A phase II trial of abemaciclib (abema) and atezolizumab (atezo) in unselected and CDK12-loss metastatic castration-resistant prostate cancer (mCRPC)

TPS213

Background: Alterations in the cell cycle signaling pathway are common in mCRPC and may contribute to resistance to AR-targeted therapies. Inhibitors of cyclin-dependent kinases 4 and 6 (CDK4/6i) have revolutionized the therapeutic landscape in ER+ breast cancer and have demonstrated robust anti-tumor activity in multiple pre-clinical mCRPC models such as enzalutamide-resistant cell lines, including those with the androgen-receptor splice variant 7 (AR-V7). Pre-clinical synergy has also been seen in multiple studies of CDK4/6i and anti-programmed death 1 (PD-1) or PD-ligand-1 (PD-L1). Additionally, loss of function alterations of CDK12, found in 5-7% of mCRPC, may confer vulnerability to anti-PD-L1 agents. Methods: This multi-center study will enroll 54 unselected mCRPC patients (pts), randomized 1:1 to abema (arm A) or abema + atezo (arm B); and 21 pts with known loss of function mutations in CDK12 (arm C) treated with atezo (n = 5) or abema + atezo (n = 16). All pts will undergo on-treatment (6-week) tumor biopsy. Treatment will be continued until disease progression and crossover is prohibited. Key eligibility criteria are age ≥ 18 years, ECOG PS 0-1, biopsy-proven prostate adenocarcinoma, progressive metastatic disease per Prostate Cancer Working Group 3 (PCWG3), progression/intolerance to ≥ 1 novel antiandrogen in hormone-sensitive or CRPC setting, ineligible for docetaxel/cabazitaxel (progression within 12 months of taxane, pt refusal, investigator discretion), no uncontrolled comorbidity or history of pneumonitis/ILD. Arms A & B will use two stage design for co-primary endpoints of progression-free survival at 6 months using PCWG3 (6m-PFS) and objective response rate (ORR). If ≥ 1/12 pts meet either co-primary endpoint, 2nd stage will open to enroll 15 more pts in that arm. Treatment will be deemed to have meaningful clinical activity (MCA) if ≥ 6/27 meet 6m-PFS or ≥ 5/27 have an ORR. This will provide 86% power for 6m-PFS (34% vs. 12%) and 85% power for ORR (30% vs. 10%) at a one-sided α = 0.08. For MCA in arm C, 16 patients treated with abema+atezo will provide 80-85% power for 6m-PFS (34% vs. 12%) at a one-sided α = 0.05 using a one-sample log-rank test. Primary safety endpoint is the incidence of dose-limiting toxicities in pts receiving abema+atezo. Key secondary endpoints are clinical benefit rate (ORR + stable disease), duration of response and overall survival in arms A and B, and safety events in all arms. Primary exploratory endpoint is comparison of tumoral FoxP3+/CD8+ ratio in pts treated with abema vs. abema + atezo. Additional exploratory endpoints will evaluate association between response and genomic alterations identified from tissue or circulating tumor-derived exosomes. Enrollment began in July 2021 and projected enrollment goal is 3 years (NCT04751929). Clinical trial information: NCT04751929.

FOXP3+ T-cell infiltration is associated with improved outcomes in metastatic urothelial carcinoma (mUC) treated with immune-checkpoint inhibitors (ICI)

549

Background: Given that ICIs benefit a minority of mUC patients and are associated with significant costs, biomarkers are necessary to optimally utilize them in the clinic. Although FOXP3+ T-cells have been associated with an immune-cold environment in many cancers, studies in urothelial carcinoma have shown an opposite trend. Methods: Formalin-fixed paraffin-embedded slides from tumor specimens were collected for patients with mUC treated with ICI at Dana-Farber Cancer Institute. A novel multiplex immunofluorescence (mIF) panel, ImmunoProfile, was performed for PD-L1, PD-1, FOXP3, CD8 and DAPI, then scanned by a Vectra Polaris platform. Regions of interest were defined and used for quantitative analysis using PerkinElmer/Akoya. Intratumoral (IT) and tumor-stroma interface (TSI) density (cells/mm2) of each cell type was calculated. Clinical data was collected through chart review, and associations between cell density and response were assessed. Wilcoxon Rank-Sum test between responders (CR/PR) and non-responders (SD/PD) was used to generate p-values, followed by Benjamini-Hochberg correction. Receiver-operating curve (ROC) and area-under-curve (AUC) calculations were performed to determine the optimal cutoff (OC) differentiating responders from non-responders. Cox proportional hazards models were used to estimate OS and PFS, accounting for type of therapy (single vs. combination ICI), baseline neutrophil-to-lymphocyte ratio (NLR), PD-L1 CPS, prior therapy, non-urothelial component, ECOG-PS and liver metastases (mets). Results: Of 35 patients assessed by ImmunoProfile, 32 were evaluable for response. Most patients (88%) were male and the median age at ICI start was 73 years. Median number of prior lines of therapy was 1 (range 0 – 3), and the majority (72%) was treated with single-agent ICI. Eight patients (25%) had CR/PR, eight had SD and 16 had PD as best response. Of all IF stains assessed, IT-TSI FOXP3 was the strongest predictor of objective response (q-value = 0.006), followed by IT-CD8 (q = 0.014). ROC analysis yielded an AUC of 0.812 (0.656 – 0.969) and the optimal cutpoint was set at 75 IT-TSI-FOXP3 cells/mm2. ORR was 46% in FOXP3-high ( > 75/mm2) vs 14% in FOXP3-low mUCs. A combined model using IT-TSI-FOXP3 and clinical covariates (NLR, ECOG-PS, line of therapy, histology, and liver mets) had an AUC of 0.929. PFS was significantly longer in the FOXP3-high group (7.9 [5.7 – NR] months) compared to the FOXP3-low group (2.3 [2.1 – 6.1] months) on multivariable analysis (p = 0.007). OS also showed the same trend (p = 0.1). Conclusions: In this pilot study of ImmunoProfile, a novel mIF panel, higher FOXP3+ infiltration in tumors was associated with better outcomes and a composite clinico-IHC panel exhibited robust prognostic impact in mUC pts treated with ICI. Further study of this mIF panel is warranted to implement it in routine practice.

Durvalumab plus tremelimumab alone or in combination with low-dose or hypofractionated radiotherapy in metastatic non-small-cell lung cancer refractory to previous PD(L)-1 therapy: an open-label, multicentre, randomised, phase 2 trial

BACKGROUND

Patients with non-small-cell lung cancer (NSCLC) that is resistant to PD-1 and PD-L1 (PD[L]-1)-targeted therapy have poor outcomes. Studies suggest that radiotherapy could enhance antitumour immunity. Therefore, we investigated the potential benefit of PD-L1 (durvalumab) and CTLA-4 (tremelimumab) inhibition alone or combined with radiotherapy.

