The rockefeller university

'Intrinsic immunity' is often used to refer to mechanisms of host defense operating in nonleukocytic cells. This term can refer to the intrinsic capacity of an individual cell to fend off invading microbes without help from other cells or of a group of similar cells to fend off invading microbes without help from other cell types. The intrinsic capacity of individual cells to defend themselves against invading microbes without assistance has received little attention and is the topic of this review. We also focus on nonleukocytic cells and on humans, the only species in which intrinsic immunity has been shown by genetic means to be essential for homeostasis in natural conditions at wholebody level. We review recent progress in our understanding of the type I interferon-independent intrinsic immunity of individual nonleukocytic cells, as inferred from human inborn errors of intrinsic immunity manifesting as infection or autoinflammation.

The life-threatening coronavirus disease 2019 (COVID-19) affects about 1 in 1,000 healthy people under 50 without underlying conditions. Among patients with critical COVID-19 pneumonia, rare germline variants at genes controlling type I IFN immunity have been reported in up to 5% of patients. Causal etiologies in 80-85% of cases are still unknown. We analyzed two families with hypoxemic COVID-19 pneumonia for known single-gene inborn errors of immunity. In Family 1, two siblings with critical COVID-19 were homozygous for a DOCK2 variant, c.3624+5G>A. DOCK2 deficiency is a known T-cell disorder underlying severe viral diseases. The variant resulted in skipping exon 35, which was predicted to produce a frameshift truncated protein (p.L1157Ifs*12). The proband showed markedly decreased blood CD4 T-helper cell counts, impaired T lymphocyte transformation test, and increased serum IgG, IgA, and IgE levels, as documented in other DOCK2-deficient patients. In Family 2, the proband had lethal COVID-19 and HPV-2-associated multiple recalcitrant warts. She was heterozygous for a deletion in GATA2:c.1075_1102del28, p.W360Sfs*18. GATA2 haploinsufficiency is a known cause of severe viral diseases due to a lack of plasmacytoid dendritic cell (pDC) development. The proband had monocytopenia and a lack of circulating pDCs, as reported in other patients with GATA2 haploinsufficiency. Overall, both DOCK2 deficiency and GATA2 haploinsufficiency are associated with critical and often fatal COVID-19 pneumonia.

Regulatory T (Treg) cells, expressing the transcription factor Foxp3, are obligatory gatekeepers of immune responsiveness, yet the mechanisms by which Foxp3 governs the Treg transcriptional network remain incompletely understood. Using a novel chemogenetic system of inducible Foxp3 protein degradation in vivo, we found that while Foxp3 was indispensable for the establishment of transcriptional and functional programs of newly generated Treg cells, Foxp3 loss in mature Treg cells resulted in minimal functional and transcriptional changes under steady state. This resilience of the Foxp3-dependent program in mature Treg cells was acquired over an unexpectedly long timescale; however, in settings of severe inflammation, Foxp3 loss led to a pronounced perturbation of Treg cell transcriptome and fitness. Furthermore, tumoral Treg cells were uniquely sensitive to Foxp3 degradation, which led to impairment in their suppressive function and tumor shrinkage in the absence of pronounced adverse effects. These studies demonstrate a context-dependent differential requirement for Foxp3 for Treg transcriptional and functional programs.

In psoriatic lesions, interleukin (IL)-17C protein expression has been reported as high as 125 times that of IL-17A; as such, it is crucial to understand the role that IL-17C plays in psoriasis, inflammation, and treatment response. Overexpression or injection of IL-17C in mice results in increased epidermal thickening and inflammation, whereas psoriatic mice with IL-17C knockout have decreased disease severity compared with control littermates. In psoriasis, IL-17C likely acts as a critical inflammatory amplifier via a feed-forward mechanism, wherein IL-17-producing CD4+ helper T (TH17) cells and IL-17-producing CD8+ cytotoxic T (TC17) cells stimulate IL-17C expression in keratinocytes. Then, keratinocyte-derived IL-17C induces IL-17A expression in TH17 and TC17 cells. Additionally, keratinocyte-derived IL-17C propagates its own signaling in an autocrine manner. Furthermore, studies suggest that IL-17C acts as an early mediator of psoriasis. No approved therapies directly target IL-17C. Brodalumab is an IL-17 receptor (IL-17R) A antagonist that inhibits IL-17A, F, C, and E signaling and has a unique mechanism of action among biologic therapies for psoriasis. By way of IL-17RA blockade, brodalumab is the only approved therapy for psoriasis that inhibits IL-17C signaling. This unique mechanism of action is hypothesized to correlate with efficacy in patients with prior failures to anti-IL-17A therapies and relatively higher rates of early skin clearance compared with those of other biologic therapies. Clinical studies are needed to confirm these correlations. In summary, IL-17C is an inflammatory amplifier and early psoriatic mediator, and inhibition of IL-17C may be beneficial in psoriasis management.

