11-strain consortium from human faecal microbiota drives IFN-gamma production in CD8 T cells

New study @nature from Japanese scientists (Konda, Atarashi, & others) identified #consortium (a nice clickbait for granting/funding agencies) of 11 microbial species from human faecal #microbiota that increase #IFN-gamma+ #CD8 T cells protective against #infection and #tumors.

— David Usharauli (@3DiMMUNE) January 24, 2019

2. Even these 11 strain #consortium could be further narrowed down into two groups of 7 #Bacteroidales and 4 non-Bacteroidales species. But effect on CD8 T cells was mostly lost when they were separated. pic.twitter.com/UOzqWNFJQz

— David Usharauli (@3DiMMUNE) January 24, 2019

3. Significantly, effect of consortium on T cells were #biologically relevant as it improved #protection against #pathogen challenge. pic.twitter.com/Wotr8HJ4p5

— David Usharauli (@3DiMMUNE) January 24, 2019

5. Though such #tumor protective effect of this consortium alone was less obvious in SPF mice (regular lab mouse). But even in SPF mice combination of #consortium + #checkpoint inhibitors show a #synergy. pic.twitter.com/H9Iyv13E0o

— David Usharauli (@3DiMMUNE) January 24, 2019

scientifically speaking it is not very important paper. It lacks mechanisms & granularity typical for great papers.On the other hand,several authors including senior author are part of microbiota biotech company @VedantaBio and there these data might be sufficient for investment.

— David Usharauli (@3DiMMUNE) January 24, 2019

Fragility of FOXP3+ Treg phenotype

This week I am reviewing two papers dealing with different aspects of FOXP3+ Treg biology. Both papers were published in journal Cell. These are predominantly mouse works so no need to get too excited. 

1st paper was published by Dario Vignali's group (department of Immunology, University of Pittsburgh School of Medicine). They have analyzed role of Neuropilin-1 (Nrp1) in Treg phenotype in tumor context. Neuropilin-1 is a marker of thymic Tregs though this notion is not universally accepted. Interestingly, in mouse tumor model, mouse that expressed Nrp1 on half of its Tregs rejected tumor with the same vigor as mouse expressing Nrp1 on all of its Tregs. 

Furthermore, in the context of tumor challenge, Treg-specific Nrp1 deficiency drastically increased IFN-γ production in both KO and WT Tregs.

It appeared that WT Tregs required sensing of IFN-γ derived from Nrp1KO Tregs to acquire "Nrp1KO-like" phenotype. 

Finally, the authors showed that therapeutic effect of checkpoint inhibitor anti-PD1 antibody against tumor required IFN-γ sensing by Tregs.

In summary, this study showed that Nrp1 deficiency makes Tregs fragile by converting them into IFN-γ producer cells which in turn affect WT Tregs phenotype as well. The reason the authors are using term fragility rather than simply instability has to do, they claim, with the difference in FOXP3 expression between fragile and unstable Tregs. 

In a separate study, the authors showed that Treg depletion inhibits hair regrowth (after depilation). 

However, it is not clear why Tregs should be involved in such physiological process when any other innate cells could do the same.   

David Usharauli

Genomic alterations in IFN-γ pathway underlie resistance to anti-CTLA-4 (Yervoy) therapy

This week journal Cell published a short "reverse translational" study conducted on small cohort of patients non-responsive to immunotherapy with anti-CTLA-4 antibody (ipilimumab, Yervoy) that  showed that genomic alterations in IFN-γ pathway in non-responder patients could underlie their resistance to immunotherapy.  

For this study the authors compared 12 patients who did not respond to ipilimumab therapy (non-responders) and 4 patients who did respond to ipilimumab therapy (responders). They found that "tumor samples from non-responders were found to have significantly more somatic mutations, including copy-number alterations (CNAs) and single-nucleotide variants (SNVs) of the IFN-γ pathway genes".

Next, the authors showed that primary melanoma cell lines derived from anti-CTLA-4 responder or non-responder patients could be differentiated based on their in vitro sensitivity to IFN-γ.

Next, they showed quite bizarre experiment. By knocking down IFN-γ receptor in mouse B16 melanoma cells the authors showed that these cell line became less sensitive to IFN-γ in vitro. Not sure about logic behind these experiment.  

Finally, the authors showed that B16 melanoma cells deficient for IFN-γ signaling and transplanted into WT mice were less sensitive to anti-CTLA-4 therapy.