METHODS

This open-label, multicentre, randomised, phase 2 trial was done by the National Cancer Institute Experimental Therapeutics Clinical Trials Network at 18 US sites. Patients aged 18 years or older with metastatic NSCLC, an Eastern Cooperative Oncology Group performance status of 0 or 1, and progression during previous PD(L)-1 therapy were eligible. They were randomly assigned (1:1:1) in a web-based system by the study statistician using a permuted block scheme (block sizes of three or six) without stratification to receive either durvalumab (1500 mg intravenously every 4 weeks for a maximum of 13 cycles) plus tremelimumab (75 mg intravenously every 4 weeks for a maximum of four cycles) alone or with low-dose (0·5 Gy delivered twice per day, repeated for 2 days during each of the first four cycles of therapy) or hypofractionated radiotherapy (24 Gy total delivered over three 8-Gy fractions during the first cycle only), 1 week after initial durvalumab-tremelimumab administration. Study treatment was continued until 1 year or until progression. The primary endpoint was overall response rate (best locally assessed confirmed response of a partial or complete response) and, along with safety, was analysed in patients who received at least one dose of study therapy. The trial is registered with ClinicalTrials.gov, NCT02888743, and is now complete.

FINDINGS

Between Aug 24, 2017, and March 29, 2019, 90 patients were enrolled and randomly assigned, of whom 78 (26 per group) were treated. This trial was stopped due to futility assessed in an interim analysis. At a median follow-up of 12·4 months (IQR 7·8-15·1), there were no differences in overall response rates between the durvalumab-tremelimumab alone group (three [11·5%, 90% CI 1·2-21·8] of 26 patients) and the low-dose radiotherapy group (two [7·7%, 0·0-16·3] of 26 patients; p=0·64) or the hypofractionated radiotherapy group (three [11·5%, 1·2-21·8] of 26 patients; p=0·99). The most common grade 3-4 adverse events were dyspnoea (two [8%] in the durvalumab-tremelimumab alone group; three [12%] in the low-dose radiotherapy group; and three [12%] in the hypofractionated radiotherapy group) and hyponatraemia (one [4%] in the durvalumab-tremelimumab alone group vs two [8%] in the low-dose radiotherapy group vs three [12%] in the hypofractionated radiotherapy group). Treatment-related serious adverse events occurred in one (4%) patient in the durvalumab-tremelimumab alone group (maculopapular rash), five (19%) patients in the low-dose radiotherapy group (abdominal pain, diarrhoea, dyspnoea, hypokalemia, and respiratory failure), and four (15%) patients in the hypofractionated group (adrenal insufficiency, colitis, diarrhoea, and hyponatremia). In the low-dose radiotherapy group, there was one death from respiratory failure potentially related to study therapy.

INTERPRETATION

Radiotherapy did not increase responses to combined PD-L1 plus CTLA-4 inhibition in patients with NSCLC resistant to PD(L)-1 therapy. However, PD-L1 plus CTLA-4 therapy could be a treatment option for some patients. Future studies should refine predictive biomarkers in this setting.

FUNDING

The US National Institutes of Health and the Dana-Farber Cancer Institute.

Low peripheral blood derived neutrophil-to-lymphocyte ratio (dNLR) is associated with increased tumor T-cell infiltration and favorable outcomes to first-line pembrolizumab in non-small cell lung cancer

BACKGROUND

An elevated peripheral blood derived neutrophil-to-lymphocyte ratio (dNLR) is a negative prognostic marker for patients with non-small cell lung cancer (NSCLC) receiving chemotherapy and immune checkpoint inhibitors. Whether dNLR is also associated with clinical outcomes to first-line pembrolizumab among patients with NSCLC and a programmed cell death ligand 1 (PD-L1) Tumor Proportion Score (TPS) of ≥50% is uncertain. How dNLR relates to the tumor immune microenvironment is also unclear.

METHODS

In two participating academic centers, we retrospectively analyzed the dNLR (defined as the absolute neutrophil count/white cell count - absolute neutrophil count) prior to initiation of first-line pembrolizumab in patients with metastatic NSCLC and a PD-L1 TPS ≥50% and lacking genomic alterations in EGFR and ALK. An unbiased recursive partitioning algorithm was used to investigate an optimal dNLR cut-off with respect to objective response rate (ORR). Multiplexed immunofluorescence for CD8+, FOXP3+, PD-1+, and PD-L1 was performed on a separate cohort of NSCLCs to determine the immunophenotype associated with dNLR.

RESULTS

A total of 221 patients treated with first-line pembrolizumab were included in this study. The optimal dNLR cut-off to differentiate treatment responders from non-responders was 2.6. Compared with patients with a dNLR ≥2.6 (n=97), patients with dNLR <2.6 (n=124) had a significantly higher ORR (52.4% vs 24.7%, p<0.001), a significantly longer median progression-free survival (mPFS 10.4 vs 3.4 months, HR 0.48, 95% CI 0.35 to 0.66, p<0.001), and a significantly longer median overall survival (mOS 36.6 vs 9.8 months, HR 0.34, 95% CI 0.23 to 0.49, p<0.001). After adjusting for age, sex, tobacco use, performance status, histology, serum albumin level, oncogenic driver status, and PD-L1 distribution (50%-89% vs ≥90%), a dNLR <2.6 was confirmed to be an independent predictor of longer mPFS (HR 0.47, 95% CI 0.33 to 0.67, p<0.001) and mOS (HR 0.32, 95% CI 0.21 to 0.49, p<0.001). Among advanced NSCLC samples with a PD-L1 TPS of ≥50%, those with a dNLR <2.6 had significantly higher numbers of tumor-associated CD8+, FOXP3+, PD-1 +immune cells, and PD-1 +CD8+T cells than those with a dNLR ≥2.6.

CONCLUSIONS

Among patients with NSCLC and a PD-L1 TPS ≥50%, a low dNLR has a distinct immune tumor microenvironment and more favorable outcomes to first-line pembrolizumab.

Combining CTLA-4 and angiopoietin-2 blockade in patients with advanced melanoma: a phase I trial

Background

Angiogenic factors promote the growth of tumor vasculature, modulate lymphocyte trafficking into tumors, and inhibit maturation of dendritic cells. We hypothesized that MEDI3617, a human IgG1 kappa monoclonal antibody directed against human angiopoietin-2, in combination with tremelimumab (treme), an IgG2 monoclonal antibody blocking cytotoxic T-lymphocyte-associated protein- (CTLA-4), is safe in patients with advanced melanoma.

