GEM T cells: A newly identified class of restricted α-chain TCRα/β T cells

The diversity of the T cell repertoire allows for recognition of a wide diversity of pathogens. During T cell development, T cell receptors (TCRs) undergo genetic rearrangements of their V, D, and J segments, as well as random deletions and nontemplated additions of nucleotides.  Furthermore, major histocompatibility complex (MHC) class I and II molecules are highly polymorphic.  Thus, each person has a unique and highly diverse T cell-MHC repertoire.  In addition, there are two known classes of lymphocytes with restricted diversity of their TCR α-chains, and which bind to the non/rarely polymorphic antigen-presenting molecule families CD1 and MR1.  These are the invariant natural killer T cells (iNKT cells), and the mucosa-associated invariant T cells (MAIT cells), respectively.  In the June issue of Nature Immunology, Van Rhijn et al. identify a new class of T cells with restricted TCR α-chains, termed GEM T cells, that recognize the Mycobacterium tuberculosis (Mtb) lipid glucose monomycolate presented on CD1b.

To study the human TCR repertoire recognizing CD1b, Van Rhijn et al., utilized CD1b tetramers loaded with glucose monomycolate (GMM), to isolate and clone T cells from peripheral blood mononuclear cells (PBMC) of Mtb infected donors.  Two groups of T cell clones with differing avidity for CD1b-GMM were isolated from each patient, differentiated by intermediate (CD1bint) and high (CD1bhi) CD1b tetramer staining intensities.  CD1bint T cells were diverse in their TCR α-chain sequences.  TCR α-chains of CD1bhi T cells however, all utilized the same variable and joining sequences (TRAV1-2, and TRAJ9, respectively) with few nontemplated additions, resulting in a specific complementarity-determining region 3 (CDR3) consensus sequence.  Thus, these were termed “germline-encoded, mycolyl lipid–reactive” (GEM) T cells.  These TCR α-chain sequences furthermore had to be paired with specific TCR β-chain sequences in order to recognize CD1b-GMM complexes.

Other properties of these uniquely identified GEM T cells included expression of CD4 and production of IFNγ and TNFα upon activation, two cytokines important for anti-mycobacterial responses.  GEM T cells expressed various rates of CD161, a marker widely expressed by NKT cells and MAITs, and thus GEM T cells could not be defined by expression of CD161.  In addition, sorting of TRAV1-2+ CD4+ cells from two healthy donors followed by deep sequencing of the TCR α-chain revealed identification of the GEM-specific CDR3 sequence, demonstrating that GEM T cells were present in Mtb uninfected individuals in the naïve T cell repertoire.  However, these cells become clonally expanded in Mtb infected patients, and thus likely to contribute to anti-mycobacterial immune responses.

In conclusion, GEM T cells are a newly identified third class of CD1-recognizing T cells with restricted TCR α-chain sequences.  These cells arise via VDJ recombination, and indicate that special selection mechanisms exist to generate T cells bearing this specific TCR α-chain.  Although what CD1b-self antigen complex could positively select for these cells in the thymus is unknown.  Furthermore, the role these cells play during mycobacterial infections will be an interesting avenue for future studies.

Further Reading:

A conserved human T cell population targets mycobacterial antigens presented by CD1b.  Van Rhijn I, Kasmar A, de Jong A, Gras S, Bhati M, Doorenspleet ME, de Vries N, Godfrey DI, Altman JD, de Jager W, Rossjohn J, Moody DB. Nat Immunol. 2013 Jun 2;14(7):706-13.

A ‘GEM’ of a cell.  Mitchell Kronenberg & Dirk M Zajonc. Nature Immunology 14, 694–695 (2013) doi:10.1038/ni.2644. Published online 18 June 2013.

Highlight: Is too much salt bad for your guts?


Whether eating too much table salt in our diet is bad for our health has long been debated. Links have been proposed to several cardiovascular diseases. But, a recent expert committee for the Institute of Medicine concluded that the data do not support such a link [1], keeping the discussion going. Two recent publications in Nature, however, suggest that too much dietary salt might impact our immune system instead and potentially increase the likelihood of autoimmune diseases.

CD4 T lymphocytes can differentiate in specialized subsets that promote or help diverse immune responses. Called T helper (Th) cells, particular subsets are named after prominent cytokines they produce, e.g. IL-17 in the case of Th17 T cells. Th17 cells are important for protection of the body against many bacterial and fungal infections and they are prevalent in the intestinal tissue were they are believed to aid the barrier function of the gut to keep the intestinal bacteria were they belong [2]. However, the “too much of a good thing” proverb applies to lymphocytes too and in the case of Th17 T cells this is exemplified by their pathogenic involvement in several autoimmune diseases. Therefore, the control of cell number and function of Th17 cells requires a delicate balance.

It was known that there is a cross talk between the gut lumen and the Th17 cell response. For example, a few years back it was shown that the frequency of a common bacterium within the gut microbiota could influence the prevalence of Th17 cells in the intestinal tissue [3]. The two new studies demonstrate that table salt (sodium chloride, NaCl) is a surprising new factor on the list to influence the frequency and function of Th17 cells [4-6].Lymphocyte activation

Adding 40 mM NaCl – a level found in the intestinal tissue of animals after feeding of a high salt diet – to in vitro cultures augmented the differentiation of Th17 cells [4, 5]. Similar to in vitro, feeding mice with a high salt diet increased the frequency of Th17 cell in the intestinal tissue, but not in the lymph nodes or the spleen. In both settings (in vitro and in vivo) the resulting Th17 cells were capable of producing large amounts of pro-inflammatory cytokines. By analysis of the mRNA expression, both reports characterized the MAP-kinase p38, NFAT5 (nuclear factor of activated T cells 5) and SGK1 (serum glucocorticoid-regulated kinase-1) as critical molecular players in sensing NaCl and mediating its effect. The elimination of any of these factors from the T cells, either by genetic ablation or by impeding the expression by means of RNA-interference (shRNA), blocked the increased Th17 cell differentiation in the presence of NaCl. Although all three proteins are part of the same pathway, SGK1 appeared to be central in the regulation of the NaCl induced effect. Although this finding is surprising, the results are in line with the known function of SGK1 in sodium transport and homeostasis [7]. SGK1 expression was not only induced by increased NaCl concentrations, but also by the cytokine IL-23, which has a critical role in stabilizing and reinforcing the TH17 phenotype [2]. As NaCl also increased the expression of the IL-23 receptor this established a positive feedback loop that strengthened the Th17 cell differentiation. Importantly, both groups also showed that raising the levels of dietary salt could augment the severity of EAE (experimental autoimmune encephalomyelitis), a mouse model for the autoimmune disease multiple sclerosis [4-6].

