B-Cell Infiltrate in the Tumor Microenvironment Is Associated With Improved Survival in Resected Lung Adenocarcinoma

Introduction

Relapse is common after resection of lung adenocarcinoma (LUAD). Features of the tumor microenvironment (TME) which influence postsurgical survival outcomes are poorly characterized. Here, we analyzed the TME of more than 1500 LUAD specimens to identify the relationship between B-cell infiltration and prognosis.

Methods

Whole exome sequencing and bulk RNA sequencing were performed on LUADs and adjacent normal lung tissue. Relapse-free survival and overall survival (OS) were retrospectively correlated with characteristics of the tumor and TME in three data sets.

Results

High B-cell content (defined as >10% B cells) was associated with improved OS in both a The Cancer Genome Atlas-resected LUAD data set (p = 0.01) and a separate institutional stage II LUAD data set (p = 0.04, median not reached versus 89.5 mo). A validation cohort consisting of pooled microarray data representing more than 1400 resected stage I to III LUADs confirmed the association between greater B-cell abundance, specifically higher B-cell expression, and longer postsurgical survival (median OS 90 versus 71 mo, p < 0.01). Relapse-free survival was longer for patients with adenocarcinomas with high B-cell content across data sets, but it did not reach statistical significance. Subcategorization of B-cell subsets indicated that high naive B-cell content was most predictive of survival. There was no correlation between programmed death-ligand 1 expression, lymphoid aggregates, or overall immune infiltrate density and survival outcomes across the cohorts.

Conclusions

The growing adjuvant immunotherapy repertoire has increased the urgency for identifying prognostic and predictive biomarkers. Comprehensive profiling of more than 1500 LUADs suggests that high tumor-infiltrating B-cell content is a favorable prognostic marker.

Abstract 244: Use of comprehensive molecular profiling to identify additional clinically-relevant alterations compared to targeted gene panels

The BostonGene Tumor PortraitTM Test (TPT) is a comprehensive molecular profiling assay with both integrated genomic and transcriptomic analysis. The combined analysis offers additional information that is potentially critical for personalized clinical decision making.

We retrospectively reviewed 2 sarcoma cohorts that received the TPT, MG (n=21) and MD (n=40) (Table 1), and evaluated reported events that were not previously identified by institute respective targeted panels. A total of 19 (MG) and 23 (MD) additional clinically-relevant SNV/indels, CNAs, and fusions were identified by the TPT, including an amplification of EZH2, 2 novel fusions with MDM2 as a binding partner, and a known diagnostic fusion, NAB2-STAT6. A high TMB was observed in 5 patients. MSI was stable for all patients. HLA class I loss of heterozygosity was found in 7 patients. In both cohorts, we observed significant changes in the expression of potentially targetable genes, with 81% of patients presenting with increased expression of such targets. Transcriptomic-based tumor microenvironment (TME) classification found that 51% and 49% of patients had an Immune-Enriched (IE) subtype (predicted favorable IO treatment outcomes) and Fibrotic/Desert (F/D) subtypes (predicted poor response to IO treatment), respectively. Predicted response to IO therapy through TME subtyping agreed with previous reports, as angiosarcomas were enriched in the IE subtype (83%), and bone sarcomas were enriched in the F (30%) compared to the IE (6%) subtype. Further, these results supported matching patients with biomarker-driven clinical trials at their respective centers.

In summary, the TPT identified more clinically-relevant biomarkers compared to respective institute targeted gene panels, highlighting the potential value of comprehensive molecular profiling for patients with highly heterogeneous diseases, such as sarcoma, to support personalized treatment decisions.

