Differential downregulation of Rbm5 and Rbm10 during skeletal and cardiac differentiation

RNA binding protein with multiple splicing (RBPMS) promotes contractile phenotype splicing in human embryonic stem cell-derived vascular smooth muscle cells

AIMS

Differentiated vascular smooth muscle cells (VSMCs) express a unique network of mRNA isoforms via smooth muscle-specific alternative pre-mRNA splicing (SM-AS) in functionally critical genes, including those comprising the contractile machinery. We previously described RNA Binding Protein with Multiple Splicing (RBPMS) as a potent driver of differentiated SM-AS in the rat PAC1 VSMC cell line. What is unknown is how RBPMS affects VSMC phenotype and behaviour. Here, we aimed to dissect the role of RBPMS in SM-AS in human cells and determine the impact on VSMC phenotypic properties.

METHODS AND RESULTS

We used human embryonic stem cell-derived VSMCs (hESC-VSMCs) as our platform. hESC-VSMCs are inherently immature, and we found that they display only partially differentiated SM-AS patterns while RBPMS protein levels are low. We found that RBPMS over-expression induces SM-AS patterns in hESC-VSMCs akin to the contractile tissue VSMC splicing patterns. We present in silico and experimental findings that support RBPMS' splicing activity as mediated through direct binding and via functional cooperativity with splicing factor RBFOX2 on a significant subset of targets. We also demonstrate that RBPMS can alter the motility and the proliferative properties of hESC-VSMCs to mimic a more differentiated state.

CONCLUSION

Overall, this study emphasizes a critical role for RBPMS in establishing the contractile phenotype splicing programme of human VSMCs.

NPTX1 inhibits pancreatic cancer cell proliferation and migration and enhances chemotherapy sensitivity by targeting RBM10

Pancreatic cancer (PC), one of the deadliest diseases worldwide, has exhibited an increasing incidence rate in recent years. The present study aimed to explore the biological mechanism of PC. Therefore, the expression levels of neuronal pentraxin 1 (NPTX1) and RNA-binding protein 10 (RBM10) were detected in PC cell lines using reverse transcription-quantitative PCR (RT-qPCR) and western blot analyses prior to or following NPTX1 and RBM10 overexpression. Additionally, the proliferative ability of PANC-1 and BxPC-3 cells treated with or without gemcitabine (GEM) and cisplatin (DDP) was evaluated using Cell Counting Kit-8 assay. Cell apoptosis and the expression levels of apoptosis-related proteins were determined by TUNEL assay and western blot analysis, respectively. Furthermore, wound healing and Transwell assays were performed to measure the migration and invasion abilities of PANC-1 and BxPC-3 cells. The interaction between RBM10 and NPTX1 mRNA was detected by RNA binding protein immunoprecipitation (RIP) assay. Additionally, cells were treated with actinomycin D to verify the regulatory effect of RBM10 on NPTX1 expression. This effect was further confirmed by RT-qPCR analysis. The results showed that NPTX1 was downregulated in PC cell lines. In addition, NPTX1 overexpression inhibited the proliferation and promoted apoptosis in PC cells. The results from the wound healing and Transwell assays revealed that the migration and invasion abilities of PANC-1 and BxPC-3 cells were reduced following NPTX1 overexpression. However, treatment of NPTX1-overexpressing cells with GEM or DDP attenuated PC cell viability. In addition, the results of the RIP assay revealed that RBM10 could bind with NPTX1. Furthermore, RBM10 overexpression could regulate NPTX1 expression, as evidenced by actinomycin D experiments. Overall, the results of the present study suggested that NPTX1 could inhibit PC and enhance the sensitivity of PC cells to chemotherapy. Additionally, NPTX1 was found to interact with RBM10, indicating that NPTX1 could inhibit PC via targeting RBM10.

In heart failure reactivation of RNA-binding proteins is associated with the expression of 1,523 fetal-specific isoforms

