Granzyme F: Exhaustion Marker and Modulator of Chimeric Antigen Receptor T Cell-Mediated Cytotoxicity

Granzymes are a family of proteases used by CD8 T cells to mediate cytotoxicity and other less-defined activities. The substrate and mechanism of action of many granzymes are unknown, although they diverge among the family members. In this study, we show that mouse CD8+ tumor-infiltrating lymphocytes (TILs) express a unique array of granzymes relative to CD8 T cells outside the tumor microenvironment in multiple tumor models. Granzyme F was one of the most highly upregulated genes in TILs and was exclusively detected in PD1/TIM3 double-positive CD8 TILs. To determine the function of granzyme F and to improve the cytotoxic response to leukemia, we constructed chimeric Ag receptor T cells to overexpress a single granzyme, granzyme F or the better-characterized granzyme A or B. Using these doubly recombinant T cells, we demonstrated that granzyme F expression improved T cell-mediated cytotoxicity against target leukemia cells and induced a form of cell death other than chimeric Ag receptor T cells expressing only endogenous granzymes or exogenous granzyme A or B. However, increasing expression of granzyme F also had a detrimental impact on the viability of the host T cells, decreasing their persistence in circulation in vivo. These results suggest a unique role for granzyme F as a marker of terminally differentiated CD8 T cells with increased cytotoxicity, but also increased self-directed cytotoxicity, suggesting a potential mechanism for the end of the terminal exhaustion pathway.

Low TCR binding strength results in increased progenitor-like CD8+ tumor-infiltrating lymphocytes

T cell receptor (TCR) binding strength to peptide-MHC antigen complex influences numerous T cell functions. However, the vast diversity of a polyclonal T cell repertoire for even a single antigen greatly increases the complexity of studying the impact TCR affinity has on T cell function. Here, we determined how TCR binding strength affected the protein and transcriptional profile of an endogenous, polyclonal T cell response to a known tumor-associated antigen (TAA) within the tumor microenvironment (TME). We confirmed that flow and CITE-Seq counts of MHC-tetramer labeling were reliable surrogates for the TCR-peptide-MHC steady-state binding affinity. We further demonstrated by single-cell RNA sequencing that tumor-infiltrating lymphocytes (TILs) with high and low binding affinity for a TAA can differentiate into cells with many antigen-specific transcriptional profiles within an established TME. However, more progenitor-like phenotypes were significantly biased towards lower affinity T cells, and proliferating phenotypes showed significant bias towards high-affinity TILs. Additionally, we found in a progressing TME that higher affinity T cells advanced more rapidly to terminal phases of T cell exhaustion and exhibited better tumor control. We confirmed the polyclonal TIL results using a TCR transgenic mouse possessing a single low-affinity TCR targeting the same TAA. These T cells maintained a progenitor-exhausted phenotype and exhibited impaired tumor control. We propose that high-affinity TCR interactions drive T cell fate decisions more rapidly than low-affinity interactions and that these cells differentiate faster. These findings illustrate divergent forms of T cell dysfunction based on TCR affinity which may impact TIL therapies and antitumor responses.

Antigens Expressed by Breast Cancer Cells Undergoing EMT Stimulate Cytotoxic CD8+ T Cell Immunity

Simple Summary

The transition of cells with epithelial characteristics to those with mesenchymal characteristics (termed EMT) facilitates breast cancer invasive capacity. The EMT program can also contribute to immunosuppressive and immunoevasive properties, altering susceptibility to immune cell recognition and killing. The goal of our study was to manipulate EMT to reveal potential neoantigens that might affect the ability of tumor cells to circumvent immune escape and/or be utilized as an anticancer vaccine to kill cancer cells exhibiting the cellular plasticity that permits therapy resistance and metastatic progression. We identified potential neoantigens resulting from EMT-associated altered gene expression and alternative splicing events and observed increased immunogenicity and susceptibility to killing of the more epithelial-like cancer cells. Although the tested peptides did not protect from tumor growth, a limited number of predicted neoantigens derived from intron retention events were tested. In the future, refined prediction programs may facilitate exciting antigen discoveries.

Abstract

Antigenic differences formed by alterations in gene expression and alternative splicing are predicted in breast cancer cells undergoing epithelial to mesenchymal transition (EMT) and the reverse plasticity known as MET. How these antigenic differences impact immune interactions and the degree to which they can be exploited to enhance immune responses against mesenchymal cells is not fully understood. We utilized a master microRNA regulator of EMT to alter mesenchymal-like EO771 mammary carcinoma cells to a more epithelial phenotype. A computational approach was used to identify neoantigens derived from the resultant differentially expressed somatic variants (SNV) and alternative splicing events (neojunctions). Using whole cell vaccines and peptide-based vaccines, we find superior cytotoxicity against the more-epithelial cells and explore the potential of neojunction-derived antigens to elicit T cell responses through experiments designed to validate the computationally predicted neoantigens. Overall, results identify EMT-associated splicing factors common to both mouse and human breast cancer cells as well as immunogenic SNV- and neojunction-derived neoantigens in mammary carcinoma cells.

Peptide Centric Vβ Specific Germline Contacts Shape a Specialist T Cell Response

Certain CD8 T cell responses are particularly effective at controlling infection, as exemplified by elite control of HIV in individuals harboring HLA-B57. To understand the structural features that contribute to CD8 T cell elite control, we focused on a strongly protective CD8 T cell response directed against a parasite-derived peptide (HF10) presented by an atypical MHC-I molecule, H-2Ld. This response exhibits a focused TCR repertoire dominated by Vβ2, and a representative TCR (TG6) in complex with Ld-HF10 reveals an unusual structure in which both MHC and TCR contribute extensively to peptide specificity, along with a parallel footprint of TCR on its pMHC ligand. The parallel footprint is a common feature of Vβ2-containing TCRs and correlates with an unusual Vα-Vβ interface, CDR loop conformations, and Vβ2-specific germline contacts with peptides. Vβ2 and Ld may represent "specialist" components for antigen recognition that allows for particularly strong and focused T cell responses.

Granzyme F production by CD8 T cells in the tumor microenvironment

Granzymes are a class of cytotoxic proteases and are the primary mechanism utilized by T cells to directly eliminate cancer cells. Each granzyme acts upon a unique set of substrates in target cells to induce cytotoxicity through a range of different mechanisms. Granzymes are some of the most differentially regulated genes in CD8+ tumor infiltrating lymphocytes, relative to T cells outside of the tumor microenvironment (TME). We and others have determined by microarray and qPCR that granzyme F is highly upregulated in the TME. Granzyme F expression is restricted to a small subset of antigen-experienced and exhausted T cells, as determined by flow cytometry-based detection of granzyme F RNA transcripts and may represent a marker of a unique T cell cytotoxic function. Single cell RNA sequencing of CD8 TIL has revealed that granzyme F-high expressing cells are unique from both granzyme A and B expressing cells, and that it is therefore likely these TIL utilize a unique mechanism of cytotoxicity in their elimination of cancer cells. Recombinant granzyme F has previously been shown to induce a unique form of cell death, characterized as being caspase-independent and resulting in rupture of target cell plasma membrane. By over expressing granzyme F we are determining if this mechanism of cell death is leverageable to improve the cytotoxic capacity of TIL, and if induction of different forms of T cell-mediated cytotoxicity can modulate the immunogenicity of the TME. These experiments are designed to provide insight into how to improve adoptive T cell therapies by directly improving cytotoxicity, the terminal step of T cell interaction with tumor cells.

This work was supported by the National Institutes of Health  NIAID training grant (Training Program in Immunology; T32-AI07405) award to Zachary Hay

Granzymes: The Molecular Executors of Immune-Mediated Cytotoxicity

Cytotoxic T lymphocytes, differentiated CD8+ T cells, use multiple mechanisms to mediate their function, including release of granules containing perforin and granzymes at target cells. Granzymes are a family of cytotoxic proteases that each act on unique sets of biological substrates within target cells, usually to induce cell death. Granzymes are differentially expressed within T cells, depending on their environment and activation state, making the granzyme cytotoxic pathway dynamic and responsive to individual circumstances. In this review, we describe what is currently known about granzyme structure, processing, and granzyme-induced cell death in the context of cancer and in some other inflammatory diseases.

MicroRNA-200c restoration reveals a cytokine profile to enhance M1 macrophage polarization in breast cancer

Many immune suppressive mechanisms utilized by triple negative breast cancer (TNBC) are regulated by oncogenic epithelial-to-mesenchymal transition (EMT). How TNBC EMT impacts innate immune cells is not fully understood. To determine how TNBC suppresses antitumor macrophages, we used microRNA-200c (miR-200c), a powerful repressor of EMT, to drive mesenchymal-like mouse mammary carcinoma and human TNBC cells toward a more epithelial state. MiR-200c restoration significantly decreased growth of mouse mammary carcinoma Met-1 cells in culture and in vivo. Cytokine profiling of Met-1 and human BT549 cells revealed that miR-200c upregulated cytokines, such as granulocyte-macrophage colony-stimulating factor (GM-CSF), promoted M1 antitumor macrophage polarization. Cytokines upregulated by miR-200c correlated with an epithelial gene signature and M1 macrophage polarization in BC patients and predicted a more favorable overall survival for TNBC patients. Our findings demonstrate that immunogenic cytokines (e.g., GM-CSF) are suppressed in aggressive TNBC, warranting further investigation of cytokine-based therapies to limit disease recurrence.