Methods

In a phase I, 3+3 dose escalation trial, patients with metastatic or unresectable melanoma received treme in combination with MEDI3617. The primary objectives of the study were safety and determination of recommended phase II dose (RP2D). The secondary objectives included determination of 6-month and 1-year overall survival and best overall response rate. Immune cell populations and soluble factors were assessed in peripheral blood and metastatic tumors using Fluorescence activated cell sorting (FACS), Luminex, and multiplexed immunofluorescence.

Results

Fifteen patients (median age: 62) were enrolled in the study (3 patients in cohort 1: treme at 10 mg/kg and MEDI3617 at 200 mg; and 12 patients in cohort 2: treme at 10 mg/kg and MEDI3617 at 600 mg). The most common all-grade treatment-related adverse events were rash, pruritus, fatigue, and extremity edema. No dose-limiting toxicities were observed. Cohort 2 was determined to be the RP2D. There were no patients with confirmed immune-related complete response or immune-related partial response. Six of 15 patients had immune-related stable disease, resulting in a disease control rate of 0.40 (95% CI 0.16 to 0.68). An increase in frequencies of circulating inducible T-cell costimulator (ICOS)⁺ and human leukocyte antigen (HLA)-DR⁺ CD4⁺ and CD8⁺ T cells and production of Interleukin-2 and Interleukin-10 was observed post therapy.

Conclusions

Tremelimumab in combination with MEDI3617 is safe in patients with advanced melanoma. Angiopoietin-2 inhibition in combination with immune checkpoint inhibition warrants further exploration.

Trial registration number

NCT02141542.

Comprehensive Immunoprofiling of High-Risk Oral Proliferative and Localized Leukoplakia

Oral leukoplakia is common and may, in some cases, progress to carcinoma. Proliferative leukoplakia is a progressive, often multifocal subtype with a high rate of malignant transformation compared with the more common localized leukoplakia. We hypothesized that the immune microenvironment and gene expression patterns would be distinct for proliferative leukoplakia compared with localized leukoplakia. We summarize key clinicopathologic features among proliferative leukoplakia and localized leukoplakia and compare cancer-free survival (CFS) between subgroups. We analyze immunologic gene expression profiling in proliferative leukoplakia and localized leukoplakia tissue samples (NanoString PanCancer Immune Oncology Profiling). We integrate immune cell activation and spatial distribution patterns in tissue samples using multiplexed immunofluorescence and digital image capture to further define proliferative leukoplakia and localized leukoplakia. Among N = 58 patients (proliferative leukoplakia, n = 29; localized leukoplakia, n = 29), only the clinical diagnosis of proliferative leukoplakia was associated with significantly decreased CFS (HR, 11.25; P < 0.01; 5-year CFS 46.8% and 83.6% among patients with proliferative leukoplakia and localized leukoplakia, respectively). CD8⁺ T cells and T regulatory (Treg) were more abundant among proliferative leukoplakia samples (P < 0.01) regardless of degree of epithelial dysplasia, and often colocalized to the dysplasia-stromal interface. Gene set analysis identified granzyme M as the most differentially expressed gene favoring the proliferative leukoplakia subgroup (log₂ fold change, 1.93; P _adj < 0.001). Programmed death ligand 1 (PD-L1) was comparatively overexpressed among proliferative leukoplakia samples, with higher (>5) PD-L1 scores predicting worse CFS (P _adj < 0.01). Proliferative leukoplakia predicts a high rate of malignant transformation within 5 years of diagnosis. A prominent CD8⁺ T-cell and Treg signature along with relative PD-L1 overexpression compared with localized leukoplakia provides strong rationale for PD-1/PD-L1 axis blockade using preventative immunotherapy.

Significance

This is the first in-depth profiling effort to immunologically characterize high-risk proliferative leukoplakia as compared with the more common localized leukoplakia. We observed a notable cytotoxic T-cell and Treg signature with relative overexpression of PD-L1 in high-risk proliferative leukoplakia providing a strong preclinical rationale for investigating PD-1/PD-L1 axis blockade in this disease as preventative immunotherapy.

Synergistic melanoma cell death mediated by inhibition of both MCL1 and BCL2 in high-risk tumors driven by NF1/PTEN loss

Melanomas driven by loss of the NF1 tumor suppressor have a high risk of treatment failure and effective therapies have not been developed. Here we show that loss-of-function mutations of nf1 and pten result in aggressive melanomas in zebrafish, representing the first animal model of NF1-mutant melanomas harboring PTEN loss. MEK or PI3K inhibitors show little activity when given alone due to cross-talk between the pathways, and high toxicity when given together. The mTOR inhibitors, sirolimus, everolimus, and temsirolimus, were the most active single agents tested, potently induced tumor-suppressive autophagy, but not apoptosis. Because addition of the BCL2 inhibitor venetoclax resulted in compensatory upregulation of MCL1, we established a three-drug combination composed of sirolimus, venetoclax, and the MCL1 inhibitor S63845. This well-tolerated drug combination potently and synergistically induces apoptosis in both zebrafish and human NF1/PTEN-deficient melanoma cells, providing preclinical evidence justifying an early-stage clinical trial in patients with NF1/PTEN-deficient melanoma.

SMARCA4 and Other SWItch/Sucrose NonFermentable Family Genomic Alterations in NSCLC: Clinicopathologic Characteristics and Outcomes to Immune Checkpoint Inhibition

INTRODUCTION

The SWItch/Sucrose Nonfermentable (SWI/SNF) chromatin remodeling complex acts as a regulatory component of transcription, and inactivating mutations (muts) within the complex are implicated in genomic instability, higher tumor mutational burden, and an aggressive cancer phenotype. Whether SMARCA4 and other SWI/SNF alterations are independent prognostic factors or associated with clinical outcomes to immune checkpoint inhibitors (ICIs) in NSCLC remains unclear.

METHODS

We collected clinicopathologic and genomic data from patients with NSCLC who underwent targeted next-generation sequencing at the Dana-Farber Cancer Institute. Tumors were characterized on the basis of the presence or absence of muts across a set of six SWI/SNF genes (ARID1A, ARID1B, ARID2, PBRM1, SMARCA4, and SMARCB1).