Reactivation of fetal-specific genes and isoforms occurs during heart failure. However, the underlying molecular mechanisms and the extent to which the fetal program switch occurs remains unclear. Limitations hindering transcriptome-wide analyses of alternative splicing differences (i.e. isoform switching) in cardiovascular system (CVS) tissues between fetal, healthy adult and heart failure have included both cellular heterogeneity across bulk RNA-seq samples and limited availability of fetal tissue for research. To overcome these limitations, we have deconvoluted the cellular compositions of 996 RNA-seq samples representing heart failure, healthy adult (heart and arteria), and fetal-like (iPSC-derived cardiovascular progenitor cells) CVS tissues. Comparison of the expression profiles revealed that reactivation of fetal-specific RNA-binding proteins (RBPs), and the accompanied re-expression of 1,523 fetal-specific isoforms, contribute to the transcriptome differences between heart failure and healthy adult heart. Of note, isoforms for 20 different RBPs were among those that reverted in heart failure to the fetal-like expression pattern. We determined that, compared with adult-specific isoforms, fetal-specific isoforms encode proteins that tend to have more functions, are more likely to harbor RBP binding sites, have canonical sequences at their splice sites, and contain typical upstream polypyrimidine tracts. Our study suggests that compared with healthy adult, fetal cardiac tissue requires stricter transcriptional regulation, and that during heart failure reversion to this stricter transcriptional regulation occurs. Furthermore, we provide a resource of cardiac developmental stage-specific and heart failure-associated genes and isoforms, which are largely unexplored and can be exploited to investigate novel therapeutics for heart failure.

Heart failure is a chronic condition in which the heart does not pump enough blood. It has been shown that in heart failure, the adult heart reverts to a fetal-like metabolic state and oxygen consumption. Additionally, genes and isoforms that are expressed in the heart only during fetal development (i.e. not in the healthy adult heart) are turned on in heart failure. However, the underlying molecular mechanisms and the extent to which the switch to a fetal gene program occurs remains unclear. In this study, we initially characterized the differences between the fetal and adult heart transcriptomes (entire set of expressed genes and isoforms). We found that RNA binding proteins (RBPs), a family of genes that regulate multiple aspects of a transcript’s maturation, including transcription, splicing and post-transcriptional modifications, play a central role in the differences between fetal and adult heart tissues. We observed that many RBPs that are only expressed in the heart during fetal development become reactivated in heart failure, resulting in the expression of 1,523 fetal-specific isoforms. These findings suggest that reactivation of fetal-specific RBPs in heart failure drives a transcriptome-wide switch to expression of fetal-specific isoforms; and hence that RBPs could potentially serve as novel therapeutic targets.

TARP syndrome associated with renal malformation and optic nerve atrophy

Talipes equinovarus, atrial septal defect, Robin sequence and persistent left superior vena cava (TARP) syndrome is a congenital disease caused by mutations in the RBBM10 gene. It has a low prevalence and a high rate of mortality in the neonatal stage. In this case report, we present a case of a 32-week gestational age preterm newborn with a prenatal diagnosis of intrauterine growth restriction, with a persistent left superior vena cava, interatrial communication and a horseshoe kidney. Additionally, postnatal optic nerve atrophy was diagnosed. By using exome sequencing, the pathogenic variant c.1877del; p.his626Lefus*78 was identified in the RMB10 gene. Due to a lack of reports in the medical literature, the phenotype has not fully been described. Here, we report on a patient with TARP syndrome and a previously unreported mutation, c.1877del; p.his627Leufs*78, which is predicted to generate a truncated and/or protein decay of the RBM10 transcript.

Mechanism of autophagy regulating chemoresistance in esophageal cancer cells

The current study aimed to explore the mechanism of autophagy-regulating chemoresistance in esophageal cancer (EC) cells. Methods: 45 cases of esophageal cancer cell tissue and 25 cases of adjacent normal tissue excised in the surgical resection were collected from the tumor pathology department of our hospital from March to November 2017. The above cancer cells and paracancerous cells were cultured according to the cell culture procedures. The autophagy was induced by cisplatin in human esophageal cancer EC9706 cells line. The effect of autophagy on the survival of EC9706 cells was observed by autophagy inhibitor 3-MA. Cell viability was also measured by cell counting kit-8 (CCK-8). Apoptosis and cell cycle were detected by flow cytometry. Furthermore, monodansylcadaverine (MDC) was used to detect autophagy. Western blot was applied to determine the molecular changes during treatment. Diketopyrrolopyrrole (DPP) is able to inhibit cell proliferation, induce cell death and cell cycle arrest in the S phase. In addition, autophagy was activated through PI3K-III pathway. Results: 3-MA inhibitor plus 10% fetal bovine serum were added for culture, and the cell culture temperature and humidity were the best conditions. There were few autophagic vesicles in the stationary cells, where their brightness was weakened. There were more and brighter green fluorescent particles in the DPP group without a 3-MA inhibitor, indicating that autophagic parameters actually exist in this process. The apoptosis rate of DDP-induced cell death was not found to be the best, but was higher than that of the control group (P<0.05). The combination of DDP and 3-MA had a more obvious catalytic effect on apoptosis, and the apoptosis rate was much higher than that of single DDP (P<0.05), indicating that DDP was capable of inducing significant apoptosis after inhibiting autophagy. The combination of DDP and 3-MA had an obvious catalytic effect on apoptosis, and the apoptosis rate was higher than that of DDP alone (P < 0.05), suggesting that DDP could significantly improve the ability to induce apoptosis after inhibiting autophagy. The expression level of autophagy-related proteins was also detected by Western blotting. Our findings indicated that autophagy may be a self-protective mechanism of esophageal cancer cells induced by DDP, and its inhibition may be a new strategy for adjuvant chemotherapy in esophageal cancer.