Testing Cancer Immunotherapy in a Human Immune System Mouse Model: Correlating Treatment Responses to Human Chimerism, Therapeutic Variables and Immune Cell Phenotypes

Over the past decade, immunotherapies have revolutionized the treatment of cancer. Although the success of immunotherapy is remarkable, it is still limited to a subset of patients. More than 1500 clinical trials are currently ongoing with a goal of improving the efficacy of immunotherapy through co-administration of other agents. Preclinical, small-animal models are strongly desired to increase the pace of scientific discovery, while reducing the cost of combination drug testing in humans. Human immune system (HIS) mice are highly immune-deficient mouse recipients rtpeconstituted with human hematopoietic stem cells. These HIS-mice are capable of growing human tumor cell lines and patient-derived tumor xenografts. This model allows rapid testing of multiple, immune-related therapeutics for tumors originating from unique clinical samples. Using a cord blood-derived HIS-BALB/c-Rag2nullIl2rγnullSIRPαNOD (BRGS) mouse model, we summarize our experiments testing immune checkpoint blockade combinations in these mice bearing a variety of human tumors, including breast, colorectal, pancreatic, lung, adrenocortical, melanoma and hematological malignancies. We present in-depth characterization of the kinetics and subsets of the HIS in lymph and non-lymph organs and relate these to protocol development and immune-related treatment responses. Furthermore, we compare the phenotype of the HIS in lymph tissues and tumors. We show that the immunotype and amount of tumor infiltrating leukocytes are widely-variable and that this phenotype is tumor-dependent in the HIS-BRGS model. We further present flow cytometric analyses of immune cell subsets, activation state, cytokine production and inhibitory receptor expression in peripheral lymph organs and tumors. We show that responding tumors bear human infiltrating T cells with a more inflammatory signature compared to non-responding tumors, similar to reports of "responding" patients in human immunotherapy clinical trials. Collectively these data support the use of HIS mice as a preclinical model to test combination immunotherapies for human cancers, if careful attention is taken to both protocol details and data analysis.

The Capacity of the Ovarian Cancer Tumor Microenvironment to Integrate Inflammation Signaling Conveys a Shorter Disease-free Interval

PURPOSE

Ovarian cancer has one of the highest deaths to incidence ratios across all cancers. Initial chemotherapy is effective, but most patients develop chemoresistant disease. Mechanisms driving clinical chemo-response or -resistance are not well-understood. However, achieving optimal surgical cytoreduction improves survival, and cytoreduction is improved by neoadjuvant chemotherapy (NACT). NACT offers a window to profile pre- versus post-NACT tumors, which we used to identify chemotherapy-induced changes to the tumor microenvironment.

EXPERIMENTAL DESIGN

We obtained matched pre- and post-NACT archival tumor tissues from patients with high-grade serous ovarian cancer (patient, n = 6). We measured mRNA levels of 770 genes (756 genes/14 housekeeping genes, NanoString Technologies), and performed reverse phase protein array (RPPA) on a subset of matched tumors. We examined cytokine levels in pre-NACT ascites samples (n = 39) by ELISAs. A tissue microarray with 128 annotated ovarian tumors expanded the transcriptional, RPPA, and cytokine data by multispectral IHC.

RESULTS

The most upregulated gene post-NACT was IL6 (16.79-fold). RPPA data were concordant with mRNA, consistent with elevated immune infiltration. Elevated IL6 in pre-NACT ascites specimens correlated with a shorter time to recurrence. Integrating NanoString (n = 12), RPPA (n = 4), and cytokine (n = 39) studies identified an activated inflammatory signaling network and induced IL6 and IER3 (immediate early response 3) post-NACT, associated with poor chemo-response and time to recurrence.

CONCLUSIONS

Multiomics profiling of ovarian tumor samples pre- and post-NACT provides unique insight into chemo-induced changes to the tumor microenvironment. We identified a novel IL6/IER3 signaling axis that may drive chemoresistance and disease recurrence.

HITM-SURE: Hepatic immunotherapy for metastases phase Ib anti-CEA CAR-T study utilizing pressure enabled drug delivery

In recent years, cell therapy technologies have resulted in impressive results in hematologic malignancies. Treatment of solid tumors with chimeric antigen receptor T-cells (CAR-T) has been less successful. Solid tumors present challenges not encountered with hematologic cancers, including high intra-tumoral pressure and ineffective CAR-T trafficking to the site of disease. Novel delivery methods may enable CAR-T therapies for solid tumor malignancies. A patient with liver metastases secondary to pancreatic adenocarcinoma received CAR-T targeting carcinoembryonic antigen (CEA). Previously we reported that Pressure-Enabled Drug Delivery (PEDD) enhanced CAR-T delivery to liver metastases 5.2-fold. Three doses of anti-CEA CAR-T were regionally delivered via hepatic artery infusion (HAI) using PEDD technology to optimize the therapeutic index. Interleukin-2 was systemically delivered by continuous intravenous infusion to support CAR-T in vivo. HAI of anti-CEA CAR-T was not associated with any serious adverse events (SAEs) above grade 3 and there were no on-target/off-tumor SAEs. Following CAR-T treatment, positron emission tomography-CT demonstrated a complete metabolic response within the liver, which was durable and sustained for 13 months. The response was accompanied by normalization of serum tumor markers and an abundance of CAR+ cells found within post-treatment tumor specimens. The findings from this report exhibit biologic activity and safety of regionally infused CAR-T for an indication with limited immune-oncology success to date. Further studies will determine how HAI of CAR-T may be included in multidisciplinary treatment plans for patients with liver metastases. ClinicalTrials.gov number, NCT02850536.

T-cell receptor affinity in the age of cancer immunotherapy

The strength of the interaction between T-cell receptors (TCRs) and their ligands, peptide/major histocompatibility complex complexes (pMHCs), is one of the most frequently discussed and investigated features of T cells in immuno-oncology today. Although there are many molecules on the surface of T cells that interact with ligands on other cells, the TCR/pMHC is the only receptor-ligand pair that offers antigen specificity and dictates the functional response of the T cell. The strength of the TCR/pMHC interaction, along with the environment in which this interaction takes place, is key to how the T cell will respond. The TCR repertoire of T cells that interact with tumor-associated antigens is vast, although typically of low affinity. Here, we focus on the low-affinity interactions between TCRs from CD8+ T cells and different models used in immuno-oncology.

The impact of the tumor microenvironment on granzyme production by CD8 T cells

Granzymes are a class of proteases produced by CD8 T cells to mediate their cytotoxic activity against target cells. The objective of this project is to determine the mechanism through which CD8 T cells are executing their granzyme-mediated cytotoxic function and how the tumor microenvironment (TME) impacts the specific granzymes produced. By micro-array and qPCR we determined that CD8 T cells in the TME have altered expression of specific granzymes. Granzyme F had one of the most altered expressions of all genes examined in antigen-specific CD8 T cells taken from a spleen relative to those taken from a tumor. We further examined the effects of the TME on granzyme expression by sorting tumor infiltrating CD8 T cells on exhaustion markers and found a relationship between exhaustion and granzyme expression, characterized by a decrease in granzyme A and an increase in granzyme B mRNA expression. We will determine the influence different ex vivo culture conditions have on differential granzyme expression and function of CD8 T cells. The expression of different granzymes may have further implications for modulation of the TME through the form of cancer cell death induced, especially the increase in granzyme F which has been suggested to induce a more immunogenic form of cell death. Additionally, the impact of exhaustion on the cytotoxic activity of CD8 T cells from the TME may represent a means for exhausted CD8 T cells to regulate their cytotoxic activity by altering the granzymes they express.

A review of emerging physical transfection methods for CRISPR/Cas9-mediated gene editing

Gene editing is a versatile technique in biomedicine that promotes fundamental research as well as clinical therapy. The development of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) as a genome editing machinery has accelerated the application of gene editing. However, the delivery of CRISPR components often suffers when using conventional transfection methods, such as viral transduction and chemical vectors, due to limited packaging size and inefficiency toward certain cell types. In this review, we discuss physical transfection methods for CRISPR gene editing which can overcome these limitations. We outline different types of physical transfection methods, highlight novel techniques to deliver CRISPR components, and emphasize the role of micro and nanotechnology to improve transfection performance. We present our perspectives on the limitations of current technology and provide insights on the future developments of physical transfection methods.

Peptide mimotopes alter T cell function in cancer and autoimmunity

T cells recognize and respond to self antigens in both cancer and autoimmunity. One strategy to influence this response is to incorporate amino acid substitutions into these T cell-specific epitopes. This strategy is being reconsidered now with the goal of increasing time to regression with checkpoint blockade therapies in cancer and antigen-specific immunotherapies in autoimmunity. We discuss how these amino acid substitutions change the interactions with the MHC class I or II molecule and the responding T cell repertoire. Amino acid substitutions in epitopes that are the most effective in therapies bind more strongly to T cell receptor and/or MHC molecules and cross-react with the same repertoire of T cells as the natural antigen.

