Wednesday, December 27, 2017

Effort to identify tumor-specific antigens: The University Industrial Complex study results

New study in journal Cell is prime example why utilization of sophisticated high-throughput methods and computer technologies does not guarantee generation of clinically useful results. I imagine the only reason this study was even accepted in Cell was the fact that list of authors included many well-known scientists with links to both academia and silicon valley (Stanford University School of Medicine, Chan Zuckerberg Biohub, Parker Institute for Cancer Immunotherapy).   

Idea of this study was to develop techniques to quickly identify tumor-specific antigens (most likely mutated antigens) that could be used in immunotherapy (though there is no evidence that any cancer vaccines based on mutant protein sequences actually work in humans using available practices). 

For this task, the authors took advantage of yeast-display library expressing random peptide covalently linked to the HLA-A*02:01 molecule, an allele which is present in up to 50% of a number of populations. The authors estimated that "approximately 400 million unique peptides ranging from 8 to 11 amino acids are represented in the combined [yeast-display] libraries."

To validate this approach, they used three recombinant 'blinded' positive control TCRs derived from a melanoma patient (their antigen specificity had been identified independently by exome sequencing, tetramer staining and binding prediction algorithms). However, antigen-specificity of only 1 TCR (NKI 2) could be validated using their yeast-display library. As the authors said "targets of NKI 1 and NKI 3 could not be unambiguously identified through this blinded validation."

Of note, in these validation experiments with NKI 2 (specific for ALDPHSGHFV, a peptide neoantigen derived from CDK4 and other DMF5 TCR specific for EAAGIGILTV derived from the MART-1 melanoma antigen, successful validation [specific enrichment + TCR staining] occurred when HA tagged 10-mer epitope library were used. 

The authors anyway went ahead with this "less than perfect" approach to try to identify tumor antigen specificity of T cells derived from 2 patients with colorectal adenocarcinoma and homozygous for the HLA-A*02 allele. The authors focused on 20 TCR most enriched in tumor tissues (based on frequency of occurrence of the same TCR genes). 

Out of these 20, only 4 TCRs could enrich peptide from the library (only with c-Myc tagged 9-mer epitope library) and only 3 TCR could stain yeast samples.  

Next, the authors try to identify epitopes from potential landscape of sequences for each TCR. Several algorithms were deployed (at least 3 or more such as a modified variant of the previous statistical method using a position weight matrix and a method utilizing a two-layer convolutional neural network). They found 1 peptide sequence EYGVSYEW, which closely matches the peptide motif for TCR 1A, however, neither this exome peptide or the anchor-modified exome peptide (EMGVSYEM), nor the human peptide predictions stimulated the cell line modified to express the TCR 1A. TCR 4B was stimulated with several peptides and as the authors write "true in vivo specificity cannot be unambiguously identified without additional tumor information". Regarding TCR 2A and 3B, only 1 peptide stimulated cell line expressing these TCRs. This peptide was MMDFFNAQM, which is derived from U2AF2, a protein involved in an RNA splicing complex. However, in both patients, no mutations were found in U2AF2.

In summary, the authors wrote "although we cannot definitively determine an immune response targeting the peptide derived from U2AF2, the evidence from the yeast-display screen, prediction algorithm, and in vitro stimulation identify this peptide as the likely target". However, when reading this study it is clear that none of the components worked: yeast-display screen performed suboptimally, prediction algorithms provide little clue and in vitro stimulation made it even more confusing. So, what have we learned from all of these? I would say maybe don't do what they did.

posted by David Usharauli    

Saturday, December 9, 2017

From microbiome-association studies to causal microbe identification

As new Nature study says "the general inability to move beyond correlations and address causation has been the Achilles heel of microbiome research." Well said. Indeed, notwithstanding of so many microbiome studies, the number of identified microbiota species specifically and reproducibly linked to a particular [medical] condition is still zero.  

