If T cell clones are so diverse, what prevents anti-tumor immune response?

Identifying cancer and pathogen-specific epitopes or TCRs may sound intuitive, but it is a futile approach. Diversity of T cell or B cell clones guarantees that the adaptive immune system will always have relevant clones to detect cancer or pathogen.  

Epitopes have no meaning attached to them with one exception.  It is when the said epitope is self. Each body will have different sets of self-epitopes. Every self-epitopes relevant for host's survival are encoded in the thymus, and thymic Tregs are trained to prevent any T cell activity against those epitopes in the periphery. This is called tolerance, and it is antigen[epitope]-specific. 

Then what prevents effective responses to cancers or pathogens? It is commonly but mistakenly believed that Tregs prevent effective T or B cell responses to cancers or pathogens. But Tregs only prevent anti-self response, and it is epitope-specific action.  So, by definition, if Tregs do their job as required, we cannot blame them. But it has nothing to do with cancer or pathogens, which obviously have other epitopes different from self, we call nonself. So, if cancer cells or pathogens express nonself epitopes that are always detected by adaptive immune system, why not everyone can fight it off effectively?

This is because T cells themselves prevent it. Yes, T cells, not Tregs, prevent effective response to cancers or pathogens in certain conditions. What are those conditions? These are condition when polarized T helper cells prevent other T cells functions. Polarization is a pathological state. A Polarized T cell's effect on other T cells is epitope non-specific, meaning, a polarized T helper cell specific to cancer or pathogen nonself epitope A will prevent T cells specific to epitope B, C, D, E, F, etc., to function properly. It is exactly Treg's job to shut down those polarized T helper cells to allow other T cells to manifest their functions and get rid of either cancer or pathogen. And Treg do it, as we already said, epitope-specific manner.

For this reason, it is not so important to identify any cancer or pathogen-specific nonself epitope, but rather to identify an epitope that could activate polarized T helper cells.

To make things even more complicated, one may ask if Tregs are self-specific and act epitope-specific manner, how can Tregs shut down polarized T helper cells that are nonself-specific? It is possible because Tregs are cross-reactive and can inhibit only those polarized T helper cells which share TCR specificity with Tregs.

In other words, control of self-tolerance and control of effective anti-nonself response are one and the same.  

These are 3 papers that together provide a full discussion related to the SPIRAL model we have developed to explain how Tregs work within an adaptive immune system:

 

 

Concurrent cross-reactivity of microbiota-derived epitopes to both self and pathogens may underlie the "Hygiene hypothesis"  

 

https://onlinelibrary.wiley.com/doi/10.1111/sji.12708 

 

Could cross-reactivity rescue Foxp3+ regulatory T cell precursors from thymic deletion? 

 

https://onlinelibrary.wiley.com/doi/10.1111/sji.12940

 

 

 

Microbiota-Specific Foxp3+ Regulatory T Cells Could Control Pathological T Helper Responses

 

https://www.dl.begellhouse.com/journals/2ff21abf44b19838,40a32b197f7156bc,7988864072d2c7c6.html

 

 

   

A specific bacteria-infecting virus, bacteriophage, found in gut microflora, augments anti-tumor T cell immunity

Molecular mimicry between microbial and host's antigens could contribute to autoimmunity but also to the protection against tumors through epitope cross-reactivity. A new study in journal Science indicates that those cross-reactive epitopes could come from viruses that infect endogenous microbial species. 

In this study the authors made a surprising observation that only certain Enterococcus hirae microbial strains (E. hirae 13144 or IGR11) augmented anti-cancer effect in experimental cancer model.

 

 

Next, the authors showed that this biological activity was linked to one dominant epitope, TSLARFANI, derived from TMP protein that originated in 39.2-kb prophage only in those specific E. hirae strains. Mice immunized with heat-inactivated E. hirae 13144 strain, or peptide TSLARFANI, or irrelevant E.coli engineered to express TMP, all augmented anti-cancer effect. 

 

 

Mechanistically, the authors showed that epitope, GSLARFRNI, derived from cancer cells used in these experiments, was recognized by the same CD8 T cells which labeled with TSLARFANI epitope tetramers confirming cross-reactivity between these 2 epitopes.

