Benefit-risk assessment for brincidofovir for the treatment of smallpox: U.S. Food and Drug Administration's Evaluation.

The development and approval of brincidofovir for the treatment of smallpox, a disease that was eradicated from the world over 40 years ago, has resulted in the second antiviral approved via the Medical Countermeasure Initiative (MCMi) to combat this disease. Approval of brincidofovir required a unique regulatory approach based on the FDA Animal Rule, and development was supported by many years of research and collaboration among academic investigators, the pharmaceutical industry and multiple government agencies. This article summarizes the FDA regulatory pathway and describes the challenges involved.

A comprehensive mechanism for 5-carboxylcytosine-induced transcriptional pausing revealed by Markov state models.

RNA polymerase II (Pol II) surveils the genome, pausing as it encounters DNA lesions and base modifications and initiating signals for DNA repair among other important regulatory events. Recent work suggests that Pol II pauses at 5-carboxycytosine (5caC), an epigenetic modification of cytosine, because of a specific hydrogen bond between the carboxyl group of 5caC and a specific residue in fork loop 3 of Pol II. This hydrogen bond compromises productive NTP binding and slows down elongation. Apart from this specific interaction, the carboxyl group of 5caC can potentially interact with numerous charged residues in the cleft of Pol II. However, it is not clear how other interactions between Pol II and 5caC contribute to pausing. In this study, we use Markov state models (a type of kinetic network models) built from extensive molecular dynamics simulations to comprehensively study the impact of 5caC on Pol II translocation. We describe two translocation intermediates with specific interactions that prevent the template base from loading into the Pol II active site. In addition to the previously observed state with 5caC constrained by fork loop 3, we discovered a new intermediate state with a hydrogen bond between 5caC and fork loop 2. Surprisingly, we find that 5caC may curb translocation by suppressing kinking of the helix bordering the active site (the bridge helix) because its high flexibility is critical to translocation. Our work provides new insights into how epigenetic modifications of genomic DNA can modulate Pol II translocation, inducing pauses in transcription.

Experimental and theoretical assessment of protonated Hoogsteen 9-methylguanine-1-methylcytosine base-pair dissociation: kinetics within a statistical reaction framework.

We investigated the collision-induced dissociation (CID) reactions of a protonated Hoogsteen 9-methylguanine-1-methylcytosine base pair (HG-[9MG·1MC + H]+), which aims to address the mystery of the literature reported "anomaly" in product ion distributions and compare the kinetics of a Hoogsteen base pair with its Watson-Crick isomer WC-[9MG·1MC + H]+ (reported recently by Sun et al.; Phys. Chem. Chem. Phys., 2020, 22, 24986). Product ion cross sections and branching ratios were measured as a function of center-of-mass collision energy using guided-ion beam tandem mass spectrometry, from which base-pair dissociation energies were determined. Product structures and energetics were assessed using various theories, of which the composite DLPNO-CCSD(T)/aug-cc-pVTZ//ωB97XD/6-311++G(d,p) was adopted as the best-performing method for constructing a reaction potential energy surface. The statistical Rice-Ramsperger-Kassel-Marcus theory was found to provide a useful framework for rationalizing the dominating abundance of [1MC + H]+ over [9MG + H]+ in the fragment ions of HG-[9MG·1MC + H]+. The kinetics analysis proved the necessity for incorporating into kinetics modeling not only the static properties of reaction minima and transition states but more importantly, the kinetics of individual base-pair conformers that have formed in collisional activation. The analysis also pinpointed the origin of the statistical kinetics of HG-[9MG·1MC + H]+vs. the non-statistical behavior of WC-[9MG·1MC + H]+ in terms of their distinctively different intra-base-pair hydrogen-bonds and consequently the absence of proton transfer between the N1 position of 9MG and the N3' of 1MC in the Hoogsteen base pair. Finally, the Hoogsteen base pair was examined in the presence of a water ligand, i.e., HG-[9MG·1MC + H]+·H2O. Besides the same type of base-pair dissociation as detected in dry HG-[9MG·1MC + H]+, secondary methanol elimination was observed via the SN2 reaction of water with nucleobase methyl groups.

