Functionally overlapping variants control tuberculosis susceptibility in collaborative cross mice

Host genetics plays an important role in determining the outcome of Mycobacterium tuberculosis infection. We previously found that Collaborative Cross (CC) mouse strains differ in their susceptibility to M. tuberculosis and that the CC042/ GeniUnc (CC042) strain suffered from a rapidly progressive disease and failed to produce the protective cytokine gamma interferon (IFN-γ) in the lung. Here, we used parallel genetic and immunological approaches to investigate the basis of CC042 mouse susceptibility. Using a population derived from a CC001/Unc (CC001) × CC042 intercross, we mapped four quantitative trait loci (QTL) underlying tuberculosis immunophenotypes (Tip1 to Tip4). These included QTL that were associated with bacterial burden, IFN-γ production following infection, and an IFN-γ-independent mechanism of bacterial control. Further immunological characterization revealed that CC042 animals recruited relatively few antigen-specific T cells to the lung and that these T cells failed to express the integrin alpha L (αL; i.e., CD11a), which contributes to T cell activation and migration. These defects could be explained by a CC042 private variant in the Itgal gene, which encodes CD11a and is found within the Tip2 interval. This 15-bp deletion leads to aberrant mRNA splicing and is predicted to result in a truncated protein product. The ItgalCC042 genotype was associated with all measured disease traits, indicating that this variant is a major determinant of susceptibility in CC042 mice. The combined effect of functionally distinct Tip variants likely explains the profound susceptibility of CC042 mice and highlights the multigenic nature of tuberculosis control in the Collaborative Cross. IMPORTANCE The variable outcome of Mycobacterium tuberculosis infection observed in natural populations is difficult to model in genetically homogeneous small-animal models. The newly developed Collaborative Cross (CC) represents a reproducible panel of genetically diverse mice that display a broad range of phenotypic responses to infection. We explored the genetic basis of this variation, focusing on a CC line that is highly susceptible to M. tuberculosis infection. This study identified multiple quantitative trait loci associated with bacterial control and cytokine production, including one that is caused by a novel loss-of-function mutation in the Itgal gene, which is necessary for T cell recruitment to the infected lung. These studies verify the multigenic control of mycobacterial disease in the CC panel, identify genetic loci controlling diverse aspects of pathogenesis, and highlight the utility of the CC resource

On the need for rigorous welfare and methodological reporting for the live capture of large carnivores: A response to de Araujo et al. (2021)

1.De Araujo et al. (Methods in Ecology and Evolution, 2021, https://doi.org/10.1111/2041-210X.13516) described the development and application of a wire foot snare trap for the capture of jaguars Panthera onca and cougars Puma concolor. Snares are a commonly used and effective means of studying large carnivores. However, the article presented insufficient information to replicate the work and inadequate consideration and description of animal welfare considerations, thereby risking the perpetuation of poor standards of reporting. 2.Appropriate animal welfare assessments are essential in studies that collect data from animals, especially those that use invasive techniques, and are key in assisting researchers to choose the most appropriate capture method. It is critical that authors detail all possible associated harms and benefits to support thorough review, including equipment composition, intervention processes, general body assessments, injuries (i.e. cause, type, severity) and post-release behaviour. We offer a detailed discussion of these shortcomings. 3.We also discuss broader but highly relevant issues, including the capture of non-target animals and the omission of key methodological details. The level of detail provided by authors should allow the method to be properly assessed and replicated, including those that improve trap selectivity and minimize or eliminate the capture of non-target animals. 4.Finally, we discuss the central role that journals must play in ensuring that published research conforms to ethical, animal welfare and reporting standards. Scientific studies are subject to ever-increasing scrutiny by peers and the public, making it more important than ever that standards are upheld and reviewed. 5. We conclude that the proposal of a new or refined method must be supported by substantial contextual discussion, a robust rationale and analyses and comprehensive documentation

Host-pathogen genetic interactions underlie tuberculosis susceptibility in genetically diverse mice

The outcome of an encounter with Mycobacterium tuberculosis (Mtb) depends on the pathogen's ability to adapt to the variable immune pressures exerted by the host. Understanding this interplay has proven difficult, largely because experimentally tractable animal models do not recapitulate the heterogeneity of tuberculosis disease. We leveraged the genetically diverse Collaborative Cross (CC) mouse panel in conjunction with a library of Mtb mutants to create a resource for associating bacterial genetic requirements with host genetics and immunity. We report that CC strains vary dramatically in their susceptibility to infection and produce qualitatively distinct immune states. Global analysis of Mtb transposon mutant fitness (TnSeq) across the CC panel revealed that many virulence pathways are only required in specific host microenvironments, identifying a large fraction of the pathogen's genome that has been maintained to ensure fitness in a diverse population. Both immunological and bacterial traits can be associated with genetic variants distributed across the mouse genome, making the CC a unique population for identifying specific host-pathogen genetic interactions that influence pathogenesis