis and suppress triple-negative breast cancer progression

OBJECTIVE

Triple-negative breast cancer (TNBC) is a highly aggressive subtype of breast cancer characterized by a high recurrence rate and a lack of effective targeted therapies. The purpose of this study was to investigate the interaction between the pro-apoptotic factor phorbol-12-myristate-13-acetate-induced protein 1 (PMAIP1) and autophagy-related protein 5 (ATG5), as well as their regulatory mechanisms in TNBC cell apoptosis and autophagy, to identify potential therapeutic targets for TNBC.

METHODS

TNBC-related datasets were retrieved from The Cancer Genome Atlas and selected by Prediction Analysis of Microarray 50 analysis to assess the expression of PMAIP1 in the samples. Additionally, the expression of PMAIP1 in the TNBC cell lines (MDA-MB-231) was detected using quantitative real-time polymerase chain reaction. In MDA-MB-231 cells, the expression of PMAIP1 and ATG5 was overexpressed or knocked down, and autophagy was inhibited using chloroquine (20 μM). Gene and protein expression levels were evaluated using quantitative real-time polymerase chain reaction and Western blot, respectively. Immunofluorescence was used to observe microtubule-associated protein 1 light chain 3 puncta formation to assess autophagy levels. Furthermore, cell apoptosis, proliferation, migration, and invasion were analyzed using terminal deoxynucleotidyl transferase dUTP nick-end labeling assay, colony formation assay, and Transwell assay.

RESULTS

Compared to the control group, the expression of PMAIP1 was significantly elevated in TNBC tissues and MDA-MB-231 cells. Furthermore, overexpression of PMAIP1 led to a marked increase in apoptosis levels and a remarkable reduction in autophagy levels in MDA-MB-231 cells, while knockdown of PMAIP1 showed the opposite effects. Additionally, knockdown of ATG5 expression or treatment with chloroquine not only resulted in an increase in PMAIP1 expression in a time-dependent manner, but also reduced autophagy levels and enhanced apoptosis levels of cells. Furthermore, simultaneous knockdown of PMAIP1 and ATG5 considerably up-regulated apoptosis levels while down-regulating autophagy levels. Moreover, knockdown of PMAIP1 alone promoted the viability, invasion, and migration abilities of TNBC cells, while dual knockdown reversed these effects.

CONCLUSION

Inhibition of ATG5-mediated autophagy maintains PMAIP1 stability, thereby promoting cell apoptosis and suppressing TNBC progression.

Identification and preliminary validation of biomarkers associated with mitochondrial and programmed cell death in pre-eclampsia

Background

The involvement of mitochondrial and programmed cell death (mtPCD)-related genes in the pathogenesis of pre-eclampsia (PE) remains inadequately characterized.

Methods

This study explores the role of mtPCD genes in PE through bioinformatics and experimental approaches. Differentially expressed mtPCD genes were identified as potential biomarkers from the GSE10588 and GSE98224 datasets and subsequently validated. Hub genes were determined using support vector machine, least absolute shrinkage and selection operator, and Boruta based on consistent expression profiles. Their performance was assessed through nomogram and artificial neural network models. Biomarkers were subjected to localization, functional annotation, regulatory network analysis, and drug prediction. Clinical validation was conducted via real-time quantitative polymerase chain reaction (RT-qPCR), immunofluorescence, and Western blot.

Results

Four genes [solute carrier family 25 member 5 (SLC25A5), acyl-CoA synthetase family member 2 (ACSF2), mitochondrial fission factor (MFF), and phorbol-12-myristate-13-acetate-induced protein 1 (PMAIP1)] were identified as biomarkers distinguishing PE from normal controls. Functional analysis indicated their involvement in various biological pathways. Immune analysis revealed associations between biomarkers and immune cell activity. A regulatory network was informed by biomarker expression and database predictions, in which KCNQ1OT1 modulates ACSF2 expression via hsa-miR-200b-3p. Drug predictions, including clodronic acid, were also proposed. Immunofluorescence, RT-qPCR, and Western blot confirmed reduced expression of SLC25A5, MFF, and PMAIP1 in PE, whereas ACSF2 was significantly upregulated.