Is there a way to overcome this challenge? Maybe one could compare microbiome content of the hosts displaying variable clinical phenotype [DSS colitis, in this case] and find one microbial species, if you are lucky, that control that phenotype in every host? But isn't this approach exactly what all other studies have done all along? 

And actually, how strong is the data in support of this approach? The authors showed that germ-free mice and germ-free mice colonized with mouse microbiota derived from SPF mice (MMb mice) were highly sensitive to DSS colitis induction compared to SPF mice or germ-free mice colonized with human microbiota (HMb mice). Of note, observed difference in survival between MMb and SPF is strange since both should have SPF microbiota.

When the authors compared several pairs of mice strains housed separately or co-housed, they found that sensitivity to DSS colitis segregated with presence of Lachnospiraceae species (Clostridium immunis).       

Indeed, colonization of germ-free mice with human microbiota enriched with Clostridium immunis could improve mice survival in DSS colitis model.

However, again, survival data between different mouse strains did not correlate with level of Lachnospiraceae species, questioning simplicity of one-on-one relationship between Clostridium immunis and colitis score (HMb and SPF have similar survival curve but vastly differ in Lachnospiraceae content).

In summary, without more data and confirmation by other labs I will view these data as very preliminary and unverified with lots of caveats. Surely, not a Nature material in my opinion.

posted by David Usharauli

Saturday, December 2, 2017

Dual TCR expressing T cells could drive autoimmunity

An article in Cell Host and Microbe (CHM) caught my attention. In proposed that dual TCR expressing T cells are responsible for autoimmune phenotype in K/BxN mice

K/BxN mice develop spontaneous arthritis thought to driven by Vβ6+ KRN T cells recognizing glucose-6-phosphate isomerase (GPI), the self-Ag presented by MHC class II Ag7 molecules. Ordinarily, it is thought that pathogen cross-reactive to self antigen, in this case GPI, could initiate autoimmune disease (theory of molecular mimicry).

However, recently the role of endogenous microbiota in driving autoimmune arthritis received new attention. Here, the authors showed segmented filamentous bacteria (SFB) was required to initiate autoimmune arthritis in K/BxN.

However, since SFB-derived peptide recognized by T cells required Vβ14+ TCR it was unclear how SFB was mediating autoimmunity against GPI recognized by completely different TCR made of Vβ6+ chain. Further analysis showed that some T cells in K/BxN express dual TCRs expressing both Vβ6+ and Vβ14+ chains. Indeed, sorted T cells expressing dual TCR, but not Vβ6+ chain alone, recognized SFB-derived peptide (A6).

In vivo, adoptive transfer of monoclonal KRN T cell population on RAG KO background that prevents expression of other Vβ or Vα chains (only expressing Vβ6+ KRN T cells), could not mediate arthritis in T cell-deficient host (harbor normal B cells also required for arthritis development). Of note, other paper in 1999 however found no difference in arthritis development between WT and RAG KO KRN T cells.

In summary, the authors think that first dual TCR T cells get activated by SFB-derived epitope via Vβ14+ TCR, indirectly prime Vβ6+ TCRs, on the same T cells, that then actually mediates autoimmunity against self antigen GPI. However, it is not clear from this study whether endogenous Vα chains could contribute to cross-reactivity between SFB and GPI when recombined with Vβ6+ or Vβ14+ chains in WT KRN T cells.

posted by David Usharauli


Sunday, November 26, 2017

Allergen-sensitized mothers transfer protection against allergy to offspring through milk

In this study the authors showed that mouse pups born to mothers sensitized to allergen were significantly protected from developing allergic response to the same antigen.    

Protection in offspring was associated with the generation of antigen-specific Foxp3+ Tregs as observed in proliferation suppression assay or following short-term Treg depletion by DT (however, the authors did not analyze antigen-specificity of Tregs by tetramer staining). 

Further experiments showed that mother's milk contained allergen-specific antibodies and immune complexes (IC) and breastfeeding by allergen-sensitized mother (irrespective of birth mother status) was sufficient to transfer allergen protection to offspring.

