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.

Case report: Metastatic urothelial cancer with an exceptional response to immunotherapy and comprehensive understanding of the tumor and the tumor microenvironment

Although immune checkpoint inhibitors (ICIs) are increasingly used as second-line treatments for urothelial cancer (UC), only a small proportion of patients respond. Therefore, understanding the mechanisms of response to ICIs is critical to improve clinical outcomes for UC patients. The tumor microenvironment (TME) is recognized as a key player in tumor progression and the response to certain anti-cancer treatments. This study aims to investigate the mechanism of response using integrated genomic and transcriptomic profiling of a UC patient who was part of the KEYNOTE-045 trial and showed an exceptional response to pembrolizumab. Diagnosed in 2014 and receiving first-line chemotherapy without success, the patient took part in the KEYNOTE-045 trial for 2 years. She showed dramatic improvement and has now been free of disease for over 6 years. Recently described by Bagaev et al., the Molecular Functional (MF) Portrait was utilized to dissect genomic and transcriptomic features of the patient's tumor and TME. The patient's tumor was characterized as Immune Desert, which is suggestive of a non-inflamed microenvironment. Integrated whole-exome sequencing (WES) and RNA sequencing (RNA-seq) analysis identified an ATM mutation and high TMB level (33.9 mut/mb), which are both positive biomarkers for ICI response. Analysis further revealed the presence of the APOBEC complex, indicating the potential for use of APOBEC signatures as predictive biomarkers for immunotherapy response. Overall, comprehensive characterization of the patient's tumor and TME with the MF Portrait revealed important insights that could potentially be hypothesis generating to identify clinically useful biomarkers and improve treatment for UC patients.

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.

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.

Recruitment of phospholipase Cγ1 to the non-structural membrane protein pK15 of Kaposi Sarcoma-associated herpesvirus promotes its Src-dependent phosphorylation

Kaposi Sarcoma-associated herpesvirus (KSHV) causes three human malignancies, Kaposi Sarcoma (KS), Primary Effusion Lymphoma (PEL) and the plasma cell variant of multicentric Castleman’s Disease (MCD), as well as an inflammatory cytokine syndrome (KICS). Its non-structural membrane protein, pK15, is among a limited set of viral proteins expressed in KSHV-infected KS tumor cells. Following its phosphorylation by Src family tyrosine kinases, pK15 recruits phospholipase C gamma 1 (PLCγ1) to activate downstream signaling cascades such as the MEK/ERK, NFkB and PI3K pathway, and thereby contributes to the increased proliferation and migration as well as the spindle cell morphology of KSHV-infected endothelial cells. Here, we show that a phosphorylated Y⁴⁸¹EEVL motif in pK15 preferentially binds into the PLCγ1 C-terminal SH2 domain (cSH2), which is involved in conformational changes occurring during the activation of PLCγ1 by receptor tyrosine kinases. We determined the crystal structure of a pK15 12mer peptide containing the phosphorylated pK15 Y⁴⁸¹EEVL motif in complex with a shortened PLCγ1 tandem SH2 (tSH2) domain. This structure demonstrates that the pK15 peptide binds to the PLCγ1 cSH2 domain in a position that is normally occupied by the linker region connecting the PLCγ1 cSH2 and SH3 domains. We also show that longer pK15 peptides containing the phosphorylated pK15 Y⁴⁸¹EEVL motif can increase the Src-mediated phosphorylation of the PLCγ1 tSH2 region in vitro. This pK15-induced increase in Src-mediated phosphorylation of PLCγ1 can be inhibited with the small pK15-derived peptide which occupies the PLCγ1 cSH2 domain. Our findings thus suggest that pK15 may act as a scaffold protein to promote PLCγ1 activation in a manner similar to the cellular scaffold protein SLP-76, which has been shown to promote PLCγ1 activation in the context of T-cell receptor signaling. Reminiscent of its positional homologue in Epstein-Barr Virus, LMP2A, pK15 may therefore mimic aspects of antigen-receptor signaling. Our findings also suggest that it may be possible to inhibit the recruitment and activation of PLCγ1 pharmacologically.

Kaposi’s Sarcoma-Associated Herpesvirus (KSHV) causes three human malignancies (Kaposi Sarcoma, Primary Effusion Lymphoma, Multicentric Castleman’s Disease) and an inflammatory condition, KICS. One of its non-structural membrane proteins, pK15, is expressed in tumor cells and has previously been shown to contribute to its ability to reactivate from latency and to its pathogenetic properties in endothelial cells by recruiting the cellular signaling enzyme phospholipase Cγ1 (PLCγ1). Here we investigate the interaction of pK15 with PLCγ1, report the structure of a PLCγ1 domain in complex with a pK15 peptide and show that pK15 primes PLCγ1 for phosphorylation by the cellular kinase Src. We also show that the pK15-dependent activation of PLCγ1 can be inhibited with a small peptide. Our findings therefore identify the pK15-PLCγ1 interaction as a putative druggable target and provide the basis for the development of small molecule inhibitors that could perhaps serve to inhibit KSHV replication and pathogenesis.

The Kaposi's sarcoma-associated herpesvirus (KSHV) non-structural membrane protein K15 is required for viral lytic replication and may represent a therapeutic target

Kaposi’s sarcoma-associated herpesvirus (KSHV) is the infectious cause of the highly vascularized tumor Kaposi’s sarcoma (KS), which is characterized by proliferating spindle cells of endothelial origin, extensive neo-angiogenesis and inflammatory infiltrates. The KSHV K15 protein contributes to the angiogenic and invasive properties of KSHV-infected endothelial cells. Here, we asked whether K15 could also play a role in KSHV lytic replication. Deletion of the K15 gene from the viral genome or its depletion by siRNA lead to reduced virus reactivation, as evidenced by the decreased expression levels of KSHV lytic proteins RTA, K-bZIP, ORF 45 and K8.1 as well as reduced release of infectious virus. Similar results were found for a K1 deletion virus. Deleting either K15 or K1 from the viral genome also compromised the ability of KSHV to activate PLCγ1, Erk1/2 and Akt1. In infected primary lymphatic endothelial (LEC-rKSHV) cells, which have previously been shown to spontaneously display a viral lytic transcription pattern, transfection of siRNA against K15, but not K1, abolished viral lytic replication as well as KSHV-induced spindle cell formation. Using a newly generated monoclonal antibody to K15, we found an abundant K15 protein expression in KS tumor biopsies obtained from HIV positive patients, emphasizing the physiological relevance of our findings. Finally, we used a dominant negative inhibitor of the K15-PLCγ1 interaction to establish proof of principle that pharmacological intervention with K15-dependent pathways may represent a novel approach to block KSHV reactivation and thereby its pathogenesis.

Both the latent and lytic replication phases of the KSHV life cycle are thought to contribute to its persistence and pathogenesis. The non-structural signaling membrane protein K15 is involved in the angiogenic and invasive properties of KSHV-infected endothelial cells. Here we show that the K15 protein is required for virus replication, early viral gene expression and virus production through its activation of the cellular signaling pathways PLCγ1 and Erk 1/2. K15 is abundantly expressed in KSHV-infected lymphatic endothelial cells (LECs) and contributes to KSHV-induced endothelial spindle cell formation. The abundant K15 protein expression observed in LECs is also observed in KS tumors. We also show that it may be possible to target K15 in order to intervene therapeutically with KSHV lytic replication and pathogenesis.