Rectal Microbiome Composition Correlates with Humoral Immunity to HIV-1 in Vaccinated Rhesus Macaques.

The microbiome is an integral and dynamic component of the host and is emerging as a critical determinant of immune responses; however, its influence on vaccine immunogenicity is largely not well understood. Here, we examined the pivotal relationship between the mucosal microbiome and vaccine-induced immune responses by assessing longitudinal changes in vaginal and rectal microbiome profiles after intradermal immunization with a human immunodeficiency virus type 1 (HIV-1) DNA vaccine in adult rhesus macaques that received two prior DNA primes. We report that both vaginal and rectal microbiomes were dominated by Firmicutes but were composed of distinct genera, denoting microbiome specialization across mucosal tissues. Following immunization, the vaginal microbiome was resilient, except for a transient decrease in Streptococcus In contrast, the rectal microbiome was far more responsive to vaccination, exhibiting an increase in the ratio of Firmicutes to Bacteroidetes Within Bacteroidetes, multiple genera were significantly decreased, including Prevotella, Alloprevotella, Bacteroides, Acetobacteroides, Falsiporphyromonas, and Anaerocella. Decreased abundance of Prevotella correlated with induction of gut-homing α4β7 + effector CD4 T cells. Prevotella abundance also negatively correlated with rectal HIV-1 specific IgG levels. While rectal Lactobacillus was unaltered following DNA vaccination, baseline Lactobacillus abundance showed strong associations with higher rectal HIV-1 gp140 IgA induced following a protein boost. Similarly, the abundance of Clostridium in cluster IV was associated with higher rectal HIV-1 gp140 IgG responses. Collectively, these data reveal that the temporal stability of bacterial communities following DNA immunization is site dependent and highlight the importance of host-microbiome interactions in shaping HIV-1 vaccine responses. Our findings have significant implications for microbial manipulation as a strategy to enhance HIV vaccine-induced mucosal immunity.IMPORTANCE There is considerable effort directed toward evaluating HIV-1 vaccine platforms to select the most promising candidates for enhancing mucosal HIV-1 antibody. The most successful thus far, the RV144 trial provided partial protection due to waning HIV-1 antibody titers. In order to develop an effective HIV vaccine, it may therefore be important to understand how biological factors, such as the microbiome, modulate host immune responses. Furthermore, as intestinal microbiota antigens may generate antibodies cross-reactive to the HIV-1 envelope glycoprotein, understanding the relationship between gut microbiota composition and HIV-1 envelope antibody responses after vaccination is important. Here, we demonstrate for the first time in rhesus macaques that the rectal microbiome composition can influence HIV-1 vaccine immunogenicity, and we report temporal changes in the mucosal microbiome profile following HIV-1 vaccination. Our results could inform findings from the HIV Vaccine Trials Network (HVTN) vaccine studies and contribute to an understanding of how the microbiome influences HIV-1 antibody responses

Demonstration of Protein-Based Human Identification Using the Hair Shaft Proteome

YesHuman identification from biological material is largely dependent on the ability to characterize genetic polymorphisms in DNA. Unfortunately, DNA can degrade in the environment, sometimes below the level at which it can be amplified by PCR. Protein however is chemically more robust than DNA and can persist for longer periods. Protein also contains genetic variation in the form of single amino acid polymorphisms. These can be used to infer the status of non-synonymous single nucleotide polymorphism alleles. To demonstrate this, we used mass spectrometry-based shotgun proteomics to characterize hair shaft proteins in 66 European-American subjects. A total of 596 single nucleotide polymorphism alleles were correctly imputed in 32 loci from 22 genes of subjects’ DNA and directly validated using Sanger sequencing. Estimates of the probability of resulting individual non-synonymous single nucleotide polymorphism allelic profiles in the European population, using the product rule, resulted in a maximum power of discrimination of 1 in 12,500. Imputed non-synonymous single nucleotide polymorphism profiles from European–American subjects were considerably less frequent in the African population (maximum likelihood ratio = 11,000). The converse was true for hair shafts collected from an additional 10 subjects with African ancestry, where some profiles were more frequent in the African population. Genetically variant peptides were also identified in hair shaft datasets from six archaeological skeletal remains (up to 260 years old). This study demonstrates that quantifiable measures of identity discrimination and biogeographic background can be obtained from detecting genetically variant peptides in hair shaft protein, including hair from bioarchaeological contexts.The Technology Commercialization Innovation Program (Contracts #121668, #132043) of the Utah Governors Office of Commercial Development, the Scholarship Activitie

Meatal stenosis: a retrospective analysis of over 4000 patients.

