Post-transcriptional gene regulation by RNA-binding proteins in vascular endothelial dysfunction

RNA-Binding Proteins Regulate Post-Transcriptional Responses to TGF-β to Coordinate Function and Mesenchymal Activation of Murine Endothelial Cells

BACKGROUND

Endothelial cells (ECs) are primed to respond to various signaling cues. For example, TGF (transforming growth factor)-β has major effects on EC function and phenotype by driving ECs towards a more mesenchymal state (ie, triggering endothelial to mesenchymal activation), a dynamic process associated with cardiovascular diseases. Although transcriptional regulation triggered by TGF-β in ECs is well characterized, post-transcriptional regulatory mechanisms induced by TGF-β remain largely unknown.

METHODS

Using RNA interactome capture, we identified global TGF-β driven changes in RNA-binding proteins in ECs. We investigated specific changes in the RNA-binding patterns of hnRNP H1 (heterogeneous nuclear ribonucleoprotein H1) and Csde1 (cold shock domain containing E1) using RNA immunoprecipitation and overlapped this with RNA-sequencing data after knockdown of either protein for functional insight. Using a modified proximity ligation assay, we visualized the specific interactions between hnRNP H1 and Csde1 and target RNAs in situ both in vitro and in mouse heart sections.

RESULTS

Characterization of TGF-β-regulated RBPs (RNA-binding proteins) revealed hnRNP H1 and Csde1 as key regulators of the cellular response to TGF-β at the post-transcriptional level, with loss of either protein-promoting mesenchymal activation in ECs. We found that TGF-β drives an increase in binding of hnRNP H1 to its target RNAs, offsetting mesenchymal activation, but a decrease in Csde1 RNA-binding, facilitating this process. Both, hnRNP H1 and Csde1, dynamically bind and regulate specific subsets of mRNAs related to mesenchymal activation and endothelial function.

CONCLUSIONS

Together, we show that RBPs play a key role in the endothelial response to TGF-β stimulation at the post-transcriptional level and that the RBPs hnRNP H1 and Csde1 serve to maintain EC function and counteract mesenchymal activation. We propose that TGF-β profoundly modifies RNA-protein interaction entailing feedback and feed-forward control at the post-transcriptional level, to fine-tune mesenchymal activation in ECs.

DeepMC-iNABP: Deep learning for multiclass identification and classification of nucleic acid-binding proteins

Nucleic acid-binding proteins (NABPs), including DNA-binding proteins (DBPs) and RNA-binding proteins (RBPs), play vital roles in gene expression. Accurate identification of these proteins is crucial. However, there are two existing challenges: one is the problem of ignoring DNA- and RNA-binding proteins (DRBPs), and the other is a cross-predicting problem referring to DBP predictors predicting DBPs as RBPs, and vice versa. In this study, we proposed a computational predictor, called DeepMC-iNABP, with the goal of solving these difficulties by utilizing a multiclass classification strategy and deep learning approaches. DBPs, RBPs, DRBPs and non-NABPs as separate classes of data were used for training the DeepMC-iNABP model. The results on test data collected in this study and two independent test datasets showed that DeepMC-iNABP has a strong advantage in identifying the DRBPs and has the ability to alleviate the cross-prediction problem to a certain extent. The web-server of DeepMC-iNABP is freely available at http://www.deepmc-inabp.net/. The datasets used in this research can also be downloaded from the website.

Competitive endogenous network of lncRNA, miRNA, and mRNA in the chemoresistance of gastrointestinal tract adenocarcinomas

Chemotherapy is one of the main therapeutic strategies used for gastrointestinal tract adenocarcinomas (GTAs), but resistance to anticancer drugs is a substantial obstacle in successful chemotherapy. Accumulating evidence shows that non-coding RNAs, especially long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), can affect the drug resistance of tumor cells by forming a ceRNA regulatory network with mRNAs. The efficiency of the competing endogenous RNAs (ceRNAs) network can be affected by the number and integrality of miRNA recognition elements (MREs). Dynamic factors such as RNA editing, alternative splicing, single nucleotide polymorphism (SNP), RNA-binding proteins and RNA secondary structure can influence the MRE activity, which may in turn be involved in the regulation of chemoresistance-associated ceRNA network by prospective approaches. Besides activities in a single tumor cell, the components of the tumor micoenvironment (TME) also affect the ceRNA network by regulating the expression of non-coding RNA directly or indirectly. The alternation of the ceRNA network often has an impact on the malignant phenotype of tumor including chemoresistance. In this review, we focused on how MRE-associated dynamic factors and components of TME affected the ceRNA network and speculated the potential association of ceRNA network with chemoresistance. We also summarized the ceRNA network of lncRNAs, miRNAs, and mRNAs which efficiently triggers chemoresistance in the specific types of GTAs and analyzed the role of each RNA as a "promoter" or "suppressor" of chemoresistance.