mRNA Metabolism in Cardiac Development and Disease: Life After Transcription

The central dogma of molecular biology illustrates the importance of mRNAs as critical mediators between genetic information encoded at the DNA level and proteomes/metabolomes that determine the diverse functional outcome at the cellular and organ levels. Although the total number of protein-producing (coding) genes in the mammalian genome is ~20,000, it is evident that the intricate processes of cardiac development and the highly regulated physiological regulation in the normal heart, as well as the complex manifestation of pathological remodeling in a diseased heart, would require a much higher degree of complexity at the transcriptome level and beyond. Indeed, in addition to an extensive regulatory scheme implemented at the level of transcription, the complexity of transcript processing following transcription is dramatically increased. RNA processing includes post-transcriptional modification, alternative splicing, editing and transportation, ribosomal loading, and degradation. While transcriptional control of cardiac genes has been a major focus of investigation in recent decades, a great deal of progress has recently been made in our understanding of how post-transcriptional regulation of mRNA contributes to transcriptome complexity. In this review, we highlight some of the key molecular processes and major players in RNA maturation and post-transcriptional regulation. In addition, we provide an update to the recent progress made in the discovery of RNA processing regulators implicated in cardiac development and disease. While post-transcriptional modulation is a complex and challenging problem to study, recent technological advancements are paving the way for a new era of exciting discoveries and potential clinical translation in the context of cardiac biology and heart disease.

Functional role of RBM10 in lung adenocarcinoma proliferation

Lung cancer is one of the most common causes of morbidity and mortality among malignant tumors worldwide. The poor prognosis of patients with lung adenocarcinomas is primarily due to its strong ability to invade and metastasize. Recent research has indicated that RNA‑binding protein 10 (RBM10) is mutated in lung adenocarcinoma, and is closely associated with tumor proliferation and apoptosis; however, the precise role of RBM10 in lung adenocarcinoma remains unclear. Our preliminary experiments (unpublished data) revealed that RBM10 expression was upregulated in lung adenocarcinoma cell lines and tissues. In this study, we first detected the protein expression level of RBM10 in lung adenocarcinoma cells and tissues, and we then examined the effects of RBM10 overexpression and downregulation (via small interfering RNA) on the proliferation and apoptosis of stable lung adenocarcinoma cells, along with its possible mechanisms of action. We also used clinical samples of lung adenocarcinomas to verify our results. We found that RBM10 protein was overexpressed in lung adenocarcinoma cells and tissues, and it reduced p53 expression (as detected by immunofluorescence assay and western blot analysis) in A549 cells and inhibited apoptosis (as shown by flow cytometric assay). RBM10 also promoted cell growth and proliferation in vitro and increased cell migration in a cell wound scratch assay. Furthermore, we found that RBM10 activated key proliferative signaling pathways [such as the epidermal growth factor receptor (EGFR), mitogen‑activated protein kinase (MAPK) and phosphoinositide 3‑kinase (PI3K)‑AKT pathways] and inhibited apoptotic pathways. In addition, we demonstrated that a high expression of RBM10 protein in patient tissue samples was associated with a shorter overall survival time and a poor prognosis. On the whole, the findings of this study indicate that RBM10 may function as an oncogene in lung cancer, and may thus prove to be a novel therapeutic target for the prophylaxis and treatment of lung adenocarcinomas.

Role of RNA-binding protein 5 in the diagnosis and chemotherapeutic response of lung cancer

Lung cancer remains one of the leading causes of cancer-associated mortality in the world. Lung carcinogenesis is frequently associated with deletions or the loss of heterozygosity at the critical chromosomal region 3p21.3, where RNA-binding protein 5 (RBM5) is localized. RBM5 regulates cell growth, cell cycle progression and apoptosis in cell homeostasis. In the lungs, altered RBM5 protein expression leads to alterations in cell growth and apoptosis, with subsequent lung pathogenesis and varied responses to treatment in patients with lung cancer. Detection of RBM5 expression may be a tumor marker for diagnosis, prediction and treatment response in lung cancer, and may be developed as a potential therapeutic target for drug resistant lung cancer. This review discusses the most recent progress on the role of RBM5 in lung cancer.