In summary, these reports demonstrate that high levels of salt in the diet could make mice susceptible to a form of autoimmune disease that involves pathogenic Th17 T cells. The data suggest that high concentration of NaCl might be an environmental risk factor for autoimmune diseases. However, it should be pointed out that high concentration of NaCl did not induce autoimmune responses by itself, as the EAE animal model requires the immunization with a know self-antigen. Autoimmunity is a complex interplay of numerous genetic pre-disposing and environmental factors. In this regard these new reports [4, 5] suggest that high dietary salt concentrations might tilt the balance a bit towards autoimmunity in genetically predisposed individuals.

However, the reality will likely be more complicated – as it usually is. For example, it will be critical to show that the correlation between dietary NaCl and Th17 cells is valid also in humans. Furthermore, with this knew knowledge other factors might come to light soon. For example, SGK1 expression is also stimulated by several hormones including endogenous steroids like stress hormones [7], suggesting that the induction of Th17 cell might be augmented by stress as well. Therefore, these intriguing new reports [4, 5] will surely spur now the required research to clarify these points. Till then, going slow on sodium-laden junk food might be generally a justified suggestion.                                 


[1] Strom, Brian (2013). Sodium Intake in Populations: Assessment of Evidence. Washington, DC: The National Academies Press: The Institute of Medicine.

[2] Weaver, C. T., Elson, C. O., Fouser, L. A. & Kolls, J. K. The Th17 pathway and inflammatory diseases of the intestines, lungs, and skin. Annu Rev Pathol 8, 477–512 (2013).

[3] Ivanov, I. I. et al. Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria. Cell 139, 485–498 (2009).

[4] Kleinewietfeld, M. et al. Sodium chloride drives autoimmune disease by the induction of pathogenic TH17 cells. Nature (2013). doi:10.1038/nature11868.

[5] Wu, C. et al. Induction of pathogenic TH17 cells by inducible salt-sensing kinase SGK1. Nature (2013). doi:10.1038/nature11984.

[6] O’Shea, J. J. & Jones, R. G. Autoimmunity: Rubbing salt in the wound. Nature 496, 437–439 (2013).

[7] Lang, F. & Shumilina, E. Regulation of ion channels by the serum- and glucocorticoid-inducible kinase SGK1. The FASEB Journal 27, 3–12 (2013).

Tumor Immunotherapies Combine Big for Synergy in Phase I Trials

There are currently two immune cell targeting cancer_immunotherapyimmunotherapeutic agents that have received FDA approval for treatment of various malignancies.  The first approved in 2010 was the autologous dendritic cell vaccine Provenge (Sipuleucel-T) by Dendreon Corporation, for hormone refractory metastatic prostate cancer.  A second immunotherapeutic gaining FDA approval in 2011 for late stage melanoma, was an antibody called Ipilimumab, which inhibits CTLA-4, a major negative regulator of T cell activation.  Antagonists to PD-1 such as Nivolumab and/or PD-L1, another receptor/ligand pair of T cell negative regulators, are expected to join this crowd by 2015.  However, early results from combinatorial immunotherapeutics trials have demonstrated that significant synergy may be achieved by combining several immunotherapeutic modalities. A report in the June edition of The New England Journal of Medicine by Wolchok et al., demonstrates impressive synergistic results with combination therapy of Ipilimumab and Nivolumab in achieving deep and durable tumor regression in patients with advanced metastatic melanoma.

CTLA-4 and PD-1 are negative regulatory immune checkpoint inhibitors expressed on activated T cells and share homology with the TCR co-stimulatory receptor CD28.  CTLA-4 strongly competes with CD28 for binding to CD80 (B7-1) and CD86 (B7-2) on antigen presenting cells thereby limiting CD28-activation signals, and furthermore recruits inhibitory molecules into the TCR signaling synapse.  PD-1 interacts with ligands homologous with the B7 family, PD-L1 (B7H1) and PD-L2 (B7-DC), which are upregulated on tumor and stromal cells and activated antigen presenting cells.  PD-1 interaction with its ligands leads to recruitment of SHP1 and SHP2 phosphatases to the immune synapse, resulting in inhibition of TCR-mediated signaling.  PD-1 and CTLA-4 are considered non-redundant in their functions, and thus blocking both of these has been proposed to have a synergistic effect on T cell function in cancer, which was previously demonstrated in murine tumor models.

In previous clinical trials, Bristol-Myers Squibb’s Ipilimumab (MDX-010, Yervoy, IgG1) with or without a gp100 peptide vaccine extended overall survival of previously treated metastatic melanoma patients by almost 4 months versus gp100 peptide alone.  In a second study, Ipilimumab plus darcarbazine versus darcarbazine alone was tested in previously untreated metastatic melanoma patients.  The addition of Ipilimumab to the darcarbazine regimen extended overall survival by approximately two months, and lent to significantly higher survival rates at 1, 2, and 3 years later.  Bristol-Myers Squibb’s PD-1 blocking antibody (BMS-936558, IgG4) showed significant clinical efficiency in metastatic or advanced non–small-cell lung cancer, melanoma, and renal-cell cancer.

In this dose-escalation phase I trial reported on by Wolchok et al., 53 patients with advanced melanoma were concurrently treated with Ipilimumab and Nivolumab, and 33 patients received sequenced treatment.  Although the primary goal of a phase I trial is to evaluate safety, the clinical responses of the concurrently treated patients were exciting enough to garner much attention.  In the concurrent regimen, 40% of patients had an objective response (modified WHO criteria), and 16 patients had a reduction in their tumor burden by 80% or more at 12 weeks, 5 being complete responses. Not only were responses faster and more pronounced than the previous clinical trials evaluating these inhibitors alone, but in the responding patients, the reduction in tumor burden was quite durable over the course of the study.  Thus, results from phase III clinical trials comparing the combination to the inhibitors alone will be eagerly awaited.  As an interesting note, tumor expression of PD-L1 has been proposed to be an indication of efficacy for Nivolumab.  However, even in patients with PD-L1-negative tumors, responses to this combination regimen were observed.

