Periodic Reporting for period 4 - Optimal-Immunity (Optimal diversity in immunity – to overcome pathogens and maximize fitness; moving from correlative associations to a more mechanistic understanding using wild songbirds.)
Okres sprawozdawczy: 2020-10-01 do 2021-09-30
All jawed vertebrates have an adaptive immune system and antigen presentation by MHC proteins is a key step in every adaptive immune response. MHC genes are among the most variable genes known in animals and it is believed that this variation is maintained by selection from pathogens. However, MHC is mostly known from humans and domestic mammals and when MHC was studied in wild songbirds that are subject to natural selection from pathogens it was clear that the MHC diversity was much higher in songbirds. What is the purpose of this high MHC diversity in wild songbirds, and has it evolved to enable particularly sophisticated adaptive immune responses? Appreciating the diversity of the different kinds of immune systems that exists in wild animals will aid not only in ecological and evolutionary research, but also in medicine and conservation. Importantly, in a much wider perspective, it is my sincere opinion that we must appreciate the diversity on all levels, genes-proteins-species-communities, in the wild. This diversity cannot be studied in humans or in captive animal-model systems in the laboratory, we need to include wild populations. The main objective in my research is to measure and characterize how selection from pathogens affects diversity of MHC genes in wild songbird populations. More specifically I seek to understand why songbirds have such large number of MHC gene copies. Does this high MHC gene copy number really translate into a broader MHC recognition repertoire against pathogens? In my project I have characterized the MHC genomic region for the first time in songbirds by using long-read DNA sequencing in combination with several additional techniques. I found an agreement in genomic organization in four different bird species of the order Passeriformes, an organization that differs from that of more basal bird orders. The genome studies also shows that the MHC genes in songbirds are highly duplicated and often found organized in tandem. MHC expression differs significantly between different MHC gene copies in songbirds and strong expression patterns are associated with MHC gene type. Moreover, the relative MHC expression in songbirds varies between bird families, suggesting that MHC diversity in genomic DNA overestimates the expressed diversity in some bird families. Crystal structures of MHC class I antigen presentation in songbirds unraveled interesting antigen presenting properties that partly agrees and partly disagrees with antigen binding of classical human MHC proteins.
1. Genomics - We have assembled the core Major Histocompatibility Complex (MHC) genomic region(s) in a songbird, the great reed warbler, based on high quality DNA from a single individual. To achieve this, we produced several different types of state-of-the-art genomic data. The comparative work on the MHC genomic region(s) in four different songbird species, with a focus on the great reed warbler, is submitted and under review. We have been invited to present our results on songbird MHC genomics on conferences, seminars and workshops, and also contributed to two review papers.
2. Gene-expression - We have done RNASeq and IsoSeq to study full gene expression in both great reed warbler and house sparrow, and amplicon sequencing (MiSeq, local pipeline at LU) has been done to specifically study MHC-I gene expression in great reed warbler and house sparrow. MHC expression differs significantly between different MHC gene copies in songbirds and strong expression patterns are associated with MHC gene type. Moreover, the relative MHC expression in songbirds varies between bird families, suggesting that MHC diversity in genomic DNA overestimates the expressed diversity in some bird families, as shown in our recent publication.
3. Proteins – The crystal structure of the great reed warbler MHC-I protein Acar_3 has been characterized with high resolution with three different antigens and it unraveled an interesting antigen presenting properties that partly agrees and partly disagrees with antigen binding of classical human MHC proteins, and a manuscript is written, and planned for submission early 2022.
4. Host-pathogen interactions have been studied both in natural populations (great reed warblers in Lake Kvismaren Sweden and in house sparrows across Europe) and in experimental set-ups (house sparrows). The seasonal variation in diversity and prevalence of avian malaria varied between locations in house sparrows, as shown in our recent publication, and tended to be highest in mid-spring and early Autumn. The diversity and expression of MHC genes shows interesting patterns across Europe and our results will be submitted shortly. The house sparrow work has enrolled a large number of collaborators across Europe and I am very grateful for their engagement in my studies of MHC and avian malaria.
2. Gene-expression - We have done RNASeq and IsoSeq to study full gene expression in both great reed warbler and house sparrow, and amplicon sequencing (MiSeq, local pipeline at LU) has been done to specifically study MHC-I gene expression in great reed warbler and house sparrow. MHC expression differs significantly between different MHC gene copies in songbirds and strong expression patterns are associated with MHC gene type. Moreover, the relative MHC expression in songbirds varies between bird families, suggesting that MHC diversity in genomic DNA overestimates the expressed diversity in some bird families, as shown in our recent publication.
3. Proteins – The crystal structure of the great reed warbler MHC-I protein Acar_3 has been characterized with high resolution with three different antigens and it unraveled an interesting antigen presenting properties that partly agrees and partly disagrees with antigen binding of classical human MHC proteins, and a manuscript is written, and planned for submission early 2022.
4. Host-pathogen interactions have been studied both in natural populations (great reed warblers in Lake Kvismaren Sweden and in house sparrows across Europe) and in experimental set-ups (house sparrows). The seasonal variation in diversity and prevalence of avian malaria varied between locations in house sparrows, as shown in our recent publication, and tended to be highest in mid-spring and early Autumn. The diversity and expression of MHC genes shows interesting patterns across Europe and our results will be submitted shortly. The house sparrow work has enrolled a large number of collaborators across Europe and I am very grateful for their engagement in my studies of MHC and avian malaria.
Professor Jochen Wolf at the Ludwig-Maximilian University in Germany offered me to use his unpublished PacBio data and assemble and study the MHC regions in the Hooded crow and the Jackdaw in parallel with the great reed warbler. We have therefore a more solid MHC comparison than outlined in my application including MHC data from four and not two different passerines.
Maria Strandh, employed in my project, has unraveled that repetitive elements are most likely the drivers of the highly duplicated MHC region in great reed warblers. She has developed bioinformatic pipelines together with Verena Kutschera at SciLifeLab to study the distribution of repetitive elements in the entire genome, an up-coming and most likely important parameter in studies of structural genetic variation.
SciLifeLab offered me to run an optical genome map using Irys long-range next-generation technique (Bionano genomics) at an extremely low cost since they thought that we were producing a really high quality genome for the great reed warbler and both me and Maria Strandh have independently been invited to talk at the workshops at SciLifeLab.
We have had progress in the protein work on MHC-I in great reed warblers and I hope that we have a pipeline for the future where antigen binding of MHC-I can be studied, not only in great reed warblers but also in other birds.
Maria Strandh, employed in my project, has unraveled that repetitive elements are most likely the drivers of the highly duplicated MHC region in great reed warblers. She has developed bioinformatic pipelines together with Verena Kutschera at SciLifeLab to study the distribution of repetitive elements in the entire genome, an up-coming and most likely important parameter in studies of structural genetic variation.
SciLifeLab offered me to run an optical genome map using Irys long-range next-generation technique (Bionano genomics) at an extremely low cost since they thought that we were producing a really high quality genome for the great reed warbler and both me and Maria Strandh have independently been invited to talk at the workshops at SciLifeLab.
We have had progress in the protein work on MHC-I in great reed warblers and I hope that we have a pipeline for the future where antigen binding of MHC-I can be studied, not only in great reed warblers but also in other birds.