RNA Ligation Precedes U6 snRNA/LINE-1 Retrotransposition
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ABSTRACT:
REPOSITORIES: dbGaP
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Project description:Colorectal cancer (CRC) is the third most common cancer and the fourth leading cause of cancer-related death in the world. Despite potentially curative surgery and the use of modern adjuvant chemotherapy, up to 40% of CRC patients subsequently develop local tumor relapse or metastatic disease. Currently, aside from post-operative pathological staging, early follow up of the patients does not include a specific test or any other evaluation that could predict disease recurrence. Therefore, exploring and identifying novel biomarkers of CRC’s following diagnosis of the primary tumor may help us in identifying patients at high risk for recurrence.
Modifications in signaling pathways and their regulation by microRNAs (miRNAs) are being evaluated as biomarkers and therapeutic targets for cancer in general and CRC in particular. It has been established, although not completely, that miRNAs have a role in initiation and progression of CRC. Modifications of miRNAs have been recorded in CRC tumors, and the expression patterns of these miRNAs could in principle biomark this cancer’s phenotype. As miRNAs are well documented to regulate critical molecules in signaling pathways, their regulation of tumor relevant pathways may also serve to further sub-classify patients into drug responsive groups. Moreover, miRNAs may be sampled from peripheral blood and are available as a non-invasive diagnostic method, their application as biomarkers is of special interest.
In this study the investigators aim to quantify miRNA levels in human colon and rectal tumors, tumor adjacent and normal tissues. By comparing this data from a large cohort of patients, the investigators aim to identify specific, relevant miRNAs that may serve as biomarkers to stratify CRC patients according to their clinical characteristics such as disease stage, specific treatment, prognosis and disease recurrence.
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Project description:1. Evaluate the diagnostic value of long noncoding RNA (CCAT1) expression by RT-PCR in peripheral blood in colorectal cancer patients versus normal healthy control personal.
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Project description:Control over cellular delivery of different functionalities and their synchronized activation is a challenging task. We report several RNA and RNA/DNA-based nanoparticles designed to conditionally activate the RNA interference in various human cells. These nanoparticles allow precise control over their formulation, stability in blood serum, and activation of multiple functionalities. Importantly, interferon and pro-inflammatory cytokine activation assays indicate the significantly lower responses for DNA nanoparticles compared to the RNA counterparts, suggesting greater potential of these molecules for therapeutic use.
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Project description:Proteins in Nicotiana benthamiana interacted with RNA fragment (or signal sequences) involving small-RNA accumulation selectivity, were trapped and analyzed.
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Project description:Self-replicating single-stranded RNA viruses such as alphaviruses, flaviviruses, measles viruses, and rhabdoviruses provide efficient delivery and high-level expression of therapeutic genes due to their high capacity of RNA replication. This has contributed to novel approaches for therapeutic applications including vaccine development and gene therapy-based immunotherapy. Numerous studies in animal tumor models have demonstrated that self-replicating RNA viral vectors can generate antibody responses against infectious agents and tumor cells. Moreover, protection against challenges with pathogenic Ebola virus was obtained in primates immunized with alphaviruses and flaviviruses. Similarly, vaccinated animals have been demonstrated to withstand challenges with lethal doses of tumor cells. Furthermore, clinical trials have been conducted for several indications with self-amplifying RNA viruses. In this context, alphaviruses have been subjected to phase I clinical trials for a cytomegalovirus vaccine generating neutralizing antibodies in healthy volunteers, and for antigen delivery to dendritic cells providing clinically relevant antibody responses in cancer patients, respectively. Likewise, rhabdovirus particles have been subjected to phase I/II clinical trials showing good safety and immunogenicity against Ebola virus. Rhabdoviruses have generated promising results in phase III trials against Ebola virus. The purpose of this review is to summarize the achievements of using self-replicating RNA viruses for RNA therapy based on preclinical animal studies and clinical trials in humans.
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Project description:Salivary biomarkers for disease detection, diagnostic and prognostic assessments have become increasingly well established in recent years. In this chapter we explain the current leading technology that has been used to characterize salivary non-coding RNAs (ncRNAs) from the extracellular RNA (exRNA) fraction: HiSeq from Illumina® platform for RNA sequencing. Therefore, the chapter is divided into two main sections regarding the type of the library constructed (small and long ncRNA libraries), from saliva collection, RNA extraction and quantification to cDNA library generation and corresponding QCs. Using these invaluable technical tools, one can identify thousands of ncRNA species in saliva. These methods indicate that salivary exRNA provides an efficient medium for biomarker discovery of oral and systemic diseases.
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Project description:RNA localization is a key mechanism for targeting proteins to particular subcellular domains. Sequences necessary and sufficient for localization have been identified, but little is known about factors that affect its kinetics. Transcripts of gurken and the I factor, a non-LTR retrotransposon, colocalize at the nucleus in the dorso-antero corner of the Drosophila oocyte directed by localization signals, the GLS and ILS. I factor RNA localizes faster than gurken after injection into oocytes, due to a difference in the intrinsic localization ability of the GLS and ILS. The kinetics of localization of RNA containing the ILS are enhanced by the presence of a stem-loop, the A loop. This acts as an RNA:RNA interaction element in vivo and in vitro, and stimulates localization of RNA containing other localization signals. RNA:RNA interaction may be a general mechanism for modulating RNA localization and could allow an mRNA that lacks a localization signal to hitchhike on another RNA that has one.
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Project description:Helicases contribute to diverse biological processes including replication, transcription and translation. Recent reports suggest that unwinding of some helicases display repetitive activity, yet the functional role of the repetitiveness requires further investigation. Using single-molecule fluorescence assays, we elucidated a unique unwinding mechanism of RNA helicase A (RHA) that entails discrete substeps consisting of binding, activation, unwinding, stalling and reactivation stages. This multi-step process is repeated many times by a single RHA molecule without dissociation, resulting in repetitive unwinding/rewinding cycles. Our kinetic and mutational analysis indicates that the two double stand RNA binding domains at the N-terminus of RHA are responsible for such repetitive unwinding behavior in addition to providing an increased binding affinity to RNA. Further, the repetitive unwinding induces an efficient annealing of a complementary RNA by making the unwound strand more accessible. The complex and unusual mechanism displayed by RHA may help in explaining how the repetitive unwinding of helicases contributes to their biological functions.
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