TIM-3+ CD8 T cells with a terminally exhausted phenotype retain functional capacity in hematological malignancies

Chronic antigen stimulation is thought to generate dysfunctional CD8 T cells. Here, we identify a CD8 T cell subset in the bone marrow tumor microenvironment that, despite an apparent terminally exhausted phenotype (TPHEX), expressed granzymes, perforin, and IFN-γ. Concurrent gene expression and DNA accessibility revealed that genes encoding these functional proteins correlated with BATF expression and motif accessibility. IFN-γ+ TPHEX effectively killed myeloma with comparable efficacy to transitory effectors, and disease progression correlated with numerical deficits in IFN-γ+ TPHEX. We also observed IFN-γ+ TPHEX within CD19-targeted chimeric antigen receptor T cells, which killed CD19+ leukemia cells. An IFN-γ+ TPHEX gene signature was recapitulated in TEX cells from human cancers, including myeloma and lymphoma. Here, we characterize a TEX subset in hematological malignancies that paradoxically retains function and is distinct from dysfunctional TEX found in chronic viral infections. Thus, IFN-γ+ TPHEX represent a potential target for immunotherapy of blood cancers.

IL-6-mediated endothelial injury impairs antiviral humoral immunity after bone marrow transplantation

Endothelial function and integrity are compromised after allogeneic bone marrow transplantation (BMT), but how this affects immune responses broadly remains unknown. Using a preclinical model of CMV reactivation after BMT, we found compromised antiviral humoral responses induced by IL-6 signaling. IL-6 signaling in T cells maintained Th1 cells, resulting in sustained IFN-γ secretion, which promoted endothelial cell (EC) injury, loss of the neonatal Fc receptor (FcRn) responsible for IgG recycling, and rapid IgG loss. T cell-specific deletion of IL-6R led to persistence of recipient-derived, CMV-specific IgG and inhibited CMV reactivation. Deletion of IFN-γ in donor T cells also eliminated EC injury and FcRn loss. In a phase III clinical trial, blockade of IL-6R with tocilizumab promoted CMV-specific IgG persistence and significantly attenuated early HCMV reactivation. In sum, IL-6 invoked IFN-γ-dependent EC injury and consequent IgG loss, leading to CMV reactivation. Hence, cytokine inhibition represents a logical strategy to prevent endothelial injury, thereby preserving humoral immunity after immunotherapy.

Signaling via a CD27-TRAF2-SHP-1 axis during naive T cell activation promotes memory-associated gene regulatory networks

The interaction of the tumor necrosis factor receptor (TNFR) family member CD27 on naive CD8+ T (Tn) cells with homotrimeric CD70 on antigen-presenting cells (APCs) is necessary for T cell memory fate determination. Here, we examined CD27 signaling during Tn cell activation and differentiation. In conjunction with T cell receptor (TCR) stimulation, ligation of CD27 by a synthetic trimeric CD70 ligand triggered CD27 internalization and degradation, suggesting active regulation of this signaling axis. Internalized CD27 recruited the signaling adaptor TRAF2 and the phosphatase SHP-1, thereby modulating TCR and CD28 signals. CD27-mediated modulation of TCR signals promoted transcription factor circuits that induced memory rather than effector associated gene programs, which are induced by CD28 costimulation. CD27-costimulated chimeric antigen receptor (CAR)-engineered T cells exhibited improved tumor control compared with CD28-costimulated CAR-T cells. Thus, CD27 signaling during Tn cell activation promotes memory properties with relevance to T cell immunotherapy.

Cancer-Associated Fibroblast-Like Tumor Cells Remodel the Ewing Sarcoma Tumor Microenvironment

PURPOSE

Despite limited genetic and histologic heterogeneity, Ewing sarcoma (EwS) tumor cells are transcriptionally heterogeneous and display varying degrees of mesenchymal lineage specification in vitro. In this study, we investigated if and how transcriptional heterogeneity of EwS cells contributes to heterogeneity of tumor phenotypes in vivo.

