Nathan W. Zammit

Conference 2022 Live Talk


Talk title

Maladaptation of a common Denisovan introgressed TNFAIP3 allele in families with haploinsufficiency of A20


Authors and Affiliations

Nathan W Zammit1, Paul E Gray2,3,4, Owen M Siggs4,5, Jin Y Yap1, Amanda Russell1,4, Daniele Cultrone1, Joanna Warren1, Stacey Walters1, Robert Brink1, David Zahra1, Deborah Burnett6, Velimir Gayevskiy1, Andre Minoche7, John B Ziegler3,4, Maria E Craig8, Melanie Wong4,9, Ted O’Laughlin9, Paul Benitez-Aguirre9, Juliana Teo9, Mark J Cowley10, Marcel E Dinger1, Stuart G Tangye1,4, Catherine Burke11, Tri G Phan1,4, Christopher C Goodnow1,4,12, Shane T Grey1.

1. Garvan Institute of Medical Reseach;
2. Sydney Children’s Hospital;
3. School of Women’s and Children’s Health, UNSW Sydney, NSW;
4. Clinical Immunogenetics Research Consortium Australia (CIRCA);
5. Flinders University;
6. The Walter and Eliza Hall Institute of Medical Research;
7. Institute for Research in Biomedicine (IRB);
8. University of Sydney;
9. Children’s Hospital Westmead;
10. Children’s Cancer Institute of Australia;
11. School of Life Sciences, University of Technology Sydney;
12. The Australian National University.




Monogenic diseases can often manifest diverse clinical phenotypes and cause diagnostic dilemmas. While monoallelic loss-of-function variants in TNFAIP3 (Haploinsufficiency of A20; HA20) cause a highly penetrant autoinflammatory disease, the variable expressivity suggest a role for additional genetic and environmental disease modifiers.


We identify critically ill children who inherited a family-specific TNFAIP3 deletion from one of their otherwise healthy parents. Each of the probands also inherited in trans a subtle loss-of-function I207L TNFAIP3 variant that is common in Oceania, originally introgressed from Denisovans. IKK-beta-dependent phosphorylation and activation of A20 was assessed in patient cells and cell lines containing p.I207L and other polymorphic TNFAIP3 variants. CRISPR/Cas9 gene-edited mice were constructed which possessed either a TNFAIP3 deletion, the I207L variant, or both, and were exposed to pro-inflammatory conditions.


Modelling the compound heterozgous state identified in patient probands in mice under specific pathogen free conditions demonstrated a reduced threshold to break immune tolerance. Exaggerated immune responses were precipitated by inheriting the two genetic hits on the TNFAIP3 checkpoint coupled with increasing the microbial challenge to immune tolerance, either by co-housing with “pet store” mice carrying a wild microbial burden or by transient dietary exposure to a chemical that diminishes the intestinal mucin barrier separating gut microbes from immune sensing systems. The single polymorphic I207L was found to alter A20 phosphorylation and the inflammatory response, improving clearance of some viruses (e.g. Coxsackievirus) but reducing control of others (e.g. poxvirus), a mechanism we have coined ‘phosphotuning’.


These data illuminate second-hit genetic and environmental modifiers contributing to complex inflammatory and autoimmune disease. Phosphotuning by I207L appears to have facilitated adaptation to the evolutionary environment of Oceania, but may potentiate the risk of inflammatory disease. Increased mechanistic understanding of the presence and contribution of disease modifiers will aid diagnostic and prognostic patient stratification and potentially reveal novel therapeutic opportunities.