Cidofovir / Cidofovir

INTRODUCCIÓN: La cistitis hemorrágica (HC) es una complicación grave del trasplante de células madre hematopoyéticas (HSCT) y presenta una incidencia variable del 7 al 70%(1). Generalmente, la HC es una complicación dolorosa que prolonga la internación, aumenta el requerimiento de transfusiones de sangre y en sus formas severas puede causar obstrucción del tracto urinario. La ocurrencia de HC ha sido asociada con mayor mortalidad. Los factores predisponentes, incluyen: HSCT alogénico, edad avanzada en el trasplante, enfermedad de injerto contra huésped (GVHD), trombocitopenia, coagulopatía e infección viral. Las HC se clasifican en dos tipos: (1) inicio temprano, que ocurre dentro de las primeras 48 a 72 horas después de HSCT y generalmente debido a los efectos tóxicos de la quimioterapia; (2) inicio tardío, ocurre luego de 72 horas, usualmente de causa infecciosa, particularmente el virus BK (BKV)(2). La HC asociada al virus BK (BKV-HC) es una complicación frecuente luego de un trasplante alogénico de células hematopoyéticas. De acuerdo a su presentación clínica, se clasifica en diferentes grados de severidad: Grado I: Hematuria microscópica; Grado II: Hematuria macroscópica; Grado III: Hematuria macroscópica con presencia de coágulos en orina; Grado IV: Hematuria macroscópica con presencia de coágulos en orina y alteración de la función renal secundaria a obstrucción de las vías urinarias. TECNOLOGÍA: El cidofovir es un nucleósido análogo de citosina activo contra varios virus ADN. Ejerce una inhibición selectiva en la síntesis de ADN, suprimiendo la replicación viral. La EMA (European Medicines Agency) y la FDA (Food and Drug Administration) lo aprobaron para el tratamiento de la retinitis por citomegalovirus en adultos con síndrome de inmunodeficiencia adquirida y sin alteración de la función renal. El cidofovir causa nefrotoxicidad con daño a células tubulares proximales y aumento de la creatinina sérica. La nefrotoxicidad es muy frecuente y es dosis dependiente. La mayoría de las veces se recomienda la asociación con Probenecid vía oral para mantener una concentración plasmática útil de cidofovir que permita su administración semanal, disminuyendo la penetración y acumulación del cidofovir en las células renales y así atenuar su nefrotoxicidad. La modalidad de tratamiento varía en dosis y vías de administración. La vía intravesical se usa en casos de viruria con baja viremia y daño renal previo, aunque su efectividad es cuestionada. Por vía endovenosa, se usa en una dosis variable de 0,5 a 5 mg/kg, una o dos veces por semana. La elección de dosis y frecuencia depende de la severidad del cuadro y fundamentalmente, de la nefrotoxicidad. OBJETIVO: Evaluar la eficacia y seguridad de cidofovir en la HC por BK virus post HSCT. DISCUSIÓN: El cidofovir constituye una tecnología sanitaria experimental para el tratamiento de la HC-BKV. Se han utilizado diferentes dosis y vías de administración. La evidencia disponible sugiere que su eficacia para el tratamiento oscila entre el 60 y 100%. En el diseño de los estudios se constata que sólo en uno fue comparado vs tratamiento convencional pero fue un estudio descriptivo de dos grupos independientes. En este estudio, el cidofovir no fue superior en respuesta clínica ni en duración de la HC. La respuesta clínica de la HC en cuanto a disminución de hematuria, eliminación de coágulos y disuria, no siempre correlaciona con una significativa disminución de la carga viral en sangre o en orina. La mitad de los pacientes pos-trasplante presenta viruria y no desarrollan HC. Este aspecto no permite definir con absoluta certeza el grado de responsabilidad del virus ni del cidofovir en el desarrollo de la HC y su tratamiento. Se describen varios eventos adversos pero el más importante y serio, es la nefrotoxicidad que se relaciona con las dosis utilizadas y la duración del tratamiento. La función renal basal y la viruria/viremia deben ser tenidas en cuenta en la prescripción y vía de administración del cidofovir. Los criterios de elección de la ruta de administración local o sistémica no fueron expresamente definidos pero se relacionan con la ubicación del virus, la nefrotoxicidad y la función renal previa. El contexto peri-trasplante agrega varios tratamientos potencialmente nefrotóxicos que se suman al cidofovir y a la nefropatía derivada de la obstrucción urinaria por HC, lo que impone la necesidad de un extremo cuidado para la función renal. RECOMENDACIONES: El cidofovir es una opción terapéutica en el tratamiento de la HC-BKV y requiere control estricto de la función renal dado el alto riesgo de nefrotoxicidad. Es por ahora un tratamiento experimental. Su uso adecuado y en ámbito adecuado, es de estricta responsabilidad del médico tratante.