 

 

In summary, this study suggests that microbiota and bacteriophages they carry represent new modality in fight against cancer. In this study overall anti-tumor effect is modest but we need to take into account that this is an effect of just one cross-reactive epitope in one type of MHC inbred mice, and it is likely that many other epitopes will be involved in outbred species such as humans. However, it is still extremely hard to do such analysis in humans in real world scenario due to lack of exact knowledge about human microbiota strains and poor reliability and performances of available bioinformatics approaches. However, once the mechanistic principles underlying anti-cancer effects are uncovered and accepted, then it is much easier to move the field forward.

posted by David Usharauli

Cross-reactivity between microbial-derived antigens and tumor neoantigens correlates with long-term survival

This is a very interesting paper published in Nature few months back. In this study the authors wanted to uncover immune correlates of long-term (>10 yrs) survival from pancreatic ductal adenocarcinoma that normally account for less than 2% of all patients. 

First they found that "patients with both the highest predicted neoantigen number and either the greatest CD3+CD8+, or polyclonal T-cell repertoire, but neither alone, exhibited the longest survival". It suggested that tumor neoantigen-derived epitope quality rather than simply quantity correlated with survival. 

More importantly, bioinformatics analysis of similarities (mimicry or cross-reactivity or poly-reactivity) and neoantigen fitness modelling between tumor neoatigens and microbial-derived antigens significantly stratified short- and long-term survivors independent of confounding factors and adjuvant chemotherapy. 

If these data will  hold true in other cancer settings, it will append how immunotherapy is applied to treat cancer patients. While this finding is potentially hugely important for immunotherapy, the authors tried not to make too big a statement about it (I would imagine it is a result of a typical reviewers conservatism), writing that "This hypothesis does not assume any associations between pre-existing antimicrobial immunity and survival, but rather aims to develop a strategy to identify candidate neoantigens based on defined immunogenic pathogen-derived epitopes" and in other place "Our results do not indicate causal associations of pre-existing microbial and anti-tumour immunity in LTSs [long-term survivors]. Instead, our data suggest that embedding microbial homology in the context of our neoantigen quality model can help to create an effective surrogate for immunogenic neoantigens." 

posted by David Usharauli

Chronic systemic inflammation in Lupus could be driven by bacterial antigen mimicry to human autoantigen Ro60

Earlier I discussed a new study in journal Science from Martin Kriegel's lab at Yale University School of Medicine that showed how translocation of commensal bacterial species E. gallinarum could amplify autoimmune phenotype in Lupus prone mouse model. It appears that his lab had another paper under review that was published this week in Science Translation Medicine, a sister publication run by Science. In this study the authors tried to show that auto-reactivity to auto-antigen Ro60 frequently observed in lupus susceptible patients could potentially be driven and sustained by commensal microbial species [turned pathobionts] expressing Ro60-like molecules.

The authors showed that there are substantial overlap between T cell epitopes in human Ro60 and Ro60 molecule from bacterial species such as Propionibacterium propionicum (P. prop) and Bacteroides thetaiotaomicron (B. theta). 

Memory T cells freshly sorted from anti-Ro60 reactive SLE (lupus) patients responded to P. prop and B. theta lysates.   

In summary, this study suggests that commensal bacterial species turned pathobionts could initiate and sustain lupus phenotype in susceptible individuals. This is not a definitive study. First, it is obvious that commensals per se cannot induce lupus but only in susceptible individuals (almost every individual carries these commensals). What exactly constitutes this susceptibility in humans to lupus [or any other autoimmune diseases] is a black box presently. Moreover, their "analysis revealed no significantly different bacterial OTUs in the fecal, oral, or skin microbiomes between anti-Ro60–positive and anti-Ro60–negative subjects". However since resolution of currently available microbiome analytical tools are quite low it is still possible that at bacterial species or strain level there maybe significant differences between healthy vs. lupus and Ro60-positive vs. Ro60-negative populations.

posted by David Usharauli

Molecular mimicry to gut microbiota antigen protects against colitis but induces diabetes

Current issue of journal Cell has one very interesting but at the same time confusing research paper. In it, the authors proposed that

(a) diabetes susceptible mice strain, NOD, harbor CD8 T cells specific for microbiota antigen that cross-react with β cell antigen, IGRP, and

(b) such molecular mimicry prevents colitis but at the same time could induce diabetes.