Conclusion

These four mtPCD-related biomarkers may play a pivotal role in PE pathogenesis, offering new perspectives on the disease's diagnostic and mechanistic pathways.

PMAIP1, a novel diagnostic and potential therapeutic biomarker in osteoporosis

BACKGROUND

Osteoporosis is a common endocrine metabolic bone disease, which may lead to severe consequences. However, the unknown molecular mechanism of osteoporosis, the observable side effects of present treatments and the inability to fundamentally improve bone metabolism seriously restrict the impact of prevention and treatment. The study aims to identify potential biomarkers from osteoclast progenitors, specifically peripheral blood monocytes on predicting the osteoporotic phenotype.

METHODS

Datasets were obtained from Gene Expression Omnibus (GEO). Based on the differentially expressed genes (DEGs) and GSEA results, GO and KEGG analyses were performed using the DAVID database and Metascape database. PPI network, TF network, drug-gene interaction network, and ceRNA network were established to determine the hub genes. Its osteogenesis, migration, and proliferation abilities in bone marrow mesenchymal stem cells (BMSCs) were validated through RT-qPCR, WB, ALP staining, VK staining, wound healing assay, transwell assay, and CCK-8 assay.

RESULTS

A total of 63 significant DEGs were screened. Functional and pathway enrichment analysis discovered that the functions of the significant DEGs (SDEGs) are mainly related to immunity and metal ions. A comprehensive evaluation of all the network analyses, PMAIP1 was defined as osteoporosis's core gene. This conclusion was further confirmed in clinical cohort data. A series of experiments demonstrated that the PMAIP1 gene can promote the osteogenesis, migration and proliferation of BMSC cells.

CONCLUSIONS

All of these outcomes showed a new theoretical basis for further research in the treatment of osteoporosis, and PMAIP1 was identified as a potential biomarker for osteoporosis diagnosis and treatment.

Effects of µ-Conotoxin GIIIB on the cellular activity of mouse skeletal musculoblast: combined transcriptome and proteome analysis

µ-Conotoxin GIIIB (µ-CTX GIIIB) is a polypeptide containing three disulfide bridges, produced by the sea snail Conus geographus. This study was aimed to explored the cytotoxic effects of µ-CTX GIIIB on mouse skeletal musculoblast (Sol8). Sol8 cells were exposed to ouabain and veratridine to establish the cell injury model, and then treated with µ-CTX GIIIB. CCK-8 was adopted to evaluate the cytotoxicity of µ-CTX GIIIB. Then, proteomics and transcriptome were conducted, and the explore the differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) affected by µ-CTX GIIIB were found. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was used to investigate the affected signaling pathways. µ-CTX GIIIB increased the cell survival rate of injured Sol8 cells. We found and identified 1,663 DEGs and 444 DEPs influenced by µ-CTX GIIIB. 106 pairs of correlated DEGs and DEPs were selected by combining transcriptome and proteome data. The results of KEGG and GO analysis showed that µ-CTX GIIB affected the cell cycle, apoptosis, DNA damage and repair, lipid metabolism and other biological processes of Sol8 cells. µ-CTX GIIIB could affected cell cycle regulation, DNA damage repair, and activation of tumor factors, with potential carcinogenic effects. Our results provide an important basis for the study of in vitro toxicity, the mechanism of toxicity and injury prevention by µ-CTX GIIIB.

Construction of a Diagnostic Model and a lncRNA-Associated ceRNA Network Based on Apoptosis-Related Genes for Schizophrenia

Methods

Gene expression profiles and apoptosis-related data were downloaded from the Gene Expression Omnibus and Molecular Signature databases, respectively. Apoptosis-related differentially expressed mRNAs (DEGs) and miRNAs (DEMs) from blood samples between the schizophrenia and healthy control individuals were screened. A diagnostic model was developed using the data from univariate and least absolute shrinkage and selection operator (LASSO) regression analyses, followed by validation using the GSE38485 dataset. Cases were divided into low-risk (LR) and high-risk (HR) groups based on the risk score of the model, and differences in immune gene sets and pathways between these two groups were compared. Finally, a ceRNA network was constructed by integrating long non-coding RNAs (lncRNAs), DEMs, and DEGs.

