Filamin B extensively regulates transcription and alternative splicing, and is associated with apoptosis in HeLa cells

Filamin B restricts vaccinia virus spread and is targeted by vaccinia virus protein C4

Vaccinia virus (VACV) is a large DNA virus that encodes scores of proteins that modulate the host immune response. VACV protein C4 is one such immunomodulator known to inhibit the activation of both the NF-κB signaling cascade and the DNA-PK-mediated DNA sensing pathway. Here, we show that the N-terminal region of C4, which neither inhibits NF-κB nor mediates interaction with DNA-PK, still contributes to virus virulence. Furthermore, this domain interacts directly and with high affinity to the C-terminal domain of filamin B (FLNB). FLNB is a large actin-binding protein that stabilizes the F-actin network and is implicated in other cellular processes. Deletion of FLNB from cells results in larger VACV plaques and increased infectious viral yield, indicating that FLNB restricts VACV spread. These data demonstrate that C4 has a new function that contributes to virulence and engages the cytoskeleton. Furthermore, we show that the cytoskeleton performs further previously uncharacterized functions during VACV infection.

IMPORTANCE

Vaccinia virus (VACV), the vaccine against smallpox and monkeypox, encodes many proteins to counteract the host immune response. Investigating these proteins provides insights into viral immune evasion mechanisms and thereby indicates how to engineer safer and more immunogenic VACV-based vaccines. Here, we report that the N-terminal domain of VACV protein C4 interacts directly with the cytoskeletal protein filamin B (FLNB), and this domain of C4 contributes to virus virulence. Furthermore, VACV replicates and spreads better in cells lacking FLNB, thus demonstrating that FLNB has antiviral activity. VACV utilizes the cytoskeleton for movement within and between cells; however, previous studies show no involvement of C4 in VACV replication or spread. Thus, C4 associates with FLNB for a different reason, suggesting that the cytoskeleton has further uncharacterized roles during virus infection.

A cross-sectional analysis of syncytiotrophoblast membrane extracellular vesicles-derived transcriptomic biomarkers in early-onset preeclampsia

Background

Preeclampsia (PE) is a pregnancy-specific hypertensive disorder affecting 2%-8% of pregnancies worldwide. Biomarker(s) for the disorder exists, but while these have excellent negative predictive value, their positive predictive value is poor. Extracellular vesicles released by the placenta into the maternal circulation, syncytiotrophoblast membrane extracellular vesicles (STB-EVs), have been identified as being involved in PE with the potential to act as liquid biopsies.

Objective

The objective of this study was to identify the difference in the transcriptome of placenta and STB-EVs between preeclampsia and normal pregnancy (NP) and mechanistic pathways.

Methods/study design

We performed RNA-sequencing on placental tissue, medium/large and small STB-EVs from PE (n = 6) and NP (n = 6), followed by bioinformatic analysis to identify targets that could be used in the future for EV-based diagnostic tests for preeclampsia. Some of the identified biomarkers were validated with real-time polymerase chain reactions.

Results

Our analysis identified a difference in the transcriptomic STB-EV cargo between PE and NP. We then identified and verified the differential expression of FLNB, COL17A1, SLC45A4, LEP, HTRA4, PAPP-A2, EBI3, HSD17B1, FSTL3, INHBA, SIGLEC6, and CGB3. Our analysis also identified interesting mechanistic processes via an in silico prediction of STB-EV-based mechanistic pathways.

Conclusions

In this study, using comprehensive profiling of differentially expressed/carried genes of three linked sample subtypes in PE, we identified potential biomarkers and mechanistic gene pathways that may be important in the pathophysiology of PE and could be further explored in future studies.

Ribosomal protein L8 regulates the expression and splicing pattern of genes associated with cancer-related pathways

Background/aim

Ribosomal proteins have been shown to perform unique extraribosomal functions in cell apoptosis and other biological processes. Ribosomal protein L8 (RPL8) not only has important nonribosomal regulatory functions but also participates in the oncogenesis and development of tumors. However, the specific biological functions and pathways involved in this process are still unknown.

Materials and methods

RPL8 was overexpressed (RPL8-OE) in HeLa cells. MTT assay and flow cytometry were used to detect cell proliferation and apoptosis, respectively. Transcriptome sequencing was performed to analyze the differentially expressed genes (DEGs) and regulated alternative splicing events (RASEs) by RPL8-OE, both of which were validated by quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay.

Results

RPL8-OE inhibited cell proliferation and promoted cell apoptosis. RPL8 regulated the differential expression of many oncogenic genes and the occurrence of RASEs. Many DEGs and RASE genes (RASGs) were enriched in tumorigenesis and tumor progression-related pathways, including angiogenesis, inflammation, and regulation of cell proliferation. RPL8 could regulate the RASGs enriched in the negative regulation of apoptosis, consistent with its proapoptosis function. Furthermore, RPL8 may influence cancer-related DEGs by modulating the alternative splicing of transcription factors.