First, the authors showed that MHC I alelle expressed in NOD mice (H2K^d) could bind IGRP_206-214 homologue derived from integrase family expressed by some gut Bacteroides species (BacIYL_36–44). 

At high dosage, such binding was functional in stimulating high affinity IGRP_206-214-specific T cells (17.4+ CD8 T cells).

Human T cells from PBMCs could apparently respond to it as well (though it is strange that it generated better stimulation index than Tetanus toxoid).

Then, the authors did the following experiment. They exposed IGRP^-/- 17.4+ TCR transgenic mice to chemical irritant (DSS) and observed that high affinity IGRP_206-214-specific T cells, 17.4+ CD8 T cells, but not low affinity ones (17.6+), could protect against colitis (I assume that they used IGRP^-/-mice to avoid diabetes development).

It appears that colitis protection depended on perforin expression by 17.4+ T cells. The authors speculated that 17.4+ CD8 T cells prevented colitis by eliminating dendritic cells laden with microbiota-derived antigen (BacIYL_36–44).

As a confirmation, the authors showed that germ-free TCR Tg NOD mice colonized with Bacteroides species expressing BacIYL_36–44 were protected against colitis.

Colitis protection was observed even in classical, adoptive naive CD4+ T cell transfer colitis model.

Interestingly, however, transfer of T cells from pre-diabetic NOD mice into germ-free NOD.scid mice colonized with Bacteroides species expressing BacIYL_36–44 did not accelerate diabetes development (here I assume DSS is required to accelerate T cells priming against IGRP by creating dysbiosis).

In summary, this study suggests the following scenario: diabetes-inducing CD8+ T cells cross-react with gut microbiota-derived antigen. When such microbiota-derived antigens become visible to T cells (during dysbiosis?) CD8+ T cells migrate to gut and eliminate dendritic cells laden with cross-reactive antigens. By eliminating DCs, other T cells are not able to induce inflammation in the gut, thus no colitis. However, the same beneficial CD8+ T cells later migrate to β cells, recognize similar looking antigen, IGRP, and mediate its destruction and diabetes.

Does such circuit makes any evolutionary sense? 

Update: Interestingly, other research group previously detected different set of gut microbiota antigens cross-reactive to IGRP_206-214. They used TCR NY8.3 transgenic NOD mice (that recognize the same IGRP epitope) and found that these CD8 T cells cross-reacted with IGRP_206–214 homologous peptide, W15944, derived from L. goodfellowii, a member of the phylum Fusobacteria (gram-negative anaerobe), a human and NOD mouse oral commensal. 

posted by David Usharauli   

Loss of microbiota depletes cross-reactive Foxp3+ Tregs leading to selective immunopathologies

Check out our follow-up manuscript in PeerJ Preprints that provides a brief guide to SPIRAL, a novel interpretive framework that demonstrates the central role of microbiota-Treg axis in the initiation of immune disorders.

Kamala T, Usharauli D. (2017)

 

Loss of microbiota depletes cross-reactive Foxp3+ Tregs leading to selective immunopathologies.

PeerJ Preprints 5:e3237v1

https://doi.org/10.7287/peerj.preprints.3237v1

 

The 'Hygiene hypothesis', a cornerstone model to account for the role of exogenous pathogens and later of endogenous microbiota in immune disorders, is currently presumed to operate at the innate immunity and metabolite levels to properly 'educate' the immune system. Doing so however fails to satisfactorily account for the antigen-specific nature of such disorders. SPIRAL is a novel interpretive framework that resolves this dilemma. It represents the periodic table of cross-reactive Foxp3+ regulatory T cell (Treg) epitopes selected from commensal microbiota over evolutionary time to mediate self-nonself discrimination and effector class regulation. Here, we utilize the SPIRAL's predictive power to provide a mechanistic antigen-specific basis for the initiation of allergies and autoimmune diseases as well as for the failure to mount effective anti-tumor and vaccine responses through selective loss of microbiota and corresponding cross-reactive Foxp3+ Tregs.



