Exosomopathies are a collection of rare diseases caused by mutations in genes that encode structural subunits of a ribonuclease complex termed the RNA exosome. The RNA exosome mediates both RNA processing and degradation of multiple classes of RNA. This complex is evolutionarily conserved and required for fundamental cellular functions, including rRNA processing. Recently, missense mutations in genes encoding structural subunits of the RNA exosome complex have been linked to a variety of distinct neurological diseases, many of them childhood neuronopathies with at least some cerebellar atrophy. Understanding how these missense mutations lead to the disparate clinical presentations that have been reported for this class of diseases necessitates investigation of how these specific changes alter cell-specific RNA exosome function. Although the RNA exosome complex is routinely referred to as ubiquitously expressed, little is known about the tissue- or cell-specific expression of the RNA exosome complex or any individual subunit. Here, we leverage publicly available RNA-sequencing data to analyze RNA exosome subunit transcript levels in healthy human tissues, focusing on those tissues that are impacted in exosomopathy patients described in clinical reports. This analysis provides evidence to support the characterization of the RNA exosome as ubiquitously expressed with transcript levels for the individual subunits that vary in different tissues. However, the cerebellar hemisphere and cerebellum have high levels of nearly all RNA exosome subunit transcripts. These findings could suggest that the cerebellum has a high requirement for RNA exosome function and potentially explain why cerebellar pathology is common in RNA exosomopathies.
Lung cancer, especially non-small cell lung cancer (NSCLC) is the most frequent cause of cancer-related mortality worldwide. MicroRNAs (miRNAs) represent a class of small non-coding RNA molecules. In recent years, many studies have confirmed that abnormal miRNAs expression in tumor can participate in many biological processes of NSCLC. However, whether miR-1294 is involved in the development of NSCLC remains unclear. In this study, miR-1294 was inhibited in NSCLC cell lines, and its expression was associated with tumor size and progression. MiR-1294 overexpression inhibited cell proliferation and cell cycle, conversely promoted cell apoptosis and senescence, and miR-1294 binding to MYH9 3’-UTR mediated suppression of it. Besides, three bioinformatics software were searched, and KLF4 was predicted as an upstream regulator of miR-1294. This study is the first to illuminate that miR-1294, mediated by KLF4, by targeting MYH9 to regulate NSCLC cell proliferation and apoptosis, and is a potential biomarker and therapeutic target for NSCLC.
Exosomopathies are a collection of rare diseases caused by mutations in genes that encode structural subunits of the RNA exosome complex (EXOSC). The RNA exosome is critical for both processing and degrading many RNA targets. Mutations in individual RNA exosome subunit genes (termed EXOSC genes) are linked to a variety of distinct diseases. These exosomopathies do not arise from homozygous loss-of-function or large deletions in the EXOSC genes likely because some level of RNA exosome activity is essential for viability. Thus, all patients described so far have at least one allele with a missense mutation encoding an RNA exosome subunit with a single pathogenic amino acid change linked to disease. Understanding how these changes lead to the disparate clinical presentations that have been reported for this class of diseases necessitates investigation of how individual pathogenic missense variants alter RNA exosome function. Such studies will require access to patient samples, a challenge for these very rare diseases, coupled with modeling the patient variants. Here, we highlight five recent studies that model pathogenic variants in EXOSC3, EXOSC2, and EXOSC5.
Increasing number of reports have shown the involvement of LncRNAs in the tumour progression in multiple cancers including colorectal and female reproductive cancers such as ovarian and breast. In particular, the profiling of lncRNAs in colorectal cancer (CRC), which is within the top three cancers in both female and male, have identified 556 upregulated and 1040 downregulated lncRNAs as compared to normal tissue. In this highlight, we looked at the mechanism in which some of these lncRNAs can act in CRC development and progression through promoting survival, proliferation and invasion and metastasis. Furthermore, we also look into the possibility of a cytoskeletal protein, gelsolin and its possible interaction with lncRNAs.
Patients with CRC (colorectal cancer) usually have a poor prognosis and the cure rate of CRC remained unsatisfied due to unfavorable curative effect. It is well known that microRNAs (miRNAs) and energy metabolism have pivotal roles in CRC progression. In a recent article in Cell Death & Disease by Xiaofeng Guo. et al. 2017, we have reported an oncogenic role of miR-181d in CRC by promoting glycolysis, and its underlying molecular mechanism about a new feedback loop among miR-181d/CRY2/FBXL3/c-myc signaling axis. Among these, we have identified the level of miR-181d was upregulated in CRC and the inhibition of miR-181d decreased glycolysis in CRC cells. We also found that c-myc played a central role in regulating cell glycolysis, which is required for the metabolic shift induced by miR-181d. Besides, we have demonstrated FBXL3 and CRY2 were direct targets of miR-181d and c-myc promoted miR-181d upregulation while inhibiting the expression of CRY2 and FBXL3 in CRC cells. The data from our recent article strongly suggest a new light onto the oncogenic function of the miR-181d in CRC. Furthermore, these findings represent a novel potential approach for silencing miR-181d/c-myc signaling pathway in CRC treatment.