Table 1. Genetic and expression alterations identified by the BostonGene Tumor PortraitTM Test Event type analyzed in targeted panels Event type Cohort (N patients)* % cohort with event or # biomarkers Events, status, or subtype Yes SNV/Indel MG (21) 10% FAT4 Y558_V590delinsCAfs*5 LOF mutation COL2A1 W1348Nfs*13 LOF mutation Yes SNV/Indel MD (40) 6% KMT2B R1779* LOF mutation KMT2C S143Vfs*3 LOF mutation PRKDC Y4046* LOF mutation Yes Germline MG (21) 5% MUTYH rs36053993, germline, pathogenic Yes Germline MD (40) 3% BTD rs13078881, germline, pathogenic Yes CNA MG (21) 43% IGF1R amplification +8 copies MGMT loss FANCA loss MCL1 amplification +10 copies MYOCD amplification +3 copies AKT2 amplification +8 copies AMACR amplification +6 copies YAP1 amplification +7 copies TRAF2 loss EZH2 amplification +2 copies HMGA2 amplification +100 copies FRS2 amplification +61 copies DDIT3 amplification +39 copies Yes CNA MD (40) 27.5% ERK1 amplification +2 copies FOXO1 amplification +5 copies HMGA2 amplification +2, +8 copies KMT2C amplification +3 copies NCOR1 amplification +7 copies TERT amplification +6 copies TSPAN31 amplification +30 copies HSF1 loss Yes Fusions MG (20) 10% MDM2-CR1 MDM2-TXNDC12 AC090825.1-IGF1R Yes Fusions MD (39) 15% FUS-KIAA1549 KIAA1549-CREB3L2 HMGA2-LRRC37A3 NAB2-STAT6 PPP1R12A-PAWR RB1-ZAR1L No TMB** MG+MD (61) 8% 35.67 mut/Mb (Desmoid fibromatosis) 8.48 mut/Mb (Cutaneous angiosarcoma) 8.9 mut/Mb (Sarcoma, NOS) 16.1 mut/Mb (Skin Angiosarcoma) 18.8 mut/Mb (Undifferentiated pleomorphic sarcoma) No MSI status MG+MD (61) 100% Stable No HLA loss of heterozygosity MG+MD (61) 11% HLA-I LOH (Leiomyosarcoma (N=1), Ewing Sarcoma (N=1)) HLA-A (Dedifferentiated liposarcoma (N=1)) HLA-I (Chondrosarcoma (N=3), High-grade sarcoma (N=1)) No Targetable surface molecule overexpression MG+MD (59) 81% CTLA4, EGFR, ERBB2, MAGEA3, PD1, PDL1, TIM3, TROP, ERBB2, FOLR1, NECTIN4, ROR1, TROP2 No Molecular Functional PortraitTM type MG+MD (59) 32% Fibrotic No Molecular Functional PortraitTM type MG+MD (59) 17% Immune Desert No Molecular Functional PortraitTM type MG+MD (59) 24% Immune-Enriched, Fibrotic No Molecular Functional PortraitTM type MG+MD (59) 27% Immune-Enriched, Non-fibrotic No MHC deficiency MG+MD (59) 3% MHC class I/II deficiency No MHC deficiency MG+MD (59) 3% MHC class II deficiency No FDA label biomarkers MG+MD (59) 7 biomarkers - Desmoid fibromatosis, TMB 35.67 mut/Mb (Pembrolizumab) - Angiosarcoma, TMB 16.1 mut/Mb (Pembrolizumab); - Undifferentiated pleomorphic sarcoma, MSI, TMB 18.8 mut/Mb (Pembrolizumab); - Cutaneous angiosarcoma, PALB2 pathogenic germline variant (Olaparib); - Chondrosarcoma IDH1 R132L (Ivosidenib) No Transcriptomic biomarkers MG+MD (59) 29 biomarkers CD8+ T cell number; PDL1 expression level; SLFN11 expression level; SMARCB1 expression; CD8+ T cell number No Diagnostic biomarkers MG+MD (59) 9 biomarkers NAB2-STAT6; MXI1-NUTM1; EWSR1-NR4A3; EWSR1-FLI1; EWSR1-CREB3L1; NAB2-STAT6 - - - - *RNA analysis failed for 2 patients. Therefore, any expression based analysis was performed on n=20 and n=39 for the MG and MD cohort, respectively. **Tumor mutational burden is considered high for FFPE samples when TMB&gt;8mut/Mb.

Citation Format: Gregory M. Cote, Anna Novokreshchenova, Irina Zhuk, Aida Aukhadieva, Sandrine Degryse, Aleksei Shevkoplias, Anna Belozerova, Krystle Nomie, Nikita Kotlov, Georgy Sagardze, Lev Bedniagin, Jessica Brown, Ekaterina Postovalova, Alexander Bagaev, Nathan Fowler, J. Andrew Livingston, Vinod Ravi. Use of comprehensive molecular profiling to identify additional clinically-relevant alterations compared to targeted gene panels [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 244.

