Autologous human preclinical modeling of melanoma interpatient clinical responses to immunotherapeutics

BACKGROUND

Despite recent advances in immunotherapy, a substantial population of late-stage melanoma patients still fail to achieve sustained clinical benefit. Lack of translational preclinical models continues to be a major challenge in the field of immunotherapy; thus, more optimized translational models could strongly influence clinical trial development. To address this unmet need, we designed a preclinical model reflecting the heterogeneity in melanoma patients' clinical responses that can be used to evaluate novel immunotherapies and synergistic combinatorial treatment strategies. Using our all-autologous humanized melanoma mouse model, we examined the efficacy of a novel engineered interleukin 2 (IL-2)-based cytokine variant immunotherapy.

METHODS

To study immune responses and antitumor efficacy for human melanoma tumors, we developed an all-autologous humanized melanoma mouse model using clinically annotated, matched patient tumor cells and peripheral blood mononuclear cells (PBMCs). After inoculating immunodeficient NSG mice with patient tumors and an adoptive cell transfer of autologous PBMCs, mice were treated with anti-PD-1, a novel investigational engineered IL-2-based cytokine (nemvaleukin), or recombinant human IL-2 (rhIL-2). The pharmacodynamic effects and antitumor efficacy of these treatments were then evaluated. We used tumor cells and autologous PBMCs from patients with varying immunotherapy responses to both model the diversity of immunotherapy efficacy observed in the clinical setting and to recapitulate the heterogeneous nature of melanoma.

RESULTS

Our model exhibited long-term survival of engrafted human PBMCs without developing graft-versus-host disease. Administration of an anti-PD-1 or nemvaleukin elicited antitumor responses in our model that were patient-specific and were found to parallel clinical responsiveness to checkpoint inhibitors. An evaluation of nemvaleukin-treated mice demonstrated increased tumor-infiltrating CD4+ and CD8+ T cells, preferential expansion of non-regulatory T cell subsets in the spleen, and significant delays in tumor growth compared with vehicle-treated controls or mice treated with rhIL-2.

CONCLUSIONS

Our model reproduces differential effects of immunotherapy in melanoma patients, capturing the inherent heterogeneity in clinical responses. Taken together, these data demonstrate our model's translatability for novel immunotherapies in melanoma patients. The data are also supportive for the continued clinical investigation of nemvaleukin as a novel immunotherapeutic for the treatment of melanoma.

A transcriptional evaluation of the melanoma and squamous cell carcinoma TIL compartment reveals an unexpected spectrum of exhausted and functional T cells

Introduction

Significant heterogeneity exists within the tumor-infiltrating CD8 T cell population, and exhausted T cells harbor a subpopulation that may be replicating and may retain signatures of activation, with potential functional consequences in tumor progression. Dysfunctional immunity in the tumor microenvironment is associated with poor cancer outcomes, making exploration of these exhausted T cell subpopulations critical to the improvement of therapeutic approaches.

Methods

To investigate mechanisms associated with terminally exhausted T cells, we sorted and performed transcriptional profiling of CD8+ tumor-infiltrating lymphocytes (TILs) co-expressing the exhaustion markers PD-1 and TIM-3 from large-volume melanoma tumors. We additionally performed immunologic phenotyping and functional validation, including at the single-cell level, to identify potential mechanisms that underlie their dysfunctional phenotype.

Results

We identified novel dysregulated pathways in CD8+PD-1+TIM-3+ cells that have not been well studied in TILs; these include bile acid and peroxisome pathway-related metabolism and mammalian target of rapamycin (mTOR) signaling pathways, which are highly correlated with immune checkpoint receptor expression.

Discussion

Based on bioinformatic integration of immunophenotypic data and network analysis, we propose unexpected targets for therapies to rescue the immune response to tumors in melanoma.

