Denisovan, Modern Human and Mouse TNFAIP3 Alleles Tune A20 Phosphorylation and Immunity
Zammit NW, Siggs OM, Grey PE, et al. Nature Immunology. 2019;20(10):1299–1310.
The nuclear factor κB (NF-κB) family of transcription factors are highly conserved through evolution and are present in almost all cells. Functions vary and include organ development, induction, and maintenance of innate and adaptive immune responses, in addition to playing a critical role in cell survival. NF-κB is integral to transplant rejection, where it is activated both at the initial stages post-surgery and in the ensuing alloresponse.1 Common immunosuppressants, including steroids and calcineurin inhibitors, are known to impact NF-κB activity. The induction of NF-κB, in turn, is tightly controlled by a complex intracellular signaling pathway. In the current issue of Nature Immunology, NF-κB signaling is shown to be differentially regulated within the human population by allelic variation in TNFAIP3, which encodes the negative regulator A20.
In initial sequencing studies, human alleles with missense substitutions in the ovarian tumor domain at T108A and I207L were identified. Carriers of this allele were healthy and exclusive to the indigenous communities of Island Southeast Asia and Oceania; the geographical separation of this allele was explained by its origins as a Denisovan (archaic hominin)-derived gene. Carrying the Denisovan haplotype was associated with enhanced NF-κB–associated transcription of C-X-C motif chemokine ligand 2 (CXCL2), tumor necrosis factor, and intercellular adhesion molecule-1 (ICAM-1) in peripheral blood mononuclear cells after stimulation. Based on those findings, Zammit et al.2 wondered whether the haplotype provided early settlers an immune advantage.
Comparison of several missense substitutions in the TNFAIP3 ovarian tumor revealed decreased A20 phosphorylation at ser381, ranging from 5% to 80% of the wild type. Phosphorylation at this residue correlated with NF-κB inhibition, and indeed A20 phosphorylation was lower in peripheral blood mononuclear cells from individuals with the Denisovan haplotype.
Mice were then genetically modified by mutagenesis or CRISPR-Cas9 gene insertion to introduce TNFAIP3 allele variants. A state of heightened immunity was associated with the degree of A20 phosphorylation. The variants had an augmented proportion of activated effector memory helper and cytotoxic T lymphocytes, as well as regulatory T cells. Reduced phosphorylation of A20 enhanced NF-κB signaling and conferred mice with a resistance to an otherwise fatal coxsackievirus infection. However, enhanced viral clearance and protection came with a price: the dysregulation of immune homeostasis. The stepwise impairment of A20 phosphorylation disrupted glucose metabolism and produced low grade resting inflammation in murine pancreatic islets, colon, kidney, and liver.
Although allelic variance in TNFAIP3 may have conferred a benefit to early humans, this study illustrates the fine balance between immune tolerance and immune activation resting on the modulation of NF-κB activity. For example, previous work by the authors described repression of NF-κB activation as beneficial to the survival of allogenic islet transplants in mouse models.3 It is possible that genetic variation in immune regulatory genes, such as TNFAIP3, is at least partly responsible for the high variability in outcomes and response to therapies post-transplantation.
Spatiotemporal Immune Zonation of the Human Kidney
Stewart BJ, Ferdinand JR, Young MD, et al. Science. 365(6460):1461–1466.
The kidney has become the prototypical organ for allotransplantation, benefiting from both living and deceased donation and achieving long-term allograft survival with long-term immunosuppression. Several groups are now working on characterizing cells in human organs as part of the Human Cell Atlas project, in an effort to provide comprehensive cellular reference maps for further studies.1 In Science, Stewart et al look inside the kidney to comprehensively characterize and map out resident cells using high-throughput single-cell RNA sequencing. The analysis of 40 268 adult kidney cells and 27 203 fetal kidney cells revealed important spatial and temporal patterns in the organ’s cellular composition.
Sequencing analyses revealed a diverse repertoire of immune cells, including resident mononuclear phagocytes, neutrophils, mast cells, plasmacytoid dendritic cells, B cells, helper T cells, cytotoxic T cells, natural killer cells and natural killer T cells cells in mature adult kidneys. Innate cells and T lymphocytes were found all along the kidney axis, whereas B cells were restricted to the cortex. According to their transcriptional profile, resident mononuclear phagocytes were separated into 4 clusters expressing genes for the myeloid marker CD11c and HLA-DR. These clusters are thought to represent classical and nonclassical monocytes, conventional dendritic cells and a fourth population that is transcriptionally distinct from circulating monocytes and monocyte-derived macrophages, which may be a tissue-specific myeloid cell with relatively low phagocytic capacity.
Furthermore, the epithelial compartment differentially expressed immune-related genes in a site and cell-dependent manner. The study found that epithelial cells, with proximity to the pelvis in regions susceptible to bacterial infection, preferentially expressed antimicrobial peptides for direct homeostatic defense. Pelvic epithelial and connecting tubule ducts also selectively expressed chemokine ligands for the recruitment of antibacterial macrophages and neutrophils to anatomically relevant regions.
Understanding the resident immune landscape of the kidney is essential to understanding the repercussions of ischemia-reperfusion injury, acute, and chronic alloresponses.2 The presence of passenger lymphocytes and antigen-presenting cells has a significant impact in providing stimulus for direct allorecognition and costimulatory signals. Indeed, classical studies where donor leukocytes are depleted, significantly impact allograft survival in animal models. A more detailed understanding of the immune composition of the kidney is, therefore, key to our understanding of tolerance, sensitization, and rejection of renal allografts.
1. Molinero LL, Alegre ML. Role of T cell-nuclear factor κb in transplantation.Transplant Rev (Orlando)2012263189–200
2. Zammit NW, Siggs OM, Gray PE, et al. Denisovan, modern human and mouse TNFAIP3 alleles tune A20 hosphorylation and immunity.Nat Immunol201920101299–1310
3. Zammit NW, Tan BM, Walters SN, et al. Low-dose rapamycin unmasks the protective potential of targeting intragraft NF-κb for islet transplants.Cell Transplant201322122355–2366
4. Regev A, Teichmann SA, Lander ES, et al. The human cell atlas.Elife20176e27041
5. Prosser AC, Kallies A, Lucas M. Tissue-resident lymphocytes in solid organ transplantation: innocent passengers or the key to organ transplant survival?Transplantation20181023378–386