Long Noncoding RNAs in Human Cancer and Apoptosis.

Genome annotations have uncovered the production of at least one transcript from nearly all loci in the genome at some given time throughout the development. Surprisingly, many of these transcripts do not code for proteins and are relatively long in size, thus called long noncoding RNAs (lncRNAs). Next- and third-generation sequencing technologies have amassed numerous lncRNAs expressed under different phenotypic conditions, yet many remain to be functionally characterized. LncRNAs regulate gene expression by functioning as scaffold, decoy, signaling, and guide molecules both at the transcriptional and post-transcriptional levels, interacting with different types of macromolecules, such as proteins, DNA, and RNA. Here, we review the potential regulatory role of lncRNAs in apoptosis and cancer as some of these lncRNAs may have the diagnostic and therapeutic potential in cancer.

Noncoding RNAs in apoptosis: identification and function.

Apoptosis is a vital cellular process that is critical for the maintenance of homeostasis in health and disease. The derailment of apoptotic mechanisms has severe consequences such as abnormal development, cancer, and neurodegenerative diseases. Thus, there exist complex regulatory mechanisms in eukaryotes to preserve the balance between cell growth and cell death. Initially, protein-coding genes were prioritized in the search for such regulatory macromolecules involved in the regulation of apoptosis. However, recent genome annotations and transcriptomics studies have uncovered a plethora of regulatory noncoding RNAs that have the ability to modulate not only apoptosis but also many other biochemical processes in eukaryotes. In this review article, we will cover a brief summary of apoptosis and detection methods followed by an extensive discussion on microRNAs, circular RNAs, and long noncoding RNAs in apoptosis.

Transcriptomics Profiling Identifies Cisplatin-Inducible Death Receptor 5 Antisense Long Non-coding RNA as a Modulator of Proliferation and Metastasis in HeLa Cells.

Cisplatin is a well-known cancer chemotherapeutic agent but how extensively long non-coding RNA (lncRNA) expression is modulated by cisplatin is unknown. It is imperative to employ a comprehensive approach to obtain a better account of cisplatin-mediated changes in the expression of lncRNAs. In this study, we used a transcriptomics approach to profile lncRNAs in cisplatin-treated HeLa cells, which resulted in identification of 10,214 differentially expressed lncRNAs, of which 2,500 were antisense lncRNAs. For functional analyses, we knocked down one of the cisplatin inducible lncRNAs, death receptor 5 antisense (DR5-AS) lncRNA, which resulted in a morphological change in HeLa cell shape without inducing any cell death. A second round of transcriptomics-based profiling revealed differential expression of genes associated with immune system, motility and cell cycle in DR5-AS knockdown HeLa cells. Cellular analyses showed that DR5-AS reduced cell proliferation and caused a cell cycle arrest at S and G2/M phases. Moreover, DR5-AS knockdown reduced the invasive capacity of HeLa cells in zebrafish xenograft model. These results suggest that cisplatin-mediated pleiotropic effects, such as reduction in cell proliferation, metastasis and cell cycle arrest, may be mediated by lncRNAs.

Transcriptomics Analysis of Circular RNAs Differentially Expressed in Apoptotic HeLa Cells.

Apoptosis is a form of regulated cell death that plays a critical role in survival and developmental homeostasis. There are numerous reports on regulation of apoptosis by protein-coding genes as well as small non-coding RNAs, such as microRNAs. However, there is no comprehensive investigation of circular RNAs (circRNA) that are differentially expressed under apoptotic conditions. We have performed a transcriptomics study in which we first triggered apoptosis in HeLa cells through treatment with four different agents, namely cisplatin, doxorubicin, TNF-α and anti-Fas mAb. Total RNAs isolated from control as well as treated cells were treated with RNAse R to eliminate the linear RNAs. The remaining RNAs were then subjected to deep-sequencing to identify differentially expressed circRNAs. Interestingly, some of the dys-regulated circRNAs were found to originate from protein-coding genes well-documented to regulate apoptosis. A number of candidate circRNAs were validated with qPCR with or without RNAse R treatment as well. We then took advantage of bioinformatics tools to investigate the coding potential of differentially expressed RNAs. Additionally, we examined the candidate circRNAs for the putative miRNA-binding sites and their putative target mRNAs. Our analyses point to a potential for circRNA-mediated sponging of miRNAs known to regulate apoptosis. In conclusion, this is the first transcriptomics study that provides a complete circRNA profile of apoptotic cells that might shed light onto the potential role of circRNAs in apoptosis.

Intracytoplasmic Re-localization of miRISC Complexes.