Despite the strong promise of these inhibitors in combination, adverse events were notably higher than the inhibitors had exhibited alone in previous trials.  Although no treatment-related deaths were reported, 72% of patients exhibited grade 3 or 4 adverse events, 53% of patients exhibited treatment-related grade 3 or 4 adverse events, and 21% of patients discontinued therapy due to treatment-related adverse events.  Adverse events were however manageable with either immunosuppressant or hormone-replacement therapies.

Many different cancer immunotherapeutics are now being tested in clinical trials, including a number of therapies combining immunotherapeutic modalities in the hopes to achieve synergy.  The results from the current trial indicate that anti-tumor T cells are not only present in tumor-bearing patients, but when uninhibited, can lend significantly to tumor-killing.  This is truly an exciting time for cancer immunology.

Further Reading:

Nivolumab plus Ipilimumab in Advanced Melanoma.  Wolchok JD, Kluger H, Callahan MK, Postow MA, Rizvi NA, Lesokhin AM, Segal NH, Ariyan CE, Gordon RA, Reed K, Burke MM, Caldwell A, Kronenberg SA, Agunwamba BU, Zhang X, Lowy I, Inzunza HD, Feely W, Horak CE, Hong Q, Korman AJ, Wigginton JM, Gupta A, Sznol M. N Engl J Med. 2013 Jun 2.

Safety, Activity, and Immune Correlates of Anti–PD-1 Antibody in Cancer. Topalian, S.L. et al. N. Engl. J. Med. 366, 2443–2454 (2012).

Improved Survival with Ipilimumab in Patients with Metastatic Melanoma.  Hodi, F.S. et al. N. Engl. J. Med. 363, 711–723 (2010).

Ipilimumab plus dacarbazine for previously untreated metastatic melanoma.  Robert C, Thomas L, Bondarenko I, O’Day S, M D JW, Garbe C, Lebbe C, Baurain JF, Testori A, Grob JJ, Davidson N, Richards J, Maio M, Hauschild A, Miller WH Jr, Gascon P, Lotem M, Harmankaya K, Ibrahim R, Francis S, Chen TT, Humphrey R, Hoos A, Wolchok JD. N Engl J Med. 2011 Jun 30;364(26):2517-26.

Ipilimumab: an anti-CTLA-4 antibody for metastatic melanoma.  Lipson EJ, Drake CG. Clin Cancer Res. 2011 Nov 15;17(22):6958-62.

A unique set of cell surface markers for induced T regulatory cells

Transplantation of antigen-specific T cells during cancer immunotherapy has generated many notable results in the fight against diverse cancers. In these scenarios, the transplanted T cell populations act as a sort of highly mobile army that can track and kill tumor cells wherever they hide. In contrast, the goal of therapy during autoimmunity is to suppress immune activity, not increase its potency. Would transplantation of a “peacekeeper” immune cell-type be able to specifically quell autoimmune reactions? T regulatory cells (Tregs) are attractive candidates for the peacekeeper role based on their ability to dominantly suppress auto-reactive cell populations. As opposed to studies of cancer immunotherapy, clinical trials for Treg adoptive transplant are hampered by the lack of specific cell surface markers for these populations that enable their purification1. The defining characteristics of Treg populations (eg. FoxP3, IL-10, TGF-beta) are intracellular proteins whose analysis and quantification requires permeabilization and, hence, destruction of the cells. Positive selection for markers such as CD4 and CD25 which are expressed on the surface of certain types of Tregs also enriches for effector T cell populations whose functions upon transplantation may serve to further stimulate immune activity in an autoreactive host.Adoptive t cell transfer

In this month’s issue of Nature Medicine, Gagliani et al. sought to address the need for Treg-specific cell surface markers2. The authors focused on a particular type of inducible Treg called Type 1 regulatory T cells (Tr1 cells). These are a highly suppressive population of CD4+ T cells that are thought to control immune reactions both through IL-10 secretion and direct, Granzyme B-mediated destruction of myeloid antigen presenting cells. Galiani et al. were able to isolate Tr1 clones from the peripheral blood of healthy donors using a limiting-dilution assay: CD4+ T cells were plated in wells at a density of 1 cell/well, grown in conditions known to be suitable for Tr1 development, and then assessed for high levels of IL-10 secretion. The isolated Tr1 clones were stimulated in vitro and their gene expression profiles were measured at different time points and compared to that of naïve CD4+ T cells (Th0 cells). Under these conditions, the authors found that Tr1 cells uniquely expressed genes for two cell surface markers, CD49b and LAG-3. Used independently, these markers would enrich for multiple T cell types. But when used in combination, CD49b and LAG-3 allowed the investigators to isolate Tr1 cells from human peripheral blood which expressed high-levels of IL-10 and were able to suppress T cell proliferation in vitro. The authors went on to show that this cell-surface marker combination could also be used to isolate Tr1 cells from well-defined mouse models of Treg function. Finally, authors showed that CD49b and LAG-3 could effectively enrich for Tr1 cells from a highly-expanded, in vitro-polarized bulk population. This raises the possibility of generating large numbers of highly pure IL-10 secreting Tr1 cells for adoptive transplantation during autoimmunity.

Gagliani et al. have effectively used gene profiling of a target cell type to identify cell-surface markers for a previously difficult-to-analyze population. These new markers should facilitate further clinical study of adoptive transplant of Treg populations for autoimmunity. Now that it is possible to identify Tr1 cells from blood, it will be interesting to see how numbers of these cells correlate to different disease states and how they change in response to immune modulatory treatments. Furthermore, coupling the polarization and enrichment of Tr1 cells to tetramer-based identification of antigen-specific T cells may allow for highly-selective targeting of autoimmune reactions.


1. Human T regulatory cell therapy: take a billion or so and call me in the morning. Riley JL, June CH, Blazar BR. Immunity. 2009 May;30(5):656-65. doi: 10.1016/j.immuni.2009.04.006.