Parallel multiphase nanofluidics utilizing nanochannels with partial hydrophobic surface modification and application to femtoliter solvent extraction

In the field of microfluidics, utilizing parallel multiphase flows with immiscible liquid/liquid or gas/liquid interfaces along a microchannel has achieved the integration of various chemical processes for analyses and syntheses. Recently, our group has developed nanofluidics that exploits 100 nm nanochannels to realize ultra-small (aL to fL scale) and highly efficient chemical operations. Novel applications such as single-molecule analyses and single-cell omics are anticipated. However, the formation of parallel multiphase flows in a nanochannel remains challenging. To this end, here we developed a novel method for nanoscale partial hydrophobic surface modification of a nanochannel utilizing a focused ion beam. Hydrophobic and hydrophilic areas could be patterned beside one another even in a 60 nm glass nanochannel. Because this patterning maintained the liquid/liquid interface in the nanochannel based on the difference in wettability, stable aqueous/organic parallel two-phase flow in a 40 fL nanochannel was realized for the first time. Utilizing this flow, nanoscale unit operations involving phase confluence, extraction and phase separation were integrated to demonstrate solvent extraction of a lipid according to the Bligh-Dyer method, which is a broadly used pretreatment process in lipidomics. We accomplished the separation of a lipid and an amino acid in a sample volume of 4 fL (250 times smaller than the pL volume of a single cell) with a processing time of 1 ms (10 000 times faster than that in a microchannel). This study therefore provides a technological breakthrough that advances the field of nanofluidics to allow multiphase chemical processing at fL volumes.

Wettability and Applications of Nanochannels

Wettability in nanochannels is of great importance for understanding many challenging problems in interface chemistry and fluid mechanics, and presents versatile applications including mass transport, catalysis, chemical reaction, nanofabrication, batteries, and separation. Recently, both molecular dynamic simulations and experimental measurements have been employed to study wettability in nanochannels. Here, wettability in three types of nanochannels comprising 1D nanochannels, 2D nanochannels, and 3D nanochannels is summarized both theoretically and experimentally. The proposed concept of "quantum-confined superfluid" for ultrafast mass transport in nanochannels is first introduced, and the mostly studied 1D nanochannels are reviewed from molecular simulation to water wettability, followed by reversible switching of water wettability via external stimuli (temperature and voltage). Liquid transport and two confinement strategies in nanochannels of melt wetting and liquid wetting are also included. Then, molecular simulation, water wettability, liquid transport, and confinement in nanochannels are introduced for 2D nanochannels and 3D nanochannels, respectively. Based on the wettability in nanochannels, broad applications of various nanochannels are presented. Finally, the perspective for future challenges in the wettability and applications of nanochannels is discussed.

RBPs Play Important Roles in Vascular Endothelial Dysfunction Under Diabetic Conditions

Diabetes is one of the major health care problems worldwide leading to huge suffering and burden to patients and society. Diabetes is also considered as a cardiovascular disorder because of the correlation between diabetes and an increased incidence of cardiovascular disease. Vascular endothelial cell dysfunction is a major mediator of diabetic vascular complications. It has been established that diabetes contributes to significant alteration of the gene expression profile of vascular endothelial cells. Post-transcriptional regulation by RNA binding proteins (RBPs) plays an important role in the alteration of gene expression profile under diabetic conditions. The review focuses on the roles and mechanisms of critical RBPs toward diabetic vascular endothelial dysfunction. Deeper understanding of the post- transcriptional regulation by RBPs could lead to new therapeutic strategies against diabetic manifestation in the future.

FMRP regulates endothelial cell proliferation and angiogenesis via the miR-181a-CaM-CaMKII pathway

RNA binding proteins (RBPs) and microRNAs have emerged as crucial post-transcriptional regulators of gene expression. Although the role of Fragile X mental retardation protein (FMRP) has been well studied in the brain, the function of FMRP in endothelial cells remains unknown. In our study, we showed that FMRP controlled human umbilical vein endothelial cells (HUVECs) proliferation and angiogenesis via the miR-181a-mediated calmodulin (CaM)/CaMKII pathway. The knockdown of FMRP induced miR-181a expression and contributed to endothelial cell proliferation and angiogenesis. Furthermore, we identified CaM as a downstream target of miR-181a in endothelial cells. Additionally, tumor necrosis factor-ɑ (TNF-ɑ) treatment specifically decreased the activity of the CaM/CaMKII pathway through the dephosphorylation of FMRP and upregulation of miR-181a. Finally, the overexpression of constitutively phosphorylated FMRP rescued the TNF-ɑ-impaired endothelial cell proliferation and angiogenesis by activating the CaM/CaMKII pathway and downregulating miR-181a, which suggested there was a pivotal role of FMRP in vascular integrity in response to inflammatory stimuli. Thus, our study supports a novel function and mechanism involving FMRP and the miR-181a-CaM-CaMKII pathway may be a therapeutic target for protecting against inflammation-induced vascular diseases.

