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

Two non-overlapping precursors generate Foxp3+ regulatory T cells in the thymus

New study in @NatImmunol compared #Treg differentiation potential of #CD25+ versus Foxp3(low) precursors in the ##thymus. https://t.co/rIFWqybNnm pic.twitter.com/9ibTGBeHF9

— David Usharauli (@3DiMMUNE) January 22, 2019

2. One interesting #difference between CD25+ vs. Foxp3(low) #precursors was dependency on #IL4 #signaling to generate Tregs only from Foxp3(low) precursors (both responded to IL-2). pic.twitter.com/hNoLxVBfIP

— David Usharauli (@3DiMMUNE) January 22, 2019

in summary, two types of thymic precursors can generate Tregs. Since their #TCR did not overlap with each other but both of them overlapped with mature #Foxp3+ #Tregs it suggests certain #functional bifurcation considering differences in protection against tissue #inflammation.

— David Usharauli (@3DiMMUNE) January 22, 2019

Foxp3+ Tregs suppress other T cells by stripping DCs of specific antigen/MHC complexes

Ag-specific or not Ag-specific, that is [maybe was] question for #Foxp3+ Tregs mechanism of action. New paper in @NatImmunol from #Shevach's lab @NIH says definitely antigen-specific. Lets dive in. BTW, ~20 years ago his lab developed assays that showed it was non-specific 🤫

— David Usharauli (@3DiMMUNE) January 16, 2019

Now his lab made U-turn and concluded that #suppression by #Tregs is actually #antigen-specific and difference between now and then comes down to in #vitro versus in #vivo assays 🤔

— David Usharauli (@3DiMMUNE) January 16, 2019

2. This #antigen-specific #suppression was still active when antigen-specific dendrtic cells were removed from Treg co-culture (1st culture) and exposed to T cells (2nd culture). pic.twitter.com/dj1pzDuNNv

— David Usharauli (@3DiMMUNE) January 16, 2019

So, from now on if someone asks you how Treg suppress other T cells don't hesitate to reply "antigen-specific manner", add Ethan Shevach said so and no one will argue with you. got it 🤨 https://t.co/I4pAYIIGy1

— David Usharauli (@3DiMMUNE) January 16, 2019

Tumor infiltrating Foxp3+ Tregs recognize synthesized but not naturally available cancer neoantigens

In new paper in @SciImmunology, Steven Rosenberg's group from @NIH asks why are #Tregs accumulate in tumor tissues and if it has something to do with #cancer #antigen recognition. But how to study #Foxp3+ Tregs in humans? No reliable surface marker exist yet.

— David Usharauli (@3DiMMUNE) January 14, 2019

1. First, they sorted fix/perm T cells from #tumor samples based on Foxp3+ expression to separate #Tregs from non-Tregs and sent the sorted samples to @AdaptiveBiotech (this is what all do now days looks like) for deep #TCR #sequencing and alpha/beta TCR #pairing.

— David Usharauli (@3DiMMUNE) January 14, 2019

2. They found differences between Treg-TCRs usage and non-Treg TCR usage. OK. Then what? #Sequencing or even TCR pairing by itself have no value unless one knows what these #TCR recognize. Many labs don't even bother to do anything about it, but #Rosenberg's people did.

— David Usharauli (@3DiMMUNE) January 14, 2019

3. To do it, they took top #Foxp3+ #Treg TCRs pairs and #transfected them individually into #autologous T cells and tested their #reactivity to autologous tumor samples. Some #TCR specifically recognized something in autologous tumor samples. They thought it must #antigen. pic.twitter.com/fbj8esBJSq

— David Usharauli (@3DiMMUNE) January 14, 2019

4. To identify antigen recognized by Treg TCRs, they used whole-#exome and RNA sequencing (RNA-seq) to detect somatic mutations and make mutant peptide pool. Indeed one Treg TCR from one patient and another Treg TCR from another patient recognized mutant #annexin A1 and #CCL5. pic.twitter.com/FRiibvwYTX

— David Usharauli (@3DiMMUNE) January 14, 2019

5. But here is the twist. None of these #Treg #TCRs recognized autologous tumor samples. Interestingly, for #annexin A1 the authors suggested its expression was too low in tumor samples and for #CCL5 they found that tumor cells actually do not express CCL5 at #RNA level.

— David Usharauli (@3DiMMUNE) January 14, 2019

Basically, Treg TCR could recognize lab #synthesized #mutant peptides from patient samples but not natural #tumor cells. So, the authors ended up back in square one. #Tregs go to tumor tissues but the methods we have right now does not allow us to know what Ag they see it there.

— David Usharauli (@3DiMMUNE) January 14, 2019

Inflammation modifies pattern of differentiation of commensal-specific T cells

1. #Commnesal S. epidermidis–specific -#MIIINA:H2-M3+ CD8+ T cells ordinarily differentiate into Tc1 or Tc17 subsets. However, when co-exposed to chitin or sand fly (source of #inflammation), Tc17 subset also produce type II cytokines. pic.twitter.com/g9Wy7BncPD

— David Usharauli (@3DiMMUNE) January 10, 2019

3. In any case, such deviation into type II cytokine+ lineage during co-exposure to S. epidermidis and inflammation is specific for CD8+CCR6+ cells (referred to as Tc17). pic.twitter.com/6uNCVHMtEz

— David Usharauli (@3DiMMUNE) January 10, 2019

5. The authors tried to show how skin #Treg deficiency could have the same effect on Tc17 de-differentiation. Again. the authors failed to show that IL-17+ and IL-5/IL-13+ Tc17 cells overlap. They don't. They put in suppl material these #data. Should be in main paper. pic.twitter.com/QupGc7HWLo

— David Usharauli (@3DiMMUNE) January 10, 2019

7. But again, no evidence is provided that IL-17+ T cells co-express IL-5 or IL-13 when exposed to IL-18. Exactly opposite. No overlap. pic.twitter.com/QG8U9EBSSH

— David Usharauli (@3DiMMUNE) January 10, 2019

So, what is my conclusions: this paper does not support the authors' conclusions about Tc17 acquiring Tc2 phenotype. Yes, it is true that RORgt+ or CCR6+ CD8+ T cells could acquire Tc2 phenotype but the same not true IL-17+ Tc17 cells or at least data are not there.

— David Usharauli (@3DiMMUNE) January 10, 2019

Gut-derived antibody-secreting cells and brain inflammation