Precise reconstruction of the TME using bulk RNA-seq and a machine learning algorithm trained on artificial transcriptomes

Cellular deconvolution algorithms virtually reconstruct tissue composition by analyzing the gene expression of complex tissues. We present the decision tree machine learning algorithm, Kassandra, trained on a broad collection of >9,400 tissue and blood sorted cell RNA profiles incorporated into millions of artificial transcriptomes to accurately reconstruct the tumor microenvironment (TME). Bioinformatics correction for technical and biological variability, aberrant cancer cell expression inclusion, and accurate quantification and normalization of transcript expression increased Kassandra stability and robustness. Performance was validated on 4,000 H&E slides and 1,000 tissues by comparison with cytometric, immunohistochemical, or single-cell RNA-seq measurements. Kassandra accurately deconvolved TME elements, showing the role of these populations in tumor pathogenesis and other biological processes. Digital TME reconstruction revealed that the presence of PD-1-positive CD8⁺ T cells strongly correlated with immunotherapy response and increased the predictive potential of established biomarkers, indicating that Kassandra could potentially be utilized in future clinical applications.

Abstract 3823: Viral transcript and tumor immune microenvironment-based transcriptomic profiling of HPV-associated head and neck cancer identifies subtypes associated with prognosis

Human papillomavirus (HPV)-associated Head and Neck Squamous Cell Carcinoma (HPV+HNSCC) is now the most common HPV-associated malignancy in the United States. Current treatments can be associated with severe side-effects or lack of efficacy yet prognostic biomarkers are limited, slowing efforts to personalize treatment in HPV+HNSCC. Here, we describe the use of a transcriptomic-based analytical platform to analyze expression patterns of viral transcripts, the tumor microenvironment (TME), and viral genome integration, and associate these features with overall survival.

Functional gene expression signatures were analyzed on publicly available HPV+HNSCC expression data (n=266). Unsupervised clustering analysis revealed 5 distinct and novel TME types across patients (immune-enriched non-fibrotic, immune-enriched fibrotic, fibrotic, immune-desert, immune-enriched luminal). These microenvironment subtypes were highly correlated with both overall survival and patient prognosis. Tumors with an immune-enriched microenvironment showed the highest survival rates, whereas fibrotic TME types were associated with poor survival (p &lt; 0.05). Unsupervised clustering of a HPV+HNSCC cohort from The Cancer Genome Atlas (TCGA) (n=53), based on HPV transcript expression, revealed 4 HPV-related subtypes. Each subtype was enriched for distinct viral transcripts: E2/E5, E6/E7, E1/E4 and L1/L2. We then validated TME and HPV transcript-related classifications on an independent HPV+HNSCC cohort (n=132). Utilizing both viral transcript and TME subtypes, we found that the E2/E5 HPV subtype was associated with an immune-enriched TME and had a higher overall survival compared to the other subtypes. The E2/E5 subtype was also enriched for samples without HPV-genome integration, suggesting that HPV episomal DNA status and E2/E5 expression pattern may drive an inflamed microenvironment and improved prognosis. In contrast, E6/E7 subtype samples were associated with the fibrotic and depleted TME types, with lower values of T-cell and B-cell gene expression signatures and a lower survival rate. Both E1/E4 and L1/L2 subtypes were associated with the immune-enriched luminal TME types.

These findings suggest that HPV-transcript expression patterns may drive modulation of the TME, and hence impact prognosis. Further validation of the relationships between viral gene expression, TME, and prognosis is warranted to understand if such subtypes could aid in the development of prognostic biomarkers for treatment selection.

Citation Format: Daria Kiriy, Dmitry Tychinin, Nikita Kotlov, Olga Kudryashova, Anastasia Nikitina, Andrey Tyshevich, Naira Samarina, Ksenia Demina, Sandrine Degryse, Susan Raju Paul, Mark Poznansky, Krystle Lang Kuhs, James S. Lewis, Robert L. Ferris, Xiaowei Wang, Alexander Bagaev, Nathan Fowler, Lori Wirth, Daniel Faden. Viral transcript and tumor immune microenvironment-based transcriptomic profiling of HPV-associated head and neck cancer identifies subtypes associated with prognosis [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 3823.