Results

A diagnostic model containing 15 apoptosis-related genes was developed and its diagnostic efficiency was found to be robust. The HR group was correlated with higher immune scores of chemokines, cytokines, and interleukins; it was also significantly involved in pathways such as pancreatic beta cells and early estrogen response. A ceRNA network composed of 2 lncRNAs, 14 miRNAs, and 5 mRNAs was established.

Conclusions

The established model is a potential tool to improve the diagnostic efficiency of patients with schizophrenia, and the nodes included in the ceRNA network might serve as biomarkers and therapeutic targets for schizophrenia.

Therapeutic advancements in targeting BCL-2 family proteins by epigenetic regulators, natural, and synthetic agents in cancer

Cancer is amongst the deadliest and most disruptive disorders, having a much higher death rate than other diseases worldwide. Human cancer rates continue to rise, thereby posing the most significant concerns for medical health professionals. In the last two decades, researchers have gone past several milestones in tackling cancer while gaining insight into the role of apoptosis in cancer or targeting various biomarker tools for prognosis and diagnosis. Apoptosis which is still a topic full of complexities, can be controlled considerably by B-cell lymphoma 2 (BCL-2) and its family members. Therefore, targeting proteins of this family to prevent tumorigenesis, is essential to focus on the pharmacological features of the anti-apoptotic and pro-apoptotic members, which will help to develop and manage this disorder. This review deals with the advancements of various epigenetic regulators to target BCL-2 family proteins, including the mechanism of several microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Similarly, a rise in natural and synthetic molecules' research over the last two decades has allowed us to acquire insights into understanding and managing the transcriptional alterations that have led to apoptosis and treating various neoplastic diseases. Furthermore, several inhibitors targeting anti-apoptotic proteins and inducers or activators targeting pro-apoptotic proteins in preclinical and clinical stages have been summarized. Overall, agonistic and antagonistic mechanisms of BCL-2 family proteins conciliated by epigenetic regulators, natural and synthetic agents have proven to be an excellent choice in developing cancer therapeutics.

Interleukin-23 mediates the reduction of GADD45a expression to attenuate oxidative stress-induced cellular senescence in human fibroblasts

The interleukin-23 (IL-23) plays a key role in various inflammatory diseases, such as spondyloarthritis, by acting on target cells through the IL-23/IL-17 pathway. Recent studies have suggested that IL-23 can also directly affect fibroblasts. Senescent fibroblasts are implicated in many physiological and pathological processes, including those related to inflammatory diseases. However, it remains unclear whether IL-23 can influence fibroblast senescence and contribute to pathogenesis. In our study, we investigated the effects of IL-23 on oxidative stress-induced senescence in human fibroblasts, using the H₂O₂-induced senescence model, and found that IL-23 pre-treatment significantly attenuated senescence in these cells. RNA-seq and in vitro experiments indicate that IL-23 may act by regulating GADD45a expression and the p38/MAPK pathway. Furthermore, we confirmed that IL-23 inhibits oxidative stress-induced up-regulation of GADD45a expression and subsequent activation of the p38/MAPK pathway through GADD45a knockdown and overexpression experiments. Our study is the first to demonstrate that IL-23 can effectively suppress the senescence of fibroblasts induced by oxidative stress, by inhibiting the H₂O₂-triggered induction of GADD45a and subsequent activation of the p38/MAPK pathway. These findings have significant implications for understanding the role of IL-23 in immune-inflammatory diseases and may provide a new avenue for the diagnosis and treatment of these conditions.

Mechanisms of long non-coding RNAs in biological phenotypes and ferroptosis of glioma

Glioma, one of the most common malignant tumors in the nervous system, is characterized by limited treatment, high mortality and poor prognosis. Numerous studies have shown that lncRNAs play an important role in the onset and progression of glioma by acting on various classical signaling pathways of tumors through signaling, trapping, guiding, scaffolding and other functions. LncRNAs contribute to the malignant progression of glioma via proliferation, apoptosis, epithelial-mesenchymal transformation, chemotherapy resistance, ferroptosis and other biological traits. In this paper, relevant lncRNA signaling pathways involved in glioma progression were systematically evaluated, with emphasis placed on the specific molecular mechanism of lncRNAs in the process of ferroptosis, in order to provide a theoretical basis for the application of lncRNAs in the anticancer treatment of glioma.

