Thread by @KedmiRanit

Thrilled to share my research from Dan Littman's lab at @nyulangone, online today in @Nature. If you are interested in the differentiation of CD4 T cell programs and the mucosal iTreg response, this is for you. #Treg, #ILC3, #Tolerance, go.nature.com/3RCXHkw, A 🧵 /1

CD4 T cell programs govern immune responses, directing inflammation or tolerance. It is widely accepted that classical DCs (cDC) present microbial peptides on MHCII to activate and direct the differentiation of all CD4 T cell programs. Our results challenge this dogma. /2

We show that both the tolerogenic iTreg and the inflammatory Th17 responses to gut microbes are initiated by two distinct antigen-presenting cell (APC) subsets, other than cDC. And what about cDC? Our data suggest that they initiate the T follicular helper (Tfh) response. /3

Let’s dive in /4

H. hepaticus induces iTreg and Tfh programs but instead drives the expansion of pathogenic Th17 cells when the iTreg response is impaired. go.nature.com/3uUNxCZ. Using this system, we asked a central question: how are different CD4 T cell responses to gut microbes induced? /5

Initially, we found that the iTreg response is abolished in mice lacking MHCII or Ccr7 in CD11c+ or Zbtb46+ lineages, presumably cDC. An inflammatory Th17 response occurred in these mice instead, suggesting that cDC are not required to initiate the Th17 program. /6

While our genetic models supported the notion that migratory cDC initiate the iTreg program, and that migratory cDC are adjacent to newly-primed T cells, several genetic models to deplete cDC showed no effect, and we concluded that the iTreg program is initiated by other APCs. /7

Together with @NYGCtech at @nygenome, we looked for other APCs targeted by CD11c-Cre. Our #CITEseq analysis suggested that we tend to trust Cre transgenic mouse lines too much. /8

Besides cDC, CD11c-Cre targeted two other Zbtb46 expressing APC subsets. Both, interestingly, expressed ROR𝛄t: ILC3 and an interesting rare, Aire expressing subset, that was recently named Janus cells (JCs) or Thetis cells, bit.ly/3cpcMHh, go.nature.com/3RFuiq7 /9

While antigen presentation by ROR𝛄t+ ILC3 was suggested to be required for Th17 elimination in the gut (Greg Sonnenburg lab), we found that antigen presentation by ROR𝛄t cells, either ILC3 or JCs, is required to actually initiate an iTreg response. /10

Indeed, our data suggest that Ccr7-dependent ROR𝛄t+ cells present the microbial peptide to naïve T cells and activate TGFβ using Integrins ⍺vβ8 to induce an iTreg response. /11

Is antigen presentation by migratory cDC required at all for iTreg responses? No. Using MHCII gain-of-function mice, we found that MHCII expression solely in ROR𝛄t+ cells is sufficient to obtain an iTreg response! /12

So, what migratory cDC2 are doing? Why do they present the helicobacter peptide and reside next to newly-primed T cells? /13

Antigen presentation by ROR𝛄t+ cells was sufficient to initiate iTreg response, but it failed to induce the Tfh program. Tfh response required antigen presentation by CD11c+ cells, potentially migratory cDC2. /14

This story is a joint effort of many people. I want to first thank my mentor Dan Littman and to thank my ‘partners in crime' current and former members of the Littman lab: @najarta, @mesakr, @GraysonAllyssa, @MariaPokrovskii, jhimmy talbot, Lina Kroehling, Mo Xu /15

I also want to thank all our wonderful collaborators. To @m_stoeckius, @slhao, and @YUHANHAO2 from the @nygenome that helped us to implement the powerful #CITEseq technology in its early days. /16

Many thanks go to @JessicaWang927 and @joegermino from @gardnerlabUCSF at @UCSFSurgery, to @CalebLareau and @Satpathology, and @HelenaPaidassi for great collaboration and help to understand the identity of the ROR𝛄t+ cells. A lot more work is still ahead of us. /17

I also want to thank all collaborators that sent us their mice. Without those mice, we could never make it. @iannisaifantis, @LauferTerri, Paul Allen, and @MAndersonUCSF /18

Lastly and very importantly I invite you to take a close look at related recent findings by our colleagues: the Greg Sonnenberg lab, the Rudensky lab, @themis_brown, and @TheAbramsonLab
bit.ly/3RGP7lK, go.nature.com/3RFuiq7, go.nature.com/3vkoh9J /19

These studies provide insights into this novel ROR𝛄t+ APCs and their central role(s) in inducing CD4 T cell responses and emphasize how much more we still don’t understand. Lucky to be a part of this vibrant community! /20

lastly, on a personal note, I want to thank @akedmi, that has been my rock throughout /21