2. Coexpression of CD49b and LAG-3 identifies human and mouse T regulatory type 1 cells. Gagliani N, Magnani CF, Huber S, Gianolini ME, Pala M, Licona-Limon P, Guo B, Herbert DR, Bulfone A, Trentini F, Di Serio C, Bacchetta R, Andreani M, Brockmann L, Gregori S, Flavell RA, Roncarolo MG. Nat Med. 2013 Jun;19(6):739-46. doi: 10.1038/nm.3179. Epub 2013 Apr 28.

Identification of New Potential Drug Targets for Treatment of Lupus

autoantibodies Systemic lupus erythematosus (SLE) is a complex autoimmune disease that afflicts tens of millions of people worldwide.  The most prominent feature is generation of “autoantibodies” to self-proteins and nucleic acids, resulting in immune complex (IC) formation and organ inflammation.  Affected patients may demonstrate rashes, joint pain, anemia, or kidney damage, and untreated complications can often be fatal.  In addition, most SLE patients demonstrate continuously elevated levels of interferon (IFN) α, which is naturally produced by activated plasmacytoid dendritic cells (pDCs) 1.  pDCs are a rare subset of DCs found in the blood and peripheral lymphoid organs that function in host defense by secreting proinflammatory cytokines to initiate the innate immune response.  pDCs are activated following engagement of Toll-like receptors (TLRs), which recognize molecular signatures of bacteria and viruses.  Studies have shown that the frequency of circulating pDCs is significantly reduced in SLE patients, due to increased migration to inflammatory sites in affected organs 2.  Although pDCs have been implicated in contributing to autoimmunity via continuous type I IFN production, their exact role in lupus pathogenesis has not been clearly elucidated.

Recently, in PNAS, Baccala et al. provided direct evidence that in the absence of pDCs, the disease manifestations of Lupus were significantly decreased 3.  Since IRF8 is a hematopoietic cell-specific transcription factor known to be essential for pDC development 4, the authors knocked out IRF8 in NZB mice, a widely used mouse model for SLE.  Appropriately, pDCs were absent in IRF8-deficientNZB mice, and type I IFNs were undetectable even after injection with CpG DNA, a standard method of inducing the interferon pathway.  Interestingly, autoantibody production was almost completely abrogated and kidney disease was drastically improved compared to wild-type NZB mice.  Taken together, their results suggest that without pDCs, SLE disease manifestations are significantly reduced.

Next, the authors sought to examine specifically how pDCs promote systemic autoimmunity.  They used another mouse model with a mutation in Slc15a4, which is characterized by normal development of pDCs but an absence of type I IFN production by pDCs.  It is still unclear how a mutation in Slc15a4 leads to a disruption in proinflammatory cytokine production in pDCs, but since Slc15a4 is a peptide/histidine transporter, others hypothesize that it transports free histidine from the endosome to the cytosol to enable cathepsin-mediated cleavage of endosomal TLRs required for subsequent signaling 5.  Similar to the IRF8-deficient NZB mice, Slc15a4 mice had significantly reduced autoantibodies, decreased kidney disease, and extended survival.  This finding rules out the possibility that pDCs contribute to disease through other functions outside of type I IFN production.

In summary, Baccala et al. provide direct evidence that pDCs contribute to the abnormal manifestations of SLE via hyperproduction of type I IFNs.  Thus, IRF8 and Slc15a4 serve as new potential drug targets for treatment of SLE.  Current therapies involve broad immunosuppressive drugs, which suppress multiple arms of the immune system, increasing a patient’s risk for various infections and cancer.  Specific pharmacologic inhibition of IRF8 or Slc15a4 could prevent Lupus-specific flare-ups, as well as manifestations of other autoimmune diseases.


1          Gilliet, M., Cao, W. & Liu, Y. J. Plasmacytoid dendritic cells: sensing nucleic acids in viral infection and autoimmune diseases. Nat Rev Immunol 8, 594-606, doi:10.1038/nri2358 (2008).

2          Ronnblom, L. The type I interferon system in the etiopathogenesis of autoimmune diseases. Ups J Med Sci 116, 227-237, doi:10.3109/03009734.2011.624649 (2011).

3          Baccala, R. et al. Essential requirement for IRF8 and SLC15A4 implicates plasmacytoid dendritic cells in the pathogenesis of lupus. Proc Natl Acad Sci U S A 110, 2940-2945, doi:10.1073/pnas.1222798110 (2013).

4          Tsujimura, H., Tamura, T. & Ozato, K. Cutting edge: IFN consensus sequence binding protein/IFN regulatory factor 8 drives the development of type I IFN-producing plasmacytoid dendritic cells. J Immunol 170, 1131-1135 (2003).

5          Park, B. et al. Proteolytic cleavage in an endolysosomal compartment is required for activation of Toll-like receptor 9. Nat Immunol 9, 1407-1414, doi:10.1038/ni.1669 (2008).

Computers meet T cells: in silico identification of mutated tumor antigens targeted by T cells

It is well accepted that T cells can recognize and kill tumors that arise in individuals but that tumor cells escape immune surveillance due to the immunosuppressive tumor microenvironment that renders these T cells dysfunctional is less understood.  Only a relatively small number of antigens that T cells recognize for tumor-killing have been identified, and the methods used to identify these antigens are quite cumbersome.  In a recent article in Nature Medicine, Robbins et al. utilize informatics methods to identify mutated tumor antigens in melanoma patients that allowed effective targeting by anti-tumor T cells.

Genome sequencing T cells

In an effort to identify clinically relevant mutated tumor cell epitopes recognized by T cells, Robbins et al. first performed whole-exome sequencing of tumor cells and matched normal cells from melanoma patients who demonstrated tumor regression following adoptive transfer of autologous tumor infiltrating lymphocytes (TILs).  Mutations in tumor cells that resulted in amino acid changes were identified and then screened using an MHC binding algorithm that predicts high affinity binding of peptide sequences to specific HLA alleles.  Candidate peptides of 9-10 amino acids in length were synthesized and pulsed with specific HLA-expressing target cell lines to load the peptides into the MHC complex.  Peptide-pulsed target cells or autologous tumor cell lines were then cultured with autologous TILs from the same donor and IFN-gamma production was assessed as a read out of T cell activation.