Abstract 5172: B cell content in the tumor microenvironment is associated with improved survival in stage II lung adenocarcinoma

In non-small cell lung cancer (NSCLC), likelihood of cure is heavily influenced by stage at diagnosis. In contrast to stage I where surgery achieves cure for &gt;70% of patients, the majority of patients with stage II NSCLC will develop recurrent disease after surgery. The addition of chemotherapy is associated with modest improvement in survival. Biomarkers that help identify patients at higher risk of relapse following curative intent therapy remain elusive.

In this study, we performed comprehensive profiling of resected stage II lung adenocarcinomas (LUAD) (n=29) to identify features associated with favorable prognostic outcomes. Whole exome (WES) and bulk RNA sequencing (RNAseq) were performed on frozen lung tumor specimens and corresponding normal lung tissue. Novel algorithms were used to digitally reconstruct the tumor microenvironment (TME). H&E slides were reviewed to characterize the immune infiltrate and identify tertiary lymphoid structures (TLS). Patient outcomes were collected and matched to pathological samples. To further validate initial findings, we then created and tested a functional B-cell signature on cohorts as described below.

In the retrospective cohort, 13 (45%) patients developed recurrent disease and 10 (34%) died during the 3+ year follow-up period. Neither the overall density of immune infiltrate nor detection of TLS predicted for improved relapse-free survival (RFS) or overall survival (OS). Similarly, tumor mutational burden (assessed by WES), histological grade (assessed by RNAseq), and expression of immune checkpoints (PD-L1, PD-1, CTLA-4) were not associated with RFS or OS (log-rank test P &gt; 0.05 for both OS and RFS in all comparisons). Interestingly, higher B-cell content in the TME (stratified as high vs low based on 10% threshold value), as deconvolved using validated algorithms (and confirmed via H&E review), was associated with improved OS (log-rank test P = 0.05) with a trend towards improved RFS (P = 0.2). We conducted the same analysis using a TCGA RNAseq cohort of stage II LUAD patients (n = 76) and confirmed that high B-cell levels in the TME were significantly associated with longer OS in stage II LUAD patients (P = 0.03). Finally, to validate our findings with a larger dataset, we developed a functional B-cell gene expression signature which significantly correlated with levels of B cells in both the TCGA (Spearman’s rho = 0.83, P &lt; 0.001) and 29-patient cohort (Spearman’s rho = 0.91, P &lt; 0.001). When this signature was applied to publicly available expression array data, B-cell enrichment status was significantly associated with OS in the external meta-cohort of stage II LUAD patients (log rank test P = 0.004, n=564).

Abundant B-cell infiltrate in the TME is associated with improved survival in patients with surgically resected stage II LUAD. Quantification of B-cell content using RNAseq warrants further investigation for use in routine clinical practice.

Citation Format: Ivan Valiev, Nikita Kotlov, Anna Belozerova, Aleksandra Lopareva, Anna Butusova, Naira Samarina, Alexandra Boiko, Sandrine Degryse, Lecia Sequist, Mari Mino-Kenudson, Nathan Fowler, Aleksander Bagaev, Michael Lanuti, Ibiayi Dagogo-Jack. B cell content in the tumor microenvironment is associated with improved survival in stage II lung adenocarcinoma [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 5172.

Antibody-mediated blockade of the IL23 receptor destabilizes intratumoral regulatory T cells and enhances immunotherapy

Regulatory T cells (Treg) can impede antitumor immunity and currently represent a major obstacle to effective cancer immunotherapy. Targeting tumor-infiltrating regulatory Treg while sparing systemic Treg represents an optimal approach to this problem. Here, we provide evidence that the interleukin 23 receptor (IL23R) expressed by tumor-infiltrating Treg promotes suppressive activity. Disruption of the IL23R results in increased responsiveness of destabilized Treg to the IL12 cytokine, the production of γ-interferon, and the recruitment of CD8 T cells that inhibit tumor growth. Since the Treg destabilization pathway that is initiated by IL23R blockade is distinct and independent from the destabilization pathway coupled to glucocorticoid-induced TNFR-related protein (GITR) activation, we examined the impact of the coordinate induction of the two destabilization pathways on antitumor immune responses. Combined GITR and IL23R antibody treatment of mice inoculated with MC38 tumors resulted in robust and synergistic antitumor responses. These findings indicate that the delineation of independent Treg destabilization pathways may allow improved approaches to the development of combination immunotherapy for cancers.