A Strategy for Accurate Quantification of 5-Methylcytosine and 5-Hydroxymethylcytosine at CpG Sites Within Gene Promoter.

5-Methylcytosine (5mC) can be converted to 5-hydroxymethylcytosine (5hmC) in mammalian DNA by the ten-eleven translocation (TET) enzymes. Traditional bisulfite-based DNA methylation analysis techniques have been widely used in the detection of 5mC. However, they can not discriminate 5hmC from 5mC, leading to overestimate 5mC levels. We here introduce a strategy, combination of selective oxidation and bisulfite pyrosequencing (BS-Pyroseq), for quantification of both 5mC and 5hmC at CpG sites within the promoters of CDH1, DAPK, RARß and RUNX3 genes in a panel of cell lines and clinical samples. As expected, oxidative bisulfite pyrosequencing (oxBS-Pyroseq) assay decreased overall or site-specific methylation levels of three of these genes in most cell lines as compared with BS-Pyroseq assay. Similarly, decreased overall or site-specific methylation levels of DAPK, RARß and RUNX3 genes in laryngeal, gastric and thyroid cancer and their matched normal tissues, respectively, were also found by a comparison between these two techniques, particularly in cancerous tissues. In addition, by using this combined strategy and hydroxymethylcytosine DNA immunoprecipitation (hMeDIP) assay, we demonstrated that TET1 up-regulated DAPK expression through promoter demethylation. Collectively, this strategy is easy to establish and accurately discriminates and quantifies 5mC and 5hmC at CpG sites within selected gene promoters.

Neighboring Genes Show Correlated Evolution in Gene Expression.

When considering the evolution of a gene's expression profile, we commonly assume that this is unaffected by its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between neighboring genes in gene expression profiles in extant taxa. Indeed, in all eukaryotic genomes genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their expression or is gene expression evolution autonomous? To address this here we consider evolution of human gene expression since the human-chimp common ancestor, allowing for both variation in estimation of current expression level and error in Bayesian estimation of the ancestral state. We find that in all tissues and both sexes, the change in gene expression of a focal gene on average predicts the change in gene expression of neighbors. The effect is highly pronounced in the immediate vicinity (<100 kb) but extends much further. Sex-specific expression change is also genomically clustered. As genes increasing their expression in humans tend to avoid nuclear lamina domains and be enriched for the gene activator 5-hydroxymethylcytosine, we conclude that, most probably owing to chromatin level control of gene expression, a change in gene expression of one gene likely affects the expression evolution of neighbors, what we term expression piggybacking, an analog of hitchhiking.

Analysis of nanopore data using hidden Markov models.

MOTIVATION: Nanopore-based sequencing techniques can reconstruct properties of biosequences by analyzing the sequence-dependent ionic current steps produced as biomolecules pass through a pore. Typically this involves alignment of new data to a reference, where both reference construction and alignment have been performed by hand. RESULTS: We propose an automated method for aligning nanopore data to a reference through the use of hidden Markov models. Several features that arise from prior processing steps and from the class of enzyme used can be simply incorporated into the model. Previously, the M2MspA nanopore was shown to be sensitive enough to distinguish between cytosine, methylcytosine and hydroxymethylcytosine. We validated our automated methodology on a subset of that data by automatically calculating an error rate for the distinction between the three cytosine variants and show that the automated methodology produces a 2-3% error rate, lower than the 10% error rate from previous manual segmentation and alignment. AVAILABILITY AND IMPLEMENTATION: The data, output, scripts and tutorials replicating the analysis are available at https://github.com/UCSCNanopore/Data/tree/master/Automation.