A high OXPHOS CD8 T cell subset is predictive of immunotherapy resistance in melanoma patients

Immune checkpoint inhibitor (ICI) therapy continues to revolutionize melanoma treatment, but only a subset of patients respond. Major efforts are underway to develop minimally invasive predictive assays of ICI response. Using single-cell transcriptomics, we discovered a unique CD8 T cell blood/tumor-shared subpopulation in melanoma patients with high levels of oxidative phosphorylation (OXPHOS), the ectonucleotidases CD38 and CD39, and both exhaustion and cytotoxicity markers. We called this population with high levels of OXPHOS “CD8⁺ T_OXPHOS cells.” We validated that higher levels of OXPHOS in tumor- and peripheral blood–derived CD8⁺ T_OXPHOS cells correlated with ICI resistance in melanoma patients. We then developed an ICI therapy response predictive model using a transcriptomic profile of CD8⁺ T_OXPHOS cells. This model is capable of discerning responders from nonresponders using either tumor or peripheral blood CD8 T cells with high accuracy in multiple validation cohorts. In sum, CD8⁺ T_OXPHOS cells represent a critical immune population to assess ICI response with the potential to be a new target to improve outcomes in melanoma patients.

MCL1 nuclear translocation induces chemoresistance in colorectal carcinoma

Colorectal cancer (CRC) is one of the most common and deadliest forms of cancer. Myeloid Cell Leukemia 1 (MCL1), a pro-survival member of the Bcl-2 protein family is associated with chemo-resistance in CRC. The ability of MCL1 to inhibit apoptosis by binding to the BH3 domains of pro-apoptotic Bcl-2 family members is a well-studied means by which this protein confers resistance to multiple anti-cancer therapies. We found that specific DNA damaging chemotherapies promote nuclear MCL1 translocation in CRC models. In p53null CRC, this process is associated with resistance to chemotherapeutic agents, the mechanism of which is distinct from the classical mitochondrial protection. We previously reported that MCL1 has a noncanonical chemoresistance capability, which requires a novel loop domain that is distinct from the BH3-binding domain associated with anti-apoptotic function. Herein we disclose that upon treatment with specific DNA-damaging chemotherapy, this loop domain binds directly to alpha-enolase which in turn binds to calmodulin; we further show these protein−protein interactions are critical in MCL1’s nuclear import and chemoresistance. We additionally observed that in chemotherapy-treated p53−/− CRC models, MCL1 nuclear translocation confers sensitivity to Bcl-xL inhibitors, which has significant translational relevance given the co-expression of these proteins in CRC patient samples. Together these findings indicate that chemotherapy-induced MCL1 translocation represents a novel resistance mechanism in CRC, while also exposing an inherent and targetable Bcl-xL co-dependency in these cancers. The combination of chemotherapy and Bcl-xL inhibitors may thus represent a rational means of treating p53−/− CRC via exploitation of this unique MCL1-based chemoresistance mechanism.

Notch activation in the mouse mammary luminal lineage leads to ductal hyperplasia and altered partitioning of luminal cell subtypes

Hyperactivated Notch signalling has been implicated in breast cancer, but how elevated levels of Notch signalling contribute to mammary dysplasia and tumorigenesis is not fully understood. In this study, we express an activated form of Notch1 in the mouse mammary luminal lineage and analyse the consequences for tumour formation and the transcriptomic landscape in the luminal lineage. Simultaneous conditional activation of a Notch1 intracellular domain (Notch1 ICD) and EGFP in the luminal lineage was achieved by removal of a stop cassette by CRE-recombinase expression from the whey acidic protein (WAP) promoter. Mice in which Notch1 ICD was activated in the luminal lineage (WAP-CRE;R26-N1ICD mice) exhibit ductal hyperplasia after lactation with an increase in branching frequency and in the number of side-branch ends in the ductal tree. A subset of the mice developed mammary tumours and the majority of the tumour cells expressed EGFP (as a proxy for Notch1 ICD), indicating that the tumours originate from the Notch1 ICD-expressing cells. Single-cell transcriptome analysis of the EGFP-positive mammary cells identified six subtypes of luminal cells. The same six subtypes were found in control mice (WAP-CRE;R26-tdTomato mice expressing the tdTomato reporter from WAP-CRE-mediated activation), but the proportion of cells in the various subtypes differed between the WAP-CRE;R26-N1ICD and control WAP-CRE;R26-tdTomato mice. In conclusion, we show that Notch1 ICD expression in the luminal lineage produces a ductal hyperplasia and branching phenotype accompanied by altered luminal cell subtype partitioning.