EXPERIMENTAL DESIGN

Single-cell proteogenomic-sequencing of EwS cell lines was performed and integrated with patient tumor transcriptomic data. Cell subpopulations were isolated by FACS for assessment of gene expression and phenotype. Digital spatial profiling and human whole transcriptome analysis interrogated transcriptomic heterogeneity in EwS xenografts. Tumor cell subpopulations and matrix protein deposition were evaluated in xenografts and patient tumors using multiplex immunofluorescence staining.

RESULTS

We identified CD73 as a biomarker of highly mesenchymal EwS cell subpopulations in tumor models and patient biopsies. CD73+ tumor cells displayed distinct transcriptional and phenotypic properties, including selective upregulation of genes that are repressed by EWS::FLI1, and increased migratory potential. CD73+ cells were distinguished in vitro and in vivo by increased expression of matrisomal genes and abundant deposition of extracellular matrix (ECM) proteins. In epithelial-derived malignancies, ECM is largely deposited by cancer-associated fibroblasts (CAF), and we thus labeled CD73+ EwS cells, CAF-like tumor cells. Marked heterogeneity of CD73+ EwS cell frequency and distribution was detected in tumors in situ, and CAF-like tumor cells and associated ECM were observed in peri-necrotic regions and invasive foci.

CONCLUSIONS

EwS tumor cells can adopt CAF-like properties, and these distinct cell subpopulations contribute to tumor heterogeneity by remodeling the tumor microenvironment. See related commentary by Kuo and Amatruda, p. 5002.

Carcinoma-associated fibroblast-like tumor cells remodel the Ewing sarcoma tumor microenvironment

Tumor heterogeneity is a major driver of cancer progression. In epithelial-derived malignancies, carcinoma-associated fibroblasts (CAFs) contribute to tumor heterogeneity by depositing extracellular matrix (ECM) proteins that dynamically remodel the tumor microenvironment (TME). Ewing sarcomas (EwS) are histologically monomorphous, mesenchyme-derived tumors that are devoid of CAFs. Here we identify a previously uncharacterized subpopulation of transcriptionally distinct EwS tumor cells that deposit pro-tumorigenic ECM. Single cell analyses revealed that these CAF-like cells differ from bulk EwS cells by their upregulation of a matrisome-rich gene signature that is normally repressed by EWS::FLI1, the oncogenic fusion transcription factor that underlies EwS pathogenesis. Further, our studies showed that ECM-depositing tumor cells express the cell surface marker CD73, allowing for their isolation ex vivo and detection in situ. Spatial profiling of tumor xenografts and patient biopsies demonstrated that CD73 ⁺ EwS cells and tumor cell-derived ECM are prevalent along tumor borders and invasive fronts. Importantly, despite loss of EWS::FLI1-mediated gene repression, CD73 ⁺ EwS cells retain expression of EWS::FLI1 and the fusion-activated gene signature, as well as tumorigenic and proliferative capacities. Thus, EwS tumor cells can be reprogrammed to adopt CAF-like properties and these transcriptionally and phenotypically distinct cell subpopulations contribute to tumor heterogeneity by remodeling the TME.

Depletion of exhausted alloreactive T cells enables targeting of stem-like memory T cells to generate tumor-specific immunity