RESULTS

Of 2689 patients with NSCLC, 20.6% (N = 555) had SWI/SNF genomic alterations. Compared with SWI/SNF wild-type (wt) NSCLC, patients with SWI/SNF-mutant NSCLCs had a lower prevalence of concurrent targetable driver muts (33.2% versus 22.2%; p < 0.001), a higher tumor mutational burden (median 8.5 versus 12.2 muts/megabase; p < 0.001), and a shorter median overall survival (mOS) from the time of advanced disease diagnosis (25.0 versus 19.3 mo, p = 0.01); the detrimental effect in OS seemed to be largely driven by SMARCA4 muts (mOS: 25.0 for SMARCA4 wt versus 15.6 mo for SMARCA4 mutant; p < 0.001). Among 532 patients who received ICIs, 25.5% (N = 136) harbored SWI/SNF muts. From the start of immunotherapy, there was no difference in objective response rate (ORR = 19.9% versus 25.0%, p = 0.2), median progression-free survival (mPFS = 3.0 versus 3.0 mo, hazard ratio [HR] = 0.96 [95% confidence interval [CI] = 0.77-1.18], p = 0.7), or mOS (13.1 versus 9.5 mo, HR = 0.81 [95% CI: 0.64-1.02], p = 0.07) in SWI/SNF-wt versus SWI/SNF-mutant NSCLC, respectively. Nevertheless, among KRAS-mutant NSCLCs treated with ICIs (N = 176), a concurrent SWI/SNF mut (N = 39) conferred a numerically lower ORR (21.9% versus 12.8%, p = 0.2), a significantly shorter mPFS (4.1 versus 1.8 mo, HR = 0.57 [95% CI: 0.38-0.84], p = 0.005), and a significantly shorter mOS (15.5 versus 8.2 mo, HR = 0.56 [95% CI: 0.36-0.86], p = 0.008). The deleterious effect on immunotherapy outcomes in KRAS-mutant NSCLC was most pronounced in the SMARCA4-mutant subset (N = 17), with a lower ORR (22% versus 0%, p = 0.03), a significantly shorter mPFS (4.1 versus 1.4 mo, HR = 0.25 [95% CI: 0.14-0.42], p < 0.001), and a significantly shorter mOS (15.1 versus 3.0 mo, HR = 0.29 [95% CI: 0.17-0.50], p < 0.001) compared with SMARCA4-wt KRAS-mutant NSCLCs.

CONCLUSIONS

Although there were no associations between SWI/SNF mut status and immunotherapy efficacy in the overall NSCLC cohort, the presence of a SMARCA4 alteration may confer a worse outcome to immunotherapy among KRAS-mutant NSCLCs.

Abstract 65: Therapeutically increasing MHC-I expression potentiates immune checkpoint blockade

Immune checkpoint blockade (ICB) therapy revolutionized cancer treatment, but many patients with impaired MHC-I expression remain refractory. Here, we combined FACS-based genome-wide CRISPR screens with a data-mining approach to identify drugs that can upregulate MHC-I without inducing PD-L1. CRISPR screening identified TRAF3, a critical suppressor of the NF-κB pathway, as a negative regulator of MHC-I but not PD-L1. The Traf3-knockout (Traf3-KO) gene expression signature is associated with better survival in ICB-naive cancer patients and better ICB response. We then screened for drugs with similar transcriptional effects as this signature and identified SMAC mimetics. We experimentally validated that the SMAC mimetic birinapant upregulates MHC-I, sensitizes cancer cells to T-cell-dependent killing, and synergizes with ICB. Our findings provide preclinical rationale for treating tumors expressing low MHC-I expression with SMAC mimetics to enhance sensitivity to immunotherapy. The approach used in this study can be generalized to identify other drugs that enhance immunotherapy efficacy.

Citation Format: Shengqing Gu, Wubing Zhang, Xiaoqing Wang, Peng Jiang, Nicole Traugh, Ziyi Li, Clifford Meyer, Blair Stewig, Yingtian Xie, Xia Bu, Michael Manos, Alba Font-Tello, Evisa Gjini, Ana Lako, Klothilda Lim, Jake Conway, Alok Tewari, Zexian Zeng, Avinash Das Sahu, Collin Tokheim, Jason L. Weirather, Jingxin Fu, Yi Zhang, Benjamin Kroger, Jin Hua Liang, Paloma Cejas, Gordon J. Freeman, Scott J. Rodig, Henry Long, Benjamin E. Gewurz, F. Stephen Hodi, Myles Brown, X. Shirley Liu. Therapeutically increasing MHC-I expression potentiates immune checkpoint blockade [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 65.

Abstract 490: A very high tumor mutational burden (TMB) is associated with improved efficacy of PD-(L)1 inhibition across different PD-L1 expression subgroups and a distinct immunophenotype in NSCLC

Background: Although high TMB correlates with improved outcomes to immune checkpoint inhibitors (ICI) in patients (pts) with non-small cell lung cancer (NSCLC), an optimal TMB cut-off to discriminate cancers most likely to respond to ICI has not been identified. Whether TMB impacts outcomes to ICI in different PD-L1 levels subgroups is also unclear.

Methods: Unbiased recursive partitioning (URP) was used to identify an optimal TMB cut-off for objective response rate (ORR) in two independent cohorts (DFCI and MSKCC) of pts with NSCLC treated with ICI. TCGA was interrogated to find differences in tumor immune cell subsets according to the TMB cut-off identified. Multiplexed immunofluorescence (IP) was also performed on NSCLC samples.

Results: In the DFCI (N=686) and MSKCC (N=672) cohorts, URP found an optimal cut-off of TMB for ORR at 19 mutations/megabase (mut/Mb), corresponding to the 90th percentile in each cohort. Median progression-free (PFS) and overall survival (OS) were significantly longer in NSCLCs with TMB ≥19 mut/Mb vs &lt;19 mut/Mb, in both cohorts (Table). After harmonizing TMB between DFCI OncoPanel and MSK-IMPACT NGS platforms, URP confirmed an optimal TMB cut-off for ORR at the 90th percentile in the combined cohort, which also associated with longer PFS/OS (Table). A TMB ≥90th percentile correlated with longer PFS/OS among NSCLCs with PD-L1 levels ≥50% and 1-49%, and longer PFS among those with PD-L1 &lt;1% (Table). Cell subset transcriptome analysis from the TCGA showed higher proportions of CD8+ T cells (P=0.02) and M1 macrophages (P&lt;0.01), among NSCLCs with a TMB ≥ vs &lt;90th percentile. IP confirmed increased CD8+ and CD8+/PD1+ T-cell infiltration (P&lt;0.01) in NSCLC with very high TMB.

Conclusion: A very high TMB is associated with better outcomes to ICI and a distinct immunophenotype in NSCLC. Rational integration of TMB and PD-L1 expression may identify NSCLCs most likely to respond to ICI.