Suppression of miR-106a-5p expression inhibits tumorigenesis via increasing CELF-2 expression in spinal cord glioma

Spinal cord glioma is a tumor characterized by high recurrence and mortality rates, and its treatment remains a major challenge. It has been reported that abnormal expression of microRNAs (miRNAs/miRs) is associated with tumor progression. Therefore, the current study aimed to identify novel miRNAs associated with spinal cord glioma. Herein, the expression levels of several miRNAs were determined in human spinal cord glioma and adjacent non-cancerous tissues by reverse transcription-quantitative (RT-qPCR). The results revealed that miR-106a-5p expression was markedly upregulated in spinal cord glioma tissues compared with in non-cancerous tissues. Furthermore, the biological effects of miR-106a-5p on spinal cord glioma cells were evaluated by MTT, Transwell and flow cytometric assays. In 0231SCG cells transfected with miR-106a-5p inhibitor, cell proliferation, migration and invasion were attenuated, whereas apoptosis was enhanced. A search of the TargetScan database revealed that miR-106a-5p directly targeted CUGBP Elav-like family member 2 (CELF-2). Western blot and RT-qPCR experiments further confirmed the association between miR-106a-5p and CELF-2 expression in spinal cord glioma tissues. The current results demonstrated that CELF-2 was a direct target of miR-106a-5p, and that the expression levels of CELF-2 were negatively associated with those of miR-106a-5p. In addition, overexpression of CELF-2 in spinal cord glioma cells reversed the tumor-promoting effects of miR-106a-5p both in vitro and in vivo. Overall, the aforementioned findings indicated that miR-106a-5p, which was highly expressed in spinal cord glioma tissues, may affect the proliferation, migration, invasion and apoptosis of spinal cord glioma cells via targeting CELF-2, thus indicating a potential approach to the future clinical management of spinal cord glioma.

Long non-coding RNA TP73-AS1 is a potential immune related prognostic biomarker for glioma

Glioma is one of the most common primary brain tumors, and is divided into low-grade and high-grade gliomas. Long non-coding RNAs have been increasingly implicated in the pathogenesis and prognosis of glioma. Here, we demonstrated that the long non-coding RNA TP73-AS1 is differentially expressed among gliomas with different clinicopathological features in The Cancer Genome Atlas (TCGA), Chinese Glioma Genome Atlas (CGGA), and GEO glioma datasets; high expression of TP73-AS1 was associated with poor clinical features, including age, stage, IDH mutation status, 1p/19q co-deletion status and overall survival. Measuring TP73-AS1 expression using real-time PCR showed the same result for 76 glioma tissue samples from our hospital. The infiltration levels of various immune cells in the tumor microenvironment were found to be significantly higher in patients with high expression of TP73-AS1. Taken together, our results suggest that TP73-AS1 has potential as a prognostic glioma biomarker. Moreover, the knowledge that TP73-AS1 affects the glioma immune microenvironment may provide new information for the immunological research and treatment of glioma.

Development of a Prognostic Signature Based on Single-Cell RNA Sequencing Data of Immune Cells in Intrahepatic Cholangiocarcinoma

Analysis of single-cell RNA sequencing (scRNA-seq) data of immune cells from the tumor microenvironment (TME) may identify tumor progression biomarkers. This study was designed to investigate the prognostic value of differentially expressed genes (DEGs) in intrahepatic cholangiocarcinoma (ICC) using scRNA-seq. We downloaded the scRNA-seq data of 33,991 cell samples, including 17,090 ICC cell samples and 16,901 ICC adjacent tissue cell samples regarded as normal cells. scRNA-seq data were processed and classified into 20 clusters. The immune cell clusters were extracted and processed again in the same way, and each type of immune cells was divided into several subclusters. In total, 337 marker genes of macrophages and 427 marker genes of B cells were identified by comparing ICC subclusters with normal subclusters. Finally, 659 DEGs were obtained by merging B cell and macrophage marker genes. ICC sample clinical information and gene expression data were downloaded. A nine-prognosis-related-gene (PRG) signature was established by analyzing the correlation between DEGs and overall survival in ICC. The robustness and validity of the signature were verified. Functional enrichment analysis revealed that the nine PRGs were mainly involved in tumor immune mechanisms. In conclusion, we established a PRG signature based on scRNA-seq data from immune cells of patients with ICC. This PRG signature not only reflects the TME immune status but also provides new biomarkers for ICC prognosis.