Tadalafil Enhances Immune Signatures in Response to Neoadjuvant Nivolumab in Resectable Head and Neck Squamous Cell Carcinoma

PURPOSE

We hypothesize that the addition of the phosphodiesterase-5 inhibitor tadalafil to the PD-1 inhibitor nivolumab, is safe and will augment immune-mediated antitumor responses in previously untreated squamous cell carcinoma of the head and neck (HNSCC).

PATIENTS AND METHODS

We conducted a two-arm multi-institutional neoadjuvant randomized trial in any-stage resectable HNSCC (NCT03238365). Patients were stratified at randomization by human papillomavirus (HPV) status. Patients in both arms received nivolumab 240 mg intravenously on days 1 and 15 followed by surgery on day 28. Those in the combination therapy arm also received tadalafil 10 mg orally once daily for 4 weeks. Imaging, blood, and tumor were obtained pretreatment and posttreatment for correlative analysis.

RESULTS

Neoadjuvant therapy was well-tolerated with no grade 3 to 5 adverse events and no surgical delays. Twenty-five of 46 (54%) evaluable patients had a pathologic treatment response of ≥20%, including three (7%) patients with a complete pathologic response. Regardless of HPV status, tumor proliferation rate was a negative predictor of response. A strong pretreatment T-cell signature in the HPV-negative cohort was a predictor of response. Tadalafil altered the immune microenvironment, as evidenced by transcriptome data identifying enriched B- and natural killer cell gene sets in the tumor and augmented effector T cells in the periphery.

CONCLUSIONS

Preoperative nivolumab ± tadalafil is safe in HNSCC and results in more than 50% of the patients having a pathologic treatment response of at least 20% after 4 weeks of treatment. Pretreatment specimens identified HPV status-dependent signatures that predicted response to immunotherapy while posttreatment specimens showed augmentation of the immune microenvironment with the addition of tadalafil.

Abstract 3182: Tumor immune microenvironment based molecular functional clustering reveals a prognostic signature that predicts overall survival in patients with gastric cancer

Gastric Cancer (GC) is the second leading cause of cancer-related mortality (9.7% of the total) and most patients with advanced disease will die within one year of diagnosis. GC is histologically classified into intestinal, diffuse and the mixed types, and into four molecular subtypes based on genetic profiling (i.e. microsatellite instable (MSI), EBV positive, chromosomal instable, and genomically stable). Although the molecular annotation is meaningful, the tumor immune microenvironment (TIME) has largely not been evaluated. Using an integrated collection of 11 public cohorts (n=2,270), we identified 5 unique GC TIME phenotypes by unsupervised clustering of gene expression signatures of RNA that describe the composition and biology of TIME and properties of malignant cells: two stromal-enriched subtypes - 1) Mesenchymal-wnt activated, high stroma activation and WNT signaling and 2) Fibrotic, only high stroma activation; two immune enriched subtypes 3) Inflamed non-fibrotic, high immune infiltration and low stromal compartment and 4) B-cell inflamed, high B cell activation; and 5) Immune Depleted, lowest immune and the highest malignant cell properties. The clusters were robust, being identified across all 11 datasets and across all stages of disease. Intestinal, diffuse, and mixed histologies were identified in each cluster. These clusters will be orthogonally validated using immunohistochemistry.

The current molecular subtypes were represented in each of our TIME clusters, with some enrichment. Specifically, we found enrichment of MSI molecular subtype, characterized by hypermutation and microsatellite instability, in “Inflamed, non-fibrotic” cluster whereas the MSS/EMT subtype, associated with poor overall survival, was enriched in “Mesenchymal, wnt activated” cluster. We also saw specific enrichment of EBV positive tumors, known to have good prognosis, in both immune-enriched clusters. These results show a high concordance with the current TCGA/ACRG molecular subtypes of GC.