CohortPD-L1 expressionPFS TMB ≥ vs &lt;90th percentile HR [95%CI],POS TMB ≥ vs &lt;90th percentile HR [95%CI],PDFCI N=6860-1000.48 [0.36-0.65],P&lt;0.010.57 [0.41-0.78],P&lt;0.01MSKCC N=6720-1000.38 [0.28-0.52],P&lt;0.010.46 [0.33-0.65],P&lt;0.01DFCI+MSKCC0-1000.44 [0.35-0.54],P&lt;0.010.50 [0.39-0.64],P&lt;0.01DFCI+MSKCC≥50%0.52 [0.34-0.81], P&lt;0.010.54 [0.32-0.94],P=0.031-49%0.33 [0.19-0.57],P&lt;0.010.36 [0.19-0.69], P&lt;0.01&lt;1%0.40 [0.25-0.65], P&lt;0.010.72 [0.34-1.18],P=0.19

Citation Format: Biagio Ricciuti, Kathryn C. Arbour, Navin R. Mahadevan, Joao V. Alessi, James Lindsay, Renato Umeton, Rileen Sinha, Amir Hoojghan, Natalie Vokes, Gonzalo Recondo, Giuseppe Lamberti, Andrew Polio1, Hira Rizvi, Giulia Leonardi, Andrew J. Plodkowski, Kristen Felt, Bijaya Sharma, Michael Y. Tolstorukov, Pasi A. Janne, Eliezer M. Van Allen, Lynette M. Sholl, Scott J. Rodig, Matthew D. Hellmann, Mark M. Awad. A very high tumor mutational burden (TMB) is associated with improved efficacy of PD-(L)1 inhibition across different PD-L1 expression subgroups and a distinct immunophenotype in NSCLC [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 490.

Molecular and cellular features of CTLA-4 blockade for relapsed myeloid malignancies after transplantation

Relapsed myeloid disease after allogeneic stem cell transplantation (HSCT) remains largely incurable. We previously demonstrated the potent activity of immune checkpoint blockade in this clinical setting with ipilimumab or nivolumab. To define the molecular and cellular pathways by which CTLA-4 blockade with ipilimumab can reinvigorate an effective graft-versus-leukemia (GVL) response, we integrated transcriptomic analysis of leukemic biopsies with immunophenotypic profiling of matched peripheral blood samples collected from patients treated with ipilimumab following HSCT on the Experimental Therapeutics Clinical Trials Network 9204 trial. Response to ipilimumab was associated with transcriptomic evidence of increased local CD8+ T-cell infiltration and activation. Systemically, ipilimumab decreased naïve and increased memory T-cell populations and increased expression of markers of T-cell activation and costimulation such as PD-1, HLA-DR, and ICOS, irrespective of response. However, responding patients were characterized by higher turnover of T-cell receptor sequences in peripheral blood and showed increased expression of proinflammatory chemokines in plasma that was further amplified by ipilimumab. Altogether, these data highlight the compositional T-cell shifts and inflammatory pathways induced by ipilimumab both locally and systemically that associate with successful GVL outcomes. This trial was registered at www.clinicaltrials.gov as #NCT01822509.

Fixing and Binding Antibodies to Suspension Cells in Preparation for Staining

Staining of suspension cells after fixation, described here, is normally used only to detect cell-surface antigens. Once cells are fixed and permeabilized, the antibodies are added. The antibodies can be labeled directly or they can be detected by using a labeled secondary reagent that will bind specifically to the primary antibody. Detection reagents for cell staining can be labeled with fluorochromes, enzymes, gold, or iodine. Because the cells are in suspension, the washing steps are tedious, and care should be taken not to centrifuge for long durations or at high speeds.

Detecting Fluorochrome-Labeled Cells

This protocol describes cell staining using fluorochrome-labeled antibodies. The resolution of subcellular structures using fluorochrome-labeled antibodies exceeds that of the transmitted light microscope because of the visualization of an expanding cone of emitted light from the excited fluorochrome in the specimen. The most commonly used fluorochromes are fluorescein and rhodamine. In recent years, a number of advances in the development of fluorochromes have resulted in brighter and longer-lasting dyes with narrow emission spectra. These are available from a number of commercial suppliers. They can be conjugated to anti-immunoglobulin antibodies, Protein A, Protein G, avidin, or streptavidin. These conjugates are available from many commercial sources. Filter sets are commonly available that will permit independent observation of these two fluorochromes in the same sample. The fluorochrome Texas Red is also used for immunofluorescence, and can be detected using the same filter sets as rhodamine.

Clinicopathologic and genomic correlates of tumor-infiltrating immune cells and immunotherapy efficacy in NSCLC

9121

Background: Tumor-infiltrating immune cells and PD-L1 expression are associated with improved clinical outcomes in patients (pts) with NSCLC treated with immune checkpoint inhibitors (ICIs). However, as tumor-infiltrating immune cells are not a well-established biomarker for NSCLC, further data are needed to integrate and identify clinicopathological and genomic factors that influence the tumor microenvironment. Methods: We collected clinicopathologic and genomic data from pts with NSCLC who underwent multiplexed immunofluorescence. Uniform Manifold Approximation and Projection (UMAP) was used to identify distinct immunophenotypic clusters according to the number of intratumoral PD-1+ immune cells (ICs), CD8+, and Foxp3+ T cells, as well as PD-L1 on tumor and immune cells. An unbiased recursive partitioning (URP) algorithm was used to investigate an optimal cluster with respect to objective response rate (ORR) in the subset of pts treated with ICIs. Results: Among 304 pts, UMAP identified 5 clusters: PD-L1-high with high vs low CD8+ and PD-1+ ICs (clusters A & B, respectively); PD-L1-low with high vs low CD8+ and PD-1+ ICs (clusters C & D respectively); PD-L1-low and moderate levels of CD8+ and PD-1+ ICs (cluster E). Clinicopathological characteristics of the clusters shown in Table. URP analysis identified immune rich clusters A and C as optimal responders to ICIs. From the start of ICIs, we observed a significantly higher ORR (53.3% vs 4.3%; P<0.001), a significantly longer median progression-free survival (mPFS 25.6 vs 3.7 months; HR: 0.12 [95% CI: 0.05-0.32]; P<0.001), and longer median overall survival (mOS 45.1 vs 22.3 months; HR: 0.25 [95% CI: 0.1-0.68]; P=0.006) in clusters A + C (N=15) vs other clusters (N=23). After adjusting for other variables such as performance status, histology, presence of oncogenic driver mutation, and line of treatment, clusters A + C were significantly associated with improved mPFS (HR: 0.08 [95% CI: 0.03-0.24], P<0.001) and mOS (HR: 0.11 [95% CI: 0.03-0.40], P<0.001). Conclusions: Incorporation of multiplex immunofluorescence may improve prediction of response and resistance to immunotherapy in NSCLC.[Table: see text]