CXCL14 suppresses human papillomavirus-associated head and neck cancer through antigen-specific CD8+ T-cell responses by upregulating MHC-I expression

Evasion of the host immune responses is critical for both persistent human papillomavirus (HPV) infection and associated cancer progression. We have previously shown that expression of the homeostatic chemokine CXCL14 is significantly downregulated by the HPV oncoprotein E7 during cancer progression. Restoration of CXCL14 expression in HPV-positive head and neck cancer (HNC) cells dramatically suppresses tumor growth and increases survival through an immune-dependent mechanism in mice. While CXCL14 recruits natural killer (NK) and T cells to the tumor microenvironment, the mechanism by which CXCL14 mediates tumor suppression through NK and/or T cells remained undefined. Here, we report that CD8⁺ T cells are required for CXCL14-mediated tumor suppression. Using a CD8⁺ T cell receptor transgenic model, we show that the CXCL14-mediated antitumor CD8⁺ T cell responses require antigen specificity. Interestingly, CXCL14 expression restores major histocompatibility complex class I (MHC-I) expression on HPV-positive HNC cells downregulated by HPV, and knockdown of MHC-I expression in HNC cells results in loss of tumor suppression even with CXCL14 expression. These results suggest that CXCL14 enacts antitumor immunity through restoration of MHC-I expression on tumor cells and promoting antigen-specific CD8⁺ T cell responses to suppress HPV-positive HNC.

IL12 Abrogates Calcineurin-Dependent Immune Evasion during Leukemia Progression

Exploitation of the immune system has emerged as an important therapeutic strategy for acute lymphoblastic leukemia (ALL). However, the mechanisms of immune evasion during leukemia progression remain poorly understood. We sought to understand the role of calcineurin in ALL and observed that depletion of calcineurin B (CnB) in leukemia cells dramatically prolongs survival in immune-competent but not immune-deficient recipients. Immune-competent recipients were protected from challenge with leukemia if they were first immunized with CnB-deficient leukemia, suggesting robust adaptive immunity. In the bone marrow (BM), recipients of CnB-deficient leukemia harbored expanded T-cell populations as compared with controls. Gene expression analyses of leukemia cells extracted from the BM identified Cn-dependent significant changes in the expression of immunoregulatory genes. Increased secretion of IL12 from CnB-deficient leukemia cells was sufficient to induce T-cell activation ex vivo, an effect that was abolished when IL12 was neutralized. Strikingly, recombinant IL12 prolonged survival of mice challenged with highly aggressive B-ALL. Moreover, gene expression analyses from children with ALL showed that patients with higher expression of either IL12A or IL12B exhibited prolonged survival. These data suggest that leukemia cells are dependent upon calcineurin for immune evasion by restricting the regulation of proinflammatory genes, particularly IL12. SIGNIFICANCE: This report implicates calcineurin as an intracellular signaling molecule responsible for immune evasion during leukemia progression and raises the prospect of re-examining IL12 as a therapeutic in leukemia.

Characterization of immune responses to anti-PD-1 mono and combination immunotherapy in hematopoietic humanized mice implanted with tumor xenografts

Background

The success of agents that reverse T-cell inhibitory signals, such as anti-PD-1/PD-L1 therapies, has reinvigorated cancer immunotherapy research. However, since only a minority of patients respond to single-agent therapies, methods to test the potential anti-tumor activity of rational combination therapies are still needed. Conventional murine xenograft models have been hampered by their immune-compromised status; thus, we developed a hematopoietic humanized mouse model, hu-CB-BRGS, and used it to study anti-tumor human immune responses to triple-negative breast cancer (TNBC) cell line and patient-derived colorectal cancer (CRC) xenografts (PDX).

Methods

BALB/c-Rag2^nullIl2rγ^nullSIRPα^NOD (BRGS) pups were humanized through transplantation of cord blood (CB)-derived CD34+ cells. Mice were evaluated for human chimerism in the blood and assigned into experimental untreated or nivolumab groups based on chimerism. TNBC cell lines or tumor tissue from established CRC PDX models were implanted into both flanks of humanized mice and treatments ensued once tumors reached a volume of ~150mm³. Tumors were measured twice weekly. At end of study, immune organs and tumors were collected for immunological assessment.

Results

Humanized PDX models were successfully established with a high frequency of tumor engraftment. Humanized mice treated with anti-PD-1 exhibited increased anti-tumor human T-cell responses coupled with decreased Treg and myeloid populations that correlated with tumor growth inhibition. Combination therapies with anti-PD-1 treatment in TNBC-bearing mice reduced tumor growth in multi-drug cohorts. Finally, as observed in human colorectal patients, anti-PD-1 therapy had a strong response to a microsatellite-high CRC PDX that correlated with a higher number of human CD8+ IFNγ+ T cells in the tumor.

Conclusion

Hu-CB-BRGS mice represent an in vivo model to study immune checkpoint blockade to human tumors. The human immune system in the mice is inherently suppressed, similar to a tumor microenvironment, and thus allows growth of human tumors. However, the suppression can be released by anti-PD-1 therapies and inhibit tumor growth of some tumors. The model offers ample access to lymph and tumor cells for in-depth immunological analysis. The tumor growth inhibition correlates with increased CD8 IFNγ+ tumor infiltrating T cells. These hu-CB-BRGS mice provide a relevant preclinical animal model to facilitate prioritization of hypothesis-driven combination immunotherapies.

Electronic supplementary material

The online version of this article (10.1186/s40425-019-0518-z) contains supplementary material, which is available to authorized users.

A Role for Tryptophan-2,3-dioxygenase in CD8 T-cell Suppression and Evidence of Tryptophan Catabolism in Breast Cancer Patient Plasma

Tryptophan catabolism is an attractive target for reducing tumor progression and improving antitumor immunity in multiple cancers. Tumor infiltration by CD8 T cells correlates with improved prognosis in triple-negative breast cancer (TNBC) and a significant effort is underway to improve CD8 T-cell antitumor activity. In this study, primary human immune cells were isolated from the peripheral blood of patients and used to demonstrate that the tryptophan catabolite kynurenine induces CD8 T-cell death. Furthermore, it is demonstrated that anchorage-independent TNBC utilizes the tryptophan-catabolizing enzyme tryptophan 2,3-dioxygenase (TDO) to inhibit CD8 T-cell viability. Publicly available data revealed that high TDO2, the gene encoding TDO, correlates with poor breast cancer clinical outcomes, including overall survival and distant metastasis-free survival, while expression of the gene encoding the more commonly studied tryptophan-catabolizing enzyme, IDO1 did not. Metabolomic analysis, using quantitative mass spectrometry, of tryptophan and its catabolites, including kynurenine, in the plasma from presurgical breast cancer patients (n = 77) and 40 cancer-free donors (n = 40) indicated a strong correlation between substrate and catabolite in both groups. Interestingly, both tryptophan and kynurenine were lower in the plasma from patients with breast cancer compared with controls, particularly in women with estrogen receptor (ER)-negative and stage III and IV breast cancer. IMPLICATIONS: This study underscores the importance of tryptophan catabolism, particularly in aggressive disease, and suggests that future pharmacologic efforts should focus on developing drugs that target both TDO and IDO1.

Eya3 promotes breast tumor-associated immune suppression via threonine phosphatase-mediated PD-L1 upregulation

Eya proteins are critical developmental regulators that are highly expressed in embryogenesis but downregulated after development. Amplification and/or re-expression of Eyas occurs in many tumor types. In breast cancer, Eyas regulate tumor progression by acting as transcriptional cofactors and tyrosine phosphatases. Intriguingly, Eyas harbor a separate threonine (Thr) phosphatase activity, which was previously implicated in innate immunity. Here we describe what we believe to be a novel role for Eya3 in mediating triple-negative breast cancer-associated immune suppression. Eya3 loss decreases tumor growth in immune-competent mice and is associated with increased numbers of infiltrated CD8+ T cells, which, when depleted, reverse the effects of Eya3 knockdown. Mechanistically, Eya3 utilizes its Thr phosphatase activity to dephosphorylate Myc at pT58, resulting in a stabilized form. We show that Myc is required for Eya3-mediated increases in PD-L1, and that rescue of PD-L1 in Eya3-knockdown cells restores tumor progression. Finally, we demonstrate that Eya3 significantly correlates with PD-L1 in human breast tumors, and that tumors expressing high levels of Eya3 have a decreased CD8+ T cell signature. Our data uncover a role for Eya3 in mediating tumor-associated immune suppression, and suggest that its inhibition may enhance checkpoint therapies.

MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection

To build a catalog of peptides presented by breast cancer cells, we undertook systematic MHC class I immunoprecipitation followed by elution of MHC class I-loaded peptides in breast cancer cells. We determined the sequence of 3196 MHC class I ligands representing 1921 proteins from a panel of 20 breast cancer cell lines. After removing duplicate peptides, i.e., the same peptide eluted from more than one cell line, the total number of unique peptides was 2740. Of the unique peptides eluted, more than 1750 had been previously identified, and of these, sixteen have been shown to be immunogenic. Importantly, half of these immunogenic peptides were shared between different breast cancer cell lines. MHC class I binding probability was used to plot the distribution of the eluted peptides in accordance with the binding score for each breast cancer cell line. We also determined that the tested breast cancer cells presented 89 mutation-containing peptides and peptides derived from aberrantly translated genes, 7 of which were shared between four or two different cell lines. Overall, the high throughput identification of MHC class I-loaded peptides is an effective strategy for systematic characterization of cancer peptides, and could be employed for design of multi-peptide anticancer vaccines.

SIGNIFICANCE

By employing proteomic analyses of eluted peptides from breast cancer cells, the current study has built an initial HLA-I-typed antigen collection for breast cancer research. It was also determined that immunogenic epitopes can be identified using established cell lines and that shared immunogenic peptides can be found in different cancer types such as breast cancer and leukemia. Importantly, out of 3196 eluted peptides that included duplicate peptides in different cells 89 peptides either contained mutation in their sequence or were derived from aberrant translation suggesting that mutation-containing epitopes are on the order of 2-3% in breast cancer cells. Finally, our results suggest that interfering with MHC class I function is one of the mechanisms of how tumor cells escape immune system attack.

Antigen-Presenting Intratumoral B Cells Affect CD4+ TIL Phenotypes in Non-Small Cell Lung Cancer Patients

Effective immunotherapy options for patients with non-small cell lung cancer (NSCLC) are becoming increasingly available. The immunotherapy focus has been on tumor-infiltrating T cells (TILs); however, tumor-infiltrating B cells (TIL-Bs) have also been reported to correlate with NSCLC patient survival. The function of TIL-Bs in human cancer has been understudied, with little focus on their role as antigen-presenting cells and their influence on CD4⁺ TILs. Compared with other immune subsets detected in freshly isolated primary tumors from NSCLC patients, we observed increased numbers of intratumoral B cells relative to B cells from tumor-adjacent tissues. Furthermore, we demonstrated that TIL-Bs can efficiently present antigen to CD4⁺ TILs and alter the CD4⁺ TIL phenotype using an in vitro antigen-presentation assay. Specifically, we identified three CD4⁺ TIL responses to TIL-Bs, which we categorized as activated, antigen-associated, and nonresponsive. Within the activated and antigen-associated CD4⁺ TIL population, activated TIL-Bs (CD19⁺CD20⁺CD69⁺CD27⁺CD21⁺) were associated with an effector T-cell response (IFNγ⁺ CD4⁺ TILs). Alternatively, exhausted TIL-Bs (CD19⁺CD20⁺CD69⁺CD27^-CD21^-) were associated with a regulatory T-cell phenotype (FoxP3⁺ CD4⁺ TILs). Our results demonstrate a new role for TIL-Bs in NSCLC tumors in their interplay with CD4⁺ TILs in the tumor microenvironment, establishing them as a potential therapeutic target in NSCLC immunotherapy. Cancer Immunol Res; 5(10); 898-907. ©2017 AACR.

Shared αβ TCR Usage in Lungs of Sarcoidosis Patients with Löfgren's Syndrome

Sarcoidosis is a granulomatous disease that primarily affects the lungs and is characterized by an accumulation of CD4⁺ T cells in the bronchoalveolar lavage (BAL). Previous work has indicated that HLA-DRB1*03:01⁺ (DR3⁺) patients diagnosed with the acute form of the disease, Löfgren's syndrome (LS), have an accumulation of CD4⁺ T cells bearing TCRs using TRAV12-1 (formerly AV2S3). However, the importance of these α-chains in disease pathogenesis and the paired TCRβ-chain remains unknown. This study aimed to identify expanded αβTCR pairs expressed on CD4⁺ T cells derived from the BAL of DR3⁺ LS patients. Using a deep-sequencing approach, we determined TCRα- and TCRβ-chain usage, as well as αβTCR pairs expressed on BAL CD4⁺ T cells from LS patients. TRAV12-1 and TRBV2 (formerly BV22) were the most expanded V region gene segments in DR3⁺ LS patients relative to control subjects, and TRAV12-1 and TRBV2 CDR3 motifs were shared among multiple DR3⁺ LS patients. When assessing αβTCR pairing, TRAV12-1 preferentially paired with TRBV2, and these TRAV12-1/TRBV2 TCRs displayed CDR3 homology. These findings suggest that public CD4⁺ TCR repertoires exist among LS patients and that these T cells are recognizing the putative sarcoidosis-associated Ag(s) in the context of DR3.

Antigen-presenting tumor B cells impact the phenotype of CD4 tumor infiltrating T cells in lung cancer patients

The focus of immunotherapy has been on CD8 and CD4 tumor infiltrating lymphocytes (TILs), however, tumor infiltrating B cells (TIL-Bs) are understudied with no focus on their role as antigen presenting cells. We hypothesize that TIL-Bs help generate potent, long-term immune responses against cancer by presenting tumor antigens to CD4 TILs.

Using un-manipulated, primary human B cells from fresh tumor, we generated a specific in vitro antigen presentation assay and observed three types of CD4 TIL responses when TIL-Bs presented autologous tumor antigens. There were activated responder CD4 TILs that proliferated when combined with TIL-Bs alone, which indicates stimulation with endogenous tumor antigens. There were antigen-associated responders that required autologous tumor lysate to elicit a CD4 TIL response, and there were patient CD4 TILs that did not respond to antigen presentation. Exhausted B cells have been described in chronic infection i.e. HIV, and thus, to parallel our studies to a model of chronic infection, we analyzed activated and exhausted TIL-Bs with our antigen presentation assay. If TIL-Bs were activated (HLADR+CD69+CD27+CD21+), the resultant CD4 TILs were T helper (anti-tumor) CD4 T cells and if the TIL-Bs were exhausted (HLADR+CD69+CD27−CD21−), the resultant CD4 TILs were T regulatory cells (pro-tumor). These data suggest that TIL-Bs influence CD4 TILs in NSCLC patient tumors.

In conclusion, determining if TIL-Bs are activated or exhausted in NSCLC patients will determine the extent of their anti-tumor function in human cancer. Ultimately, results from this study will dictate how to target TIL-Bs in future immunotherapies.

Abstract PR03: Characterizing the immune context of responses to immunotherapy in humanized patient derived xenograft models of CRC

Introduction: Inhibiting the activity of the epidermal growth factor receptor (EGFR) with monoclonal antibodies has been utilized as a therapeutic strategy for patients with metastatic colorectal cancer (CRC), leading to improved clinical results alone and in combination with standard chemotherapy. Many systematic reviews and metanalyses were performed to better understand the role of EGFR inhibition in CRC, revealing that KRAS exon 2 mutations and furthermore exons 3 and 4 and NRAS exons 2, 3, and 4 were predictive of non-responsiveness to these agents. Concurrent with these results has been the development of immunotherapy targeting immune regulatory checkpoints such as CTLA-4 and PD-1 that have initiated a new era in the treatment of cancer. In order to gain a better biological understanding of the context of immune responses and facilitate preclinical evaluation of cancer immunotherapy, we developed a hematopoietic humanized mouse model utilizing patient-derived CRC xenograft tumor models to assess immune therapy for RAS mutant CRC. Not only could evaluation of humanized RAS mutant PDX models provide additional information on the potential for clinical activity of immune therapies, but could also improve the understanding of immune responses to RAS mutant cancers. We therefore hypothesize that humanized RAS mutant colorectal PDX models can be used to evaluate the preclinical activity of immune targeted agents for treatment of RAS mutant colorectal cancer.

Methods: Humanized BRG mice developed from the BALB/cRag2-/-IL2Rγc-/- (BRG) strain which is known to accept human hematopoietic stem cells, have been used to enhance engraftment. BRG newborn pups were humanized through transplantation of approximately 1x105 CD34+ cells purified from umbilical cord blood. The mice were evaluated for chimerism at 8 and 12 weeks. At 14 weeks, tumor tissue from established PDX models were implanted on the right and left flank of humanized mice. The tumor was selected among a cluster within the “immune-enriched” subtype (C2) based upon the RNAseq characterization of the models. When the average tumor size reached a volume of approximately ~150-300 mm3, the mice were randomized into either vehicle or nivolumab treatment groups. Mice were monitored daily for signs of toxicity and weighed twice weekly. They were treated with nivolumab (30 mg/kg) twice a week by intraperitoneal injection for 15 days. Tumor size was evaluated twice weekly by caliper measurements using the following equation: tumor volume= (length × width2) × 0.52. At the end of the treatment, mice were euthanized while sera, lymph nodes, spleen, bone marrow and tumors were collected for further investigation.

Results: Humanized RAS mutant CRC PDX models were successfully established in vivo. While no differences were observed in tumor growth among the control and treated arms, we were able to detect differences in PD1 expression among treated versus control mice, with lower expression in the nivolumab treated group. We also observed higher numbers of T cells in the lymph nodes of nivolumab treated mice, suggesting T cell expansion. Interestingly, we also observed an increase of T cells in the spleen and blood and late occupancy of T cells in the bone marrow. Two of the treated mice exhibited identifiable TILs that were comprised of a majority of CD4+ T cells with an activated phenotype (CD69+).