JBP1-seq: a fast and efficient method for genome-wide profiling of 5hmC.

We developed a novel approach, J-binding protein 1 sequencing (JBP1-seq), that combines the benefits of an improved recombinant JBP1 protein, Nextera-based library construction, and next-generation sequencing (NGS) for genome-wide profiling of 5-hydroxymethylcytosine (5hmC). Compared with the original JBP1, this new recombinant JBP1 was biotinylated in vivo and conjugated to magnetic beads via biotin-streptavidin interactions. These modifications allowed a more efficient and consistent pull-down of ß-glucosyl-5-hydroxymethylcytosine (ß-glu-5hmC), and sequence-ready libraries can be generated within 4.5h from DNA inputs as low as 50ng. 5hmC enrichment of human brain DNA using the new JBP1 resulted in over 25,000 peaks called, which is significantly higher than the 4003 peaks enriched using the old JBP1. Comparison of the technical duplicates and validations with other platforms indicated the results are reproducible and reliable. Thus, JBP1-seq provides a fast, efficient, and cost-effective method for accurate 5hmC genome-wide profiling.

Application of a low cost array-based technique - TAB-Array - for quantifying and mapping both 5mC and 5hmC at single base resolution in human pluripotent stem cells.

5-hydroxymethylcytosine (5hmC), an oxidized derivative of 5-methylcytosine (5mC), has been implicated as an important epigenetic regulator of mammalian development. Current procedures use DNA sequencing methods to discriminate 5hmC from 5mC, limiting their accessibility to the scientific community. Here we report a method that combines TET-assisted bisulfite conversion with Illumina 450K DNA methylation arrays for a low-cost high-throughput approach that distinguishes 5hmC and 5mC signals at base resolution. Implementing this approach, termed "TAB-array", we assessed DNA methylation dynamics in the differentiation of human pluripotent stem cells into cardiovascular progenitors and neural precursor cells. With the ability to discriminate 5mC and 5hmC, we identified a large number of novel dynamically methylated genomic regions that are implicated in the development of these lineages. The increased resolution and accuracy afforded by this approach provides a powerful means to investigate the distinct contributions of 5mC and 5hmC in human development and disease.

High burden of BK virus-associated hemorrhagic cystitis in patients undergoing allogeneic hematopoietic stem cell transplantation.

BK virus (BKV) reactivation has been increasingly associated with the occurrence of late-onset hemorrhagic cystitis (HC) after allogeneic hematopoietic SCT (allo-HSCT) resulting in morbidity and sometimes mortality. We investigated the incidence, risk factors and outcome of BKV-HC in 323 consecutive adult patients undergoing allo-HSCT over a 5-year period. BK viremia values for HC staging were evaluated, as well as the medico-economic impact of the complication. Forty-three patients developed BKV-HC. In univariate analysis, young age (P=0.028), unrelated donor (P=0.0178), stem cell source (P=0.0001), HLA mismatching (P=0.0022) and BU in conditioning regimen (P=0.01) were associated with a higher risk of developing BKV-HC. In multivariate analysis, patients receiving cord blood units (CBUs) (P=0.0005) and peripheral blood stem cells (P=0.011) represented high-risk subgroups for developing BKV-HC. BK viremia was directly correlated to HC severity (P=0.011) with a 3 to 6-log peak being likely associated with grades 3 or 4 HC. No correlation was found between BKV-HC and acute graft versus host disease or mortality rate. Patients with BKV-HC required a significantly longer duration of hospitalization (P<0.0001), more RBC (P=0.0003) and platelet transfusions (P<0.0001). Over the 5-year study period, the financial cost of the complication was evaluated at \[euro]2 376 076 ($3 088 899). Strategies to prevent the occurrence of late-onset BKV-HC after allo-HSCT are urgently needed, especially in CBU and peripheral blood stem cell recipients. BK viremia correlates with the severity of the disease. Prospective studies are required to test prophylactic approaches.