Some hematological malignancies such as multiple myeloma are inherently resistant to immune-mediated antitumor responses, the cause of which remains unknown. Allogeneic bone marrow transplantation (alloBMT) is the only curative immunotherapy for hematological malignancies due to profound graft-versus-tumor (GVT) effects, but relapse remains the major cause of death. We developed murine models of alloBMT where the hematological malignancy is either sensitive [acute myeloid leukemia (AML)] or resistant (myeloma) to GVT effects. We found that CD8+ T cell exhaustion in bone marrow was primarily alloantigen-driven, with expression of inhibitory ligands present on myeloma but not AML. Because of this tumor-independent exhaustion signature, immune checkpoint inhibition (ICI) in myeloma exacerbated graft-versus-host disease (GVHD) without promoting GVT effects. Administration of post-transplant cyclophosphamide (PT-Cy) depleted donor T cells with an exhausted phenotype and spared T cells displaying a stem-like memory phenotype with chromatin accessibility present in cytokine signaling genes, including the interleukin-18 (IL-18) receptor. Whereas ICI with anti-PD-1 or anti-TIM-3 remained ineffective after PT-Cy, administration of a decoy-resistant IL-18 (DR-18) strongly enhanced GVT effects in both myeloma and leukemia models, without exacerbation of GVHD. We thus defined mechanisms of resistance to T cell-mediated antitumor effects after alloBMT and described an immunotherapy approach targeting stem-like memory T cells to enhance antitumor immunity.

Abstract 1360: CD8 T cells display distinct trajectories of T cell exhaustion in the bone marrow of mice with multiple myeloma

Multiple myeloma (MM) is the second most common hematological malignancy and despite the developments of novel therapies, it remains largely incurable. A minority of patients do achieve durable disease control after autologous stem cell transplantation (SCT), and we previously demonstrated the induction of profound T cell-mediated myeloma-specific immunity after SCT in preclinical models. Nonetheless, in both mice and patients, myeloma progression is associated with inhibitory receptor expression on CD8 T cells in the bone marrow (BM). Characterization of CD8 T cell exhaustion and the presence of precursor exhausted T cells (TPEX) has been limited to solid tumor models. Whether CD8 T cells exhibit the same trajectory of exhaustion from TPEX in the MM BM microenvironment after SCT was hitherto unknown. This is an important clinical question as immunotherapies are largely utilized in relapsed/refractory MM and currently do not target this patient population. We performed single cell RNA sequencing in mice with relapsed MM after SCT to provide in-depth characterization of CD8 T cell differentiation and exhaustion. CD8 T cells were sorted via flow cytometry based on CD38 and CD101 expression to capture diverse stages of differentiation. Notably, CD38+CD101+ CD8 T cells have been previously described as irreversibly exhausted and represent over 50% of polyclonal CD8 T cells in our model. We performed unsupervised clustering and identified ten CD8 T cell clusters that spanned T cell differentiation, including a TPEX population with a phenotype akin to solid tumor settings. We also observed two distinct exhausted T cell clusters that both expressed Tox, Pdcd1, and lacked Tcf7 while only one cluster expressed high levels of Prdm1 (Blimp-1), Havcr2 (TIM-3), Maf and Il10. Utilizing flow cytometry, we confirmed expression of TOX and PD-1, with loss of TCF-1, in mice with relapsed MM and expression of c-Maf was largely restricted to the TIM-3+ subset. We next sought to determine whether the exhausted clusters represented degrees of exhaustion or were distinct lineages. Thus, we performed RNA velocity analysis and noted a clear trajectory from the TPEX cluster towards the two exhausted clusters, confirming a common trajectory of CD8 T cell exhaustion states across solid and hematological malignancies. Surprisingly, there was a divergence point between the exhausted clusters suggesting that these could be distinct lineages. To address this, we performed bone marrow aspirates in mice from 3 weeks post-SCT to track exhaustion phenotypes over time in myeloma-bearing mice. We observed concurrent emergence of both exhausted T cell phenotypes from early post-SCT, supporting our hypothesis that these may represent distinct T cell exhaustion lineages. These data highlight a trajectory of CD8 T cell exhaustion from precursor subsets in MM that supports the utilization of immunotherapies in the early stages of disease.

Citation Format: Simone A. Minnie, Nicole S. Nemychenkov, Olivia G. Waltner, Kathleen S. Ensbey, Christine R. Schmidt, Shruti S. Bhise, Scott N. Furlan, Geoffrey R. Hill. CD8 T cells display distinct trajectories of T cell exhaustion in the bone marrow of mice with multiple myeloma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1360.