Conclusions: Humanized KRAS mutant CRC PDX models were successfully established and tumor engraftment occurred in all humanized mice with nivolumab-treated mice demonstrating the development of lymph nodes that were populated by activated T cells. These preliminary results demonstrate that human immunity and PD-1 expressing T cells exist in these models and provide the basis for planned immunotherapy combination studies.

This abstract is also being presented as Poster A23.

Citation Format: Anna Capasso, Julie Lang, Todd M. Pitts, S. Lindsey Davis, Chris H. Lieu, Stacey M. Bagby, Aik Choon Tan, John J. Tentler, Jill E. Slansky, Roberta Pelanda, S. Gail Eckhardt. Characterizing the immune context of responses to immunotherapy in humanized patient derived xenograft models of CRC. [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr PR03.

Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model

Mechanisms of self-tolerance often result in CD8(+) tumor-infiltrating lymphocytes (TIL) with a hypofunctional phenotype incapable of tumor clearance. Using a transplantable colon carcinoma model, we found that CD8(+) T cells became tolerized in <24 h in an established tumor environment. To define the collective impact of pathways suppressing TIL function, we compared genome-wide mRNA expression of tumor-specific CD8(+) T cells from the tumor and periphery. Notably, gene expression induced during TIL hypofunction more closely resembled self-tolerance than viral exhaustion. Differential gene expression was refined to identify a core set of genes that defined hypofunctional TIL; these data comprise the first molecular profile of tumor-specific TIL that are naturally responding and represent a polyclonal repertoire. The molecular profile of TIL was further dissected to determine the extent of overlap and distinction between pathways that collectively restrict T cell functions. As suggested by the molecular profile of TIL, protein expression of inhibitory receptor LAG-3 was differentially regulated throughout prolonged late-G1/early-S phase of the cell cycle. Our data may accelerate efficient identification of combination therapies to boost anti-tumor function of TIL specifically against tumor cells.

Flow Cytometric Analysis of Mononuclear Phagocytes in Nondiseased Human Lung and Lung-Draining Lymph Nodes

RATIONALE

The pulmonary mononuclear phagocyte system is a critical host defense mechanism composed of macrophages, monocytes, monocyte-derived cells, and dendritic cells. However, our current characterization of these cells is limited because it is derived largely from animal studies and analysis of human mononuclear phagocytes from blood and small tissue resections around tumors.

OBJECTIVES

Phenotypic and morphologic characterization of mononuclear phagocytes that potentially access inhaled antigens in human lungs.

METHODS

We acquired and analyzed pulmonary mononuclear phagocytes from fully intact nondiseased human lungs (including the major blood vessels and draining lymph nodes) obtained en bloc from 72 individual donors. Differential labeling of hematopoietic cells via intrabronchial and intravenous administration of antibodies within the same lobe was used to identify extravascular tissue-resident mononuclear phagocytes and exclude cells within the vascular lumen. Multiparameter flow cytometry was used to identify mononuclear phagocyte populations among cells labeled by each route of antibody delivery.

MEASUREMENTS AND MAIN RESULTS

We performed a phenotypic analysis of pulmonary mononuclear phagocytes isolated from whole nondiseased human lungs and lung-draining lymph nodes. Five pulmonary mononuclear phagocytes were observed, including macrophages, monocyte-derived cells, and dendritic cells that were phenotypically distinct from cell populations found in blood.

CONCLUSIONS

Different mononuclear phagocytes, particularly dendritic cells, were labeled by intravascular and intrabronchial antibody delivery, countering the notion that tissue and blood mononuclear phagocytes are equivalent systems. Phenotypic descriptions of the mononuclear phagocytes in nondiseased lungs provide a precedent for comparative studies in diseased lungs and potential targets for therapeutics.

Abstract B55: Suppression of CD8 T-cell activation by tryptophan catabolism in triple-negative breast cancer

Background: The ability of cancer cells to evade and suppress an antitumor immune response is increasingly recognized as a critical feature of aggressive, metastatic disease. Conversion of the amino acid tryptophan (trp) into the catabolite kynurenine (kyn) and the subsequent secretion of kyn is a current area of interest in the field of antitumor immunity, given that trp depletion is a trigger for T-cell death, and that kyn binds to and activates the aryl-hydrocarbon receptor (AhR) in immune cells, often with immunosuppressive consequences. In a screen to identify mechanisms promoting survival of triple-negative breast cancer (TNBC) cells in transit during the metastatic cascade, our lab discovered that trp-to-kyn catabolism is significantly increased by TNBC cells in forced-suspension culture due to upregulation of the gene encoding the rate-limiting trp-catabolizing enzyme tryptophan 2,3-dioxygenase (TDO2).

Hypothesis: In addition to promoting survival of TNBC cells during metastasis, TDO2-dependent trp-to-kyn catabolism may facilitate tumor-mediated immune suppression, further contributing to the aggressive nature of this breast cancer subtype.

Methods: TNBC cell lines were plated in adherent or forced-suspension culture for 24 hours, using poly (2-hydroxyethyl methacrylate)-coated plates to prevent adhesion. TDO2 mRNA (using quantitative PCR) and protein (immunoblotting) were measured in adherent versus suspended cells. Secreted kyn was measured using liquid chromatography-mass spectrometry and inhibited with a selective TDO2 inhibitor, 680C91. To test the effect of kyn on CD8 T-cell function, primary human CD8 T-cells were isolated from the blood of healthy human donors using a positive selection kit. T-cell proliferation was measured by dilution of the cell-permeable dye carboxyfluorescein succinimidyl ester and T-cell death was measured by incorporation of a fixable viability dye. Flow cytometry was used to measure both surface and intracellular T-cell proteins.

Results: The rate limiting enzyme TDO2 was upregulated in BT549 cells in suspension by 20.1-fold at the mRNA level and 5.4-fold at the protein level. Secreted kyn increased by 2.4-fold in suspension culture (0.46 μM secreted kyn by adherent cells, 1.09 μM kyn secreted by suspended cells, n=3 replicates), and this increase was reversed by addition of the TDO2 inhibitor 680C91 (p&lt;0.0001). Over the course of a five day CD3/CD28 activation, purified kyn reduced CD8 T-cell proliferation and increased CD8 T-cell death in a dose-dependent manner (n=6-9 donors, p&lt;0.05 at 25, 50, and 100 μM kyn), and these effects were partially reversed by the addition of an AhR antagonist (n=6 donors, p&lt;0.05 at 25 μM kyn). Kyn also reduced expression of granzyme B by live CD8 T-cells at high doses (n=4 donors, p=0.05 at 100 μM kyn), but did not alter expression of perforin or tumor necrosis factor alpha. Consistent with these results, culture of human CD8 T-cells in conditioned media from suspended BT549 cells over the course of a five day CD3/CD28 activation resulted in reduced proliferation and increased cell death in CD8 T-cells (n=6 donors, p&lt;0.05) compared to culture in conditioned media from adherent BT549 cells. Expression of the pro-inflammatory cytokine interferon gamma by CD8 T-cells cultured in conditioned media from suspended BT549 cells may also be reduced (n=4 donors, p=0.08).

Conclusions: Together, these results suggest a role for TNBC-mediated trp-to-kyn catabolism in suppressing cytotoxic T-cells. Further in vivo studies will indicate whether TDO2 activity might be a rational therapeutic target for improving antitumor immunity in patients with this aggressive subtype of breast cancer.

Citation Format: Lisa I. Greene, Tullia C. Bruno, Thomas J. Rogers, Jill E. Slansky, Virginia F. Borges, Jennifer K. Richer. Suppression of CD8 T-cell activation by tryptophan catabolism in triple-negative breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr B55.

Abstract A57: Determine a transcriptional mechanism novel to tumor infiltrating T cell dysfunction

This abstract is being presented as a short talk in the scientific program. A full abstract is printed in the Proffered Abstracts section (PR03) of the Conference Proceedings.

Citation Format: Katherine A. Waugh, Sonia Leach, Jill E. Slansky. Determine a transcriptional mechanism novel to tumor infiltrating T cell dysfunction. [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy: A New Chapter; December 1-4, 2014; Orlando, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2015;3(10 Suppl):Abstract nr A57.

Targeting Transcriptional Regulators of CD8+ T Cell Dysfunction to Boost Anti-Tumor Immunity

Transcription is a dynamic process influenced by the cellular environment: healthy, transformed, and otherwise. Genome-wide mRNA expression profiles reflect the collective impact of pathways modulating cell function under different conditions. In this review we focus on the transcriptional pathways that control tumor infiltrating CD8+ T cell (TIL) function. Simultaneous restraint of overlapping inhibitory pathways may confer TIL resistance to multiple mechanisms of suppression traditionally referred to as exhaustion, tolerance, or anergy. Although decades of work have laid a solid foundation of altered transcriptional networks underlying various subsets of hypofunctional or “dysfunctional” CD8+ T cells, an understanding of the relevance in TIL has just begun. With recent technological advances, it is now feasible to further elucidate and utilize these pathways in immunotherapy platforms that seek to increase TIL function.