Thoeris systems use proteins with Toll/interleukin-1 receptor domains to protect prokaryotes from phage infection through the synthesis of a cyclic adenosine diphosphate ribose signalling molecule, which activates an effector that depletes the host of the essential metabolite NAD+ to limit viral propagation. How infection is recognized during Thoeris immunity is not known. Here we investigate the staphylococcal Thoeris defense system, ThsA-B1-B2, and found that, upon infection, the major capsid proteins of Siphoviridae phages from serogroup B, but not A, form a complex with ThsB1 and ThsB2 to activate Thoeris defense. Thoeris cyclases from Streptococcus also recognize major capsid proteins. Our results suggest that the accumulation of capsid mutations that enable avoidance of Thoeris recognition may be an important evolutionary force behind the structural diversity of prokaryotic viruses. More broadly, given that some mammalian immune pathways contain Toll/interleukin-1 receptor domains that recognize viral structures, our findings highlight a conserved mechanism of innate antiviral immunity.

Likelihood-free inference for simulator-based statistical models has developed rapidly from its infancy to a useful tool for practitioners. However, models with more than a handful of parameters still generally remain a challenge for the Approximate Bayesian Computation (ABC) based inference. To advance the possibilities for performing likelihood-free inference in higher dimensional parameter spaces, we introduce an extension of the popular Bayesian optimisation based approach to approximate discrepancy functions in a probabilistic manner which lends itself to an efficient exploration of the parameter space. Our approach achieves computational scalability for higher dimensional parameter spaces by using separate acquisition functions, discrepancies, and associated summary statistics for distinct subsets of the parameters. The efficient additive acquisition structure is combined with exponentiated loss-likelihood to provide a misspecification-robust characterisation of posterior distributions for subsets of model parameters. The method successfully performs computationally efficient inference in a moderately sized parameter space and compares favourably to existing modularised ABC methods. We further illustrate the potential of this approach by fitting a bacterial transmission dynamics model to a real data set, which provides biologically coherent results on strain competition in a 30-dimensional parameter space.

Quaternary climatic fluctuations had a substantial influence on ecosystems, species distribution, phenology and genetic diversity, driving extinction, adaptation and demographic shifts during glacial periods and postglacial expansions. Integration of genomic data and environmental niche modelling can provide valuable insights on how organisms responded to past environmental variations and contribute to assessing vulnerability and resilience to ongoing climatic challenges. Among vertebrates, turtles are particularly vulnerable to habitat changes because of distinctive life history traits and the effect of environmental conditions on physiology and survival. We estimated contemporary heterozygosity (H) and effective population size (N e) using a high-quality chromosome-level reference genome we produced for the European pond turtle (Emys orbicularis) and reference genomes and whole genome sequence data available for 21 species of tortoises and freshwater turtles. We implemented environmental niche modelling (ENM) to estimate past habitat dynamics. We found recurrent cycles of population expansion and contraction over the last 10 Mya in all species, with a general pattern of decrease in N e correlated with temperature reduction after the last interglacial period. No correlation was found between habitat fluctuations during the Quaternary and past N e. Moreover, neither H nor mean N e was correlated to threat status as defined by IUCN Red List categories. Our results add to studies on other vertebrates showing the extent to which genetic parameters can aid the assessment of conservation status, and although genomic data may not always be consistent indicators of the level of threat, investigations of which genomic parameters could best represent essential biodiversity variables should be consistently supported.