In summary, this study suggests that breastfeeding by allergen-sensitized mothers can benefit offspring by preventing development of allergic response to the same allergen. However, it is not clear how exactly the authors see this mechanism working in humans. In mice, mothers were intentionally sensitized with allergen using epicutaneous (skin) application that supposed to mimic how humans with skin barrier dysfunction get sensitized to allergens. But the authors have not tested if milk from atopic human mothers can have the same effect on their offspring. For some reason the authors tested milk from nonatopic human mothers and showed that it 'worked' when fed to mice but did not provide any explanation why healthy, nonatopic human mother milk should contain any "protection" against allergen when mothers themselves are not sensitized as experiments in mice showed they must be for a milk derived immune complexes to work. So lots of unknowns and contradictions.

posted by David Usharauli

Saturday, November 18, 2017

Salt-sensitive lactobacilli drive down TH17 cells and contribute to normal blood pressure

Most clinically diagnosed hypertensions, high blood pressure, are idiopathic in origin, meaning one can't determine what causes it. First thing patients are asked to do is to modify their diet habits and reduce salt intake. Diet high in salt thought to contribute to hypertension by water retention.

However, it could be that there is another, immunological pathway that contributes to high blood pressure. New study in Nature showed that in mice and maybe in humans as well, high salt diet depletes Lactobacilli, a gut microbiota species shown to lower TH17 differentiation and contributing in maintaining normal blood pressure.

Initially, the authors showed that in mice high salt diet (HSD) depleted several microbiota species, most notable, Lactobacillus murinus (initially identified through sensitive machine learning approach using the AdaBoost classifier from scikit-learn module run on Python).

In autoimmune model, adding Lactobacillus murinus could abolish high salt diet-induced increase in disease severity. Lactobacillus murinus appears to drive down TH17 differentiation (of note, high salt diet did not change TH17 population in germ-free mice).

Mechanistically, the authors showed that Lactobacillus murinus could inhibit TH17 differentiation by producing indole-3-lactic acid (ILA), a product of tryptophan metabolism.

Finally, volunteers on high salt diet display high TH17 differentiation and decrease in gut content for Lactobacilli.

In summary, the authors want to make the case that high salt diet could induce high blood pressure by depleting Lactobacilli and increasing TH17 cells which appear to initiate hypertension-related changes. 

It is clear that depletion of Lactobacilli per se is not sufficient for initiation of hypertension but we don't know what are other remaining microbiota species that actually induce TH17 in humans. Also, it is not clear whether microbiota-derived conserved molecules or metabolites (ILA) are sufficient for initiating hypertension or there are more complex events, such as chronic antigen-specific interactions that are ultimately responsible for sustaining chronicity of TH17 response and hypertension.    

posted by David Usharauli 

Sunday, November 5, 2017

Hidden arm against tumors: microbiota-enabled checkpoint immunotherapy

This week Science published two studies showing how diverse microbiota directly contributes to efficacy of PD-1 checkpoint immunotherapy in several tumors.

First, we need to mention that senior authors from both papers disclosed associations with for-profit pharma/biotech companies (as cofounders, stockholders, paid consultants or advisory board members). Such associations could, in general, be seen as problematic if one promotes therapy lacking particularities.     

Second, data presented do not advance our understanding how microbiota contributes to the effectiveness of checkpoint immunotherapy. The sole conclusion from both papers is that the more diverse cancer patient's microbiota the more benefit it provides during PD-1 immunotherapy. However, when it comes to narrow down beneficial correlation to particular species we find that one paper reported enrichment of Akkermansia muciniphila while other paper reported enrichment of Faecalibacterium and Clostridiales in Responders (as opposed to Non-Responders).

We still don't know much about the role of microbiota in cancer immunotherapy. I think real advance will come when we define how antigens derived from specific microbiota contribute to anti-cancer immunotherapy either by amplifying existing cross-reactive effector T cells or Foxp3+ Tregs. 

posted by David Usharauli

Wednesday, October 25, 2017

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 (H2Kd) could bind IGRP206-214 homologue derived from integrase family expressed by some gut Bacteroides species (BacIYL36–44). 