Three metastatic melanoma patients were assessed using this methodology.  The first patient was homozygous for HLA-A*0201, and thus mutated melanoma cell line peptides predicted to bind to the HLA-A*0201 allele were identified by the MHC-binding algorithm.  From this donor, 4 out of 55 candidate peptides elicited IFN-gamma responses from autologous T cells cultured with peptide-pulsed target cells.  Two of these mutated peptides were found to correspond to the casein kinase1α1 protein (CSNK1A1), one peptide was mapped to the growth arrest specific 7 gene (GAS7) gene, and the fourth was a fragment of the HAUS augmin-like complex, subunit 3 (HAUS3) protein.  The wild-type versions of each of these peptides bound very poorly (100-10,000 fold less) or not at all to the HLA and were not recognized by T cells.  Two other donors were assessed for predicted binding of mutated peptides to HLA-A*0101 and HLA-A*1101.  Autologous T cell responses were found to be activated in response to mutated peptides from pleckstrin homology domain containing, family M member 2 (PLEKHM2), protein phosphatase 1 regulatory subunit 3B (PPP1R3B), matrilin 2 (MATN2), and cyclin-dependent kinase 12 (CDK12) genes, but not their wild-type counterparts.  Furthermore, tumor lines were validated to express these mutated proteins.

Finally, the authors compared the reactivity of peripheral blood mononuclear cells (PBMCs) drawn before and after adoptive TIL transfer into two of these patients to determine if anti-tumor reactive T cell clones persisted in vivo.  T cells that recognized the same tumor antigens as the TILs were identified post-adoptive transfer at greater levels than prior to adoptive transfer.  Thus, T cells that recognize mutated tumor epitopes may play a clinically relevant role in mediating tumor regression.  Many questions remain, including a direct demonstration that such tumor-reactive TILs are responsible for mediating the observed tumor regression in these patients, and whether further mutation of these residues might facilitate immune escape later it the course of disease. 

Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells.  Robbins PF, Lu YC, El-Gamil M, Li YF, Gross C, Gartner J, Lin JC, Teer JK, Cliften P, Tycksen E, Samuels Y, Rosenberg SA. Nat Med. 2013 May 5. doi: 10.1038/nm.3161.

NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence.  Nielsen M, Lundegaard C, Blicher T, Lamberth K, Harndahl M, Justesen S, Røder G, Peters B, Sette A, Lund O, Buus S. PLoS One. 2007 Aug 29;2(8):e796.

A bifunctional FoxP3+ regulatory T cell subset converts to pro-inflammatory helper T cells

Recently a number of studies have arisen characterizing Tregulatory cellvarious functional subsets of CD4+ FoxP3+ regulatory T cells (TREGS), as well as their plasticity and ability to differentiate into other TH subtypes.  For instance, TREGS that express RORγt were found to be the specific TREG subset that promotes pro-tumor immune functions in colorectal cancer patients.  In a recent article in Immunity, Sharma et al. identify another TREG subset: FoxP3+ TREGS that loose expression of Eos convert to a pro-inflammatory helper subtype that promotes naïve CD8+ T cells differentiation into potent effectors.

Eos is a transcription factor in the Ikaros family, and acts as an obligate co-repressor in complex with FoxP3 to inhibit expression of FoxP3-repressed genes.  In a quest to understand why TREGS in inflammatory environments were observed to become pro-inflammatory without losing FoxP3 expression, Sharma et al. examined the expression of Eos in FoxP3+ TREGS under inflammatory conditions.

Conversion of FoxP3+ TREGS into an inflammatory phenotype was demonstrated by acquired expression of IL-2, IL-17, and CD40L in the draining lymph nodes of a vaccination site compared with FoxP3+ TREGS at distant lymph nodes that did not gain this function.  In these converted inflammatory FoxP3+ TREGS, expression of Eos was rapidly lost.  IL-6 was required for downregulation of Eos, as TREGS in mice lacking IL-6 did not lose Eos expression under the same conditions.  However, IL-6 alone was insufficient for Eos downregulation, which also required interactions with MHC class II on activated dendritic cells.  Loss of Eos expression was furthermore shown to be required for acquisition of the pro-inflammatory phenotype, as TREGS with forced overexpression of Eos did not undergo this conversion.

Interestingly, not all FoxP3+ TREGS were equivalent in their propensity to lose Eos expression and become pro-inflammatory.  Thymic FoxP3+ TREGS were assessed for stability of Eos under treatment with cyclohexamide. CD38+CD69+CD103 TREGS were “Eos-labile” and specifically lost Eos expression within one hour of cyclohexamide treatment, while CD38CD69CD103+ TREGS maintained Eos expression.  Expression of other markers associated with FoxP3+ TREGS including CD25 and CTLA-4 were equivalent between these two phenotypes highlighting the inability of using these TREG markers to discriminate between these populations.  When these FoxP3+ TREGS were sorted into CD38+CD103and CD38CD103+ subsets and transferred into mice, followed by the vaccination schema, only CD38+CD103 TREGS lost Eos expression and gained CD40L and IL-2 expression. The Eos-labile TREGS do however have characteristic suppressive functions when examined in several models including protection from colitis in a Rag-deficient CD45RBHI effector cell-driven autoimmune colitis model and in vitro suppression of T cell proliferation driven by anti-CD3.

Because the Eos-labile subset was observed in the thymus as part of the natural TREG repertoire, the authors examined the signals required for development of this subset.  Again, IL-6 was required as this subset did not arise in IL-6-/- mice.  Epigenetic analysis of DNA methylation patterns comparing these FoxP3+ TREGS subsets revealed distinctive patterns of methylation yet these subsets were still much more closely related to each other as compared with FoxP3 CD4+ T cells.  Future studies will be needed to determine the nature of these epigenetic differences and which signals are controlled by IL-6.

Interestingly, the authors explored the functional contribution of the Eos-labile pro-inflammatory TREGS subset on CD8+ priming in the vaccination model.  Depletion of TREGS resulted in loss of CD8+ T cell proliferation and granzyme B expression as well as loss of CD86 upregulation on DCs, while adding back just the Eos-labile subset or IL-2 plus CD40-agonist antibodies rescued these defects.  The Eos-labile subset did not however, contribute to reactivation of memory CD4+ T cells, and thus these cells appear to play a specific role in the initial priming stages of naïve T cell activation.  Thus, despite having regulatory activity, these cells are critical in priming CD8+ T cell responses by supplying IL-2 and CD40L signals.