These TIME clusters are prognostic in GC. The “Inflamed, non-fibrotic” cluster demonstrated a better overall and relapse free survival whereas stromal enriched clusters exhibited the worst (p&lt;0.001, HR=2.27). Interestingly, the most aggressive “Mesenchymal, wnt activated” subtype was also enriched of metastatic samples. These results were confirmed using an independent validation cohort (n=231) from four other datasets. Additionally, comparison of matching on-treatment vs baseline biopsies from 7 patients treated with cabazitaxel further suggested that TIME changed upon treatment and, in some cases, was indicative of poor response to taxanes.

We have defined and characterized the TIME for GC. The GC microenvironment is both prognostic for patient outcome and predictive of response to cytotoxic therapy.

Citation Format: Prashant V. Thakkar, Olga Kudryashova, Daria Melikhova, Naira Samarina, Sandrine Degryse, Alexander Bagaev, Felix Frenkel, Svetlana Podsvirova, Dmitry Tychinin, Sandipto Sarkar, Rhonda K. Yantiss, Nathan Fowler, Manish A. Shah. Tumor immune microenvironment based molecular functional clustering reveals a prognostic signature that predicts overall survival in patients with gastric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 3182.

Abstract 1441: Predictors of treatment response in a preoperative window of opportunity trial of nivolumab in resectable squamous cell carcinoma of the head and neck

Nivolumab, a PD-1 inhibitor, has variable response rates in patients and is not fully characterized in treatment-naïve patients. Here, we describe exploratory analyses of immune-related gene expression in squamous cell carcinoma of the head and neck (SCCHN) as predictors of response to nivolumab, administered for 4 weeks before planned surgical resection in the context of a window-of-opportunity trial.

RNA-seq was performed on pre- and post-treatment tumor tissues from 39 patients with SCCHN of any stage, who were candidates for complete surgical resection (NCT03238365). Expression was quantified using kallisto. Noncoding, histone-coding and mitochondrial transcripts were removed. HPV-specific reads were filtered using pathseq and aligned to HPV reference using viGEN. TME signature scores were quantified using ssGSEA.

While HPV-status did not predict clinical responses to nivolumab, the expression of individual HPV16 genes in post-treatment samples reflected response in this patient cohort. Patients who responded to nivolumab showed lower levels of E6 expression, while non-responsive patients had significantly higher E6 expression levels. In contrast, E4 expression was found to be increased in patients who responded to nivolumab treatment. As expected, HPV-positive tumors presented with a more inflamed TME compared to HPV-negative tumors.

A tumor microenvironment (TME) classification platform developed by BostonGene was used to analyze several gene expression signatures. Four distinct microenvironment subtypes were reproduced, consistent with pooled analysis. In addition, a high proliferation rate signature in baseline samples was closely associated with non-response to immunotherapy regardless of HPV status.

HPV-negative tumors with significantly higher CD8, FoxP3, and CD163 as measured by IHC, had a greater response to immunotherapy in contrast to HPV-positive tumors, where no association was found. This finding was supported by single gene expression and the BostonGene-developed deconvolution algorithm to reconstruct the TME composition of the tumors using RNA sequencing; predicted CD8+ T-cells and Macrophages were significantly enriched in HPV-negative responders. Interestingly, patients with HPV-negative tumors disproportionately responded better to treatment when they presented with an immune-inflamed TME; however, this pattern was not observed in HPV-positive tumors.

Our analysis indicates that HPV16 gene transcription appears to impact response to treatment. In addition, the immune-inflamed TME impacts response to nivolumab treatment in HPV-negative tumors. These properties can be assessed in a multiparametric analysis and could lead to the identification of predictors of response to immunotherapy in head and neck cancer.

Citation Format: Nikita Kotlov, Zoya Antysheva, Dina Antonova, Naira Samarina, Sandrine Degryse, Alban Linnenbach, Sanket Shukla, Larry Harshyne, Andrew P. South, Jennifer M. Johnson, Young Kim, Alexander Bagaev, Nathan H. Fowler, Adam Luginbuhl. Predictors of treatment response in a preoperative window of opportunity trial of nivolumab in resectable squamous cell carcinoma of the head and neck [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1441.

