bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficacy of PD-1/PD-L1 therapy: Do proton pump inhibitors affect the outcome?
Authors: Mukherjee Sarbajit , Khalid Bilal , Ibrahimi Sami , Morton Jordan Malie , Roman Darwin , Zhao Yan D , Aljumaily Raid
Published: February 2018

208

Background: Recent studies have shown that manipulating the gut microbiome modulates the efficacy of anti-PD1/PD-L1 directed therapy leading to increase in the activity of CD8+ T-cells. Proton Pump inhibitors (PPIs) affect the gut microbiome. The objective of this study was to investigate the effects of PPIs use on agents that target the PD-1/PD-L1 pathway in patients treated with these agents. Methods: We looked at the outcomes of 158 patients aged 18 years or older, treated at the University of Oklahoma Health Sciences Center between 2014 and 2016. The primary aim of this study was to investigate whether survival of patients treated with agents that target PD-1/PD-L1 pathway was affected by PPI use. The secondary objective was to identify if there is any difference in the immune related side effect profile between PPI users and non-users. The overall survival (OS) and progression free survival (PFS) were compared between PPI users and nonusers using the log-rank tests. Survival curves were generated using the Kaplan-Meyer method. The proportions of Grade 3 or 4 colitis or pneumonitis were compared between PPI users and nonusers using the Fisher’s exact test. SAS 9.4 was used for the statistical analysis and a 0.05 significance level was used. Results: The majority of patients were females (57%). The median age was 63 years. Lung cancer was the most common diagnosis (20%) followed by melanoma (20%) and ovarian cancer (12%). Nivolumab was the most commonly used agent (47%) followed by Pembrolizumab (22%), other investigational agents (22%) and Atezolizumab (7%). The median follow-up time from the date of first PPI dose was 7 months. There was no statistically significant difference in OS or PFS between PPI users and nonusers (p = 0.77). There were no significant differences in proportions of Grade 3 or 4 colitis between PPI users and nonusers (5% vs. 5.26%, p > .99). Similarly, there were no significant differences in proportions of Grade 3 or 4 pneumonitis between PPI users and nonusers (6.25% vs. 1.75%, p = 0.40). Conclusions: Use of PPI does not affect the outcome of patients receiving agents that target PD1/PD-L1 pathway. The incidence of important immune related side effects was similar between PPI users and non-users.
Association of PD-L1 mRNA levels in plasma-derived exosomes with response to nivolumab and pembrolizumab in melanoma and NSCLC.
Authors: Del Re Marzia , Marconcini Riccardo , Pasquini Giulia , Rofi Eleonora , Vivaldi Caterina , Bloise Francesco , Restante Giuliana , Arrigoni Elena , Bianco Mariagrazia , Caparello Chiara , Crucitta Stefania , Petrini Iacopo , Vasile Enrico , Morganti Riccardo , Falcone Alfredo , Danesi Romano
Published: February 2018

210

Background: The anti-PD-1 monoclonal antibodies (moAb) nivolumab and pembrolizumab have improved the survival of melanoma and non-small cell lung cancer (NSCLC) patients. However, treatment selection is based on tumor PD-L1 expression by immuno-histochemistry and no specific approaches are available to monitor treatment response. The aim of this study was to investigate the association between PD-L1 mRNA levels in plasma-derived exosomes and response to nivolumab and pembrolizumab in patients affected by melanoma (n = 18) and NSCLC (n = 8). Methods: Blood (6 ml) was obtained at 1) baseline (before initiation of anti-PD1 moAb or at the time of last available radiological evaluation of disease response) and 2) after two months of treatment (at the time of first response evaluation or disease re-assessment). Exosomes were extracted from plasma and PD-L1 mRNA expression was measured by digital PCR and expressed as copies/ml. Results: Overall, the number of copies of mRNA PD-L1/ml plasma varied according to tumor response; in particular, an increase was found in patients with PD and a decrease was observed in patients who achieved a CR/PR. The mean±SEM values of PD-L1 in patients responding to treatment (CR+PR) were 830.4±231.3 and 242.5±82.5 copies/ml (baseline vs. 2 months, p = 0.016), respectively. In patients with stable disease the mean±SEM values were as expected 298.8±97.2 vs. 247.5±29.8 copies/ml (p = 0.586), while in progressive disease PD-L1 expression levels were 204.0±68.8 vs. 416.0±87.8 copies/ml (p = 0.001), respectively. Conclusions: In the present study, we demonstrate for the first time that changes in exosomal PD-L1 expression occur in melanoma and NSCLC patients treated with nivolumab or pembrolizumab and may correlate with the radiological tumor response. This proof-of-concept study demonstrates the feasibility of detecting PD-L1 in plasma and its relationship with response to treatment.
Efficacy of immune checkpoint inhibitors in patients with brain metastasis from NSCLC, RCC, and melanoma.
Authors: Lauko Adam , Thapa Bicky , Jia Xuefei , Ahluwalia Manmeet Singh
Published: February 2018