At high dosage, such binding was functional in stimulating high affinity IGRP206-214-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 IGRP206-214-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 (BacIYL36–44).

As a confirmation, the authors showed that germ-free TCR Tg NOD mice colonized with Bacteroides species expressing BacIYL36–44 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 BacIYL36–44 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 IGRP206-214. They used TCR NY8.3 transgenic NOD mice (that recognize the same IGRP epitope) and found that these CD8 T cells cross-reacted with IGRP206–214 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   

Thursday, October 12, 2017

Microbiota-generated butyrate works on Aire to amplify Treg numbers

A short but very interesting paper in Journal of Immunology caught my attention this week. In this study the scientists showed that butyrate, a short chain fatty acid derived from fiber fermentation by microbiota acts on GPR41 receptor in the thymus to increase Aire expression and amplify Foxp3+ Treg frequency (of note, compared to WT, GPR41-KO thymus already contains almost 5-fold less Tregs).  

Generally it is believed that microbiota works locally in the gut or other peripheral tissues to either convert naive T cells into Foxp3+ Tregs or expand existing Treg numbers. However no one yet managed to definitely show which pathway is functionally operational in vivo in physiological conditions. This study now could help to further narrow down biological mechanisms responsible for Treg biology. If microbiota-generated butyrate could work on thymus to increase Aire expression that in turn increases level of Thymus-derived Treg generation, then peripheral conversion pathway may play even less relevant role in physiological mechanisms of tolerance.  

The most obvious question after reading this article is why the authors did not test Aire KO mice to verify their conclusions.

posted by David Usharauli


Friday, September 29, 2017

Gut IgA are naturally microbiota-reactive and polyreactive (cross-reactive)

Gut immune system naturally produces large quantities of IgA, an antibody isotype frequently found at mucosal surfaces. Since these IgA antibodies are found in mice in absence of immunization and infection they were dubbed natural and were thought to be specific for microbiota or food antigens. However a formal proof for such conclusions were lacking. 

This week journal Science published a new study from Bendelac's Lab to show that these naturally occurring IgA antibodies are present even in mice devoid of microbiota or food antigens.

In this study the authors analyzed specificity of IgA antibodies using single cell analysis. Interestingly, IgA bound to some but not to all microbiota species. 

Furthermore, most of gut IgA bound to all kind of microbiota-derived components showing a broad polyreactivity (cross-reactivity). Separate test using broadly-neutralizing antibody (bnAb) panel directed against influenza stalk region showed co-staining for microbiota coated by IgA. 

Interestingly, unlike other tissues, numbers of IgA+ plasma cells in small intestine were not reduced in germ-free mice.

Even more surprising, numbers of IgA+ plasma cells in small intestine were not reduced in germ-free mice fed antigen-free diet (amino acid diet).

These results suggest that 

(a) not all microbiota species are targeted by IgA that by itself requires further studies to understand why it is the case.

(b) natural, microbiota-reactive IgA in small intestine develop in absence of exogenous antigenic stimulation that suggests that such specificities are inherited and accumulate spontaneously. 

(c) selection of broadly neutralizing antibodies against viruses could be influenced by microbiota-derived antigens (polyreativity, cross-reactivity)  

posted by David Usharauli

Saturday, September 16, 2017

Tolerance to insulin is maintained by Foxp3+ Tregs

A new study in Journal of Immunology suggests that tolerance to insulin is maintained by Foxp3+ Tregs rather than by deletion of insulin-reactive T cell clones. 
Here, the authors reconstituted mice with T cells on scid background transduced either with high (4-8) or low (12-4.1) affinity TCR specific for native insulin peptide (insulin epitope B:9–23). In addition, each of TCR construct were fused with either native insulin (INS) or modified insulin carrying super-affinity peptide (R22E). All mice expressing either INS or R22E but not irrelevant HEL were protected from developing diabetes.