Abstract 4064: Targeting the anti-tumor function of B cells in non-small cell lung cancer patient tumors

Despite improvements in surgical techniques and combined chemotherapies, the 5-year survival rate for all stages of non-small cell lung cancer (NSCLC) is only 18%. Understanding the function of tumor infiltrating lymphocytes (TILs) in NSCLC patient tumors will contribute to the development of rationally designed treatments and improved statistics. B cells in tumors (TIL-Bs) are detected in NSCLC and their frequency correlates with improved survival, however, they are understudied in human tumors. We hypothesize that TIL-Bs help generate potent, long-term immune responses against cancer.

We used un-manipulated, primary human B cells from fresh tumor, tumor-adjacent, and normal (cancer-free) lung tissue. We performed a comprehensive flow cytometric analysis of all TILs in NSCLC: CD4 and CD8 TILs, T regulatory cells, TIL-Bs, NK and NKT cells. We further examined the phenotype of TIL-Bs by analyzing markers of lymphocyte activation (anti-tumor; CD69, CD86, HLA-DR, CD27) and exhaustion (pro-tumor; CD95, CD21, PD-1, PD-L1). We developed an in vitro antigen presentation assay that analyzed if TIL-Bs present tumor-specific antigens to CD4 TILs to help stimulate an anti-tumor response in NSCLC patient tumors.

The total number of B cells at the site of the tumor versus the tumor-adjacent tissue was increased compared to other immune subsets. In analyzing the markers of activation and exhaustion, we observed a spectrum of activation of TIL-Bs. Further, we observed that TIL-Bs present autologous tumor antigens to CD4 TILs in a subset of NSCLC patients. These data suggest that some patients have functional TIL-Bs and some patients have nonfunctional TIL-Bs. XAGE-1b is an immunogenic, lung cancer-specific antigen that generates CD4 and CD8 T cell responses in lung cancer patients. It was overexpressed in the tumor cells of our NSCLC patients, and we demonstrated that some TIL-Bs could present recombinant XAGE-1b antigen to CD4 TILs. The TIL-Bs that could not present tumor-specific antigens had higher expression of B cell exhaustion markers on the cell surface. Further, because PD-1 expression is increased on CD4 TILs in our NSCLC patients, we are combining blockade of the immune inhibitory PD-1:PD-L1 pathway in our antigen presentation assays.

In conclusion, the anti-tumor function of TIL-Bs can be stimulated in some NSCLC patients, and TIL-Bs that cannot be stimulated have increased immune exhaustion. Ultimately, results from this study will advance the understanding of the anti-tumor function of TIL-Bs in solid tumors and will help develop a model of B cell exhaustion in human cancer. It will also help predict which TIL-B functions to target in future TIL-B-specific immunotherapies or in combination with current successful immunotherapies for NSCLC patients like blockade of the immune inhibitory PD-1:PD-L1 pathway.

Citation Format: Tullia Carmela Bruno, Brandon L. Moore, Daniel J. Munson, Peggy Ebner, Jeffrey Kern, Jill E. Slansky. Targeting the anti-tumor function of B cells in non-small cell lung cancer patient tumors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4064. doi:10.1158/1538-7445.AM2015-4064

Mimotope vaccine efficacy gets a "boost" from native tumor antigens

Tumor-associated antigen (TAA)-targeting mimotope peptides exert more prominent immunostimulatory functions than unmodified TAAs, with the caveat that some T-cell clones exhibit a relatively low affinity for TAAs. Combining mimotope-based vaccines with native TAAs in a prime-boost setting significantly improves antitumor immunity.

Abstract A11: The function of B cells in non-small cell lung cancer patients

Lung cancer is the leading cause of cancer death in both men and women. Although novel therapies are emerging, we are interested in boosting tumor-specific immune responses in infiltrating lymphocytes. In a flow cytometric analysis of the immune infiltrate in non-small cell lung cancer (NSCLC) tumors (n=25), we found that the total number of infiltrating B cells (TIL-Bs) in the tumor versus the matched tumor-adjacent tissue was increased compared to other immune subsets, specifically T cells. Most NSCLC TIL-Bs were activated (CD69+ and CD86+) and had a memory phenotype (CD27+). Proliferation, antigen presentation, and antibody production studies were done to assess the range of function in TIL-Bs. Positively isolated TIL-Bs that were stimulated for three days through the antigen receptor had varied proliferation when compared to B cells from the tumor adjacent tissue, which suggests a spectrum of function in TIL-Bs at the site of the tumor. For antigen presentation, TIL-Bs stimulated CD4 tumor infiltrating lymphocytes (CD4 TILs) to proliferate without the addition of tumor lysate compared to the negative and positive controls (T cells alone and T cells activated through the T cell receptor, respectively). This suggests that TIL-Bs can present endogenous tumor antigens to CD4 TILs; however, antigen presentation is not as robust with TIL-Bs from other patient tumors, which is another example of a spectrum in TIL-B function. Finally, we assayed total antibody production (IgG) by TIL-Bs to determine if this is a function at the site of the tumor. Tumor and tumor adjacent B cells produce antibody in comparison to B cells from the periphery of a normal donor; this function is uniform unlike proliferation and antigen presentation. We predict that TIL-Bs have a range of function in their response against tumors. Our overall hypothesis is that tumor immunity in NSCLC is influenced by the molecular signature of TIL-Bs, which directs proliferation, presentation of tumor antigens to T cells, and production of anti-tumor antibodies. We are determining if proliferation, antigen presentation, and antibody production are tumor antigen-specific, particularly for the lung cancer-testis antigen XAGE-1b. This antigen was the most highly expressed in our patient tumor cells when analyzed by real time PCR and has been shown to play a role in NSCLC. We are performing experiments with TIL-Bs to test XAGE-1b specific proliferation and antigen presentation. Further, we generated a XAGE-1b ELISA to test the specificity of the antibodies generated by the TIL-Bs. Three out of twelve patient sera were positive for XAGE-1b-specific antibodies indicating that the XAGE-1b ELISA is working for the detection of XAGE-1b antibodies. Further, we are isolating cells from tumor, tumor adjacent, and normal (cancer-free) lung tissue to analyze the molecular signature of TIL-Bs to identify a pathway upstream of B cell signaling that may be altered and influencing TIL-B function. Results from this study will advance the understanding of the function of TIL-Bs in solid tumors, and which functions can be targeted. Ultimately, this project will provide a platform for a therapeutic vaccine for lung cancer patients, and more importantly, will help us understand why some patients do not respond well to immunotherapy. Such results may lead to the development of a prognostic tool to screen patients that will respond to vaccine.

Citation Format: Tullia C. Bruno, Daniel Munson, Brandon Moore, Katherine Waugh, Jeffrey Kern, Jill E. Slansky. The function of B cells in non-small cell lung cancer patients. [abstract]. In: Proceedings of the AACR-IASLC Joint Conference on Molecular Origins of Lung Cancer; 2014 Jan 6-9; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2014;20(2Suppl):Abstract nr A11.

Improving antigenic peptide vaccines for cancer immunotherapy using a dominant tumor-specific T cell receptor

Vaccines that incorporate peptide mimics of tumor antigens, or mimotope vaccines, are commonly used in cancer immunotherapy and function by eliciting increased numbers of T cells that cross-react with the native tumor antigen. Unfortunately, they often elicit T cells that do not cross-react with or that have low affinity for the tumor antigen. Using a high affinity tumor-specific T cell clone, we identified a panel of mimotope vaccines for the dominant peptide antigen from a mouse colon tumor that elicits a range of tumor protection following vaccination. The TCR from this high affinity T cell clone was rarely identified in ex vivo evaluation of tumor-specific T cells elicited by mimotope vaccination. Conversely, a low affinity clone found in the tumor and following immunization was frequently identified. Using peptide libraries, we determined if this frequently identified TCR improved the discovery of efficacious mimotopes. We demonstrated that the representative TCR identified more protective mimotopes than the high affinity TCR. These results suggest that targeting a dominant fraction of tumor-specific T cells generates potent immunity and that consideration of the available T cell repertoire is necessary for targeted T cell therapy. These results have important implications when optimizing mimotope vaccines for cancer immunotherapy.

Influence of human immune cells on cancer: studies at the University of Colorado

There will be over half a million cancer-related deaths in the United States in 2012, with lung cancer being the leader followed by prostate in men and breast in women. There is estimated to be more than one and a half million new cases of cancer in 2012, making the development of effective therapies a high priority. As tumor immunologists, we are interested in the development of immunotherapies because the immune response offers exquisite specificity and the potential to target tumor cells without harming normal cells. In this review, we highlight the current advances in the field of immunotherapy and the current work being completed by laboratories at University of Colorado School of Medicine in multiple malignancies, including breast cancer, lung cancer, melanoma, thyroid cancer, and glioblastoma. This work focuses on augmenting the anti-tumor response of CD8 T cells in the blood, lymph nodes, and tumors of patients, determining biomarkers for patients who are more likely to respond to immunotherapy, and identifying additional anti-tumor and immunosuppressive cells that influence the overall response to tumors. These collaborative efforts will identify mechanisms to improve immune function, which may elucidate therapeutic targets for clinical trials to improve patient health and survival.