Role of glutamine metabolism in CD8+PD-1+TIM-3+ T cells in ICI resistant melanoma

e22055

Background: Immune checkpoint inhibitors (ICI) targeting checkpoints has achieved cures in half of stage IV melanoma patients yet there remains a critical need to identify why other half remain either ICI resistant or relapse. Recent studies show that multiple subpopulations of tumor-infiltrating CD8+PD-1+ T cells, previously known to be exhausted, are in fact metabolically active. We have identified a sub population of CD8+PD-1+ T cells resistant melanoma that are metabolically active, highly proliferative; and has high glutamine metabolic pathway. Rapidly proliferating cells utilize the glucose-lactic acid pathway for faster energy production and can metabolize glutamine for energy. A recent study showed that glutamine metabolism blockade improves immunotherapy response by enhancing cytotoxic T cell function. However, the role of glutamine in dysfunctional CD8+T cells has not be studied. Methods: Using patient-derived ICI resistant tumors (n = 8), tumor infiltrating lymphocytes (TILs) were isolated and sorted for total CD8+ T cells for single cell RNA sequencing, and then into CD8+PD-1+TIM-3+ T cells for bulk RNA analysis. FACS analysis was performed to assess the protein expression of SLC1A5 (a major glutamine transporter) and ki67. Seahorse Fuel Flex Test was employed to examine oxidative phosphorylation and mass spectrometry analysis was performed on sorted CD8+PD-1+TIM-3 TILs to assess the glutamine and lactic acid content. Results: A volcanic plot from bulk RNAseq data demonstrated an increase in glutamine pathway activity as well as the expression of SLC1A5 in CD8+PD-1+TIM3+ T cells compared to the peripheral CD8+ T cells. Similarly, scRNAseq analysis showed an increased expression of ki67 and SLC1A5 in MAD CD8+ T cells compared to the effector and naïve CD8+ T cells. FACS analysis of TILs gated for CD3+CD8+,showed an increased protein expression of SLC1A5 and ki67 in the PD-1+TIM-3+ population. A seahorse assay using sorted CD8+PD-1+ TIM3+ TILs from human samples confirmed an increased oxidative consumption rate (OCR) and increased dependency of glutamine metabolism in MAD CD8+ T cells compared to healthy CD8+ T cells. Importantly, mass spectrometry of CD8+PD-1+ TIM3+ T cells showed a significant increase in glutamine and lactate supporting our hypothesis that MAD CD8+ T cells have increased glutamine metabolism due to anaerobic glycolysis. Conclusions: Glutamine is a major metabolic source for rapidly proliferating CD8+PD-1+TIM-3+ dysfunctional T cells and inhibition of glutamine metabolism can be leveraged as immunotherapy in ICI resistant melanoma.

Loss of CSL Unlocks a Hypoxic Response and Enhanced Tumor Growth Potential in Breast Cancer Cells

Notch signaling is an important regulator of stem cell differentiation. All canonical Notch signaling is transmitted through the DNA-binding protein CSL, and hyperactivated Notch signaling is associated with tumor development; thus it may be anticipated that CSL deficiency should reduce tumor growth. In contrast, we report that genetic removal of CSL in breast tumor cells caused accelerated growth of xenografted tumors. Loss of CSL unleashed a hypoxic response during normoxic conditions, manifested by stabilization of the HIF1α protein and acquisition of a polyploid giant-cell, cancer stem cell-like, phenotype. At the transcriptome level, loss of CSL upregulated more than 1,750 genes and less than 3% of those genes were part of the Notch transcriptional signature. Collectively, this suggests that CSL exerts functions beyond serving as the central node in the Notch signaling cascade and reveals a role for CSL in tumorigenesis and regulation of the cellular hypoxic response.