The authors showed that while R22E deleted developing insulin-specific T cell clones in the thymus, native INS did not.

In fact, the authors showed that if the T cells also lacked Foxp3 molecule (scid-scurfy), then protection against diabetes was lost in mice exposed to native INS.

This study could be interpreted to show that with the exception of  epitopes which are able to delete (purge) cognate T cell clones in the thymus, tolerance to self in the periphery is maintained by thymic-derived Foxp3+ Tregs.

posted by David Usharauli 


Tuesday, September 12, 2017

It is really hard to replicate human autoimmune diseases in mice

A new study in PNAS highlights the challenges scientists face when trying to reproduce human diseases in mice.  

Here, the authors tried to reproduce human type I diabetes by creating humanized mice by transplantation of HLA-DQ8+ human fetal thymus and CD34+ stem cells into immunodeficient mice (to recreate human immune system in mouse) followed by transfer of autologous [hu-mice]-derived HLA-DQ8/insulin-B:9–23 specific TCR transduced human CD4+ T cells and followed by two successive low doses of streptozotocin (a chemical to damage islet β cells and release auto-antigen).

However, even these steps were not enough to induce diabetes in hu-mice. Only immunization with insulin B:9–23 peptide + adjuvant (HLA class II-restricted T-cell response to InsB:9–23 peptide is highly associated with T1D in humans) in addition to above mentioned "conditioning" were able to induce diabetes in hu-mice.

No one really knows how autoimmune diseases are initiated in humans and these study shows that it is really hard to "reproduce" it in mice. Of course, it is not known what factors could play the role of "streptozotocin" and "B:9–23 peptide immunization" in natural context in humans. 

posted by David Usharauli

Friday, September 8, 2017

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
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.


Thursday, September 7, 2017

IL-27 protects against autoimmunity through its effect on Tregs

IL-27 is a heterodimeric cytokine composed of the p28 and Ebi3 subunits produced by APCs. It binds to IL-27 receptors (IL 27Rα:gp130) expressed on several cell types, including T lymphocytes. IL-27Ra-/- mice are shown to be highly susceptible to experimental autoimmune encephalomyelitis (EAE), a mouse of human MS. Earlier studies suggested that effect of IL-27 is mediated through its suppression of pro-inflammatory Th17 cells and generation of anti-inflammatory IL-10 producing Tr1 cells.

A new study in PNAS, however, showed that mice with Treg-specific IL-27Rα-deficiency displayed similar susceptibility to EAE as total IL-27Rα-deficient mice pointing to the role of Tregs in mediating IL-27 effect on EAE.

Compared to WT mice, mice with Treg-selective IL-27Rα-deficiency were not able to recover from EAE, a similar trend seen in total IL-27Rα-deficient mice. IL-10 levels were not different between WT and KO littermates.

Furthermore, in contrast to WT mice, injection of "therapeutic" dosage of IL-27 had no effect on EAE dynamics in Treg-selective IL-27Rα-deficient mice. Nor did antibody-blockade of IL-10 diminish effect of IL-27 on WT mice.

These results suggest that in addition to other cell types or even in contrast to other studies, the role of IL-27 in controlling severity of EAE could be solely mediated through its effect on Foxp3+ Tregs.

posted by David Usharauli 


Wednesday, August 23, 2017

MHC class II epitope presentation modulates microbiota and protects against autoimmunity

It is not clear how exactly microbiota modulates host's immune system. Evidence are largely based on empirical observations and nonspecific factors secreted by microbiota. Presently very little is known if microbiota-immune system interface is also controlled at the level of antigen-specific adaptive immune system.    
New study from Diane Mathis lab published in PNAS suggests it may be the case.
Her lab studies human type I diabetes (T1D) mouse model known as NOD. NOD mice lack MHC II allele, Eα. In this study they used NOD mice expressing Eα, referred as Eα16/NOD. In mating experiments, they noticed when Eα was expressed by female but not by male parent, baby mice with NOD genotype showed significant protection from developing T1D, suggesting protection was transmitted vertically from Eα16/NOD mother to NOD pups. Interestingly, this protection was lost when pregnant mothers (dams) were treated with antibiotics pointing towards role of microbiota.