MicroRNAs (miRNAs) are a conserved class of non-coding RNAs of 22 nucleotides that post-transcriptionally regulate gene expression through translational repression and/or mRNA degradation. A great progress has been made regarding miRNA biogenesis and miRNA-mediated gene regulation. Additionally, an ample amount of information exists with respect to the regulation of miRNAs. However, the cytoplasmic localization of miRNAs and its effect on gene regulatory output is still in progress. We provide a current review of the cytoplasmic miRNA localization in metazoans. We then discuss the dynamic changes in the intracytoplasmic localization of miRNAs as a means to regulate their silencing activity. We then conclude our discussion with the potential molecules that could modulate miRNA localization.

Small RNA data set that includes tRNA-derived fragments from Jurkat cells treated with camptothecin.

In this article, we report a small RNA data set obtained from human T cell acute leukemia Jurkat cells, which were treated with the universal apoptotic agent camptothecin. Based on the Annexin-V labeling pattern, we sorted two Jurkat subpopulations in treated cells: one that is sensitive to the drug and the other being relatively more resistant. We report new original data that include the frequency of tRNA-derived fragments (tRF) in drug-sensitive and resistant cells. We also present partially analyzed data to show the origin of reads on tRNAs as well as the borders of the fragments. We believe that this data can benefit the science community working in the field of tRF and/or apoptosis.

Deep sequencing reveals two Jurkat subpopulations with distinct miRNA profiles during camptothecin-induced apoptosis.

MicroRNAs (miRNAs) are small noncoding RNAs of about 19-25 nt that regulate gene expression posttranscriptionally under various cellular conditions, including apoptosis. The miRNAs involved in modulation of apoptotic events in T cells are partially known. However, heterogeneity associated with cell lines makes it difficult to interpret gene expression signatures, especially in cancer-related cell lines. Treatment of the Jurkat T-cell leukemia cell line with the universal apoptotic drug, camptothecin, resulted in identification of two Jurkat subpopulations: one that is sensitive to camptothecin and another that is rather intrinsically resistant. We sorted apoptotic Jurkat cells from nonapoptotic ones prior to profiling miRNAs through deep sequencing. Our data showed that a total of 184 miRNAs were dysregulated. Interestingly, the apoptotic and nonapoptotic subpopulations exhibited distinct miRNA expression profiles. In particular, 6 miRNAs were inversely expressed in these two subpopulations. The pyrosequencing results were validated by real-time qPCR. Altogether, these results suggest that miRNAs modulate apoptotic events in T cells and that cellular heterogeneity requires careful interpretation of miRNA expression profiles obtained from drug-treated cell lines.

Bioactive Sheath/Core nanofibers containing olive leaf extract.

This study aimed at producing silk fibroin (SF)/hyaluronic acid (HA) and olive leaf extract (OLE) nanofibers with sheath/core morphology by coaxial electrospinning method, determining their antimicrobial properties, and examining release profiles of OLE from these coaxial nanofibers. Optimum electrospinning process and solution parameters were determined to obtain uniform and bead-free coaxial nanofibers. Scanning electron microscopy and transmission electron microscopy (TEM) were used to characterize the morphology of the nanofibers. The antimicrobial activities of nanofibers were tested according to AATCC test method 100. Total phenolic content and total antioxidant activity were tested using in vitro batch release system. The quality and quantity of released components of OLE were determined by high-performance liquid chromatography. The changes in nanofibers were examined by Fourier-transform infrared spectroscopy. Uniform and bead-free nanofibers were produced successfully. TEM images confirmed the coaxial structure. OLE-loaded nanofibers demonstrated almost perfect antibacterial activities against both of gram-negative and gram-positive bacteria. Antifungal activity against C. albicans was rather poor. After a release period of 1 month, it was observed that ∼70-95% of the OLE was released from nanofibers and it was still bioactive. Overall results indicate that the resultant shell/core nanofibers have a great potential to be used as biomaterials.

Pulsatile versus non-pulsatile flow to reduce cognitive decline after coronary artery bypass surgery: A randomized prospective clinical trial.

BACKGROUND: In this prospective study, we aimed to compare the effect of pulsatile and non-pulsatile flow on the cognitive functions in patients undergoing coronary artery bypass surgery. METHODS: Patients scheduled for their first coronary artery bypass surgery (n = 148) were randomly assigned to the pulsatile flow group (Group A, n = 75) or non-pulsatil group (Group B, n = 73). Cognitive performance was assessed with (MoCA) montreal cognitive assessment test performed by psychologists before coronary artery bypass surgery and 1 month after the operation. RESULTS: Mild cognitive impairment was seen in 12 (16%) patients and serious cognitive impairment was seen in 1 (1.33%) patient in the pulsatile flow group. In the other group, mild cognitive impairment was detected in 23 (31.50%) patients and serious cognitive decline was found in 3 (4.10%) patients. Mean MoCA scores were 25.86 ± 2.62 in group A and 22.12 ± 2.20 in group B. The difference between two groups was statistically significant (P = 0.041). CONCLUSIONS: We suggest that pulsatile flow has beneficial effects to decrease cognitive dysfunction in patients undergoing on-pump coronary artery bypass surgery.