However, indoleamine 2,3-dioxygenase (IDO) was able to block Eos downregulation and acquisition of IL-2, IL-17, and CD40L expression.  Importantly, in a murine tumor vaccination model, blocking IDO was important for FoxP3+ inflammatory TREG induction and acquisition of anti-tumor effector CD8+ T cell responses.  The mechanism of IDO inhibition of Eos downregulation was found to be at least in part, dependent on the antagonization of the IL-6-STAT3 pathway by IDO-mediated production of kynurenine-pathway metabolites which activate the aryl hydrocarbon receptor (AhR).  Interestingly, different AhR ligands have been previously shown to differentially regulate induction of TH17 cells vs. TREGS (Quintana et al.), and kyenurine was a TREG inducing AhR ligand (Mezrich et al.).  Additionally, the contrasting effects of IL-6 and IDO will be an important factor in priming immune cell responses.

Overall, this thorough investigation identified the mechanisms that induce and inhibit this newly defined Eos-labile TREG subset that maintains FoxP3 expression and has typical suppressive TREG activity, yet is critically important in priming effector T cell immune responses.  Future studies will be needed to address how these cells balance regulatory and priming activities as well as the relationships between this subset and the many other TREG subsets described.

An inherently bifunctional subset of foxp3(+) T helper cells is controlled by the transcription factor eos.   Sharma MD, Huang L, Choi JH, Lee EJ, Wilson JM, Lemos H, Pan F, Blazar BR, Pardoll DM, Mellor AL, Shi H, Munn DH. Immunity. 2013 May 23;38(5):998-1012. doi: 10.1016/j.immuni.2013.01.013. Epub 2013 May 16.

Eos, goddess of treg cell reprogramming.  Rieder SA, Shevach EM. Immunity. 2013 May 23;38(5):849-50. doi: 10.1016/j.immuni.2013.05.001.

Control of T(reg) and T(H)17 cell differentiation by the aryl hydrocarbon receptor.  Quintana FJ, Basso AS, Iglesias AH, Korn T, Farez MF, Bettelli E, Caccamo M, Oukka M, Weiner HL. Nature. 2008 May 1;453(7191):65-71. doi: 10.1038/nature06880. Epub 2008 Mar 23.

An interaction between kynurenine and the aryl hydrocarbon receptor can generate regulatory T cells.  Mezrich JD, Fechner JH, Zhang X, Johnson BP, Burlingham WJ, Bradfield CA. J Immunol. 2010 Sep 15;185(6):3190-8. doi: 10.4049/jimmunol.0903670. Epub 2010 Aug 18.

A theory of everything: commensal gut bacteria link environmental exposures to sex hormones in modulating autoimmunity

Whether an individual develops autoimmunity depends on how environmental and genetic factors interact to influence immune function. Genome wide association studies have revealed numerous risk alleles associated with diverse autoimmune diseases and small animal models have helped parse the effects of some of these gene variants on specific components of the immune system (see previous post). These approaches, however, largely ignore two of the more perplexing aspects of autoimmunity: (1) the strong female predominance of many autoimmune diseases and (2) the high incidence of autoimmunity in industrialized areas of the world compared to poorer, rural areas. The issue of sexual dimorphism in autoimmunity has led investigators to surmise that sex hormones are potent modulators of immune function. Indeed, altering estrogen, progesterone, or testosterone levels can influence the progression of autoimmune reactions in animals and people, although the specific mechanisms underpinning these phenomena remain controversial1. The increasing incidence of autoimmunity in the industrialized world has given rise to the “hygiene hypothesis”: exposure to specific microbes early in life is necessary for a fully-functioning immune system. These beneficial exposures are lacking in modernized, clean cities which contributes to immunological derangement and self-reactivity. Evidence supporting the hygiene hypothesis has accumulated in recent years to the point that clinical trials are in progress testing whether purposeful infestation with parasitic worms (thought to be the major microbial exposure missing from a modern upbringing) can control inflammatory bowel disease and multiple sclerosis2.


In a recent paper in Science Magazine, Dr. Jayne Danska’s group at the University of Toronto present an intriguing hypothesis that unifies the roles of early-life microbial exposure and sex hormone levels in driving an autoimmune response3. The group, with lead author Dr. Janet Markle, used a well-established mouse model of type-1 diabetes (T1D)—the non-obese diabetic (NOD) mouse—that is genetically predisposed to develop spontaneous, immune-mediated destruction of beta-islets at around 15 weeks of age, causing diabetes. Similar to several human autoimmune diseases, NOD mice have a 2:1 female-to-male sex bias in progressing to diabetes. In agreement with this, Markle et al. found that male mice housed under standard laboratory conditions were protected from developing diabetes compared to female mice. However, if NOD mice were born and raised in germ-free conditions (i.e. their intestines were never colonized by commensal bacteria) males developed the disease at the same rate as females. In addition, the environment in which the mice were raised impacted their levels of sex hormones: male mice raised in germ-free conditions had lower serum testosterone levels than those raised in standard conditions while germ free female mice had higher testosterone levels than those kept in standard cages. These data supported the conclusion that colonization with commensal bacteria was responsible for the protection of male NOD mice against T1D and that bacterial colonization somehow regulated the production and/or use of testosterone.

To get a sense of the extent to which gut microbiota influenced general physiology of adult male and female NOD mice, the authors used mass spectrometry to profile almost 200 unique small-molecule metabolites in serum. They found that male and female NOD mice raised in standard conditions had distinct profiles of serum metabolites. In contrast, there were few detectable differences between the metabolite profile of males and females raised in germ free conditions. This data suggested two hypotheses: (1) male and female mice had different physiologic responses to the same commensal bacteria, or (2) male and female mice had different commensal communities influencing their hormone and metabolite levels. The authors then sequenced bacterial 16S ribosomal RNA from the intestines of NOD mice at various stages of maturation (just after weaning, at puberty, and as adults). While male and female NOD mice had indistinguishable gut microbiota after weaning, sex-based differences in commensal bacteria were apparent at puberty and became even more pronounced in adulthood.