Pathology of durable stable disease in melanoma patients treated with ipilimumab, nivolumab, or ipilimumab, and nivolumab combination therapy

9567

Background: As immunotherapy with checkpoint blockade becomes the backbone of melanoma treatment there is a need to better understand the biology associated with long term benefit. One particularly interesting set of patients are those with prolonged stable disease or response with residual findings on imaging. It is unknown if immunotherapy has led to scarring at the site of prior disease or if there are residual tumor cells being controlled by an ongoing immune response. Evaluating tissue from patients with prolonged responses provides a unique opportunity to determine the composition of residual lesions. Correlation with PET/CT helps determine if this is an accurate modality to reflect presence of residual viable tumor tissue. Methods: Metastatic melanoma patients that have attained long term stable disease after treatment with ipilimumab, nivolumab, or ipilimumab plus nivolumab were identified. Patients must have received ipilimumab, nivolumab or combination therapy 2+ years prior to enrollment and must have had stable disease for ≥ 6 months. Patients were consented and underwent PET/CT scans and biopsies of residual areas of stable disease. Pre- and post-treatment tissue samples underwent pathologic assessment to look at tumor cell content, fibrotic content, and inflammation. Results: Ten patients were consented for evaluation but only 7 met the screening criteria and underwent PET/CT and tissue biopsy. Six patients had FDG avid lesions on PET/CT which ranged in intensity from SUV 2.4-22. One patient had no FDG avidity in the areas of residual disease observed on CT. Biopsies from the residual stable lesions demonstrated predominantly necrosis and fibrosis with prominent pigment containing macrophages. One patient with an axillary nodal lesion with an SUV of 22 had active melanoma on pathology which was resected, and the patient has subsequently remained without progression of disease. Conclusions: Patients with durable stable disease after treatment with ipilimumab, nivolumab or ipilimumab and nivolumab combination therapy represent a unique population of melanoma patients treated with immune checkpoint inhibition. An examination of the residual lesions observed in these patients demonstrated predominantly necrosis and fibrosis consistent with resolving lesions. The presence of melanophages in these samples may suggest some ongoing immune surveillance. One patient did demonstrate residual melanoma suggesting the need for ongoing monitoring of this patient population.

Association of a very high tumor mutational load with increased CD8+ and PD-1+ T-cell infiltration and improved clinical outcomes to PD-(L)1 blockade across different PD-L1 expression levels in non-small cell lung cancer

9018

Background: Although high TMB correlates with improved outcomes to immune checkpoint inhibitors (ICI) in patients (pts) with non-small cell lung cancer (NSCLC), an optimal TMB cutoff to discriminate cancers most likely to respond to ICI has not been identified. Whether TMB impacts outcomes to ICI in different PD-L1 levels subgroups is also unclear. Methods: Unbiased recursive partitioning (URP) was used to identify an optimal TMB cutoff for objective response rate (ORR) in two independent cohorts of pts with NSCLC treated with ICI at DFCI and MSKCC. TCGA was interrogated to find differences in tumor immune cell subsets according to the TMB cutoff identified. Multiplexed immunofluorescence (IF) for CD8, PD-1, PD-L1, Foxp3, and CK7 was also performed on NSCLC samples at the DFCI. Results: In the DFCI (N=686) and MSKCC (N=672) cohorts, URP found an optimal TMB cutoff for ORR at 19 mutations/megabase (mut/Mb), corresponding to the ̃90th percentile in each cohort. Median progression-free (PFS) and overall survival (OS) were significantly longer in NSCLCs with TMB ≥19 mut/Mb vs <19 mut/Mb, in both cohorts (Table). After harmonizing TMB between DFCI OncoPanel and MSK-IMPACT NGS platforms, URP confirmed an optimal TMB cutoff for ORR at the 90th percentile in the combined cohort, which also associated with longer PFS/OS to ICI (Table). A TMB ≥90th percentile correlated with longer PFS/OS to ICI among NSCLCs with PD-L1 levels ≥50% and 1-49%, and longer PFS among those with PD-L1 <1% (Table). Cell subset transcriptome analysis from the TCGA showed higher proportions of CD8+ T cells (P=0.02) and M1 macrophages (P<0.01) among NSCLCs with a TMB ≥ vs <90th percentile. IF confirmed increased CD8+, CD8+ PD1+ T-cell infiltration (P<0.01), and increased CD8+/Foxp3+ ratio in NSCLC with very high TMB Conclusions: A very high TMB is associated with better outcomes to ICI and a distinct immunophenotype in NSCLC. Rational integration of TMB and PD-L1 expression may identify NSCLCs most likely to respond to ICI.[Table: see text]

Randomized multicenter phase Ib/II study of neoadjuvant chemoradiation therapy (CRT) alone or in combination with pembrolizumab in patients with resectable or borderline resectable pancreatic cancer

4128

Background: Pancreatic cancer (PC) is a challenging target for immunotherapy due to suppressive immune-microenvironment. Neoadjuvant chemoradiation (CRT) can increase the presence of tumor-infiltrating lymphocytes (TILs). We hypothesized that the combination of CRT and pembrolizumab can lead to further increase in TILs and their activation. Methods: Patients with resectable or borderline resectable PC were randomized 2:1 to the investigational treatment (Arm A) of pembrolizumab 200mg IV every 3 weeks concurrently with CRT (capecitabine 825 mg/m2 orally twice daily and radiation 50.4 Gy in 28 fractions over 28 days) or CRT only (Arm B) prior to surgical resection. The primary endpoints were treatment safety and density of TILs with the objective to estimate differences in TILs density between the investigational and the control arms. Immune cell densities were assessed using multiplexed immunofluorescence on resected tumor specimens. Densities of CD8+TILs were measured in 2-10 representative regions containing residual cancer per case and then averaged to obtain overall densities. The study was amended after enrollment of 37 patients to allow FOLFIRINOX prior to CRT, given changes in standard of care. Results: 37 patients were enrolled (24 Arm A and 13 Arm B). Post-neoadjuvant therapy, 13 patients had unresectable disease (9 on A and 4 on B), and 24 patients underwent surgery and were evaluable for the TILs primary endpoint (17 arm A and 7 arm B). The mean difference (A-B) in CD8+ cell density was 36 cells/mm2 (95% CI -85 to 157, stdev 130) (p 0.48). Additional analysis did not show significant differences in CD8+Ki67+ (activated cytotoxic T-cells), CD4+, and CD4+FOXP3+ (regulatory T cells), M1- or M2-like polarized macrophages, or granulocytes. The median recurrence free survival (RFS) was 18.2 months on Arm A and 14.1 on Arm B (p 0.41) and Overall Survival was 27.8 months on Arm A and 24.3 on Arm B (p 0.68) with a median follow up of 2.2 years. The most common grade 3 treatment-related toxicities were lymphopenia reported in 29% on Arm A and 31% on Arm B followed by diarrhea in 8% on Arm A attributed to CRT. There was only 1 DLT of increased ALT attributed to the combination on Arm A that resolved after holding the treatment and receiving steroids. There were no major surgical complications reported within 30 days post-surgery. Conclusions: The combination of CRT and pembrolizumab is safe. Preliminary analysis shows that the addition of pembrolizumab to CRT has minimal effects on several immune cell populations including CD8+TILs in the PC microenvironment. The study is currently enrolling 25 more patients who receive FOLFIRINOX prior to randomization to CRT+/- Pembrolizumab, which will help to dissect the immune modulatory effect of chemotherapy followed by CRT. Clinical trial information: NCT02305186.