In summary, this small cohort study suggests that screening of melanoma patients for genomic alterations in IFN-γ pathway could be useful in better predicting therapeutic outcome for this checkpoint inhibitor therapy.

David Usharauli

Cross-reactivity to fungal antigen drives acquired IFN-γ auto-antibody mediated mycobacteria susceptibility

Inherited genetic deficiency in IFN-γ signaling underlies susceptibility to weakly virulent mycobacteria, such as bacille Calmette-Guérin (BCG) vaccines and nontuberculous mycobacteria. Here, new study in Nature Medicine reported group of patients with acquired susceptibility to mycobacteria due to presence of neutralizing anti-IFN-γ auto-antibodies that could have been results of its cross-reactivity to fungal Aspergillus antigens.

Molecular mimicry hypothesis suggests that if foreign [nonself] antigen shows antigenic similarity to self antigen, then immune response to such nonself antigen could lead to autoimmune diseases due to shared, cross-reactivity. Here, the authors showed that set of patients with mycobacteria infection expressed neutralizing anti-IFN-γ auto-antibodies.

Next, the authors found that conserved KRKR motif of IFN-γ, known to be crucial for the protein’s bioactivity, showed homology to amino acids 105–113 of the ribosome assembly protein Noc2 of Aspergillus terreus.

Indeed, sera from patients with neutralizing anti-IFN-γ auto-antibodies reacted with Noc2 antigen from Aspergillus.

In summary, this study suggested that immune response to Aspergillus in certain individuals carrying specific HLA polymorphism (HLA class II molecules HLA-DRB1*15:02–HLA-DQB1*05:01 and HLA-DRB1*16:02–HLA-DQB1*05:02) could lead to generation of cross-reactive neutralizing anti-IFN-γ auto-antibodies and acquisition of mycobacteria susceptibility.

David Usharauli

Hybrid NKB cells are source of early IL-18

This week journal Immunity published new study that revealed existence of hybrid innate cells expressing both NK and B cell markers (NK1.1⁺CD19⁺IgM⁺). The authors called it NKB cells.

By screening for NK1.1⁺ cell population in different tissues, the authors noticed that spleen and mLNs [but not other tissues] contained cell population expressing CD19 and IgM, a canonical B cell markers.

Image flow analysis confirmed that both NK1.1 and CD19 markers were expressed by the same cells.

This new NKB cell population were absent in RAG-KO, IL-2RgcKO, B cell or NK-deficient mice, suggesting unique lineage (its precursors appear to express CD122, IL-2Rbeta chain).

In vitro functional analysis showed that NKB cells were innate producers of IL-18 and IL-12 (IL-12p40, most likely). Of note, NKB cells did not secrete antibody after stimulation.

In an in vivo infection model NKB cell-deficient mice (created by reconstituting lethally irradiated mice with Id2 and mMT deficient bone marrow cells) showed high susceptibility to L.M. infection.

Finally, the authors showed that IL-18 produced by wt NKB cells played important role in disease resistance against L.M. infection.

In summary, this study identified new type of innate cells expressing NK and B cell markers, called NKB cells, that were involved in early IL-18 production that contributed early waves of IFN-gamma from NK and ILC1 cells and resistance to L.M. infection. It is not clear what roles surface CD19 or IgM play in NKB cell functionality.

David Usharauli

Anti-PD1 antibody treatment shows beneficial effect in human Alzheimer disease (AD) mouse model

This week journal Nature Medicine published a short paper from Michal Schwartz lab at Weizmann Institute of Science (Israel) showing beneficial effect of anti-PD1 treatment in human Alzheimer disease (AD) mouse model.

Michal Schwartz lab is famous in immunology circles for producing data showing the role of immune system in CNS function. For example, earlier their lab showed that mice deficient for adaptive immune system display decline in cognitive functions.

In this new paper the authors showed that two consecutive injections of anti-PD1 antibody (checkpoint inhibitor used in cancer immunotherapy) reduces CNS tissue pathology in mice with human AD phenotype [in two different models, (a) five familial AD mutations (5XFAD) and (b) APP/PS1 mouse models]. This beneficial effect correlated with the accumulation of peripheral macrophages into CNS and were dependent on IFN-γ.

It is not clear why systemic immune activation improves AD tissue pathology. Simple explanation is that peripheral "activated" macrophages that migrate to CNS are better equipped to digest and clean up AD-associated amyloid depositions. However, it is not clear whether CNS with AD pathology sends out any specific signals to recruit those peripheral macrophages or it is just nonspecific migration into CNS and other tissues [not examined in this paper].