Improving T cell responses to modified peptides in tumor vaccines

Immune recognition and elimination of cancerous cells is the primary goal of cancer immunotherapy. However, obstacles including immune tolerance and tumor-induced immunosuppression often limit beneficial immune responses. Vaccination is one proposed intervention that may help to overcome these issues and is an active area of study in cancer immunotherapy. Immunizing with tumor antigenic peptides is a promising, straight-forward vaccine strategy hypothesized to boost preexisting antitumor immunity. However, tumor antigens are often weak T cell agonists, attributable to several mechanisms, including immune self-tolerance and poor immunogenicity of self-derived tumor peptides. One strategy for overcoming these mechanisms is vaccination with mimotopes, or peptide mimics of tumor antigens, which alter the antigen presentation and/or T cell activation to increase the expansion of tumor-specific T cells. Evaluation of mimotope vaccine strategies has revealed that even subtle alterations in peptide sequence can dramatically alter antigen presentation and T cell receptor recognition. Most of this research has been performed using T cell clones, which may not be accurate representations of the naturally occurring antitumor response. The relationship between clones generated after mimotope vaccination and the polyclonal T cell repertoire is unclear. Our work with mimotopes in a mouse model of colon carcinoma has revealed important insights into these issues. We propose that the identification of mimotopes based on stimulation of the naturally responding T cell repertoire will dramatically improve the efficacy of mimotope vaccination.

Abstract B39: Activated B cells infiltrate lung cancer

Lung cancer is the leading cause of cancer death in men and women, both in the United States and the world. The current 5-year survival rate for lung cancer in the United States is 16%, which can be attributed to the fact that the majority of lung cancer subjects present with late-stage disease that is not curable by current therapies i.e. chemotherapy and radiation. However, in the last several years, novel therapies have emerged to make lung cancer therapy better tolerated and more effective. We are particularly interested in developing an immunotherapy that will help to engage the immune system in targeting and destroying tumor cells. In a comprehensive survey of the immune infiltrate in non-small cell lung cancer (NSCLC) patients, we found that the frequency and total numbers of B cells (TIL-Bs) in the tumor versus the tumor-adjacent tissue was increased in comparison to other immune subsets, specifically, CD4, CD8, and regulatory T cells as well as NK and NKT cells. Further, these TIL-Bs were activated (CD21lo and CD69+), proliferated, and acquired a memory phenotype (CD27+). To test the function of the TIL-Bs, we are determining the types of cytokines they produce, their ability to secrete total IgG, and their potential to present antigen to CD4 T cells. Preliminary studies indicate that these cells generate activation cytokines (IFN-γ and IL-12) rather than suppressive cytokines, which suggests that the TIL-Bs have an effector phenotype that could aid in targeting the tumor. In addition, we are exploring why the TIL-Bs migrate to the site of the tumor. Preliminary data suggest that the common B cell chemokine receptors (CXCR3, CXCR4, CXCR5, CXCR7) are not elevated in TIL-Bs in the tumor compared to tumor adjacent tissue. However, normal peripheral blood B cells migrate toward tumor cell supernatant compared to tumor adjacent cell supernatant, which leads to the hypothesis that the tumor microenvironment generates more chemokines that attract TIL-Bs to the site of the tumor. Ultimately, we aim to identify a novel target for an immunotherapy clinical trial in lung cancer patients.

Citation Format: Tullia C. Bruno, Jeffrey Kern, Jill E. Slansky. Activated B cells infiltrate lung cancer. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology: Multidisciplinary Science Driving Basic and Clinical Advances; Dec 2-5, 2012; Miami, FL. Philadelphia (PA): AACR; Cancer Res 2013;73(1 Suppl):Abstract nr B39.

Augmenting antitumor T-cell responses to mimotope vaccination by boosting with native tumor antigens

Vaccination with antigens expressed by tumors is one strategy for stimulating enhanced T-cell responses against tumors. However, these peptide vaccines rarely result in efficient expansion of tumor-specific T cells or responses that protect against tumor growth. Mimotopes, or peptide mimics of tumor antigens, elicit increased numbers of T cells that crossreact with the native tumor antigen, resulting in potent antitumor responses. Unfortunately, mimotopes may also elicit cells that do not crossreact or have low affinity for tumor antigen. We previously showed that one such mimotope of the dominant MHC class I tumor antigen of a mouse colon carcinoma cell line stimulates a tumor-specific T-cell clone and elicits antigen-specific cells in vivo, yet protects poorly against tumor growth. We hypothesized that boosting the mimotope vaccine with the native tumor antigen would focus the T-cell response elicited by the mimotope toward high affinity, tumor-specific T cells. We show that priming T cells with the mimotope, followed by a native tumor-antigen boost, improves tumor immunity compared with T cells elicited by the same prime with a mimotope boost. Our data suggest that the improved tumor immunity results from the expansion of mimotope-elicited tumor-specific T cells that have increased avidity for the tumor antigen. The enhanced T cells are phenotypically distinct and enriched for T-cell receptors previously correlated with improved antitumor immunity. These results suggest that incorporation of native antigen into clinical mimotope vaccine regimens may improve the efficacy of antitumor T-cell responses.

Multiple associations between a broad spectrum of autoimmune diseases, chronic inflammatory diseases and cancer

BACKGROUND

Many recent studies suggest the immune system plays a significant role in the pathogenesis of autoimmune diseases, chronic inflammatory diseases, and cancer.

MATERIALS AND METHODS

Literature published between 2001 and 2011 was reviewed for risk of cancer development in patients with autoimmune and chronic inflammatory diseases. Mode of risk assessment employed did not limit inclusion of studies. Autoimmune conditions developing after diagnosis of a pre-existing cancer were also considered.

RESULTS

We report a pervasive, largely positive association between 23 autoimmune and inflammatory diseases and subsequent cancer development. We discuss associations for celiac disease, inflammatory bowel disease rheumatoid arthritis, systemic lupus erythematosus, and multiple sclerosis in detail. We also address the less frequently reported development of some autoimmune conditions within the course of some malignancies, such as vitiligo developing in the course of melanoma.

CONCLUSION

Evidence demonstrates that chronic inflammation and autoimmunity are associated with the development of malignancy. Additionally, patients with a primary malignancy may develop autoimmune like disease. These relationships imply a need for surveillance of patients on immunomodulatory therapies for potential secondary disease processes.

TCR hypervariable regions expressed by T cells that respond to effective tumor vaccines

A major goal of immunotherapy for cancer is the activation of T cell responses against tumor-associated antigens (TAAs). One important strategy for improving antitumor immunity is vaccination with peptide variants of TAAs. Understanding the mechanisms underlying the expansion of T cells that respond to the native tumor antigen is an important step in developing effective peptide-variant vaccines. Using an immunogenic mouse colon cancer model, we compare the binding properties and the TCR genes expressed by T cells elicited by peptide variants that elicit variable antitumor immunity directly ex vivo. The steady-state affinity of the natural tumor antigen for the T cells responding to effective peptide vaccines was higher relative to ineffective peptides, consistent with their improved function. Ex vivo analysis showed that T cells responding to the effective peptides expressed a CDR3β motif, which was also shared by T cells responding to the natural antigen and not those responding to the less effective peptide vaccines. Importantly, these data demonstrate that peptide vaccines can expand T cells that naturally respond to tumor antigens, resulting in more effective antitumor immunity. Future immunotherapies may require similar stringent analysis of the responding T cells to select optimal peptides as vaccine candidates.

Abstract A5: Characterizing and targeting B cells in lung cancer patients

Lung cancer is the leading cause of cancer death in men and women, both in the United States and the world. The current 5-year survival rate for lung cancer in the United States for all races is a discouraging 16% and has not changed dramatically during the past 30 years. The biggest reason for the discouraging survival statistics is that the majority of lung cancer subjects present with late-stage disease that is not curable by current therapies i.e. chemotherapy and radiation. However, in the last several years novel therapies have emerged to make lung cancer therapy better tolerated and more effective. As tumor immunologists, we are particularly interested in developing an immunotherapy that will help to engage the immune system in targeting and destroying tumor cells. In a comprehensive survey of the immune infiltrate in non-small cell lung cancer (NSCLC) patients, we discovered that the frequency of the B cell infiltrate in the tumor versus the normal tumor-adjacent tissue was significantly increased in comparison to other immune subsets, specifically, CD4, CD8, and regulatory T cells as well as NK and NKT cells. Further preliminary studies on the characterization of these B cells suggest that they have proliferated and acquired a memory phenotype. We will continue to characterize the B cells in the tumor microenvironment to determine if they are activated as well as functional. If the B cells in the tumor microenvironment are activated, we will test if the cells are responsive to antigens currently in clinical trial like MUC-1 as well as new antigens in the cancer-testis classification like XAGE-1b. We will test if the antigens are stimulating the B cells through the BCR and if these antigens will be presented to CD4 T cells in vitro, which would lead to the stimulation of the CD4 T cells. If the B cells are not activated, we will then query whether or not the B cells could have a suppressive phenotype, which will be determined by assaying the types of cytokines produced by the B cells using a cytokine array. As we continue to further characterize the B cells, we will also continue to monitor the various immune subsets in the three subtypes of NSCLC: adenocarcinoma, squamous cell carcinoma and large cell carcinoma. This immunophenotyping of the immune subsets will aid us in the identification of the appropriate immune cell populations to target for immunotherapy in the three subtypes of NSCLC. Ultimately, we aim to identify a novel target for an immunotherapy clinical trial in lung cancer patients.