The literature on treatment of meatal stenosis is limited to single center series. Controversy exists regarding choice of meatotomy versus meatoplasty and need for general anesthesia. Our objective was to analyze treatment efficacy, current practice patterns and utilization of anesthesia. We hypothesized that meatoplasty would be associated with a lower re-operative rate.We used a hospital consortium database to identify children who were diagnosed with meatal stenosis between January 1, 2009 and December 31, 2012. Both univariate and multivariate analyses were completed to evaluate correlations between patient, surgeon and hospital characteristics and type of procedure. The propensity of surgeons to operate with or without general anesthesia was analyzed.We identified 4373 male patients with a diagnosis of meatal stenosis treated by 123 surgeons. Fifty-percent of boys had procedural intervention during the 4-year period. Median follow-up was 25 and 22 months after meatotomy and meatoplasty, respectively. There was a re-operative rate of 3.5% and 0.2% for office meatotomy versus meatoplasty with general anesthesia. Multivariate analysis demonstrated that being White and living in the Northeast independently increased odds of intervention. Half of the surgeons treated meatal stenosis exclusively under general anesthesia.This study is limited by an inability to determine recurrence rates. Only patients having secondary surgery at the same institution within the time period captured by the database (6 months-4 years) could be identified. As such, the true recurrence of meatal stenosis is likely higher. Although the re-operative rate is not equivalent to the recurrence rate, the two are correlated. Likewise, the surgeon's propensity to operate could be biased by their propensity to diagnosis meatal stenosis and this could affect the rates cited. In addition to the cost benefit achieved with avoidance of general anesthesia (estimated to be a 10-fold cost reduction, the 2012 Consensus Statement of the International Anesthesia Research Society has highlighted that there is increasing evidence from research studies suggesting the benefits of general anesthesia should be considered in the context of its possible harmful effects. Although this study and others have highlighted that in-office procedures are a viable alternative to meatoplasty with general anesthesia, there are multiple factors in being able to perform an office meatotomy. Arguably, the two most important are the patient's ability to cooperate and his anatomy.The large sample size, over 4000 patients, allowed us to show that the hypothesis, that meatoplasty would be associated with a lower re-operative rate (0.2%), is true. With a low re-operative rate (3.5%), office meatotomy is a reasonable choice of surgical treatment if the child can cooperate and the anatomy is appropriate. On the other hand, if general anesthesia is utilized, formal meatoplasty is associated with a lower re-operative rate

Meatal stenosis: a retrospective analysis of over 4000 patients.

The literature on treatment of meatal stenosis is limited to single center series. Controversy exists regarding choice of meatotomy versus meatoplasty and need for general anesthesia. Our objective was to analyze treatment efficacy, current practice patterns and utilization of anesthesia. We hypothesized that meatoplasty would be associated with a lower re-operative rate.We used a hospital consortium database to identify children who were diagnosed with meatal stenosis between January 1, 2009 and December 31, 2012. Both univariate and multivariate analyses were completed to evaluate correlations between patient, surgeon and hospital characteristics and type of procedure. The propensity of surgeons to operate with or without general anesthesia was analyzed.We identified 4373 male patients with a diagnosis of meatal stenosis treated by 123 surgeons. Fifty-percent of boys had procedural intervention during the 4-year period. Median follow-up was 25 and 22 months after meatotomy and meatoplasty, respectively. There was a re-operative rate of 3.5% and 0.2% for office meatotomy versus meatoplasty with general anesthesia. Multivariate analysis demonstrated that being White and living in the Northeast independently increased odds of intervention. Half of the surgeons treated meatal stenosis exclusively under general anesthesia.This study is limited by an inability to determine recurrence rates. Only patients having secondary surgery at the same institution within the time period captured by the database (6 months-4 years) could be identified. As such, the true recurrence of meatal stenosis is likely higher. Although the re-operative rate is not equivalent to the recurrence rate, the two are correlated. Likewise, the surgeon's propensity to operate could be biased by their propensity to diagnosis meatal stenosis and this could affect the rates cited. In addition to the cost benefit achieved with avoidance of general anesthesia (estimated to be a 10-fold cost reduction, the 2012 Consensus Statement of the International Anesthesia Research Society has highlighted that there is increasing evidence from research studies suggesting the benefits of general anesthesia should be considered in the context of its possible harmful effects. Although this study and others have highlighted that in-office procedures are a viable alternative to meatoplasty with general anesthesia, there are multiple factors in being able to perform an office meatotomy. Arguably, the two most important are the patient's ability to cooperate and his anatomy.The large sample size, over 4000 patients, allowed us to show that the hypothesis, that meatoplasty would be associated with a lower re-operative rate (0.2%), is true. With a low re-operative rate (3.5%), office meatotomy is a reasonable choice of surgical treatment if the child can cooperate and the anatomy is appropriate. On the other hand, if general anesthesia is utilized, formal meatoplasty is associated with a lower re-operative rate

Transcriptomic Markers of Recombinant Human Erythropoietin Micro-Dosing in Thoroughbred Horses.