Linc00475 promotes the progression of glioma by regulating the miR-141-3p/YAP1 axis

Glioma is the most prevalent and lethal primary brain tumour. Abundant long non‐coding RNAs ( lncRNAs) are aberrant and play crucial roles in the oncogenesis of glioma. The exact functions of linc00475 in glioma remain blurred. Here, we analysed the expression levels of linc00475 by qRT‐PCR and discovered that linc00475 was up‐regulated in glioma and predicted a poor prognosis in patients with glioma. Besides, inhibiting linc00475 restrained the progression of glioma in vitro and in vivo. Further experiments confirmed that linc00475 regulated the progression of glioma by acting as a sponge for miR‐141‐3p. Moreover, we detected the binding sites of linc00475 and miR‐141‐3p, the YAP1‐ 3′UTR and miR‐141‐3p by luciferase reporters. The rescue assays confirmed that inhibiting linc00475 restrained the progression of glioma through the miR‐141‐3p/YAP1 pathway. Collectively, our research demonstrates the key roles of linc00475 in glioma, which could be a promising therapeutic target.

LncRNA FAM83H-AS1 maintains intervertebral disc tissue homeostasis and attenuates inflammation-related pain via promoting nucleus pulposus cell growth through miR-22-3p inhibition

Background

Intervertebral disc degeneration (IVDD) is regarded as the leading cause of low back pain, resulting in disability and a heavy burden on public health. Several studies have unveiled that long noncoding RNAs (lncRNAs) play a key role in the pathogenesis and progression of IVDD. In this study, we aimed to investigate the biological function and latent molecular mechanism of the lncRNA FAM83H antisense RNA 1 (FAM83H-AS1) in IVDD development.

Methods

Firstly, we established an IVDD model in rats using advanced glycation end products (AGEs) intradiscal injection. Subsequently, gain-of-function assays were conducted to investigate the role of FAM83H-AS1 in the progression of IVDD. Bioinformatics analysis, RNA pull down assay and rescue experiments were employed to shed light on the molecular mechanism underlying FAM83H-AS1 involving in IVDD.

Results

Our findings verified that AGEs treatment aggravated IVDD damage, and FAM83H-AS1 was downregulated in the IVDD group. Additionally, overexpression of FAM83H-AS1 contributed to the growth of nucleus pulposus (NP) cells and ameliorated IVDD injury. It was revealed that FAM83H-AS1 possessed the speculated binding sites of miR-22-3p. More importantly, we confirmed that FAM83H-AS1 functioned as a sponge of miR-22-3p in IVDD. Lastly, we demonstrated that miR-22-3p mediated the impact of FAM83H-AS1 on cell proliferation, ECM degradation, and inflammation.

Conclusions

Our study indicated that FAM83H-AS1 relieved IVDD deterioration through sponging miR-22-3p, and provides novel insights into the mechanisms underlying FAM83H-AS1 in IVDD progression.

Immune-Related lncRNA Correlated with Transcription Factors Provide Strong Prognostic Prediction in Gliomas

Glioma is the most common and deadly tumor in central nervous system. According to previous studies, long noncoding RNAs (lncRNA) and transcription factors were significant factors of gliomas progression by regulating gliomas immune microenvironment. In our study, we built two independent cohorts from CGGA and TCGA. And we extracted 253 immune-related lncRNA correlated with prognosis. After LASSO analysis and multivariate Cox regression analysis, 8 immune-related lncRNA were used to construct classifier. The effectiveness of classifier was confirmed in both CGGA (AUC = 0.869) and TCGA (AUC = 0.902) cohorts. The correlation between transcription factors and immune-related lncRNA was calculated by WCGNA. Eventually, we built a network between 8 lncRNA and transcription factors. The function of core immune-related lncRNA in gliomas immune microenvironment was also investigated by CIBERTSORT. Our research provided a strong classifier of immune-related lncRNA to predict gliomas patient outcome. We also found the correlation between core immune-related lncRNA and transcription factors. These results may stimulate new strategy of immunotherapy in gliomas patients.