Baseline gene signatures of reactogenicity to Ebola vaccination: a machine learning approach across multiple cohorts

Introduction: The rVSVDG-ZEBOV-GP (Ervebo®) vaccine is both immunogenic and protective against Ebola. However, the vaccine can cause a broad range of transient adverse reactions, from headache to arthritis. Identifying baseline reactogenicity signatures can advance personalized vaccinology and increase our understanding of the molecular factors associated with such adverse events. Methods: In this study, we developed a machine learning approach to integrate prevaccination gene expression data with adverse events that occurred within 14 days post-vaccination. Results and Discussion: We analyzed the expression of 144 genes across 343 blood samples collected from participants of 4 phase I clinical trial cohorts: Switzerland, USA, Gabon, and Kenya. Our machine learning approach revealed 22 key genes associated with adverse events such as local reactions, fatigue, headache, myalgia, fever, chills, arthralgia, nausea, and arthritis, providing insights into potential biological mechanisms linked to vaccine reactogenicity

Systems Vaccinology of rVSV-ZEBOV Ebola Vaccine

A febre hemorrágica causada pelo vírus Ebola é uma doença grave com alta mortalidade, sendo a vacinação uma importante estratégia de intervenção. A rVSV-ZEBOV, uma vacina recombinante do vírus da estomatite vesicular (VSV) em que a glicoproteína de envelope é a do vírus Ebola da cepa Zaire, foi a primeira aprovada para uso clínico. Apesar de imunogênica e segura, a vacina é reatogênica podendo causar febre, calafrios, mialgia e artrite. Usando dados de transcriptoma do sangue nós realizamos análises de transcriptoma para compreender a resposta à vacina em diferentes tempos para 4 diferentes coortes. A partir dos mesmos dados obtidos antes da vacinação, nós identificamos conjuntos de genes preditores de eventos adversos relacionados à vacina rVSV-ZEBOV. Os dados foram obtidos por RNA-seq para 64 voluntários e por dual-color Reverse Transcriptase Multiplex Ligation-dependent Probe Amplification (dcRT-MLPA) para 375 voluntários entre vacinados e placebos. A identificação de genes preditores das reações adversas foi realizada utilizando o algoritmo Random Forest. Com o algoritmo \"AdaBoost\" obtivemos modelo capaz de predizer indivíduos com artrite, com valor preditivo positivo de 1 e valor preditivo negativo de 0.818, utilizando dados de expressão de apenas cinco genes. Este trabalho foi importante para compreender melhor a resposta induzida pela vacina rVSV-ZEBOV e identificar genes possivelmente relacionados à predisposição das pessoas a desenvolver reatogenicidade pós vacinal.Hemorrhagic fever caused by the Ebola virus is a high mortality disease, and vaccination is an important intervention strategy. The rVSV-ZEBOV, a recombinant vesicular stomatitis virus (VSV) vaccine in which the envelope glycoprotein is that of the Ebola virus of the Zaire strain, was the first one to be approved for medical use. Although immunogenic and safe, the vaccine is very reactogenic and can cause fever, chills, myalgia and arthritis. From blood transcriptome data we performed transcriptome analysis to understand the response to the vaccine at different time points for 4 different cohorts. With the same data obtained before vaccination, we identified sets of genes that predict adverse events related to the rVSV-ZEBOV vaccine. Data were obtained by RNA-seq for 64 volunteers and by dual-color Reverse Transcriptase Multiplex Ligation-dependent Probe Amplification (dcRT-MLPA) for 375 volunteers. The identification of predictor genes was performed with Random Forest Algorithm. Using the \"AdaBoost\'\' algorithm, we selected a model capable of predicting individuals with arthritis, with positive predictive value of 1, and negative predictive value of 0.818 based on expression data from only five genes. This work was important to better understand the response induced by the rVSV-ZEBOV vaccine and to identify genes possibly related to people\'s predisposition to develop post-vaccine reactogenicity

Characterisation of microbial attack on archaeological bone

As part of an EU funded project to investigate the factors influencing bone preservation in the archaeological record, more than 250 bones from 41 archaeological sites in five countries spanning four climatic regions were studied for diagenetic alteration. Sites were selected to cover a range of environmental conditions and archaeological contexts. Microscopic and physical (mercury intrusion porosimetry) analyses of these bones revealed that the majority (68%) had suffered microbial attack. Furthermore, significant differences were found between animal and human bone in both the state of preservation and the type of microbial attack present. These differences in preservation might result from differences in early taphonomy of the bones. © 2003 Elsevier Science Ltd. All rights reserved

NEOTROPICAL XENARTHRANS: a data set of occurrence of xenarthran species in the Neotropics

Xenarthrans—anteaters, sloths, and armadillos—have essential functions for ecosystem maintenance, such as insect control and nutrient cycling, playing key roles as ecosystem engineers. Because of habitat loss and fragmentation, hunting pressure, and conflicts with domestic dogs, these species have been threatened locally, regionally, or even across their full distribution ranges. The Neotropics harbor 21 species of armadillos, 10 anteaters, and 6 sloths. Our data set includes the families Chlamyphoridae (13), Dasypodidae (7), Myrmecophagidae (3), Bradypodidae (4), and Megalonychidae (2). We have no occurrence data on Dasypus pilosus (Dasypodidae). Regarding Cyclopedidae, until recently, only one species was recognized, but new genetic studies have revealed that the group is represented by seven species. In this data paper, we compiled a total of 42,528 records of 31 species, represented by occurrence and quantitative data, totaling 24,847 unique georeferenced records. The geographic range is from the southern United States, Mexico, and Caribbean countries at the northern portion of the Neotropics, to the austral distribution in Argentina, Paraguay, Chile, and Uruguay. Regarding anteaters, Myrmecophaga tridactyla has the most records (n = 5,941), and Cyclopes sp. have the fewest (n = 240). The armadillo species with the most data is Dasypus novemcinctus (n = 11,588), and the fewest data are recorded for Calyptophractus retusus (n = 33). With regard to sloth species, Bradypus variegatus has the most records (n = 962), and Bradypus pygmaeus has the fewest (n = 12). Our main objective with Neotropical Xenarthrans is to make occurrence and quantitative data available to facilitate more ecological research, particularly if we integrate the xenarthran data with other data sets of Neotropical Series that will become available very soon (i.e., Neotropical Carnivores, Neotropical Invasive Mammals, and Neotropical Hunters and Dogs). Therefore, studies on trophic cascades, hunting pressure, habitat loss, fragmentation effects, species invasion, and climate change effects will be possible with the Neotropical Xenarthrans data set. Please cite this data paper when using its data in publications. We also request that researchers and teachers inform us of how they are using these data