 

How Foxp3+ Tregs and microbiota work together to control immune system

Check out our new paper in PeerJ Preprints that unlocks the mystery of how Foxp3+ regulatory T cells work that enables proper immune functioning.

Usharauli D, Kamala T. (2017) An identical mechanism governs self-nonself discrimination and effector class regulation. PeerJ  Preprints 5:e3081v1  https://doi.org/10.7287/peerj.preprints.3081v1

Prevailing immunological dogma dictates self-nonself discrimination, meaning to respond or not, and effector class regulation, meaning choosing the most effective response, are two separate decisions the immune system makes when faced with a new antigen. Representing a cardinal departure from the past, our model instead predicts both self-nonself discrimination and effector class regulation are in fact one and the same process controlled by Foxp3+ regulatory T cells (Tregs) whose antigen-specific repertoire is entirely maintained by commensal microbiota-derived cross-reactive antigens.

 

 

posted by David Usharauli

Fusobacteria, a gut commensal, contributes to autoimmune type I diabetes in mice

Initiation of autoimmune disease is still an immunological mystery. Some forms of autoimmune diseases are results of genuine genetic defects in signaling molecules within immune system. Other forms show strong linkage to certain HLA haplotypes that present antigenic epitopes. More recently scientists focused on the role of gut commensals in autoimmune diseases.

A new study in Jounral of Experimental Medicine showed that cross-reactivity at the epitope level between gut commensal Fusobacteria-derived magnesium transporter and β islet-specific glucose-6-phosphatase catalytic subunit–related protein (IGRP) contributed in autoimmune diabetes development in IGRP-specific CD8 T cell transgenic, CD8+ TCR NY8.3 NOD mice.

Initially, the authors observed that unlike MyD88KO NOD mice, MyD88KO CD8+ TCR NY8.3 transgenic NOD mice showed accelerated diabetes development (though unlike the authors, I don't find this surprising).

Interestingly, when co-housed with WT NOD mice, MyD88KO TCR NY8.3 transgenic NOD mice showed enhanced protection against diabetes, suggesting dominant role of fecal bacteria present in WT NOD mice in providing this protection.

Since it is known that NOD mice susceptibility to diabetes is commensal-dependent, the authors sequenced fecal microbiome in MyD88KO NY8.3 NOD mice to determine its composition. Not surprising, certain families of commensals underwent changes on MyD88KO background.

When the authors compared the IGRP_206–214 peptide sequence against bacterial protein sequences in the nonredundant protein sequence database, they found several hits shared strong homology with IGRP_206–214 peptid, the native autoantigen detected by NY8.3 CD8+ T cells. One such peptide, W15944, was derived from L. goodfellowii, a member of the phylum Fusobacteria (gram-negative anaerobe), a human and NOD mouse oral commensal.

Indeed, W15944 stimulated NY8.3 CD8+ T cells could transfer diabetes in NOD mice.

Finally, introduction of L. goodfellowii into WT NY8.3 NOD mice accelerated diabetes development, further suggesting role of L. goodfellowii in this process (while in general, this paper is of high quality, it lacks some of the crucial experiments such as, for example, (1) introduction of L. goodfellowii into NY8.3 NOD mice on germ-free background and (2) experiments with L. goodfellowii lacking cross-reactive W15944 peptide).

In summary, the author showed that in this artificially constructed NOD mice, IGRP-specific CD8 T cells could be activated by commensal-derived cross-reactive peptide and initiate autoimmune destruction of  β cells (it is remains to be seen why Foxp3+ regulatory T cells are incapable of preventing such T cell attack).

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

Cross-reactivity to gut microbiota could explain failure of HIV vaccine

More than 30 years since its discovery and there is still no FDA licensed HIV vaccine. It is not even entirely clear if the failure to develop effective HIV vaccine has really anything to do with frequent HIV antigenic shift. Flu virus, for example, also undergo quite frequent antigenic shift and still there is Flu vaccines with 60-90% efficacy.   