Conclusion

RPL8 might affect the phenotypes of cancer cells by altering the transcriptome profiles, including gene expression and splicing, which provides novel insights into the biological functions of RPL8 in tumor development.

Transcriptomics analysis of ethanol treatment of male Aedes aegypti reveals a small set of putative radioprotective genes

Introduction: Sterile Insect Technique (SIT) is based on releasing sterilized male insects into wild insect populations to compete for mating with wild females. Wild females mated with sterile males will produce inviable eggs, leading to a decline in population of that insect species. Sterilization with ionizing radiation (x-rays) is a commonly used mechanism for sterilization of males. Since irradiation can cause damage to both, somatic and germ cells, and can severely reduce the competitiveness of sterilized males relative to wild males, means to minimize the detrimental effects of radiation are required to produce sterile, competitive males for release. In an earlier study, we identified ethanol as a functional radioprotector in mosquitoes. Methods: Here, we used Illumina RNA-seq to profile changes in gene expression of male Aedes aegypti mosquitoes fed on 5% ethanol for 48 hours prior to receiving a sterilizing x-ray dose, compared to males fed on water prior to sterilization. Results: RNA-seq revealed a robust activation of DNA repair genes in both ethanol-fed and water-fed males after irradiation, but surprisingly few differences in gene expression between ethanol-fed and water-fed males regardless of radiation treatment. Discussion: While differences in gene expression due to ethanol exposure were minimal, we identified a small group of genes that may prime ethanol-fed mosquitoes for improved survivability in response to sterilizing radiation.

Age and Blood Pressure Contribute to Aortic Cell and Tissue Stiffness Through Distinct Mechanisms

BACKGROUND

Aortic stiffening is strongly associated with both aging and hypertension, but the underlying mechanisms remain unclear. We hypothesized that aging-induced aortic stiffness is mediated by a mechanism differing from hypertension.

METHODS

We conducted comprehensive in vivo and in vitro experiments using multiple rat models to dissect the different mechanisms of aortic stiffening mediated by aging and hypertension.

RESULTS

A time-course study in spontaneously hypertensive rats (SHR) and Wistar-Kyoto (WKY) normotensive rats showed more pronounced aging-associated aortic stiffening in SHR versus WKY. Angiotensin II-induced hypertension was associated with more significant aortic stiffening in older versus young WKY rats. Hypertension aggravated aging effects on aortic wall thickness and extracellular matrix content, indicating combinational effects of aging and hypertension on aortic stiffening. Intrinsic stiffness of isolated aortic vascular smooth muscle cells (VSMCs) increased with age in WKY rats, although no significant difference between older SHR and older WKY VSMCs was observed in 2-dimensional culture, reconstituted 3-dimensional tissues were stiffer for older SHR versus older WKY. A selective inhibitor that reduced hypertension-mediated aortic stiffening did not decrease age-related stiffening in aortic VSMCs and aortic wall. Integrin β1 and SM22 (smooth muscle-specific SM22 protein) expression were negligibly changed in WKY VSMCs during aging but were markedly increased by hypertension in older versus young WKY VSMCs. A notable shift of filamin isoforms from B to A was detected in older WKY VSMCs.

CONCLUSIONS

Our results indicate distinct mechanisms mediating aging-associated aortic VSMC and vessel stiffness, providing new insights into aortic stiffening and the pathogenesis of hypertension in the elderly.

RNA-binding protein CELF6 modulates transcription and splicing levels of genes associated with tumorigenesis in lung cancer A549 cells

CELF6 (CUGBP Elav-Like Family Member 6), a canonical RNA binding protein (RBP), plays important roles in post-transcriptional regulation of pre-mRNAs. However, the underlying mechanism of lower expressed CELF6 in lung cancer tissues is still unclear. In this study, we increased CELF6 manually in lung cancer cell line (A549) and utilized transcriptome sequencing (RNA-seq) technology to screen out differentially expressed genes (DEGs) and alternative splicing events (ASEs) after CELF6 over-expression (CELF6-OE). We found that CELF6-OE induced 417 up-regulated and 1,351 down-regulated DEGs. Functional analysis of down-regulated DEGs showed that they were highly enriched in immune/inflammation response- related pathways and cell adhesion molecules (CAMs). We also found that CELF6 inhibited the expression of many immune-related genes, including TNFSF10, CCL5, JUNB, BIRC3, MLKL, PIK3R2, CCL20, STAT1, MYD88, and CFS1, which mainly promote tumorigenesis in lung cancer. The dysregulated DEGs were also validated by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) experiment. In addition, CELF6 regulates the splicing pattern of large number of genes that are enriched in p53 signaling pathway and apoptosis, including TP53 and CD44. In summary, we made an extensive analysis of the transcriptome profile of gene expression and alternative splicing by CELF6-OE, providing a global understanding of the target genes and underlying regulation mechanisms mediated by CELF6 in the pathogenesis and development of lung cancer.

