Analysis of human immune responses in quasi-experimental settings: tutorial in biostatistics

<p>Abstract</p> <p>Background</p> <p>Human immunology is a growing field of research in which experimental, clinical, and analytical methods of many life science disciplines are utilized. Classic epidemiological study designs, including observational longitudinal birth cohort studies, offer strong potential for gaining new knowledge and insights into immune response to pathogens in humans. However, rigorous discussion of methodological issues related to designs and statistical analysis that are appropriate for longitudinal studies is lacking.</p> <p>Methods</p> <p>In this communication we address key questions of quality and validity of traditional and recently developed statistical tools applied to measures of immune responses. For this purpose we use data on humoral immune response (IR) associated with the first cryptosporidial diarrhea in a birth cohort of children residing in an urban slum in south India. The main objective is to detect the difference and derive inferences for a change in IR measured at two time points, before (pre) and after (post) an event of interest. We illustrate the use and interpretation of analytical and data visualization techniques including generalized linear and additive models, data-driven smoothing, and combinations of box-, scatter-, and needle-plots.</p> <p>Results</p> <p>We provide step-by-step instructions for conducting a thorough and relatively simple analytical investigation, describe the challenges and pitfalls, and offer practical solutions for comprehensive examination of data. We illustrate how the assumption of time irrelevance can be handled in a study with a pre-post design. We demonstrate how one can study the dynamics of IR in humans by considering the timing of response following an event of interest and seasonal fluctuation of exposure by proper alignment of time of measurements. This alignment of calendar time of measurements and a child's age at the event of interest allows us to explore interactions between IR, seasonal exposures and age at first infection.</p> <p>Conclusions</p> <p>The use of traditional statistical techniques to analyze immunological data derived from observational human studies can result in loss of important information. Detailed analysis using well-tailored techniques allows the depiction of new features of immune response to a pathogen in longitudinal studies in humans. The proposed staged approach has prominent implications for future study designs and analyses.</p

Modulation of enhancer looping and differential gene targeting by Epstein-Barr virus transcription factors directs cellular reprogramming

Epstein-Barr virus (EBV) epigenetically reprogrammes B-lymphocytes to drive immortalization and facilitate viral persistence. Host-cell transcription is perturbed principally through the actions of EBV EBNA 2, 3A, 3B and 3C, with cellular genes deregulated by specific combinations of these EBNAs through unknown mechanisms. Comparing human genome binding by these viral transcription factors, we discovered that 25% of binding sites were shared by EBNA 2 and the EBNA 3s and were located predominantly in enhancers. Moreover, 80% of potential EBNA 3A, 3B or 3C target genes were also targeted by EBNA 2, implicating extensive interplay between EBNA 2 and 3 proteins in cellular reprogramming. Investigating shared enhancer sites neighbouring two new targets (WEE1 and CTBP2) we discovered that EBNA 3 proteins repress transcription by modulating enhancer-promoter loop formation to establish repressive chromatin hubs or prevent assembly of active hubs. Re-ChIP analysis revealed that EBNA 2 and 3 proteins do not bind simultaneously at shared sites but compete for binding thereby modulating enhancer-promoter interactions. At an EBNA 3-only intergenic enhancer site between ADAM28 and ADAMDEC1 EBNA 3C was also able to independently direct epigenetic repression of both genes through enhancer-promoter looping. Significantly, studying shared or unique EBNA 3 binding sites at WEE1, CTBP2, ITGAL (LFA-1 alpha chain), BCL2L11 (Bim) and the ADAMs, we also discovered that different sets of EBNA 3 proteins bind regulatory elements in a gene and cell-type specific manner. Binding profiles correlated with the effects of individual EBNA 3 proteins on the expression of these genes, providing a molecular basis for the targeting of different sets of cellular genes by the EBNA 3s. Our results therefore highlight the influence of the genomic and cellular context in determining the specificity of gene deregulation by EBV and provide a paradigm for host-cell reprogramming through modulation of enhancer-promoter interactions by viral transcription factors

Association between precipitation upstream of a drinking water utility and nurse advice calls relating to acute gastrointestinal illnesses

BACKGROUND: The River Göta Älv is a source of fresh-water for the City of Gothenburg (Sweden). We recently identified a clear association between upstream precipitation and indicator bacteria concentrations in the river water outside the intake to the drinking water utility. This study aimed to determine if variation in the incidence of acute gastrointestinal illnesses is associated with upstream precipitation. METHODS: We acquired data, covering 1494 days, on the daily number of telephone calls to the nurse advice line from citizens in Gothenburg living in areas with Göta Älv as a fresh-water supply. We separated calls relating to gastrointestinal illnesses from other medical concerns, and analyzed their association with precipitation using a distributed lag non-linear Poisson regression model, adjusting for seasonal patterns and covariates. We used a 0-21-day lag period for precipitation to account for drinking water delivery times and incubation periods of waterborne pathogens. RESULTS: The study period contained 25,659 nurse advice calls relating to gastrointestinal illnesses. Heavy rainfall was associated with increased calls the same day and around 5-6 days later. Consecutive days of wet weather were also found to be associated with an increase in the daily number of gastrointestinal concerns. No associations were identified between precipitation and nurse advice calls relating to other medical concerns. CONCLUSION: An increase in nurse advice calls relating to gastrointestinal illnesses around 5-6 days after heavy rainfall is consistent with a hypothesis that the cause could be related to drinking water due to insufficient barriers in the drinking water production, suggesting the need for improved drinking water treatment

Late Cretaceous spore-pollen zonation of the Central African Rift System (CARS), Kaikang Trough, Muglad Basin, South Sudan: angiosperm spread and links to the Elaterates Province

This paper presents a first detailed study on and new zonation scheme for the Kaikang Trough, Muglad Basin of South Sudan. The Kaikang Trough lies within the central sediment locus of the Muglad Basin, a non-marine African cratonic basin within the Central African Rift System (CARS) Two wells, KW-1 and K-4, were examined leading to the recognition of five palynological assemblage zones: K-I (early–middle Cenomanian), K-II (late Cenomanian), K-III (Turonian?–Santonian), K-IV (Campanian–Maastrichtian) and K-V (Maastrichtian). The elaterate group are peculiarly absent in otherwise rich Cenomanian palynological assemblages of the Muglad Basin. Why this is so, and the implications for the global middle Cretaceous Elaterate Province, needs some explanation. The CARS provided a range of diverse freshwater alluvial and lake-shore substrates. Its cross-continent sweep may have played a role in the evolution and dispersal of floras including early angiosperms as the rift basin of the proto-South Atlantic became a permanently flooded fjord