Cost-effectiveness of cidofovir treatment of polyomavirus nephropathy in kidney transplant recipients.

BACKGROUND: BK virus nephropathy (BKVAN) causes about 10% of late kidney graft loss. Cidofovir is widely used to treat BKVAN, but the magnitude of the health benefits and costs are largely unknown. We aimed to evaluate the incremental health benefits and costs of cidofovir and immunosuppression reduction compared with immunosuppression reduction alone in kidney transplant patients with BKVAN. METHODS: A probabilistic decision analytic model was developed to simulate a cohort of kidney transplant recipients aged 45 years and above with BKVAN who received cidofovir treatment compared with those who received standard care. The duration of the cycle was 1 year, and the model terminated when all recipients were deceased. RESULTS: Compared with immunosuppression reduction alone, in the base-case, the incremental health benefits of cidofovir were 0.0061 life-years saved (2.2 days), with savings of $20,756 over the lifetime of a transplant recipient. When varying the most influential variables (the probability of response to treatment and graft loss) between best and worst case scenarios, the incremental health outcomes ranged from -0.967 to 1.093 life-years saved, with incremental costs ranging from an extra $27,313 to saving $20,756. CONCLUSIONS: Compared with immunosuppression reduction alone, based on best available data, cidofovir treatment and immunosuppression reduction for BKVAN seem to be cost saving and improves health outcomes. However, because of weak clinical data, particularly around comparative effectiveness, there is still moderate uncertainty in the incremental cost effectiveness. Adequately powered trials are still needed to better define optimal treatment strategies for BKVAN before cidofovir can be recommended strongly as routine therapy.

Applicability of a "Pick a Winner" trial design to acute myeloid leukemia.

Randomized clinical trials remain the gold standard to establish efficacy and safety of new treatments. In acute myeloid leukemia, large trials have been associated with gradual improvement in outcome over 2 decades in younger patients without major differences emerging between treatments. By contrast, in older patients, improvement has been minimal, which justifies a new approach to identifying effective treatments. Given the urgent unmet need, and with the emergence of several novel agents or combinations that are likely to be expensive, large benefits are probably required to change clinical practice. To address this issue, we have evolved a "Pick a Winner" randomized progressive design with a rolling incorporation of novel treatments (drug X), which has been tested in older patients with acute myeloid leukemia. The rationale, operational characteristics, and initial experience of such an approach in the context of the United Kingdom National Cancer Research Institute AML16 trial are presented.

Quantum mechanics study and Monte Carlo simulation on the hydrolytic deamination of 5-methylcytosine glycol.

The efficient formation of 5-methylcytosine glycol (mCg) and its facile deamination to thymine glycol (Tg) may account for the prevalent C → T transition mutation found at methylated CpG site (mCpG) in human p53 gene, a hallmark for many types of human tumors. In this work, the hydrolytic deamination of mCg was investigated at the MP2 and B3LYP levels of theory using the 6-311G(d,p) basis set. In the gas phase, three pathways were explored, paths A-C, and it indicates that the direct deamination of mCg with H(2)O by either pathway is unlikely because of the high activation free energies involved in the rate-determining steps, the formation of the tetrahedral intermediate for paths A and B as well as the formation of the Tg tautomer for path C. In aqueous solution, the role of the water molecules in the deamination of mCg with H(2)O was analyzed in two separate parts: the direct participation of one water molecule in the reaction pathway, called the water-assisted mechanism; and the complementary participation of the aqueous solvation. The water-assisted mechanism was carried out for mCg and the cluster of two water molecules by quantum mechanical calculations in the gas phase. This indicates that the presence of the auxiliary water molecule significantly contributes to decreasing all the activation free energies. The bulk solution effect on the water-assisted mechanism was included by free energy perturbation implemented on Monte Carlo simulations, which is found to be substantial and decisive in the deamination mechanism of mCg. In this case, the water-assisted path A is the most plausible mechanism reported for the deamination of mCg, where the calculated activation free energy (22.6 kcal mol(-1) at B3LYP level of theory) agrees well with the experimentally determined activation free energy (24.8 kcal mol(-1)). The main striking results of the present DFT computational study which is in agreement with previous experimental data is the higher rate of deamination displayed by mCg residues with respect to 5-methylcytosine (mC) bases, which supports that the deamination of mCg contributes significantly to the C → T transition mutation at mCpG dinucleotide site.

