Biography
Dr. Scheib was the head of the aDNA research laboratory at the Institute of Genomics, University of Tartu, Tartu, Estonia from 2017 - 2023. Her early research as a PhD student at the University of Cambridge optimised aDNA extraction protocols and explored the complex genetic history of Native American populations. Always fascinated by disease, her postdoc focused on retrieving and analysing pathogen DNA from medieval Cambridgeshire skeletons.
Her current project, "Ancient Antibodies: Identifying pathogen exposure via immunological memory in ancient populations using proteins and DNA" a UKRI Frontier Research Guarantee (ERC Starting Grant) will develop palaeoproteomics and aDNA methods for the identification and analysis of ancient immune-response and pathogen proteins to gain a better understanding of host–pathogen dynamics and how they have affected our genomes today.
Research
Palaeoproteomics, ancient DNA, immunology, infectious disease, evolution
Ancient Antibodies Abstract
The vision: detecting all infections an ancient person was exposed to during life, not just what may have killed them! Infectious disease has likely had the greatest impact on human evolution, yet it has not been possible to assess the true burden of communicable disease on historic human populations. Next Generation Sequencing has made it possible to identify certain ancient pathogens in victims and the applications of paleoproteomics are rapidly developing; however, we have been unable to distinguish between survivors of communicable disease and those who were never exposed, nor routinely detect the most common circulating illnesses and causes of child mortality (many of which are viruses, chemically unstable at the DNA level). To understand how shifts in environment and/or cultural practices have shaped our susceptibility through time, it is necessary to be able to directly study both pathogens and our immune response to them. AncientAntibodies will provide this ability by exploiting emerging paleoproteomics methods, ancient DNA, immunological memory and well-preserved, well-studied human skeletal remains from epidemic contexts– allowing unprecedented insight into the history of infectious disease. It will develop protocols for (1) isolating, sequencing and matching ancient antibodies to pathogens and (2) identifying important, ancient viruses (e.g. measles, mumps, influenza) in skeletal remains. Both are made possible by recent advances in paleoproteomics and metagenomics. These novel protocols will build the foundation for a new field of study: Ancient Immunomics and provide the methodological framework for settling long-standing debates regarding the impact of environmental, cultural and genetic shifts on the evolution of the human immune system. It will allow researchers to directly assess past individual and community immune status. The groundwork laid by AncientAntibodies will be an indispensable, transferable resource for future studies of the human past.
Publications
1. Scheib, C. L., Li, H., Desai, T., Link, V., Kendall, C., Dewar, G., Griffith, P. W., Mörseburg, A., Johnson, J. R., Potter, A., Kerr, S. L., Endicott, P., Lindo, J., Haber, M., Xue, Y., Tyler-Smith, C., Sandhu, M. S., Lorenz, J. G., Randall, T. D., … Kivisild, T. (2018). Ancient human parallel lineages within North America contributed to a coastal expansion. Science, 360(6392), 1024–1027.
2. Keller, M., Spyrou, M. A., Scheib, C. L., Neumann, G. U., Kröpelin, A., Haas-Gebhard, B., Päffgen, B., Haberstroh, J., Ribera I Lacomba, A., Raynaud, C., Cessford, C., Durand, R., Stadler, P., Nägele, K., Bates, J. S., Trautmann, B., Inskip, S. A., Peters, J., Robb, J. E., … Krause, J. (2019). Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541-750). Proceedings of the National Academy of Sciences of the United States of America, 116(25), 12363–12372.
3. Guellil, M., van Dorp, L., Inskip, S. A., Dittmar, J. M., Saag, L., Tambets, K., Hui, R., Rose, A., D’Atanasio, E., Kriiska, A., Varul, L., Koekkelkoren, A. M. H. C., Goldina, R. D., Cessford, C., Solnik, A., Metspalu, M., Krause, J., Herbig, A., Robb, J. E., … Scheib, C. L. (2022). Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia. Science Advances, 8(30), eabo4435.
4. Saupe, T., Montinaro, F., Scaggion, C., Carrara, N., Kivisild, T., D’Atanasio, E., Hui, R., Solnik, A., Lebrasseur, O., Larson, G., Alessandri, L., Arienzo, I., De Angelis, F., Rolfo, M. F., Skeates, R., Silvestri, L., Beckett, J., Talamo, S., Dolfini, A., … Scheib, C. L. (2021). Ancient genomes reveal structural shifts after the arrival of Steppe-related ancestry in the Italian Peninsula. Current Biology: 31(12), 2576–2591.e12.
5. Badillo-Sanchez, D. A., Jones, D. J. L., Guellil, M., Inskip, S. A., & Scheib, C. L. (2023). Human Archaeological Dentin as Source of Polar and Less Polar Metabolites for Untargeted Metabolomic Research: The Case of Yersinia pestis. Metabolites, 13(5).
Supervisions
I am looking for PhD students and postdocs with experience and/or interest in biochemistry, proteomics, immunology and/or medical genomics. At the moment, if you would like to work with me, you will need to have your own funding. Please email if interested.