Experiments with germ-free sterile mice confirmed this observation.

In summary, this study showed that MHC class II [epitope] presentation modulates composition of microbiota in such a way to harbor species protective against T1D. Again, the authors were unable to specifically pinpoint any specific mechanism of protection, though they reported increase in Foxp3+ Treg numbers in Eα16/NOD mice compared to NOD (but found no difference in microbiota bound to IgA between mouse strains). It is likely that epitope presentation at the level of adaptive CD4 T cells contributed to development of protective environment.

posted by David



Tuesday, August 22, 2017

Does TGF-β control T cell autoimmunity independent of Tregs?

When T cells attack body's own antigens its called autoimmunity. Each and every one with the adaptive immune system carry this potential. Mostly two mechanisms prevent autoimmunity: thymic deletion of overtly auto-reactive T cells (recessive tolerance) and Foxp3+ Tregs (dominant tolerance).
Within immune system, TGF-β plays important inhibitory role at T cell level. However, since TGF-β is involved in Treg biology, it is not clear if it has Treg-independent role in preventing autoimmunity.
New paper published in PNAS tried to answer this question.
The authors used OT-II RIP-mOva mice model (on RAG KO background) in which all CD4 T cells express OVA-specific T cell receptor and pancreas express OVA protein. These mice harbor OT-II Foxp3+ Tregs and they don't develop autoimmune diabetes.

To separate effect of Tregs versus TGF-β, the authors either compared TGF-βRII-KO mice vs. Foxp3KO (both on RAG1-KO OT-II RIP-mOva background) or adoptively transferred into RAG1-KO RIP-mOVA mice either Foxp3KO OT-II or OT-II T cells expressing TGF-βRII under the control of estrogen receptor. They noticed that OT-II T cell population lacking TGF-βRII but not Foxp3 could cause or accelerate autoimmune diabetes.

These two set of experiments are central for this paper. However, contrary to the authors' conclusions, these experiments do not fully answer Tregs versus TGF-β question. The main problem is that total TGF-βRII deficiency in all CD4 T cells affects both effector and Tregs (functionally at least if not number wise) while Foxp3 deficiency only affects Tregs. That is to say that if Tregs were TGF-βRII-sufficient and effector T cells TGF-βRII-deficient outcome could be different (WT Tregs might be able to stop effector OT-II cells). Another way to separate the role of Tregs versus TGF-β would be to specifically inactivate TGF-βRII in effector T cells leaving Tregs intact.

posted by David Usharauli


Thursday, August 3, 2017

Th2A subset drives allergic phenotype in humans

TH2 cells were initially identified based on their capacity to make IL-4 and drive B cell antibody class switch recombination to IgG1  and IgE. However, more recently it became clear that TH2 cells consist of several subtypes each with its own unique specialization in particular effector function such as IL-13 or IL-25 production that have nothing to do with antibody production. 

Similarly, canonical TH2 cells were thought to be responsible for allergy phenotype in humans (and mice as well). However, new study in Science Translational Medicine suggests new subset of TH2 cells, called TH2A subset, is mainly responsible for food allergy phenotype

The authors carried out magnetic enrichment of T cells harvested from allergic patients using HLA-II tetramers. Compared to non-allergic individuals, allergic patents showed expansion of a special population of TH2 cells expressing CD161 and CD49d

Interestingly, patients undergoing antigen-specific desensitization showed selective loss of these TH2A cells.