Investigation of the effects of overexpression of jumping translocation breakpoint (JTB) protein in MCF7 cells for potential use as a biomarker in breast cancer

Jumping translocation breakpoint (JTB) gene acts as a tumor suppressor or an oncogene in different malignancies, including breast cancer (BC), where it was reported as overexpressed. However, the molecular functions, biological processes and underlying mechanisms through which JTB protein causes increased cell growth, proliferation and invasion is still not fully deciphered. Our goal is to identify the functions of JTB protein by cellular proteomics approaches. MCF7 breast cancer cells were transfected with sense orientation of hJTB cDNA in HA, His and FLAG tagged CMV expression vector to overexpress hJTB and the expression levels were confirmed by Western blotting (WB). Proteins extracted from transfected cells were separated by SDS-PAGE and the in-gel digested peptides were analyzed by nano-liquid chromatography tandem mass spectrometry (nanoLC-MS/MS). By comparing the proteome of cells with upregulated conditions of JTB vs control and identifying the protein dysregulation patterns, we aim to understand the function of this protein and its contribution to tumorigenesis. Gene Set Enrichment Analysis (GSEA) algorithm was performed to investigate the biological processes and pathways that are associated with the JTB protein upregulation. The results demonstrated four significantly enriched gene sets from the following significantly upregulated pathways: mitotic spindle assembly, estrogen response late, epithelial-to-mesenchymal transition (EMT) and estrogen response early. JTB protein itself is involved in mitotic spindle pathway by its role in cell division/cytokinesis, and within estrogen response early and late pathways, contributing to discrimination between luminal and mesenchymal breast cancer. Thus, the overexpressed JTB condition was significantly associated with an increased expression of ACTNs, FLNA, FLNB, EZR, MYOF, COL3A1, COL11A1, HSPA1A, HSP90A, WDR, EPPK1, FASN and FOXA1 proteins related to deregulation of cytoskeletal organization and biogenesis, mitotic spindle organization, ECM remodeling, cellular response to estrogen, proliferation, migration, metastasis, increased lipid biogenesis, endocrine therapy resistance, antiapoptosis and discrimination between different breast cancer subtypes. Other upregulated proteins for overexpressed JTB condition are involved in multiple cellular functions and pathways that become dysregulated, such as tumor microenvironment (TME) acidification, the transmembrane transport pathways, glycolytic flux, iron metabolism and oxidative stress, metabolic reprogramming, nucleocytosolic mRNA transport, transcriptional activation, chromatin remodeling, modulation of cell death pathways, stress responsive pathways, and cancer drug resistance. The downregulated proteins for overexpressed JTB condition are involved in adaptive communication between external and internal environment of cells and maintenance between pro-apoptotic and anti-apoptotic signaling pathways, vesicle trafficking and secretion, DNA lesions repair and suppression of genes involved in tumor progression, proteostasis, redox state regulation, biosynthesis of macromolecules, lipolytic pathway, carbohydrate metabolism, dysregulation of ubiquitin-mediated degradation system, cancer cell immune escape, cell-to-cell and cell-to-ECM interactions, and cytoskeletal behaviour. There were no significantly enriched downregulated pathways.

ATP5A1 Participates in Transcriptional and Posttranscriptional Regulation of Cancer-Associated Genes by Modulating Their Expression and Alternative Splicing Profiles in HeLa Cells

Background: Aberrant expression and alternative splicing of oncogenes are the driving events in tumor initiation and development. But how these events are regulated in cancer cells is largely unknown. Functions of ATP5A1, an important mitochondrial ATP synthase gene, in transcriptional and posttranscriptional regulation were explored in this study. Methods: ATP5A1 was overexpressed using plasmid-transformed HeLa cells, and its influence on cell apoptosis and proliferation is evaluated. Transcriptome sequencing was then performed using RNA-seq to study the changes in gene expression and regulation of alternative splicing events. Validation of the implicated genes was achieved using RT-qPCR analysis. Results: It was found that ATP5A1 could significantly promote cellular apoptosis, but it had no influence on cell proliferation. ATP5A1 overexpression significantly increased the expression levels of genes associated with the innate immune response, angiogenesis, and collagen catabolic processes. This included enrichment of MMP2 and MMP19. It was also found that ATP5A1 could interfere with the alternative splicing of hundreds of genes associated with glucose homeostasis, HIF-1 signaling activation, and several pathways associated with cancers. Eight ATP5A1-regulated differentially expressed genes and 3 genes altered by splicing were selected and validated using RT-qPCR analysis. Conclusions: In summary, we illustrate the regulatory functions of ATP5A1 on the transcriptome of HeLa cells by exploring its influence on gene expression and alternative splicing. The results suggest that ATP5A1 may play an important regulatory role in cervical cancer cells by regulating expression and alternative splicing of cancer-associated genes. This study provides novel insights into the current understanding of the mechanisms of ATP5A1 on carcinogenesis and cancer progression.