Recombinant human erythropoietin (rHuEPO) is a well-known performance enhancing drug in human athletes, and there is anecdotal evidence of it being used in horse racing for the same purpose. rHuEPO, like endogenous EPO, increases arterial oxygen content and thus aerobic power. Micro-doping, or injecting smaller doses over a longer period of time, has become an important concern in both human and equine athletics since it is more difficult to detect. Horses offer an additional challenge of a contractile spleen, thus large changes in the red blood cell mass occur naturally. To address the challenge of detecting rHuEPO doping in horse racing, we determined the transcriptomic effects of rHuEPO micro-dosing over seven weeks in exercised Thoroughbreds. RNA-sequencing of peripheral blood mononuclear cells isolated at several time points throughout the study identified three transcripts (C13H16orf54, PUM2 and CHTOP) that were significantly (PFDR < 0.05) different between the treatment groups across two or three time point comparisons. PUM2 and CHTOP play a role in erythropoiesis while not much is known about C13H16orf54, but it is primarily expressed in whole blood. However, gene expression differences were not large enough to detect via RT-qPCR, thereby precluding their utility as biomarkers of micro-doping

Transcriptomic Markers of Recombinant Human Erythropoietin Micro-Dosing in Thoroughbred Horses

Recombinant human erythropoietin (rHuEPO) is a well-known performance enhancing drug in human athletes, and there is anecdotal evidence of it being used in horse racing for the same purpose. rHuEPO, like endogenous EPO, increases arterial oxygen content and thus aerobic power. Micro-doping, or injecting smaller doses over a longer period of time, has become an important concern in both human and equine athletics since it is more difficult to detect. Horses offer an additional challenge of a contractile spleen, thus large changes in the red blood cell mass occur naturally. To address the challenge of detecting rHuEPO doping in horse racing, we determined the transcriptomic effects of rHuEPO micro-dosing over seven weeks in exercised Thoroughbreds. RNA-sequencing of peripheral blood mononuclear cells isolated at several time points throughout the study identified three transcripts (C13H16orf54, PUM2 and CHTOP) that were significantly (PFDR < 0.05) different between the treatment groups across two or three time point comparisons. PUM2 and CHTOP play a role in erythropoiesis while not much is known about C13H16orf54, but it is primarily expressed in whole blood. However, gene expression differences were not large enough to detect via RT-qPCR, thereby precluding their utility as biomarkers of micro-doping

Association of the Lactase Persistence Haplotype Block With Disease Risk in Populations of European Descent

Among people of European descent, the ability to digest lactose into adulthood arose via strong positive selection of a highly advantageous allele encompassing the lactase gene. Lactose-tolerant and intolerant individuals may have different disease risks due to the shared genetics of their haplotype block. Therefore, the overall objective of the study was to assess the genetic association of the lactase persistence haplotype to disease risk. Using data from the 1000Genomes project, we estimated the size of the lactase persistence haplotype block to be 1.9 Mbp containing up to 9 protein-coding genes and a microRNA. Based on the function of the genes and microRNA, we studied health phenotypes likely to be impacted by the lactase persistence allele: prostate cancer status, cardiovascular disease status, and bone mineral density. We used summary statistics from large genome-wide metanalyses-32,965 bone mineral density, 140,306 prostate cancer and 184,305 coronary artery disease subjects-to evaluate whether the lactase persistence allele was associated with these disease phenotypes. Despite the fact that previous work demonstrated that the lactase persistence haplotype block harbors increased deleterious mutations, these results suggest little effect on the studied disease phenotypes

Proteomic profiling of Pachyonychia congenita plantar callus.

Callus samples from the ball and the arch of the foot, collected on tape circles, were compared by shotgun proteomic profiling. Pachyonychia congenita subjects were sampled who exhibited a mutation in KRT6A, KRT6B, KRT6C, KRT16 or KRT17, and the proteins were digested and analyzed by tandem mass spectrometry. In comparison with samples from unaffected control subjects, those from subjects with KRT6A or KRT16 mutations displayed the most differences in profile from normal, while those from subjects with KRT6C or KRT17 mutations showed few differences from normal. The profiles from subjects with KRT6B mutations were intermediate in protein profile differences. Degree of departure from the normal profile could be estimated by expression of numerous proteins in callus from the ball of the foot that were consistently different. By contrast, the protein profile from the arch of the foot was hardly affected. The results provide a foundation for noninvasive monitoring of the efficacy of treatments with quantitative assessment of departure from the normal phenotype.SignificancePachyonychia congenita is an orphan disease in which the connection between the basic defect (keratin mutation) and debilitating symptoms (severe plantar pain) is poorly understood. Present work addresses the degree to which the protein profile is altered in the epidermis where the severe pain originates. The results indicate that the mutated keratins differ greatly in the degree to which they elicit perturbations in protein profile. In those cases with markedly altered protein levels, monitoring the callus profile may provide an objective measure of treatment efficacy