Splicing Site Recognition by Synergy of Three Domains in Splicing Factor RBM10

Splicing factor RBM10 and its close homologues RBM5 and RBM6 govern the splicing of oncogenes such as Fas, NUMB, and Bcl-X. The molecular architecture of these proteins includes zinc fingers (ZnFs) and RNA recognition motifs (RRMs). Three of these domains in RBM10 that constitute the RNA binding part of this splicing factor were found to individually bind RNAs with micromolar affinities. It was thus of interest to further investigate the structural basis of the well-documented high-affinity RNA recognition by RMB10. Here, we investigated RNA binding by combinations of two or three of these domains and discovered that a polypeptide containing RRM1, ZnF1, and RRM2 connected by their natural linkers recognizes a specific sequence of the Fas exon 6 mRNA with an affinity of 20 nM. Nuclear magnetic resonance structures of the RBM10 domains RRM1 and ZnF1 and the natural V354del isoform of RRM2 further confirmed that the interactions with RNA are driven by canonical RNA recognition elements. The well-known high-fidelity RNA splice site recognition by RBM10, and probably by RBM5 and RBM6, can thus be largely rationalized by a cooperative binding action of RRM and ZnF domains.

RBM10: Harmful or helpful-many factors to consider

RBM10 is an RNA binding motif (RBM) protein expressed in most, if not all, human and animal cells. Interest in RBM10 is rapidly increasing and its clinical importance is highlighted by its identification as the causative agent of TARP syndrome, a developmental condition that significantly impacts affected children. RBM10's cellular functions are beginning to be explored, with initial studies demonstrating a tumor suppressor role. Very recently, however, contradictory results have emerged, suggesting a tumor promoter role for RBM10. In this review, we describe the current state of knowledge on RBM10, and address this dichotomy in RBM10 function. Furthermore, we discuss what may be regulating RBM10 function, particularly the importance of RBM10 alternative splicing, and the relationship between RBM10 and its paralogue, RBM5. As RBM10‐related work is gaining momentum, it is critical that the various aspects of RBM10 molecular biology revealed by recent studies be considered moving forward. It is only if these recent advances in RBM10 structure and function are considered that a clearer insight into RBM10 function, and the disease states with which RBM10 mutation is associated, will be gained.

RBM5 reduces small cell lung cancer growth, increases cisplatin sensitivity and regulates key transformation-associated pathways

Small cell lung cancer (SCLC) is the most aggressive type of lung cancer, with almost 95% of patients succumbing to the disease. Although RBM5, a tumor suppressor gene, is downregulated in the majority of lung cancers, its role in SCLC is unknown. Using the GLC20 SCLC cell line, which has a homozygous deletion encompassing the RBM5 gene locus, we established stable RBM5 expressing sublines and investigated the effects of RBM5 re-expression. Transcriptome and target identification studies determined that RBM5 directly regulates the cell cycle and apoptosis in SCLC cells, as well as significantly downregulates other important transformation-associated pathways such as angiogenesis and cell adhesion. RNA sequencing of paired non-tumor and tumor SCLC patient specimens showed decreased RBM5 expression in the tumors, and expression alterations in the majority of the same pathways that were altered in the GLC20 cells and sublines. Functional studies confirmed RBM5 expression slows SCLC cell line growth, and increases sensitivity to the chemotherapy drug cisplatin. Overall, our work demonstrates the importance of RBM5 expression to the non-transformed state of lung cells and the consequences of its deletion to SCLC development and progression.

New Insights Into the Role of RNA-Binding Proteins in the Regulation of Heart Development

The regulation of gene expression during development takes place both at the transcriptional and posttranscriptional levels. RNA-binding proteins (RBPs) regulate pre-mRNA processing, mRNA localization, stability, and translation. Many RBPs are expressed in the heart and have been implicated in heart development, function, or disease. This chapter will review the current knowledge about RBPs in the developing heart, focusing on those that regulate posttranscriptional gene expression. The involvement of RBPs at each stage of heart development will be considered in turn, including the establishment of specific cardiac cell types and formation of the primitive heart tube, cardiac morphogenesis, and postnatal maturation and aging. The contributions of RBPs to cardiac birth defects and heart disease will also be considered in these contexts. Finally, the interplay between RBPs and other regulatory factors in the developing heart, such as transcription factors and miRNAs, will be discussed.