Mechanism-based pharmacokinetic/pharmacodynamic model for troxacitabine-induced neutropenia in cancer patients.

PURPOSES: The objective of this study was to develop a mechanism-based population pharmacokinetic/pharmacodynamic (PK/PD) model in describing troxacitabine-induced neutropenia in patients with cancer. METHODS: A total of 727 PK/PD samples from 31 patients with cancer were included in the analysis. A mechanism-based population PD model was developed to describe neutropenia and the final model consisted of (1) a drug-sensitive uncommitted progenitor cell compartment (2) three transit compartments, and (3) a circulating neutrophil compartment with feedback mechanism. The troxacitabine affected the proliferation of sensitive progenitor cells through an inhibitory E (max) model. The model parameters were estimated using the MCPEM algorithm that was implemented in a parallel computing platform consisting of a single computer equipped with a quad-core INTEL central processor unit. RESULTS AND CONCLUSIONS: The mechanism-based PK/PD model developed using parallelized MCPEM method adequately describes the complex relationship between the exposure and absolute neutrophil counts in troxacitabine-treated patients with cancer. The simulation results suggested that the less frequent dosing schedule of troxacitabine used currently in clinical studies was associated with less incidence of neutropenia compared to more frequent dosing schedule.

Viral infections affecting the skin in organ transplant recipients: epidemiology and current management strategies.

Viral skin infections are common findings in organ transplant recipients. The most important etiological agents are the group of human herpesviruses (HHV), human papillomaviruses (HPV), and molluscum contagiosum virus. HHV that are important in this group of patients are herpes simplex virus (HSV) types 1 and 2, varicella-zoster virus (VZV), cytomegalovirus (CMV), Epstein-Barr virus (EBV), HHV-6 and -7, and HHV-8, which causes Kaposi sarcoma (KS). HSV infections are characterized by their ability to establish latency and then reactivate at a later date. The most common manifestations of HSV infection in organ transplant recipients are mucocutaneous lesions of the oropharynx or genital regions. Treatment is usually with acyclovir, valaciclovir, or famciclovir. Acyclovir resistance may arise although the majority of acyclovir-resistant strains have been isolated from AIDS patients and not organ transplant recipients. In such cases, alternatives such as foscarnet, cidofovir, or trifluridine may have to be considered. VZV causes chickenpox as well as herpes zoster. In organ transplant recipients, recurrent herpes zoster can occur. Acute chickenpox in organ transplant patients should be treated with intravenous acyclovir. CMV infection occurs in 20-60% of all transplant recipients. Cutaneous manifestations, which include nonspecific macular rashes, ulcers, purpuric eruptions, and vesiculobullous lesions, are seen in 10-20% of patients with systemic infection and signify a poor prognosis. The present gold standard for treatment is ganciclovir, but newer drugs such as valganciclovir appear promising. EBV is responsible for some cases of post-transplant lymphoproliferative disorder, which represents the greatest risk of serious EBV disease in transplant recipients. HHV-6 and HHV-7 are two relatively newly discovered viruses and, at present, the body of information concerning these two agents is still fairly limited. KS is caused by HHV-8, which is the most recently discovered lymphotrophic HHV. Iatrogenic KS is seen in solid-organ transplant recipients, with a prevalence of 0.5-5% depending on the patient's country of origin. HPV is ubiquitous, and organ transplant recipients may never totally clear HPV infections, which are the most frequently recurring infections in renal transplant recipients. HPV infection in transplant recipients is important because of its link to the development of certain skin cancers, in particular, squamous cell carcinoma. Regular surveillance, sun avoidance, and patient education are important aspects of the management strategy.