In summary, it is clear that different subset of TH2 cells exist, some naturally others only during pathology, to deal with various foreign antigenic entities.

posted by David Usharauli


Wednesday, July 26, 2017

IBD converts tolerant antigens into immunogenic

Inflammatory bowel disease (IBD) is a pathological condition wherein body's immune cells wrongly attack its own or commensal microbiota-derived antigens that initiates a vicious cycles of permanent inflammation.
However, it is still not clear whether immune system attacks "new" antigens from microbiota or simply it loses adaptive tolerance to "old" ones. 
New study in Science Immunology tried to answer it to the extent it was possible to do in mouse model.
First, the authors generated IBD condition in mice by treating them with DSS + anti-IL10R. Keep in mind this is highly artificial model. Then, they transferred naïve T cells from previously established transgenic T cell lines specific for unknown commensal antigens that were known to drive Treg phenotype. Naïve T cells transferred into control WT mice generated Tregs while the naïve T cells transferred into IBD-conditioned mice preferably developed into effector T cells.
When analyzed for antigen specificity, the authors found that transgenic naïve T cells were reactive to antigens derived from Helicobacter species that have expanded during IBD-conditioning.
In vivo studies also confirmed that Helicobacter species could induce Treg generation from naïve transgenic T cells in "normal" condition.
Interestingly, transfer of T cells specific for other microbiota species that also underwent expansion during IBD-conditioning did not produce T cell expansion.
Finally, transfer of Treg-TCR transgenic naïve T cells into RAG-KO mice produced IBD when co-injected with Helicobacter species.
What these data indicate? In my view the authors made one correct and one wrong interpretation. First, they were correct to conclude that T cell response to IBD could be directed to "old" microbiota antigens rather than "new" never before seen microbiota-derived antigens. So basically in IBD we are losing tolerance rather than gaining immunity to microbiota antigens.
However, they made wrong conclusion that naïve T cells are converted into Tregs in vivo based on context (normal versus IBD). In their study loss of Treg generation is inhibited either during IBD-conditioning or in RAG KO hosts which could argue alternatively that such outcome has to do with failure of naïve T cells to interact with existing Tregs specific for the same or similar antigens in these scenarios (IBD or RAG-KO).
posted by David Usharauli

Sunday, July 16, 2017

Identification of prostate-antigen specific natural Tregs (in mice)

Foxp3+ Tregs are central player in maintaining tolerance to self and other environmental antigens. However, till to this date we know little of their antigen specificity. It is because unlike conventional CD4+ T cells, Tregs do not secrete [upon antigen recognition] any cytokine that uniquely identifies them. The best marker is still Foxp3 molecule, an intracellular transcription factor.   

So it is always interesting to see new study that could identify Treg epitope, such as this new paper in Immunity that provided evidence that in mice peptide spanning residues 646–658 of prostate-specific TRPM8 channel-associated factor 3 protein (Tcaf3) is a natural epitope for thymic MJ23 TCR transgenic Treg development.

The authors showed that development of MJ23+ Tregs from adoptively transferred MJ23+ thymocytes (un-differentiated T cells) were only supported in hosts expressing intact Tcaf3 (and not in Tcaf3 KO mice).   

Next, using sensitive tetramer based antigen-specific T cell detection, the authors showed that WT mice also harbored Tcaf3[646–658]-tetramer specific T cells that were enriched in Tregs compared to other antigen-specific T cells (2W1S). Interestingly, Aire-KO mice which do not efficiently express peripheral antigens in the thymus harbored reduced numbers of Tcaf3[646–658]-tetramer specific Tregs.

Finally, the authors showed that prostate tissue from Aire KO mice harbored significantly more Tcaf3[646–658]-tetramer specific Tregs compared to prostate tissue from normal mice. I found these particular results problematic because should not normal mice prostate supposed to contain Tregs to prevent autoimmunity? Or are Tregs keeping autoreactive T cells in check in draining lymph nodes? 

In summary, this study showed that in mice prostate-specific Tcaf3[646–658] epitope is a natural ligand that selects Tregs in a Aire-dependent manner.

posted by David Usharauli