Clinicopathologic, genomic, and tumor microenvironment correlates of aneuploidy and immunotherapy outcomes in NSCLC

9119

Background: Cancer aneuploidy, an unbalanced number of chromosomes, is associated with somatic mutation rate, expression of proliferative genes, and altered immune signaling. Whether aneuploidy correlates to a distinct immunophenotype or impacts clinical outcomes to immune checkpoint inhibitors (ICIs) in NSCLC is unclear. Methods: In NSCLCs which underwent targeted next-generation sequencing, we retrospectively analyzed the aneuploidy score (AS), defined as the sum of the number of altered chromosome arms. An unbiased recursive partitioning (URP) algorithm was used to investigate an AS cutoff to discriminate responders from non-responders to ICIs. Multiplexed immunofluorescence to quantify CD8+, Foxp3+, PD-1+, and PD-L1 expression was performed to determine differences in tumor immune cells subsets according to AS cutoff. Results: Among 436 NSCLCs identified, stage I tumors (median AS 1) had significantly lower median AS (mAS) than stage IV cancers (mAS 7, P < 0.001), stage III (mAS 4, P = 0.03), and numerically lower compared to stage II cancers (mAS 3, P = 0.18). We found no difference in the mAS across tumors with a PD-L1 tumor proportion score of ≥50%, 1-49%, or < 1% (mAS 5 vs 7 vs 6, respectively, P = 0.26), nor was there any correlation between aneuploidy and TMB when taken as continuous variables (Spearman R: 0.074, P = 0.12). A total of 279 advanced NSCLCs with available aneuploidy scores were treated with ICIs. An URP analysis identified an AS of 2 as the strongest discriminator of objective response to ICI. Compared to pts with an AS > 2 (N = 207, 74.2%), pts with AS ≤2 (N = 72, 25.8%) had a significantly higher objective response rate (ORR 43.0% vs 19.8%, P < 0.001), a significantly longer median progression-free survival (mPFS 6.2 vs 2.9 months, HR: 0.70 [95% CI: 0.52-0.94], P = 0.02), and a significantly longer median overall survival (mOS 19.8 vs 13.8 months, HR: 0.66 [95% CI: 0.47-0.94], P = 0.02) to treatment with ICIs. After adjusting for other variables such as performance status, presence of oncogenic driver mutation, PD-L1, TMB, and line of treatment, AS was significantly associated with improved mPFS (HR: 0.72 [95% CI: 0.52-0.99], P = 0.04) and mOS (HR: 0.64 [95% CI: 0.44-0.94], P = 0.02). By contrast, among pts who received first-line platinum doublet chemotherapy without ICI, an AS ≤2 (N = 29), when compared to an AS > 2 (N = 56), did not correlate with improved ORR (55.2% vs 44.6%, P = 0.4) or PFS (5.3 vs 4.8 months, HR 0.83 [95% CI: 0.5-1.3], P = 0.43). Among 179 NSCLCs profiled by multiplex immunofluorescence, compared to cancers with an AS > 2, those with low aneuploidy had significantly higher numbers of CD8+, Foxp3+, PD-1+ immune cells, and PD-1+ CD8+ T cell, both intratumorally and when looking at the total numbers of cells within the tumor and at the tumor-stroma interface. Conclusions: NSCLCs with low aneuploidy have a distinct immune microenvironment and more favorable outcomes to ICIs.

First-in-human CAN-3110 (ICP-34.5 expressing HSV-1 oncolytic virus) in patients with recurrent high-grade glioma

2009

Background: Recurrent glioma patients have few therapeutic options and an expected survival of only 7 to 10 months. New treatments to improve the prognosis of this patient population are a dire medical need. Oncolytic viruses (OVs) are emerging as important new agents for cancer treatment. The first FDA approved OV was talimogene laherparepvec (Imlygic, T-Vec) for treatment of melanoma. T-Vec, as most other clinical HSV-1 based OVs, is deleted in the ICP34.5 gene, which is responsible for HSV-1 neurovirulence. However, deletion of ICP34.5 also impedes efficient viral replication. CAN-3110 (rQNestin34.5v2) maintains a copy of the HSV1 ICP34.5 gene under transcriptional control of the tumor-specific promoter for nestin to drive robust tumor-selective replication. CAN-3110 replicates in malignant glioma cells far above levels seen with ICP34.5 deleted viruses. This potency also created the hypothetical risk for increased neurovirulence, thus the regulatory advice to conduct a cautious nine-dose-level Phase-1 dose escalation study in patients with recurrent high-grade glioma (HGG). Methods: From September 2017 to February 2020, thirty patients with biopsy-confirmed recurrent high-grade glioma were treated in an open label clinical trial. Patients with multifocal, multicentric, tumors larger than 5 cm, and tumors that had recurred multiple times were eligible. All patients received best standard of care treatments as indicated by their physician. CAN-3110 was injected intratumorally starting at 1x106 plaque forming units (pfu) and dose-escalating (3+3 design) by half log increments up to 1x1010 pfu. Tissue (when possible) and blood samples were obtained before and during treatment for experimental medicine analyses. Results: CAN-3110 was well tolerated with no dose limiting toxicity observed. The initial tissue diagnosis of the recurrent tumor for the 30 subjects was 26 glioblastoma, 3 anaplastic oligodendroglioma, and 1 anaplastic astrocytoma. The median overall survival (mOS) of the entire study group is 13.25 months. Post-treatment tissue is available for 18/30 subjects and revealed persistence of HSV antigen and CD8+ T cell infiltrates. Additional response, immunologic (including T cell receptor repertoire), transcriptomic and single cell RNA sequencing analyses are ongoing. Conclusions: Administration of CAN-3110 into recurrent glioma was well tolerated without evidence of ICP34.5-induced encephalitis/meningitis. Histological and molecular analyses showed evidence of biological activity and that CAN-3110 injection was associated with immune activation and viral antigen persistence. Although definitive clinical efficacy cannot be determined in this small phase 1 study, OS of CAN-3110 treated subjects compares favorably to historical reports and warrants further clinical studies. Clinical trial information: NCT03152318.