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Loss of CSL accelerates tumor growth

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CSL deficiency unleashes a hypoxic response during normoxia

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Loss of CSL leads to a polyploid giant-cell, cancer stem cell-like morphology

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CSL-deficient cells show a Notch-independent transcriptional signature

Wnt-C59 arrests stemness and suppresses growth of nasopharyngeal carcinoma in mice by inhibiting the Wnt pathway in the tumor microenvironment

Wnt/β-catenin signaling is responsible for the generation of cancer stem cells (CSCs) in many human tumors, including nasopharyngeal carcinoma (NPC). Recent studies demonstrate that Wnt or PORCN inhibitor, Wnt-C59, inhibits tumor growth in MMTV-WNT1 transgenic mice. The effect of Wnt-C59 in human tumors is not clear. In this study, the NPC cell lines investigated manifest heterogeneous responses to Wnt-C59 treatment. Wnt-C59 decreased tumor growth of SUNE1 cells in mice immediately following the administration of Wnt-C59. Mice injected with HNE1 cells did not develop visible tumors after the treatment of Wnt-C59, while control mice developed 100% tumors. Wnt-C59 inhibited stemness properties of NPC cells in a dosage-dependent manner by arresting sphere formation in both HNE1 and SUNE1 cells. Thus, Wnt-C59 has the potential to eradicate CSCs in human tumors. Active β-catenin and Axin2 proteins were strongly expressed in stromal cells surrounding growing tumors, confirming the importance of Wnt signaling activities in the microenvironment being driving forces for cell growth. These novel findings confirm the ability of Wnt-C59 to suppress Wnt-driven undifferentiated cell growth in NPC. Both anti-Wnt signaling and anti-CSC approaches are feasible strategies in cancer therapy.

Abstract 1938: Inhibition of both physiological and aberrant Wnt/β-catenin signaling activities associated with stemness in nasopharyngeal carcinoma

We previously demonstrated that basic or physiological levels of β-catenin signaling and tissue context play decisional roles in the regulation of self-renewal networks in nasopharyngeal carcinoma (NPC) HONE1 cells. Introduction of physiological levels of β-catenin signaling in HONE1 hybrid cells plays a central role in the control of other pathway activities, such as TGF-β, Activin, and pluripotency maintenance (LIFR and IL6ST), during the stemness transition process. These results revealed novel regulatory relationships among Wnt signaling, stemness, epithelial-mesenchymal transition (EMT), tumor suppressive pathways and expression of common cancer stem cell surface markers, such as CD44 and CD133, in human tumor cells. In current studies, we found that several NPC cell lines, including CNE1, HK1, HNE1, SUNE1, and C666-1, have aberrant and significant up-regulation of β-catenin expression, when compared to HONE1 cells that have low levels endogenous β-catenin expression. In these NPC cells with aberrant β-catenin signaling activities, the Wnt pathway (Axin2, APC, TCF1 and TCF3), stemness factors (Nanog, and Oct4) and pluripotency markers (IFITM1 and GRB7) are strongly overexpressed, compared to HONE1 cells. Our findings suggest that aberrant Wnt/β-catenin signaling activities may play a prominent role in promoting tumor progression in NPC cells. To further verify the role of aberrant β-catenin signaling in NPC, we utilize shRNA to knock down β-catenin expression in these cells, including CNE1 and HK1. As found in HONE1 hybrids, the diminished expression of core stem cell factors (Nanog, Oct4, Klf4, and Sox2) is also detected in both CNE1 and HK1 cell lines. Concomitantly, the gene expression of EMT markers (E-cadherin and Zeb1) is also inhibited when β-catenin is knocked down by shRNA β-catenin infection. These preliminary results suggest that β-catenin signaling plays a dominant role in regulating both physiological and aberrant Wnt/β-catenin signaling activities as well as EMT events in NPC development.