Having established that adult male and female NOD mice have distinct bacterial populations in their intestines, Markle et al. showed that transplanting the “male” gut microbiota into pre-pubescent female NOD mice altered the composition of the recipient’s commensal populations for several weeks and resulted in increased serum testosterone levels. Importantly, transplantation of male commensal bacteria protected the female recipients from T1D. Markers of T1D disease activity, such as inflammation of beta-islets and production of auto-antibodies, were reduced in recipients of male gut bacteria compared to unmanipulated females. This effect was abrogated upon treatment with the anti-androgen Flutamide, indicating that testosterone levels were a critical regulator of autoimmune pathogenesis.

Markle et al. have put forth an interesting model in which sexual maturation results in sex-specific programming of intestinal commensal bacteria. These distinct populations have differential effects on host physiology and hormonal balance which, in turn, modulate immune function. The centrality of gut microbiota to immunity raises the intriguing possibility of treating a dysfunctional immune system by altering the make-up of the intestine’s commensal communities. Such studies are already underway for intestinal disorders using “fecal transplants”, but the concept may extend to more systemic autoimmune disorders4. This approach would benefit from knowing the specific effects of different bacterial species on host physiology in order to identify the critical components of effective therapeutic microbial regimens.  Similarly, it will be interesting to see which of the changes in metabolite and hormone levels that accompany shifts in commensal populations are most impactful on immune function. The metabolite profiling approach shown in this article could be useful for identifying endogenous compounds that serve as immune modulators.


1. Sex differences in spontaneous versus induced animal models of autoimmunity. Lee TP, Chiang BL. Autoimmun Rev. 2012 May;11(6-7):A422-9. doi: 10.1016/j.autrev.2011.11.020. Epub 2011 Dec 4.

2. Vaccine against autoimmune disease: can helminths or their products provide a therapy? Zaccone P, Cooke A. Curr Opin Immunol. 2013 Mar 2. pii: S0952-7915(13)00027-7. doi: 10.1016/j.coi.2013.02.006.

3. Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity. Markle JG, Frank DN, Mortin-Toth S, Robertson CE, Feazel LM, Rolle-Kampczyk U, von Bergen M, McCoy KD, Macpherson AJ, Danska JS. Science. 2013 Mar 1;339(6123):1084-8. doi: 10.1126/science.1233521. Epub 2013 Jan 17.

4. Stool transplants: ready for prime time? Weissman JS, Coyle W. Curr Gastroenterol Rep. 2012 Aug;14(4):313-6. doi: 10.1007/s11894-012-0263-7.


From bedside to bench: linking autoimmunity-associated gene variants to immune function

Autoimmunity results when the immune system, normally tasked to defend against infections and cancer, attacks the body’s own tissues. There are over 80 clinically-distinct autoimmune diseases that differ in terms of which tissues are targeted and which therapies are most effective. Rheumatoid arthritis (RA) and inflammatory bowel disease (IBD) result in the destruction of joints and the intestinal tract, respectively. These diseases respond well to agents such as adalimumab (Humira) and etanercept (Enbrel) that block the action of TNF-alpha, a cytokine that can promote inflammation. During multiple sclerosis (MS) the immune system attacks the central nervous system resulting in progressive neurologic deficits. Despite being an inflammatory disease, multiple sclerosis is actually worsened through the use of anti-TNF-alpha therapies.

Identifying the fundamental dysfunction at the root of an autoimmune disease would aid in choosing the best of available therapies or devising new ones. Advances in genome sequencing technology have allowed researchers to generate an expanding list of genetic differences present in individuals with various autoimmune diseases compared to healthy people. Although several of these disease-associated gene variants have known roles in the immune system, how they contribute to specific autoimmune processes is largely unknown. There is a need for functional characterization of these gene variants in order to determine how they alter immunity and to stratify them as therapeutic targets.

Dr. David Rawlings’ group at Seattle Children’s Hospital sought to address this challenge in a recent paper published in the May 2013 issue of the Journal of Clinical Investigation. The group, with lead author Dr. Xuezhi Dai, investigated a genetic variant of protein tyrosine phosphatase non-receptor 22 (PTPN22) which had previously been linked to several autoimmune diseases, including type 1 diabetes (T1D), RA, Graves’ Disease, and systemic lupus erythematosus (SLE). PTPN22 encodes an enzyme called LYP, a protein tyrosine phosphatase whose general function is to modulate the intensity of certain signals within cellular signaling networks. The disease-linked variant results in an amino acid switch from arginine to tryptophan at position 620 (LYP-R620W). How LYP or LYP-R620W work to modulate immune activity is incompletely understood.

transgenic mouse

To gain insight into the role of LYP-R620W in autoimmune patients, Dai et al. created a genetically engineered mouse with an analogous arginine to tryptophan switch in the mouse version of LYP (called PEP-R619W). The “knock-in” mice expressing PEP-R619W were viable but had slightly shorter life spans compared to their counterparts with normal PEP. As the engineered mice aged they manifested signs of autoimmunity, such as inflamed lung tissue and blood vessels, as well as signs of chronic kidney damage. In addition, PEP-R619W rendered the mice more susceptible to an experimental form of type 1 diabetes.  These mice also produced numerous auto-antibodies, a hallmark of certain autoimmune diseases.

The PEP-R619W knock-in mouse allowed the authors to look in close detail at the effect of this gene variant on specific immune cell populations. Dai et al. found that the knock-in mice had larger numbers of activated/memory T cells than their normal counterparts, indicating a chronically active immune system. T cells from the knock-in mice were shown to be hyper-responsive to stimulation of their antigen receptors indicating augmentation of the intracellular signals that dictate T cell activation. Similarly, the authors found that knock-in mice had larger numbers of specific B cell populations that occur in active immune states. B cells from the knock-in mice proliferated more than those from normal animals in response to stimulation and were more easily induced to secrete antibody. These findings led the authors to conclude that expression of PEP-R619W results in a lower threshold for activation in both T and B cells which contributed to the autoimmune phenotype. Interestingly, the authors discovered that expression of the disease-linked variant exclusively in B cells was sufficient to generate mice with signs of autoimmunity.