Is radiation necrosis in radiated melanoma brain metastasis increasing because immunotherapy is contributing to this or are patients just living longer?

e21518

Background: The use of immune checkpoint inhibitors, particularly combination ipilimumab and nivolumab, has drastically changed the management of patients with melanoma brain metastasis. Select patients also benefit from brain-directed stereotactic radiation. Radiation necrosis is a risk associated with stereotactic radiation that oncologists have been observing more frequently in the era of immunotherapy. Methods: Patients were identified who had a history of metastatic melanoma treated with stereotactic brain radiation who subsequently developed radiation necrosis. Brain tissue from those patients with a subsequent resection of their radiation necrosis was obtained and examined for immune infiltrate and other factors. The tissue obtained was evaluated by blinded pathologists who graded % viable tissue, % necrosis, % tumor and % fibrosis. In addition, they graded inflammation on a scale of 1-3. Results: Seven patients were identified who had surgery for radiation necrosis following radiation to melanoma brain metastasis. Tissue was available for five patients. Two patients had received no prior immunotherapy, one patient had received ipilimumab and two patients received combination ipilimumab and nivolumab. The samples obtained consisted of almost entirely viable brain tissue or necrosis. There was minimal inflammation seen in all patients’ samples including those who had not received immunotherapy and those who had. Conclusions: Radiation necrosis in patients on immunotherapy who receive brain-directed stereotactic radiation is a rising problem. On pathologic evaluation increased immune infiltrate is not observed in patients on immunotherapy with radiation necrosis compared to those who never received immunotherapy. This suggests that the increased rates of radiation necrosis may be more likely associated with longer survival as opposed to a direct causative effect from the immunotherapy although with our limited sample size this will need further exploration.[Table: see text]

A Randomized Trial of Combined PD-L1 and CTLA-4 Inhibition with Targeted Low-Dose or Hypofractionated Radiation for Patients with Metastatic Colorectal Cancer

PURPOSE

Prospective human data are lacking regarding safety, efficacy, and immunologic impacts of different radiation doses administered with combined PD-L1/CTLA-4 blockade.

PATIENTS AND METHODS

We performed a multicenter phase II study randomly assigning patients with metastatic microsatellite stable colorectal cancer to repeated low-dose fractionated radiation (LDFRT) or hypofractionated radiation (HFRT) with PD-L1/CTLA-4 inhibition. The primary endpoint was response outside the radiation field. Correlative samples were analyzed using multiplex immunofluorescence (IF), IHC, RNA/T-cell receptor (TCR) sequencing, cytometry by time-of-flight (CyTOF), and Olink.

RESULTS

Eighteen patients were evaluable for response. Median lines of prior therapy were four (range, 1-7). Sixteen patients demonstrated toxicity potentially related to treatment (84%), and 8 patients had grade 3-4 toxicity (42%). Best response was stable disease in 1 patient with out-of-field tumor shrinkage. Median overall survival was 3.8 months (90% confidence interval, 2.3-5.7 months). Correlative IF and RNA sequencing (RNA-seq) revealed increased infiltration of CD8+ and CD8+/PD-1+/Ki-67+ T cells in the radiation field after HFRT. LDFRT increased foci of micronuclei/primary nuclear rupture in two subjects. CyTOF and RNA-seq demonstrated significant declines in multiple circulating immune populations, particularly in patients receiving HFRT. TCR sequencing revealed treatment-associated changes in T-cell repertoire in the tumor and peripheral blood.

CONCLUSIONS

We demonstrate the feasibility and safety of adding LDFRT and HFRT to PD-L1/CTLA-4 blockade. Although the best response of stable disease does not support the use of concurrent PD-L1/CTLA-4 inhibition with HFRT or LDFRT in this population, biomarkers provide support that both LDFRT and HFRT impact the local immune microenvironment and systemic immunogenicity that can help guide future studies.

Subtype-specific and co-occurring genetic alterations in B-cell non-Hodgkin lymphoma

B-cell non-Hodgkin's lymphoma (B-NHL) encompasses multiple clinically and phenotypically distinct subtypes of malignancy with unique molecular etiologies. Common subtypes of B-NHL such as diffuse large B-cell lymphoma (DLBCL) have been comprehensively interrogated at the genomic level. But rarer subtypes such as mantle cell lymphoma (MCL) remain sparsely characterized. Furthermore, multiple B-NHL subtypes have thus far not been comprehensively compared using the same methodology to identify conserved or subtype-specific patterns of genomic alterations. Here, we employed a large targeted hybrid-capture sequencing approach encompassing 380 genes to interrogate the genomic landscapes of 685 B-NHL tumors at high depth; including DLBCL, MCL, follicular lymphoma (FL), and Burkitt lymphoma (BL). We identified conserved hallmarks of B-NHL that were deregulated in the majority of tumor from each subtype, including the frequent genetic deregulation of the ubiquitin proteasome system (UPS). In addition, we identified subtype-specific patterns of genetic alterations, including clusters of co-occurring mutations and DNA copy number alterations. The cumulative burden of mutations within a single cluster were more discriminatory of B-NHL subtypes than individual mutations, implicating likely patterns of genetic cooperation that contribute to disease etiology. We therefore provide the first cross-sectional analysis of mutations and DNA copy number alterations across major B-NHL subtypes and a framework of co-occurring genetic alterations that deregulate genetic hallmarks and likely cooperate in lymphomagenesis.

Preparing Paraffin Tissue Sections for Staining

Most histological studies are performed on formalin-fixed, paraffin-embedded (FFPE) tissue samples. Therefore, there is an extensive atlas of most tissues and organs prepared from these sources, and comparing the location of antigens to these data is immediately informative. Fixation and embedding procedures for preparation of paraffin tissue sections are described here. Because of the harsh fixation, embedding, and preparation conditions used in this procedure, many antigens are not well preserved. Thus, cell staining of paraffin-embedded tissue sections usually requires sensitive detection methods and may require amplification using multiple-layer techniques. The protein cross-linking associated with these fixation conditions can mask epitopes. To uncover them and thus improve antibody-antigen binding, the epitopes can be unmasked by reversing the protein cross-linking. One thermal method, heat-induced epitope retrieval, is presented here.