David Usharauli 

NK cell activation initiates type II diabetes

Type II diabetes is a complex syndrome involving endocrine, immune and metabolic abnormalities. It is well known that obesity can lead to type II diabetes. But how?

New study in Nature Immunology suggests that obesity-induced adipocyte stress activates NK cells  via NCR1 receptor driving IFN-γ mediated insulin insensitivity characteristic to type II diabetes.

The authors observed that NK cell depletion in mice fed high fat diet (HFD) ameliorated insulin insensitivity and glucose intolerance.

Ex vivo examination of visceral adipose tissue (VAT), a target tissue of type II diabetes, revealed that HFD induced expression of NK cell ligand in VAT detected by NCR1 (NKp46 in humans).

Interestingly, VAT but not subcutaneous (Sc fat) adipose tissue from HFD fed mice could stimulate NK cells.

In vivo experiments confirmed that NCR1 deficiency improved insulin sensitivity.

Finally, the authors showed that IFN-γ derived from NCR1 activated NK cells promotes inflammatory macrophages in VAT leading to glucose intolerance, that can be ameliorated with NCR1 blockade.

In summary, these results showed that HFD induces visceral adipose tissue stress that activates local NK cells via NCR1 ligand leading to inflammatory macrophage polarization and reduced insulin sensitivity. Targeting NK cell activation may interrupt this disease cycle and improve type II diabetes management.

I was always wondered why diet-induced obesity leading to VAT stress should activate inflammatory, M1 type macrophages? What is an evolutionary advantage for such response, in general? No idea.  

David Usharauli

Is helminth infection sensed by latent virus?

During life time a human body is infected and re-infected with the same or the diverse types of infectious agents, sometimes simultaneously.

Since early 90's, an immune responses to infections were categorized into two major types: type 1, TH1 response, dominated by IFN-gamma (thought to be protective against viruses, intra-cellular pathogens, tumors) and type 2, TH2 response dominated by IL-4 (thought to to be protective against helminth infection). This division of labors, of course, is for simplicity purpose only.

Most importantly, since TH1 and TH2 responses thought to antagonize each other, it is clearly scientifically interesting to study and to know how immune system would deal with simultaneous presence of infections driving TH1 and TH2 responses.

The following Science paper has tried to answer this question. This study has examined the effect of an acute helminth infection on latent viral infection.

The authors has used a luciferase expression as a readout for latent viral reactivation. After initial viral infection and resting period (42 days), the mice were exposed to helminth or their eggs. Such exposure led to viral re-activation. 

 

It is of note, that very few peritoneal macrophages (< 0.02%) show sign of viral infection (RFP expression). Interestingly, the authors also observed that some of the virus infected macrophages expressed Arginase-1, a TH2 response signature molecule (though the numbers are so low that I am not sure whether it is real expression or an artifact). 

To understand the role of TH2 signature molecule, Arg1, in infected macrophages, the authors conducted the series of in vitro experiments with bone marrow derived macrophages infected with MHV86. These experiments showed that IL-4 and IL-13 (but not IL-5) were promoting viral infection of macrophages via STAT6 pathway.

This effect of IL-4 on MHV86 infection was antagonized by IFN-gamma.

Finally, in vivo experiments confirmed that IL-4 was promoting viral reactivation but only in absence of IFN-gamma signaling.

This effect was through STAT6. It should be noted here, however, that STAT6KO mice already showed high viral expression at day 0. This is unusual observation since IFN-gamma signaling should be more dominant in STAT6KO mice.

In summary, the authors proposed that in some situations, there is a competition between IL-4 and IFN-gamma responses on the level of viral promoters in infected cells.   

Few comments: First, a time has come to retire a simplified view of immune responses dominated either by IL-4 or IFN-gamma. Second, IL-4 was shown to not sufficient for viral reactivation. It requires inhibition of IFN-gamma signaling as well. No evidence is provided that helminth infection inhibits IFN-gamma signaling in latently infected macrophages. This study reminds me the story about in vitro TH17 induction that required the presence of anti-IFN-gamma and anti-IL-4 blocking antibodies to activate IL-17 program. Of course, this is a completely artificial system. Whether latent virus reactivation is IL-4 dependent in vivo is not clear either.

David Usharauli