TRAIL (TNF-related apoptosis-inducing ligand) is a promising anticancer agent because of its tumor-specifc apoptosis inducer activity without affecting normal cells. MicroRNAs (miRNAs) emerge as important regulators of cell viability. Our recent studies showed that miR-7 is a potential sensitizer for TRAIL-induced apoptosis in glioblastoma (GBM) cells, and XIAP is a critical gene in the apoptotic process as a direct downstream gene of miR-7. Additionally, this regulatory axis could also exert in other types of tumor cells. More importantly, we confirmed that co-delivery of sTRAIL and tumor suppressor miR-7 by MSCs leads to synergistic cancer killing effect. Thus, miR-7 has been demonstrated to be a critical sensitizer for TRAIL-induced apoptosis through regulating XIAP and highlights a novel therapeutic strategy for the treatment of GBM.
Obesity is a serious health problem that is caused by an equilibrium shift towards elevated energy intake over expenditure, and is often involved in a range of metabolic diseases. A diet rich in saturated fatty acids (SFA), which is one of the leading causes of obesity and ectopic lipid accumulation in the key organs for metabolic regulation, results in an imbalance of the cellular metabolism and an inadequate response of hepatocytes to insulin, which is known as hepatic insulin resistance. Although endogenous non-coding small microRNAs (miRNAs) play important roles in the post-transcriptional repression of the target genes, the implications of obesity-induced miRNAs in metabolic diseases, particularly in the development of hepatic insulin resistance, are largely unknown. In recent studies, SFA and a high fat diet were found to increase the expression of certain miRNAs significantly in the liver and skeletal muscle. These obesity-induced miRNAs were also up-regulated in human subjects with metabolic diseases. Our recent study highlights a novel mechanism whereby miR-96, which is one of the obesity-induced miRNA, participates actively in the development of hepatic insulin resistance in obesity. Studies focusing on obesity-induced miR-96 have indicated the strong diagnostic and therapeutic importance of miRNAs in insulin resistance and metabolic diseases. This will also help better understand the pathogenesis of insulin resistance and T2DM in obesity, and enable the development of inhibitors against obesity-induced miRNAs as a novel diagnostic and therapeutic strategy for metabolic diseases.
The targeted and conditional activation of pharmaceuticals is an increasingly important feature in modern personalized medicine. Nucleic acid nanoparticles show tremendous potential in this exploit due to their programmability and biocompatibility. Among the most powerful nucleic acid specific treatments is RNA interference-based therapeutics. RNA interference is a naturally occurring phenomenon in which specific genes are effectively silenced. Recently we have developed two different strategies based on customized multivalent nucleic acid nanoparticles with the ability to conditionally activate RNA interference in diseased cells as well as elicit detectable fluorescent responses.[1,2] These novel technologies can be further utilized for the simultaneous delivery and conditional intracellular activation of multiple therapeutic and biosensing functions to combat various diseases.
Prostate cancer (PCa) is the second most common cause of cancer-specific deaths in the U.S. Unfortunately, the underlying molecular mechanisms for its development and progression remain unclear. Studies have established that microRNAs (miRNAs) are dysregulated in PCa. The intron-derived microRNA-1207-3p (miR-1207-3p) is encoded at the non-protein coding gene locus PVT1 on the 8q24 human chromosomal region, an established PCa susceptibility locus. However, miR-1207-3p in PCa had not previously been investigated. Therefore, we explored if miR-1207-3p plays any regulatory role in PCa. We discovered that miR-1207-3p is significantly underexpressed in PCa cell lines in comparison to normal prostate epithelial cells, and that increased expression of microRNA-1207-3p in PCa cells significantly inhibits proliferation, migration, and induces apoptosis via direct molecular targeting of fibronectin type III domain containing 1 (FNDC1). Our studies also revealed significant overexpression of FNDC1, fibronectin (FN1) and the androgen receptor (AR) in human PCa cell lines as well as tissues, and FNDC1, FN1, and AR positively correlate with aggressive PCa. These findings, recently published in Experimental Cell Research, are the first to describe a novel miR-1207-3p/FNDC1/FN1/AR novel regulatory pathway in PCa.