A tumor-infiltrating IL23R-expressing CD4+ Treg population represents a safe and potent immunotherapeutic candidate in mice

Interleukin 23 receptor (IL23R) is a signaling protein normally implicated in gut T cell development, but which has also been correlated with poor cancer prognoses. Previous studies have found that interfering with this pathway results in improved cancer outcomes in mice. These studies found that blocking IL23R was more effective than neutralizing IL23, suggesting that an IL23R-expressing cell was responsible for the tumor-protective effects observed in targeting IL23R. Here, we show that Treg-specific targeting of IL23R provides potent tumor immunity that explains previous successes with anti-IL23R therapy in cancer. We show that there is indeed a tumor-infiltrating Treg subset, marked by IL23R expression, that is enriched for markers of potent suppressive activity. Moreover, we find that targeting their IL23R expression is correlated with Treg conversion and increased IFNγ expression on tumor-infiltrating CD8 T cells. Preliminary results suggest that this Treg conversion is associated with enhanced IL12 sensitivity as a result of targeting the IL23R chain. In keeping with the tumor-specific expression pattern of IL23R, we did not find these changes in systemic T cells in the tumor-bearing mice. Ultimately, these Treg-specific IL23R-deleted mice do not display overt autoimmune disease at even advanced ages, suggesting this approach could represent a safe avenue of cancer immunotherapeutic research.

HOXA9 Cooperates with Activated JAK/STAT Signaling to Drive Leukemia Development

Leukemia is caused by the accumulation of multiple genomic lesions in hematopoietic precursor cells. However, how these events cooperate during oncogenic transformation remains poorly understood. We studied the cooperation between activated JAK3/STAT5 signaling and HOXA9 overexpression, two events identified as significantly co-occurring in T-cell acute lymphoblastic leukemia. Expression of mutant JAK3 and HOXA9 led to a rapid development of leukemia originating from multipotent or lymphoid-committed progenitors, with a significant decrease in disease latency compared with JAK3 or HOXA9 alone. Integrated RNA sequencing, chromatin immunoprecipitation sequencing, and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) revealed that STAT5 and HOXA9 have co-occupancy across the genome, resulting in enhanced STAT5 transcriptional activity and ectopic activation of FOS/JUN (AP1). Our data suggest that oncogenic transcription factors such as HOXA9 provide a fertile ground for specific signaling pathways to thrive, explaining why JAK/STAT pathway mutations accumulate in HOXA9-expressing cells.Significance: The mechanism of oncogene cooperation in cancer development remains poorly characterized. In this study, we model the cooperation between activated JAK/STAT signaling and ectopic HOXA9 expression during T-cell leukemia development. We identify a direct cooperation between STAT5 and HOXA9 at the transcriptional level and identify PIM1 kinase as a possible drug target in mutant JAK/STAT/HOXA9-positive leukemia cases. Cancer Discov; 8(5); 616-31. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 517.

Mutant JAK3 phosphoproteomic profiling predicts synergism between JAK3 inhibitors and MEK/BCL2 inhibitors for the treatment of T-cell acute lymphoblastic leukemia

Mutations in the interleukin-7 receptor (IL7R) or the Janus kinase 3 (JAK3) kinase occur frequently in T-cell acute lymphoblastic leukemia (T-ALL) and both are able to drive cellular transformation and the development of T-ALL in mouse models. However, the signal transduction pathways downstream of JAK3 mutations remain poorly characterized. Here we describe the phosphoproteome downstream of the JAK3(L857Q)/(M511I) activating mutations in transformed Ba/F3 lymphocyte cells. Signaling pathways regulated by JAK3 mutants were assessed following acute inhibition of JAK1/JAK3 using the JAK kinase inhibitors ruxolitinib or tofacitinib. Comprehensive network interrogation using the phosphoproteomic signatures identified significant changes in pathways regulating cell cycle, translation initiation, mitogen-activated protein kinase and phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K)/AKT signaling, RNA metabolism, as well as epigenetic and apoptotic processes. Key regulatory proteins within pathways that showed altered phosphorylation following JAK inhibition were targeted using selumetinib and trametinib (MEK), buparlisib (PI3K) and ABT-199 (BCL2), and found to be synergistic in combination with JAK kinase inhibitors in primary T-ALL samples harboring JAK3 mutations. These data provide the first detailed molecular characterization of the downstream signaling pathways regulated by JAK3 mutations and provide further understanding into the oncogenic processes regulated by constitutive kinase activation aiding in the development of improved combinatorial treatment regimens.