Co- and post-transcriptional regulation of Rbm5 and Rbm10 in mouse cells as evidenced by tissue-specific, developmental and disease-associated variation of splice variant and protein expression levels

BACKGROUND

Expression and function of the two RNA binding proteins and regulators of alternative splicing, RBM5 and RBM10, have largely been studied in human tissue and cell lines. The objective of the study described herein was to examine their expression in mouse tissue, in order to lay the framework for comprehensive functional studies using mouse models.

METHODS

All RNA variants of Rbm5 and Rbm10 were examined in a range of normal primary mouse tissues. RNA and protein were examined in differentiating C2C12 myoblasts and in denervated and dystonin-deficient mouse skeletal muscle.

RESULTS

All Rbm5 and Rbm10 variants examined were expressed in all mouse tissues and cell lines. In general, Rbm5 and Rbm10 RNA expression was higher in brain than in skin. RNA expression levels were more varied between cardiac and skeletal muscle, depending on the splice variant: for instance, Rbm10v1 RNA was higher in skeletal than cardiac muscle, whereas Rbm10v3 RNA was higher in cardiac than skeletal muscle. In mouse brain, cardiac and skeletal muscle, RNA encoding an approximately 17kDa potential paralogue of a small human RBM10 isoform was detected, and the protein observed in myoblasts and myotubes. Expression of Rbm5 and Rbm10 RNA remained constant during C2C12 myogenesis, but protein levels significantly decreased. In two muscle disease models, neither Rbm10 nor Rbm5 showed significant transcriptional changes, although significant specific alternative splicing changes of Rbm5 pre-mRNA were observed. Increased RBM10 protein levels were observed following denervation.

CONCLUSIONS

The varied co-transcriptional and post-transcriptional regulation aspects of Rbm5 and Rbm10 expression associated with mouse tissues, myogenesis and muscle disease states suggest that a mouse model would be an interesting and useful model in which to study comprehensive functional aspects of RBM5 and RBM10.

Nuclear Magnetic Resonance Structure of a Novel Globular Domain in RBM10 Containing OCRE, the Octamer Repeat Sequence Motif

The OCtamer REpeat (OCRE) has been annotated as a 42-residue sequence motif with 12 tyrosine residues in the spliceosome trans-regulatory elements RBM5 and RBM10 (RBM [RNA-binding motif]), which are known to regulate alternative splicing of Fas and Bcl-x pre-mRNA transcripts. Nuclear magnetic resonance structure determination showed that the RBM10 OCRE sequence motif is part of a 55-residue globular domain containing 16 aromatic amino acids, which consists of an anti-parallel arrangement of six β strands, with the first five strands containing complete or incomplete Tyr triplets. This OCRE globular domain is a distinctive component of RBM10 and is more widely conserved in RBM10s across the animal kingdom than the ubiquitous RNA recognition components. It is also found in the functionally related RBM5. Thus, it appears that the three-dimensional structure of the globular OCRE domain, rather than the 42-residue OCRE sequence motif alone, confers specificity on RBM10 intermolecular interactions in the spliceosome.

Post-transcriptional regulation of Rbm5 expression in undifferentiated H9c2 myoblasts

We previously examined the expression of Rbm5 during myoblast differentiation and found significantly more protein in the early stages of skeletal myoblast differentiation than during the later stages. We decided to determine if this elevated level was necessary for differentiation. Our hypothesis was that if high levels of Rbm5 protein expression were necessary for the initiation of skeletal myoblast differentiation, then inhibition of expression would prevent differentiation. Our long-term objective is to inhibit Rbm5 expression and examine the effect on H9c2 differentiation. Towards this end, stable knockdown clones and transient knockdown populations were generated. Expression analyses in H9c2 myoblasts demonstrated significant Rbm5 messenger RNA (mRNA) inhibition but, surprisingly, no effect on RBM5 protein levels. Expression of the Rbm5 paralogue Rbm10 was examined in order to (a) ensure no off-target knockdown effect, and (b) investigate any possible compensatory effects. RBM10 protein levels were found to be elevated, in both the clonal and transiently transfected populations. These results suggest that myoblast RBM5 expression is regulated by a process that includes RNA sequestration and/or controlled translation, and that (a) RBM5 function is compensated for by RBM10, and/or (b) RBM5 regulates RBM10 expression. We have developed a model to describe our findings, and suggest further experiments for testing its validity. Since upregulation of Rbm10 might compensate for downregulated Rbm5, and consequently might mask any potential knockdown effect, it could lead to incorrect conclusions regarding the importance of Rbm5 for differentiation. It is therefore imperative to determine how both RBM5 and RBM10 protein expression is regulated.