Emerging roles of RNA-binding proteins in diabetes and their therapeutic potential in diabetic complications

Diabetes is a debilitating health care problem affecting 422 million people around the world. Diabetic patients suffer from multisystemic complications that can cause mortality and morbidity. Recent advancements in high-throughput next-generation RNA-sequencing and computational algorithms led to the discovery of aberrant posttranscriptional gene regulatory programs in diabetes. However, very little is known about how these regulatory programs are mis-regulated in diabetes. RNA-binding proteins (RBPs) are important regulators of posttranscriptional RNA networks, which are also dysregulated in diabetes. Human genetic studies provide new evidence that polymorphisms and mutations in RBPs are linked to diabetes. Therefore, we will discuss the emerging roles of RBPs in abnormal posttranscriptional gene expression in diabetes. Questions that will be addressed are: Which posttranscriptional mechanisms are disrupted in diabetes? Which RBPs are responsible for such changes under diabetic conditions? How are RBPs altered in diabetes? How does dysregulation of RBPs contribute to diabetes? Can we target RBPs using RNA-based methods to restore gene expression profiles in diabetic patients? Studying the evolving roles of RBPs in diabetes is critical not only for a comprehensive understanding of diabetes pathogenesis but also to design RNA-based therapeutic approaches for diabetic complications. WIREs RNA 2018, 9:e1459. doi: 10.1002/wrna.1459 This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing Translation > Translation Regulation.

Increased cell apoptosis in human lung adenocarcinoma and in vivo tumor growth inhibition by RBM10, a tumor suppressor gene

Tumor suppressor genes are frequently deleted or mutated in lung cancer. The RNA-binding motif protein 10 (RBM10) gene has the ability to suppress tumor activity, but the role of RBM10 during the development of lung cancer has yet to be elucidated. The current study investigated the expression levels of RBM10 in non-tumor and tumor tissues obtained from patients with adenocarcinoma using reverse transcription-polymerase chain reaction and western blot analysis, and identified a reduction in RBM10 expression in lung tumor tissue. To investigate the in vitro and in vivo function of RBM10, A549 human non-small cell lung cancer cells were transfected with the pcDNA-RBM10 vector. Flow cytometry was used to analyze the levels of apoptosis in the transfected cells. Western blot analysis was used to evaluate the expression of B-cell lymphoma 2 (Bcl-2), cleaved caspase-3, caspase-9 and poly (ADP-ribose) polymerase (PARP) proteins in A549 cells and tissues from the A549 xenograft Bagg Albino coat (BALB/c) nude mice model. RBM10 mRNA levels were significantly decreased in adenocarcinoma cells, but not in the non-tumor tissues. The A549 cells and tumor tissues exhibited significant growth inhibition following transfection with the pcDNA-RBM10 vector, which was determined using a cell proliferation assay. Flow cytometry analysis of cells stained with Annexin V/propidium iodide indicated that the overexpression of RBM10 induced apoptosis in A549 cells. The present study demonstrated that the expression levels of Bcl-2 protein were decreased and the expression levels of cleaved caspase-3, caspase-9 and PARP proteins were significantly increased in the A549 cells and cells from ex vivo tumor tissues that were injected with RBM10 vector-containing Salmonella enterica subspecies enterica serovar typhimurium. Notably, the current study identified that the accumulated and stable overexpression of RBM10 in the xenograft BALB/c nude mice model significantly inhibited the tumor growth rate. These results may provide novel insights into the use of RBM10 for lung cancer diagnosis and therapy.

Lepidotol A from Mesua lepidota Inhibits Inflammatory and Immune Mediators in Human Endothelial Cells

Phytochemical investigation on the fruits of Mesua lepidota (Calophyllaceae) led to the isolation of seven new phenylcoumarin derivatives named lepidotols A-E (1-5) and lepidotins A and B (6, 7). These structures were elucidated by spectroscopic and spectrometric methods including UV, NMR, and HRMS. Lepidotol A (1), the major compound, was evaluated for its inhibitory effect on inflammation and immunity using endothelial cell-based cellular assays. At 10 μM, 1 exhibited an anti-inflammatory activity, with a significant inhibition of vascular cell adhesion molecule 1 and intercellular adhesion molecule 1 expression induced by tumor necrosis factor-α. Lepidotol A also showed a mild immunosuppressive effect, with inhibition of the major histocompatibility complex molecules, namely, human leukocyte antigen (HLA)-DR and HLA-E.

Anomalous effects of water flow through charged nanochannel membranes

Anomalous osmosis may be observed in a suitable concentration range when the directions of concentration diffusion and induced electroosmosis are opposite.