The analgesic effect of 8 and 16 mg lornoxicam administered before shock wave lithotripsy: a randomized, double-blind, controlled study.

OBJECTIVES: To evaluate the efficacy of 2 different doses of intravenous lornoxicam for pain relief during shock wave lithotripsy (SWL). METHODS: In this randomized, controlled, double-blind study, 60 ASA I-II patients undergoing SWL were randomly divided into 3 groups. Fifteen minutes before SWL, 4 mL of saline solution was given to the patients in group I, 8 mg lornoxicam in group II, and 16 mg lornoxicam in group III. All groups received 1 mcg/kg fentanyl intravenously 3 minutes before SWL. Pain scores, blood pressure, heart rate, respiratory rate, and oxygen saturation were noted before SWL, at 1 minute and every 5 minutes during the procedure. Also, additional fentanyl consumption, oxygen support requirements, time for recovery room discharge, adverse effects, and patient satisfaction were recorded. RESULTS: The mean blood pressure, heart rate, and SpO(2) values were significantly lower in group I at 5 and 10 minutes (P < .01). The mean visual analogue scale scores and fentanyl consumption were higher in group I (P < .001). The additional meperidine requirement was higher in group I (P = .014). In group I, oxygen requirement was higher and recovery room period was longer than in the other 2 groups (P < .001), and 2 patients from group I had respiratory depression develop. The incidence of nausea and vomiting was higher in group I (P < .05). The patients' satisfaction scores were higher in groups II and III than in group I (P = .001). CONCLUSIONS: Eight milligrams of intravenously administered lornoxicam 15 minutes before SWL provides pain relief and patient satisfaction during the procedure, reducing opioid requirements as well as decreasing the incidence of side effects.

Effect of lornoxicam on postoperative analgesia after myomectomy.

BACKGROUND: In this prospective, randomized study, we evaluate the postoperative analgesic effect of lornoxicam after myomectomy operations. MATERIAL-METHOD: Forty ASA I-II patients scheduled for myomectomy operation were enrolled to this study. Patients were randomly divided into two groups and epidural block was performed with 0,75 % ropivacaine. After the operation, morphine Patient Controlled Epidural Analgesia (PCEA) combined with placebo (saline 2 ml iv) and morphine PCEA combined with lornoxicam 8 mg iv were administered to patients in Group I and Group II, respectively. Pain was assessed at the 0,1st, 2nd, 4th, 6th, 8th, 12th and 24th hours postoperatively. Chi-square and student's t tests were used for statistical analysis. RESULTS: VAS( Visual Analog Scale) scores were higher in Group I than Group II at 2nd, 4th, 6th and 24th hours. Total morphine consumption was 10.45+/- 4.03 in Group I and 4.25 +/- 1.74 in Group II. CONCLUSION: Single dose iv lornoxicam is a safe and an effective treatment option of post-myomectomy pain as it produces effective analgesia, reduces morphine consumption and does not increase the side effects.

Efficacy of lornoxicam in postoperative analgesia after total knee replacement surgery.

In total knee replacement operation, patients have a severe pain in the postoperative period. Because of side effects of opioids, multiple postoperative pain treatment regimens are more suitable in these elderly patients. In this double-blind, randomized, placebo controlled study, the effect of lornoxicam administration (32 mg/48 hour) on morphine consumption and drug-related side effects were investigated in elderly patients undergoing total knee replacement. Group M (n=23) and Group L (n=23) received morphine with patient controlled analgesia (PCA) device postoperatively. Additionally Group L received lornoxicam 16 mg intravenously 15 minutes before surgery and 8 mg at postoperative 12th and 24th hours. Morphine consumption in Group L were significantly lower than in Group M at 2, 3, 6, 8, 24, 36 and 48th postoperative hours (p<0.05). At the end of 48th hour mean total morphine consumptions (mean+/-SD) for Group M and Group L were 63.70+/-15.70 mg and 34.60+/-16.32 mg, respectively. AUC (area under the curve) Morphine 0-48h in Group M was 59+/-13 and in Group L it was 30+/-13 (p<0.001). Incidence of side effects in Group M were 60% and 25% in Group L (p<0.05). In Group M, 8 patients (40%) experienced nausea and 3 (15%) patients experienced itching where as in Group L, 3 patients (15%) experienced nausea, 1 patient (5%) itching, 1 patient (5%) dry mouth. Lornoxicam administration in total knee replacement is associated with decreased morphine consumption for postoperative analgesia and fewer side effects.