Elevated tumor-associated antigen expression suppresses variant peptide vaccine responses

Variant peptide vaccines are used clinically to expand T cells that cross-react with tumor-associated Ags (TAA). To investigate the effects of elevated endogenous TAA expression on variant peptide-induced responses, we used the GP70 TAA model. Although young BALB/c mice display T cell tolerance to the TAA GP70(423-431) (AH1), expression of GP70 and suppression of AH1-specific responses increases with age. We hypothesized that as TAA expression increases, the AH1 cross-reactivity of variant peptide-elicited T cell responses diminishes. Controlling for immunosenescence, we showed that elevated GP70 expression suppressed AH1 cross-reactive responses elicited by two AH1 peptide variants. A variant that elicited almost exclusively AH1 cross-reactive T cells in young mice elicited few or no T cells in aging mice with Ab-detectable GP70 expression. In contrast, a variant that elicited a less AH1 cross-reactive T cell response in young mice successfully expanded AH1 cross-reactive T cells in all aging mice tested. However, these T cells bound the AH1/MHC complex with a relatively short half-life and responded poorly to ex vivo stimulation with the AH1 peptide. Variant peptide vaccine responses were also suppressed when AH1 peptide is administered tolerogenically to young mice before vaccination. Analyses of variant-specific precursor T cells from naive mice with Ab-detectable GP70 expression determined that these T cells expressed PD-1 and had downregulated IL-7Rα expression, suggesting they were anergic or undergoing deletion. Although variant peptide vaccines were less effective as TAA expression increases, data presented in this article also suggest that complementary immunotherapies may induce the expansion of T cells with functional TAA recognition.

Gene expression profiling identifies inflammation and angiogenesis as distinguishing features of canine hemangiosarcoma

Background

The etiology of hemangiosarcoma remains incompletely understood. Its common occurrence in dogs suggests predisposing factors favor its development in this species. These factors could represent a constellation of heritable characteristics that promote transformation events and/or facilitate the establishment of a microenvironment that is conducive for survival of malignant blood vessel-forming cells. The hypothesis for this study was that characteristic molecular features distinguish hemangiosarcoma from non-malignant endothelial cells, and that such features are informative for the etiology of this disease.

Methods

We first investigated mutations of VHL and Ras family genes that might drive hemangiosarcoma by sequencing tumor DNA and mRNA (cDNA). Protein expression was examined using immunostaining. Next, we evaluated genome-wide gene expression profiling using the Affymetrix Canine 2.0 platform as a global approach to test the hypothesis. Data were evaluated using routine bioinformatics and validation was done using quantitative real time RT-PCR.

Results

Each of 10 tumor and four non-tumor samples analyzed had wild type sequences for these genes. At the genome wide level, hemangiosarcoma cells clustered separately from non-malignant endothelial cells based on a robust signature that included genes involved in inflammation, angiogenesis, adhesion, invasion, metabolism, cell cycle, signaling, and patterning. This signature did not simply reflect a cancer-associated angiogenic phenotype, as it also distinguished hemangiosarcoma from non-endothelial, moderately to highly angiogenic bone marrow-derived tumors (lymphoma, leukemia, osteosarcoma).

Conclusions

The data show that inflammation and angiogenesis are important processes in the pathogenesis of vascular tumors, but a definitive ontogeny of the cells that give rise to these tumors remains to be established. The data do not yet distinguish whether functional or ontogenetic plasticity creates this phenotype, although they suggest that cells which give rise to hemangiosarcoma modulate their microenvironment to promote tumor growth and survival. We propose that the frequent occurrence of canine hemangiosarcoma in defined dog breeds, as well as its similarity to homologous tumors in humans, offers unique models to solve the dilemma of stem cell plasticity and whether angiogenic endothelial cells and hematopoietic cells originate from a single cell or from distinct progenitor cells.

Vaccination of mice with baculovirus-infected insect cells expressing antigenic proteins

Methods to induce antigen-specific immune responses in mice using insect cells infected with recombinant baculoviruses are described in this unit. Although this vaccine strategy has been used to generate both antibody and T cell responses, it has been more thoroughly characterized for the peptide-specific cytotoxic T cell responses. Nonspecific responses to the vaccine vehicle are controlled for by vaccinating with insect cells infected with baculoviruses encoding irrelevant antigens or no antigen. The baculovirus-infected insect cells alone are an effective immune adjuvant to elicit antigen-specific T cells. Overall, immune responses generated using this approach are similar to those generated by more conventional vaccine strategies.

Vaccination with Mimotopes Prevents Tumor Growth by Enhancing the Activation of T cells that Respond to Natural Tumor Antigens (41.40)

Vaccination with mimotopes, or peptide mimics of self-tumor antigens, is a potential strategy for antigen-specific immunotherapy of cancer. We tested mimotopes with substitutions in residues involved in T cell interactions, rather than in conventional MHC-anchor residues, for protection against the transplantable tumor, CT26. Although vaccination with all of the mimotopes elicited tumor-specific T cells more effectively than the wild type tumor antigen, AH1, only some mimotopes prevented tumor growth. Vaccination with the protective mimotopes generated considerably more cross-reactive T cells that produced the cytokine IFNgamma after stimulation with lower concentrations of the AH1 peptide. These T cells expressed TCR molecules with a more restricted Vbeta repertoire ex vivo, but were similar in CDR3 sequence to the T cells generated by vaccination with the AH1 peptide. Importantly, the T cells responding to the non-effective mimotopes did not inhibit the antitumor responses of the protective mimotopes. These results suggest that protective mimotopes generate antitumor immunity, in part, by enhancing the activation and differentiation of a subset of T cells that naturally respond to the tumor, not a new repertoire of T cells only elicited by the mimotope.

Monitoring antigen-specific T cells using MHC-Ig dimers

The lack of high affinity reagents has made distinguishing T cells on the basis of antigen specificity difficult to accomplish. This unit provides protocols that utilize innovations in molecular design to permit construction of soluble multivalent MHC complexes (MHC-Ig dimers) with high avidity for cognate T cell receptors. MHC-Ig dimers display stable binding properties when they interact with antigen-specific T cells thus allowing their use in the staining of antigen-specific T cells by flow cytometry. Methods for constructing and detecting these MHC-Ig dimers are included along with protocols for applying their use for the quantitation of antigen-specific T cells.

Baculovirus-infected insect cells expressing peptide-MHC complexes elicit protective antitumor immunity

Evaluation of T cell responses to tumor- and pathogen-derived peptides in preclinical models is necessary to define the characteristics of efficacious peptide vaccines. We show in this study that vaccination with insect cells infected with baculoviruses expressing MHC class I linked to tumor peptide mimotopes results in expansion of functional peptide-specific CD8+ T cells that protect mice from tumor challenge. Specific peptide mimotopes selected from peptide-MHC libraries encoded by baculoviruses can be tested using this vaccine approach. Unlike other vaccine strategies, this vaccine has the following advantages: peptides that are difficult to solublize can be easily characterized, bona fide peptides without synthesis artifacts are presented, and additional adjuvants are not required to generate peptide-specific responses. Priming of antitumor responses occurs within 3 days of vaccination and is optimal 1 wk after a second injection. After vaccination, the Ag-specific T cell response is similar in animals primed with either soluble or membrane-bound Ag, and CD11c+ dendritic cells increase expression of maturation markers and stimulate proliferation of specific T cells ex vivo. Thus, the mechanism of Ag presentation induced by this vaccine is consistent with cross-priming by dendritic cells. This straightforward approach will facilitate future analyses of T cells elicited by peptide mimotopes.

Live attenuated Listeria monocytogenes effectively treats hepatic colorectal cancer metastases and is strongly enhanced by depletion of regulatory T cells

The liver represents a major and frequently sole site of metastases for many types of cancer, particularly gastrointestinal cancers. We showed previously that coadministration of an engineered hepatic-targeting Listeria monocytogenes (LM) with a cancer vaccine enhanced the antitumor effect of vaccine-induced T cells selectively against hepatic metastases. Here, we show that administration of multiple doses of LM, in the absence of vaccine, generates therapeutic responses against hepatic metastases. LM treatment of mice bearing hepatic metastases induced tumor-specific CD8+ T-cell responses that were enhanced by depletion of regulatory T (Treg) cells by either anti-CD25 or cyclophosphamide treatment. Antitumor activity of LM further depended on natural killer (NK) cell activation but was inhibited by presence of a subset of NK T cells. These results show the utility of LM in the treatment of hepatic metastases even in the absence of vaccine administration and further suggest that blockade of Treg cells and NK T cells will enhance antitumor activity.