Gene expression profiling is an important strategy to study animal development, response to stimuli and diseases. RNAs measured in gene expression profiling experiments are frequently purified from mixture of multiple cell types. The resultant data have low resolution, incapable of distinguishing transcriptome of different cell types and likely biased towards up-regulated genes in dominant tissues. These problems can be solved by obtaining tissue-specific gene expression profile. For dozens of years, there have been several strategies developed to isolate specific tissues or purify RNAs from tissue of interest, and combined with high-throughput RNA assays to generate transcriptome of various specific tissues or cell types. This review will introduce basic principles of these methods and their application in large-scale transcriptome analysis, and discuss on their advantages and limitation.
We have previously presented the histone methyltransferase enhancer of zeste homolog 2 (EZH2) of the polycomb repressive complex 2 (PRC2) as a potential therapeutic target in Multiple Myeloma (MM). In a recent article in Oncotarget by Alzrigat. et al. 2017, we have reported on the novel finding that EZH2 inhibition using the highly selective inhibitor of EZH2 enzymatic activity, UNC1999, reactivated the expression of microRNA genes previously reported to be underexpressed in MM. Among these, we have identified miR-125a-3p and miR-320c as potential tumor suppressor microRNAs as they were predicted to target MM-associated oncogenes; IRF-4, XBP-1 and BLIMP-1. We also found EZH2 inhibition to reactivate the expression of miR-494, a previously reported regulator of the c-MYC oncogene. In addition, we could report that EZH2 inhibition downregulated the expression of a few well described oncogenic microRNAs in MM. The data from our recent article are here highlighted as it shed a new light onto the oncogenic function of the PRC2 in MM. These data further strengthen the notion that the PRC2 complex may be of potential therapeutic interest.
We have recently developed tools to study Kaposi’s sarcoma-associated virus (KSHV) reactivation at the single-episome level. Using immunofluorescent labeling of latent nuclear antigen (LANA) protein to localize viral episomes, combined with fluorescence in situ RNA hybridization (RNA-FISH) of an intron region of immediate early transcripts, we have visualized active transcription of viral genomes in infected cells. At this level, we observed that not all episomes within a single cell were uniformly transcribed following reactivation stimuli. However, those episomes that were transcribed, formed large aggregates containing a significant fraction of cellular RNA polymerase II (RNAPII), foci consistent with previously described viral transcriptional factories. This focal assembly of RNAPII on viral episomes was accompanied by an overall decrease in the pool of cellular RNAPII. Additionally, the viral transcriptional factories localized with replicating viral genomic DNAs. This co-localization suggests that KSHV may assemble an “all-in-one” workroom for both gene transcription and DNA replication. While previous studies have reported on the variable response of individual KSHV infected cells or episomes derived from a population during reactivation, our results expose this variation further by demonstrating heterogeneity in the response of individual KSHV episomes within a single reactivating cell.
Bone marrow failure disorders (BMFDs), which are characterized by an early pro-apoptotic phase which results in faulty hematopoiesis and anemia, more often than not progress to outright acute myelogenous leukemia (AML). Recent findings have indicated that most if not all of these disorders have a very significant RNA processing component to their pathology. This review aims to highlight some of normal processes of RNA metabolism that have been recently demonstrated to be altered in BMFDs.
AMPA and kainate receptors, along with NMDA receptors, are distinct subtypes of glutamate ion channels. Excessive activity of AMPA and kainate receptors has been implicated in neurological diseases, such as epilepsy and neuropathic pain. Antagonists that block their activities are therefore potential drug candidates. In a recent article in the Journal of Biological Chemistry by Jaremko et al. 2017, we have reported on the discovery and molecular characterization of an RNA aptamer of a dual functionality: the full-length RNA (101 nucleotide) inhibits AMPA receptors while the truncated or the short (55 nucleotide) RNA inhibits both the AMPA and kainate receptors. The full-length RNA aptamer was isolated through a specially designed, systematic evolution of ligands by exponential enrichment (SELEX) using only a single type of AMPA receptors expressed in HEK-293 cells. The design feature and the results of our recent article are highlighted here, as they demonstrate the utility of the SELEX approach and the potential of using a single AMPA receptor type to develop potent, novel RNA aptamers targeting multiple subunits and AMPA/kainate receptor subtypes with length-dependent functionalities.