Dai et al. provide a great example of how the tools of bench science can be used to deepen the knowledge gained from analysis of patient specimens. Further determination of PEP/LYP substrate specificity and the dynamics of its phosphatase activity during lymphocyte activation could generate targets for the development of highly selective immune suppressants. In addition, the autoimmune phenotype generated with this knock-in mouse is relatively mild. It would be interesting to see how other disease-linked gene variants would cooperate with PEP-R619W to generate either a more aggressive disease or one that resembles a particular autoimmune syndrome. Finally, the ability of B-cell-specific PEP-R619W expression to stimulate autoimmunity suggests that B cells are a critical component of the autoimmune process in patients with this genetic variant. This model provides the opportunity to compare different therapeutic modalities in the PEP-R619W background (for example, B cell depletion versus anti-TNF agents). Such studies could provide the basis for predicting clinical responses to autoimmune therapies based on genotype.


A disease-associated PTPN22 variant promotes systemic autoimmunity in murine models. Dai X, James RG, Habib T, Singh S, Jackson S, Khim S, Moon RT, Liggitt D, Wolf-Yadlin A, Buckner JH, Rawlings DJ. J Clin Invest. 2013 May 1;123(5):2024-36. doi: 10.1172/JCI66963. Epub 2013 Apr 24.

RORγt+ TREGS: A unique subset of TREGS that specifically promote Colorectal Cancer

tregThe role of CD4+ FoxP3+ regulatory T cells (TREGS) in colorectal cancer (CRC) has continued to be unclear.  TREGS act to suppress inflammatory mechanisms that are associated with tumor progression and can thus act to suppress the development of cancer.  However, TREGS also function to inhibit anti-tumor T cell responses, thereby promoting cancer escape from immune surveillance.  Many studies have been published on the frequencies of TREGS in the peripheral blood and tumors of CRC patients, but there is yet to be a consensus regarding the relationship between TREGS and disease outcome.  In a report by Blatner et. al, the expression of RORγt in a subset of CD4+ FoxP3+ T cells was found to specifically mediate pathogenic pro-tumor activity compared with RORγtCD4+FoxP3+ TREGS in CRC patients.

CD4+ FoxP3+ cells have been classified into three functional populations based on the expression of CD45RA and FoxP3: CD45RA+FoxP3int, CD45RAFoxP3int, and CD45RAFoxP3high.  The CD45RAFoxP3high population exhibits the most suppressive activity of these subsets.  In the study by Blatner et. al, the CD45RAFoxP3high population was found to be specifically expanded in peripheral blood mononuclear cells (PBMCs) and within the tumor of CRC patients and increased with cancer stage.  Because IL-17 expressing CD4+ FoxP3+ cells have been described in the gut and enhanced in patients with CRC and Crohn’s disease, the authors examined CD4+ FoxP3+ populations for expression of the TH17 transcription factor, RORγt. 

In CRC patients, a large fraction of all three subsets of TREGS in PBMCs and in the tumor were found to express RORγt.  Interestingly, when TREG populations were sorted from healthy donors versus CRC patients, CRC patient TREGS  retained suppressive activity over T cell proliferation but had lost their ability to suppress mast cell degranulation.  Expression of IL-17 was also found in a large percentage of CRC TREGS, in a fashion mutually exclusive from IL-10 expression.

To further explore the role of RORγt in CRC, APC∆468 polyposis-prone mice were crossed with mice deficient in RORγt.  RORγt-/-APC∆468 mice were highly resistant to polyp development, had reduced expansion of splenic proinflammatory macrophages, myeloid-derived suppressor cells (MDSCs) and polyp-associated mast cells, compared with RORγt+APC∆468 mice.  Interestingly, the effect of RORγt deficiency in APC∆468 mice was not phenocopied by the loss of IL-17.  Instead, although IL-17 deficiency reduced the frequency of polyps, mast cell recruitment to polyps was enhanced, and ultimately IL-17-/-APC∆468 mice developed invasive lesions.

Overall, this study revealed several fascinating points: CD4+FoxP3+RORγt+ cells appear to be a pathogenic TREG subset that have lost their anti-inflammatory properties and are specifically expanded in CRC patients where they assist in disease progression.  The function of RORγt was not synonymous with IL-17 in TREGS, indicating that other effects of RORγt contribute to the role of these cells in tumor pathogenesis.  Thus, the roles and relationships between FoxP3, RORγt, and IL-17 in TREGS deserve further attention in CRC pathogenesis.  Hopefully, a clearer understanding of this newly identified subset of RORγt+  TREGS and their role in CRC progression will enable much improved methodology for targeting specific TREGS populations in CRC and other disease settings.

Further Reading:

Expression of RORγt marks a pathogenic regulatory T cell subset in human colon cancer.  Blatner NR, Mulcahy MF, Dennis KL, Scholtens D, Bentrem DJ, Phillips JD, Ham S, Sandall BP, Khan MW, Mahvi DM, Halverson AL, Stryker SJ, Boller AM, Singal A, Sneed RK, Sarraj B, Ansari MJ, Oft M, Iwakura Y, Zhou L, Bonertz A, Beckhove P, Gounari F, Khazaie K. Sci Transl Med. 2012 Dec 12;4(164):164ra159. doi: 10.1126/scitranslmed.3004566.

Translational mini-review series on Th17 cells: induction of interleukin-17 production by regulatory T cells.  Afzali B, Mitchell P, Lechler RI, John S, Lombardi G. Clin Exp Immunol. 2010 Feb;159(2):120-30. doi: 10.1111/j.1365-2249.2009.04038.x. Epub 2009 Nov 11.

Inflammation-driven reprogramming of CD4+ Foxp3+ regulatory T cells into pathogenic Th1/Th17 T effectors is abrogated by mTOR inhibition in vivo.  Yurchenko E, Shio MT, Huang TC, Da Silva Martins M, Szyf M, Levings MK, Olivier M, Piccirillo CA. PLoS One. 2012;7(4):e35572. doi: 10.1371/journal.pone.0035572. Epub 2012 Apr 24.

In colorectal cancer mast cells contribute to systemic regulatory T-cell dysfunction.  Blatner NR, Bonertz A, Beckhove P, Cheon EC, Krantz SB, Strouch M, Weitz J, Koch M, Halverson AL, Bentrem DJ, Khazaie K. Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6430-5. doi: 10.1073/pnas.0913683107. Epub 2010 Mar 22.