Citation Format: Yue Cheng, Yee Peng Phoon, Maria L. Lung. Inhibition of both physiological and aberrant Wnt/β-catenin signaling activities associated with stemness in nasopharyngeal carcinoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1938. doi:10.1158/1538-7445.AM2014-1938

Abstract 420: Physiological β-catenin signaling regulates pluripotency genes in cancer microcell hybrids

Both β-catenin signaling and Nanog were previously reported to be involved in cell fusion-mediated somatic cell reprogramming. It remains unclear as to how the β-catenin signaling pathway is initiated and whether this pathway may directly control the expression of core stem cell factors such as Nanog and Oct4. Since β-catenin signaling is a predominating force for the regulation of cellular fate and basic levels of this signaling are needed for somatic cell reprogramming, we speculate that transfer of a single copy of chromosome 3, where β-catenin maps and is controlled by its natural regulators, into somatic cancer cells may appropriately induce this pathway and switch on the expression of endogenous pluripotency genes in recipient cells. We previously generated human nasopharyngeal (HONE1) and esophageal (SLMT1) carcinoma hybrid cells with an intact copy of transferred chromosome 3. At both transcriptional and translational levels, we detected obvious expression of genes related to the Wnt/β-catenin pathway in HONE1/chromosome 3 hybrid cells. In these hybrid cells, β-catenin, c-Myc, Axin2, Tcf1, Sox2, Klf4, Oct4, and Nanog were either strongly expressed or up-regulated. The loss of region that contains B-catenin locus in transferred chromosome 3 abolishes the expression of core stem cell genes. The control of these gene activities by physiological β-catenin signaling was further confirmed in HONE1/chromosome 17 hybrids that contain the downstream components of β-catenin signaling Axin2 and Stat3, but was not detected in hybrids with an irrelevant transferred chromosome and SLMT1 cells that had a relatively high level of endogenous β-catenin expression. We also found that HONE1 hybrid cells have stem cell-like properties, including spheroid formation, up-regulation of CD24+ and CD44+ populations and expression of various embryonic markers. Additionally, chromosome 3 transfer induced epithelial-mesenchymal transformation (EMT) events in HONE1 cells that caused different expression of adhesion molecules and up-regulation of their regulators and other markers such as Twist, Snail, Slug, ZEB1, Sip1, and E-cadherin. As expected, we detected that p53, Rb1, and Smad2 involved pathways were activated in HONE1 hybrid cells, suggesting that physiological β-catenin signaling, via multiple signaling pathways, regulates both pluripotency networks and EMT events.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 420. doi:1538-7445.AM2012-420

Graft-vs-tumor effect in patients with advanced nasopharyngeal cancer treated with nonmyeloablative allogeneic PBSC transplantation

While nonmyeloablative peripheral blood stem cell transplantation (NST) has shown efficacy against several solid tumors, it is untested in nasopharyngeal cancer (NPC). In a phase II clinical trial, 21 patients with pretreated metastatic NPC underwent NST with sibling PBSC allografts, using CY conditioning, thymic irradiation and in vivo T-cell depletion with thymoglobulin. Stable lymphohematopoietic chimerism was achieved in most patients and prophylactic CYA was tapered at a median of day +30. Seven patients (33%) showed partial response and three (14%) achieved stable disease. Four patients were alive at 2 years and three showed prolonged disease control of 344, 525 and 550 days. With a median follow-up of 209 (4-1147) days, the median PFS was 100 days (95% confidence interval (CI), 66-128 days), and median OS was 209 days (95% CI, 128-236 days). Patients with chronic GVHD had better survival-median OS 426 days (95% CI, 194-NE days) vs 143 days (95% CI, 114-226 days) (P=0.010). Thus, NST may induce meaningful clinical responses in patients with advanced NPC.