Distinct Acute Lymphoblastic Leukemia (ALL)-associated Janus Kinase 3 (JAK3) Mutants Exhibit Different Cytokine-Receptor Requirements and JAK Inhibitor Specificities

JAK1 and JAK3 are recurrently mutated in acute lymphoblastic leukemia. These tyrosine kinases associate with heterodimeric cytokine receptors such as IL-7 receptor or IL-9 receptor, in which JAK1 is appended to the specific chain, and JAK3 is appended to the common gamma chain. Here, we studied the role of these receptor complexes in mediating the oncogenic activity of JAK3 mutants. Although JAK3(V674A) and the majority of other JAK3 mutants needed to bind to a functional cytokine receptor complex to constitutively activate STAT5, JAK3(L857P) was unexpectedly found to not depend on such receptor complexes for its activity, which was induced without receptor or JAK1 co-expression. Introducing a mutation in the FERM domain that abolished JAK-receptor interaction did not affect JAK3(L857P) activity, whereas it inhibited the other receptor-dependent mutants. The same cytokine receptor independence as for JAK3(L857P) was observed for homologous Leu(857) mutations of JAK1 and JAK2 and for JAK3(L875H). This different cytokine receptor requirement correlated with different functional properties in vivo and with distinct sensitivity to JAK inhibitors. Transduction of murine hematopoietic cells with JAK3(V674A) led homogenously to lymphoblastic leukemias in BALB/c mice. In contrast, transduction with JAK3(L857P) induced various types of lymphoid and myeloid leukemias. Moreover, ruxolitinib, which preferentially blocks JAK1 and JAK2, abolished the proliferation of cells transformed by the receptor-dependent JAK3(V674A), yet proved much less potent on cells expressing JAK3(L857P). These particular cells were, in contrast, more sensitive to JAK3-specific inhibitors. Altogether, our results showed that different JAK3 mutations induce constitutive activation through distinct mechanisms, pointing to specific therapeutic perspectives.

JAK kinase inhibitors for the treatment of acute lymphoblastic leukemia

Recent studies of acute lymphoblastic leukemia have identified activating mutations in components of the interleukin-7 receptor complex (IL7R, JAK1, and JAK3). It will be of interest to investigate both JAK1 and JAK3 kinase inhibitors as targeted agents for these leukemias.

Targeted sequencing identifies associations between IL7R-JAK mutations and epigenetic modulators in T-cell acute lymphoblastic leukemia

T-cell acute lymphoblastic leukemia is caused by the accumulation of multiple oncogenic lesions, including chromosomal rearrangements and mutations. To determine the frequency and co-occurrence of mutations in T-cell acute lymphoblastic leukemia, we performed targeted re-sequencing of 115 genes across 155 diagnostic samples (44 adult and 111 childhood cases). NOTCH1 and CDKN2A/B were mutated/deleted in more than half of the cases, while an additional 37 genes were mutated/deleted in 4% to 20% of cases. We found that IL7R-JAK pathway genes were mutated in 27.7% of cases, with JAK3 mutations being the most frequent event in this group. Copy number variations were also detected, including deletions of CREBBP or CTCF and duplication of MYB. FLT3 mutations were rare, but a novel extracellular mutation in FLT3 was detected and confirmed to be transforming. Furthermore, we identified complex patterns of pairwise associations, including a significant association between mutations in IL7R-JAK genes and epigenetic regulators (WT1, PRC2, PHF6). Our analyses showed that IL7R-JAK genetic lesions did not confer adverse prognosis in T-cell acute lymphoblastic leukemia cases enrolled in the UK ALL2003 trial. Overall, these results identify interconnections between the T-cell acute lymphoblastic leukemia genome and disease biology, and suggest a potential clinical application for JAK inhibitors in a significant proportion of patients with T-cell acute lymphoblastic leukemia.