The membrane-bound transcription factors, SREBPs (sterol regulatory element-binding proteins), play a central role in regulating lipid metabolism. The transcriptional activation of SREBPs requires the key protein SCAP (SREBP-cleavage activating protein) to translocate their precursors from the endoplasmic reticulum to the Golgi for subsequent proteolytic activation, a process tightly regulated by a cholesterol-mediated negative feedback loop. Our previous work showed that the SCAP/SREBP-1 pathway is significantly upregulated in human glioblastoma (GBM), the most deadly brain cancer, and that glucose-mediated N-glycosylation of SCAP is a prerequisite step for SCAP/SREBP trafficking. More recently, we demonstrated that microRNA-29 (miR-29) mediates a previously unrecognized negative feedback loop in SCAP/SREBP-1 signaling to control lipid metabolism. We found that SREBP-1, functioning as a transcription factor, promotes the expression of the miR-29 family members, miR-29a, -29b and -29c. In turn, the miR-29 isoforms reversely repress the expression of SCAP and SREBP-1. Moreover, treatment with miR-29 mimics effectively suppressed GBM tumor growth by inhibiting SCAP/SREBP-1 and de novo lipid synthesis. These findings, recently published in Cell Reports, strongly suggest that delivery of miR-29 in vivo may be a promising approach to treat cancer and metabolic diseases by suppressing SCAP/SREBP-1-regulated lipid metabolism.
The human RNA methyltransferase BCDIN3D is overexpressed in breast cancer cells and involved in cellular invasion and poor prognosis of breast cancer. Several years ago, BCDIN3D was reported to dimethylate the 5'-monophosphate of specific precursor miRNAs (pre-miRNAs), such as the tumor suppressor miR145. Dimethylation of the 5'-monophosphate of the pre-miRNA negatively regulates the subsequent processing by Dicer in vitro , and results in the downregulated expression of the mature form of the miRNA. The depletion of BCDIN3D also reportedly results in the suppression of the tumorigenic phenotype of breast cancer cells. Thus, these findings suggested that BCDIN3D promotes the cellular invasion of breast cancer cells, by downregulating the expression of tumor suppressor miRNAs via the dimethylation of the 5'-monophosphate of the corresponding pre-miRNAs . Recently, we found that cytoplasmic tRNA His is actually the primary target of human BCDIN3D, rather than pre-miR145. BCDIN3D monomethylates the 5'-phosphate of cytoplasmic tRNA His much more efficiently than that of pre-miRNA in vitro , and is responsible for the monomethylation of the 5'-phosphate of cytoplasmic tRNA His in vivo . BCDIN3D recognizes the eight-nucleotide long extended acceptor helix with the G -1 -A 73 mis-pair at the top of the acceptor stem of tRNA His , which are exceptional features among cytoplasmic tRNA species. These results not only reveal the primary target of BCDIN3D, which is overexpressed in breast cancer cells, but also highlight the possible involvement of the 5'-phosphomethylation of tRNA and/or tRNA in the tumorigenesis of breast cancer cells, beyond its established function in protein synthesis.
ARS2 is a stable component of the nuclear cap-binding complex (CBC) and is critical for RNA Polymerase II transcript processing. Moreover, ARS2, and its orthologue SERRATE in plants, has been implicated in having a role in most established CBC-dependent functions. This review will provide insight into the functions of ARS2/SERRATE in numerous RNA Polymerase II transcript processing events, which happen co-transcriptionally from initiation to termination, and post-transcriptionally during maturation and export into the cytoplasm. Additionally, we will discuss what is known regarding ARS2/SERRATE structure in plants and in mammals.
RNA profiling in biofluids holds promise as both diagnostic and prognostic markers. High expression levels of distinctive cell free circulating miRNAs in serum, plasma and cerebral spinal fluid (CSF), have been utilized as classifiers to detect and characterize disorders of the central nervous system (CNS). We formulated the quantitative theory showing how the results of surprisal analysis enable a reliable inference if tumor cells are present in the sample from a single measurement. Subsequently, we develop a molecular beacon-based microfluidic chip that enables for fluorescence detection of miRNAs without amplification in low volumes of human CSF. Using surprisal analysis, we identified a miRNA classifier that enables high fidelity detection and characterization of human brain tumors. We anticipate that this micro-fluidic platform will provide a critical translational tool with point of care potential for CNS disorders.
microRNAs (miRs) are small, non-coding RNAs, which play crucial roles in the development and progression of human cancer. Given that miRs are stable, easy to synthetize and readily introduced into cells, they have been viewed as having potential therapeutic benefit in cancer. c-Myc (Myc) is one of the most commonly deregulated oncogenic transcription factors and has important roles in the pathogenesis of cancer, thus making it an important, albeit elusive therapeutic target. Here we review the miRs that have been identified as being both positive and negative targets for Myc and how these participate in the complex phenotypes that arise as a result of Myc-driven transformation. We also discussseveral recent reports of Myc-synthetic lethal interactions with miRs.These highlight the importance and complexity of miRs in Myc-mediated biological functions and the opportunities for Myc-driven human cancer therapies.
