Inhibition of HIV-LTR gene expression by oligonucleotides targeted to the TAR element

All human immunodeficiency virus mRNAs contain a sequence known as TAR (trans-activating responsive sequence). The TAR element forms a stable RNA stem-loop structure which binds the HIV tat (trans-activator) protein and mediates increased viral gene expression. In principle, molecules which bind to the TAR RNA structure would inhibit trans-activation by perturbing the native RNA secondary structure. We have constructed a series of phosphodiester and phosphorothioate antisense oligonucleotides which specifically bind to the HIV TAR element. Specific binding to the TAR element was demonstrated in vitro with enzymatically synthesized TAR RNA. The TAR-directed phosphorothioates inhibited trans-activation in a sequence-dependent fashion in a cell culture model using an HIV LTR/human placental alkaline phosphatase gene fusion and tat protein supplied in trans. The molecules also inhibited HIV replication in both acute and chronically infected viral assays, but without sequence specificity. We have constructed a series of vectors consisting of the MMTV promoter and 5'-untranslated region of four different mRNAs, including the TAR region, to study the effect of TAR on gene expression in heterologous systems. The results suggest that, in the absence of the HIV LTR, the TAR element has a repressive effect on gene expression, which is relieved by tat.

A TIBO derivative, R82913, is a potent inhibitor of HIV-1 reverse transcriptase with heteropolymer templates

R82913, (+)-S-4,5,6,7-tetrahydro-9-chloro-5-methyl-6-(3-methyl-2-butenyl)- imidazo[4,5,1-jk][1,4]-benzodiazepin-2(1H)-thione (a TIBO derivative), inhibited the replication of thirteen different strains of HIV-1 in CEM cells with a median IC50 of 0.15 microM. The concentration of compound that killed 50% of the cells was much higher (46 microM), indicating that R82913 has a high selectivity index. R82913 was 20-fold more potent than AZT-TP in the inhibition of HIV-1 reverse transcriptase in an assay using a naturally occurring template (ribosomal RNA) that more accurately resembles native viral RNA than a synthetic homopolymer. With this template, R82913 inhibited HIV-1 reverse transcriptase with an ID50 (0.01 microM) that is equal to, or lower than, the IC50 for this compound in all of our cell culture assays (0.01-0.65 microM). R82913 has no effect on the replication of HIV-2 in CEM cells and does not inhibit the reverse transcriptase from this virus.

Mechanism of inhibition of human immunodeficiency virus type 1 reverse transcriptase and human DNA polymerases alpha, beta, and gamma by the 5'-triphosphates of carbovir, 3'-azido-3'-deoxythymidine, 2',3'-dideoxyguanosine and 3'-deoxythymidine. A novel RNA template for the evaluation of antiretroviral drugs

Carbovir (the carbocyclic analog of 2'-3'-didehydro-2',3'-dideoxyguanosine) is a potent inhibitor of human immunodeficiency virus type 1 (HIV-1) replication. Assays were developed to assess the mechanism of inhibition by the 5'-triphosphate of carbovir of HIV-1 reverse transcriptase using either RNA or DNA templates that contain all four natural nucleotides. Carbovir-TP was a potent inhibitor of HIV-1 reverse transcriptase using either template with Ki values similar to that observed by AZT-TP, ddGTP, and ddTTP. The kinetic constants for incorporation of these nucleotide analogs into DNA by HIV-1 reverse transcriptase using either template were similar to the values seen for their respective natural nucleotides. In addition, the incorporation of either carbovir-TP or AZT-TP in the presence of dGTP or dTTP, respectively, indicated that the mechanism of inhibition by these two nucleotide analogs was due to their incorporation into the DNA resulting in chain termination. Carbovir-TP was not a potent inhibitor of DNA polymerase alpha, beta, or gamma, or DNA primase. Given the potent activity of carbovir-TP against HIV-1 reverse transcriptase and its lack of activity against human DNA polymerases, we believe that further evaluation of this compound as a potential drug for the treatment of HIV-1 infection is warranted.

Pharmacogenomic Germline Testing: Applications in Oncology Nursing

The implementation of pharmacogenomics in clinical practice has increased in clinical oncology practice. Pharmacogenomic germline testing can be used to develop and prescribe safer and more effective medications and treatment.

Exploring the Genomic Landscape of Hepatobiliary Cancers to Establish a Novel Molecular Classification System

Taxonomy of hepatobiliary cancer (HBC) categorizes tumors by location or histopathology (tissue of origin, TO). Tumors originating from different TOs can also be grouped by overlapping genomic alterations (GA) into molecular subtypes (MS). The aim of this study was to create novel HBC MSs. Next-generation sequencing (NGS) data from the AACR-GENIE database were used to examine the genomic landscape of HBCs. Machine learning and gene enrichment analysis identified MSs and their oncogenomic pathways. Descriptive statistics were used to compare subtypes and their associations with clinical and molecular variables. Integrative analyses generated three MSs with different oncogenomic pathways independent of TO (n = 324; p < 0.05). HC-1 "hyper-mutated-proliferative state" MS had rapidly dividing cells susceptible to chemotherapy; HC-2 "adaptive stem cell-cellular senescence" MS had epigenomic alterations to evade immune system and treatment-resistant mechanisms; HC-3 "metabolic-stress pathway" MS had metabolic alterations. The discovery of HBC MSs is the initial step in cancer taxonomy evolution and the incorporation of genomic profiling into the TNM system. The goal is the development of a precision oncology machine learning algorithm to guide treatment planning and improve HBC outcomes. Future studies should validate findings of this study, incorporate clinical outcomes, and compare the MS classification to the AJCC 8th staging system.

An LC-MS/MS method for the quantification of 3-bromotyrosine in plasma from patients diagnosed with eosinophilic esophagitis

Eosinophilic esophagitis (EoE) is a disease marked by a surplus of eosinophils, a type of white blood cell that causes inflammation and irritation. The current diagnostic and monitoring procedure for EoE is endoscopy with biopsy, which is invasive, expensive, and leads to tissue tearing in patients. A biomarker in plasma would offer a much less invasive form of disease monitoring for patients with EoE. Eosinophils have been shown to make eosinophil peroxidase, an enzyme that produces hypobromous acid, reacts with primary amines, and forms bromoamides. One product of this biochemical reaction is 3-bromotyrosine. We have optimized a selective, sensitive, and reproducible method to detect and quantify L-tyrosine and 3-bromotyrosine in human plasma using high-pressure liquid chromatography and tandem mass spectrometry (HPLC-MS/MS). Our sample preparation and analysis method requires fewer steps and provides a faster analysis than previous methods. Method validation yielded limits of quantification of 50 ng mL-1 for L-tyrosine and 10 ng mL-1 for 3-bromotyrosine. Calibration curves for quantification were linear from 50 to 500 ng mL-1 with an R2 value of 0.9995 for L-tyrosine and 10 to 300 ng mL-1 with an R2 value of 0.9998 for 3-bromotyrosine. Method variability was assessed resulting in relative standard deviations of 0.98-4.6% for 3-bromotyrosine (n = 18) and 0.20-0.58% for L-tyrosine (n = 18). Method applicability was tested with patients with a confirmed diagnosis of EoE, initially suggesting little to no correlation between eosinophil count and 3-bromotyrosine concentration in plasma. However, we do observe a relationship between eosinophil count and esophageal deformities. More research must be conducted to determine a more definitive correlation.