New study published this week in journal Science suggested new explanation for frequent failure with HIV vaccine(s). It appears that cross-reactivity between gp41 component of HIV vaccine and endogenous microbiota antigen (component of E. coli RNA polymerase) prevented development of neutralizing gp120-specific antibody titre.

The authors have analysed Ab repertoire to HIV-1 DNA prime, recombinant Adenovirus Type 5 (rAd5) boost vaccine. They found that 93% of Env specific antibodies derived from sorted memory B cells were directed against non-neutralizing gp41 antigen. 

Interestingly, majority of those gp41-specific antibodies utilized polyreactive, innate-like IGHV1-69 variable segment. VH1-69 locus is involved in Ab repertoire directed to Flu stem region. But unlike Flu specific VH1-69 Abs, gp41-specific VH1-69 Abs were made of allele variants with Leucine substitution at position 54 in HCDR2.

Finally, analysis of antigen specificity of individual gp41 mAbs revealed high level of polyreactivity towards commensal and self antigens.

In summary, these results points to the most important aspect of immune system, namely that strength and specificity of immune response is controlled by environmental antigens, including microflora antigens. It is my opinion that future vaccine testing would require incorporation of cross-reactivity tests against wide range of environmental antigens to select the most effective immunogens.  

David Usharauli

    

   

Naive T cell clonal size is influenced by breadth of self-antigen cross-reactivity

While both B cells and T cells developed to detect foreign antigens, the basic mechanisms behind this process for these two population are fundamentally different. Unlike B cells, T cells recognize foreign epitope presented on MHC plate. The size of epitope detected by T cell receptor (TCR) is usually 9 amino acid long. Such constraint imposed on T cell receptor creates potential for cross-reactivity leading to autoimmunity.

This new study in journal Immunity went further to show that out of 9 amino acids that make up TCR recognition field, changes in only 5 amino acids have the major impact on TCR recognition and T cell population size.

First, the authors, led by Marc Jenkins at the University of Minnesota, Center for Immunology, have determined the population size of mouse naive CD4 T cells specific for a dozen of foreign antigens. Immunization with these specific antigens showed that magnitude of CD4 T cell response correlated with the number of antigen-specific naive T cells.

Next the authors synthesized 11 variant peptides for each 13 peptide examined by substituting each amino acid with alanine at positions P1-P10 ( TCR recognition field). Parental peptide immunized mice were then tested for T cell reactivity to variant peptides in ELISpot assay. The authors found that changes in amino acids in Position 2, 5, 7, 8 could reduce T cell responsiveness by >90%.

To understand how TCR cross-reactivity could affect the variant peptide, 2W109-specific T cell population size and its responsiveness to 2W109, the authors have used act-2W mice that express 2W epitope in the thymus. 2W differs from 2W109 at position 1, 4, 6, 9. Double tetramer staining revealed that compared to B6 mice, in act-2W mice, T cells cross-reactive for both 2W and 2W109 peptide were significantly reduced (B6 mice ~ 180 T cells, act-2W mice ~ 40 T cells). 

Additional experiments indicated that 2W109-specific T cells, that remained in act-2W mice after negative selection, developed heightened sensitivity to amino acid substitution across all 9-mer, including anchor amino acids, implying increased dependency on peptide conformation for TCR recognition.

Indeed, re-analysis of parental foreign peptide-specific T cells responsiveness to variant peptides revealed that increased sensitivity to anchor amino acids substitution correlated with reduction of clonal size, suggesting negative selection against potential self-epitopes.

This study suggests that clonal size of naive T cell specific to any given foreign antigen is determined by the number of self-antigen it happens to cross-react. It addition, these results indicate that TCR cross-reactive for self-epitopes becomes heavily dependent on peptide conformation and may have low affinity for foreign antigens.  

This results, while quite complex, provided a guiding principle how to study T cell responses or how to design T cell specific vaccines.   

Please, leave your comments below. Let me know what do you think about this paper or my analysis.

David Usharauli