214

Background: Immune checkpoint inhibitors are revolutionizing the treatment of multiple advanced malignancies, however, there is limited data on the efficacy of immune checkpoint blockade in brain metastasis. We conducted a study to analyze the overall survival (OS) and progression-free survival (PFS) among patients with brain metastasis from Non-Small Cell Lung Carcinoma (NSCLC), Renal Cell Carcinoma (RCC), and Melanoma treated with either Nivolumab, Pembrolizumab, Ipilimumab or a combination. Methods: After IRB approval, we retrospectively evaluated patients with brain metastasis treated at our tertiary care institution from 2011-2017 who underwent immunotherapy and one or more of the following; whole brain radiation therapy (WBRT), surgery, stereotactic radiosurgery (SRS) or systemic chemotherapy. Univariable and multivariable analysis was utilized to analyze OS and PFS. Volumetric analysis to assess treatment response is ongoing. Results: A total of 128 patients were identified with a median age of 60.6 years. 49% of patients were male; 77% of patients had a good (0 or 1) ECOG performance scores at the time of the brain metastasis; 83 patients had supratentorial brain metastasis, 11 had infratentorial and 24 had both. The prevalence of mutations was 34% in NSCLC patients, 58% in melanoma, and 0% in RCC. The median OS from the start of immunotherapy was not reached for RCC and was 17.1 and 28.9 months for Melanoma and NSCLC respectively. Median PFS was 5.9, 6.7 and 3.6 months for RCC, Melanoma, and NSCLC respectively. On multivariable analysis, SRS, sex and the number of cycles of immunotherapy had statistically significant hazard ratios. Conclusions: Immune checkpoint inhibitors are efficacious in the treatment of brain metastasis. Further analysis including response criteria using volumetric analysis is ongoing and final results will be presented at the meeting. [Table: see text]
Immune deserts: Correlation of low CD8 gene expression with non-response to checkpoint inhibition.
Authors: Gardner Mark , Pabla Sarabjot , Ernstoff Marc S. , Puzanov Igor , Conroy Jeffrey M. , Nesline Mary , Glenn Sean T. , Papanicolau-Sengos Antonios , Burgher Blake , Andreas Jonathan , Giamo Vincent , Qin Maochun , Lenzo Felicia L. , Morrison Carl
Published: February 2018

23

Background: Associations between presence and density of effector T-cells (CD8+) and response to checkpoint inhibitors (CPIs) has been established for protein biomarkers using immunohistochemistry but less work has been done to characterize this relationship through gene expression. Methods: We collected clinical response data (RECIST v1.1) for 184 patients who had been treated with CPIs across tumor types with FDA indications. We tested formalin-fixed paraffin embedded (FFPE) samples by NGS with a comprehensive immune response panel which interrogates the gene expression profile of 54 validated immune-related genes. Ranked gene expression was compared to a reference population. 85/184 (46%) cases were considered “responders” after six months, and 66/184 cases (36%) were considered responders after twelve months on treatment. We hypothesized that patients with in the bottom quartile of CD8 expression, as measured by the rank of the sum of normalized CD8A and CD8B transcripts compared to a reference population, would be unlikely to respond to checkpoint therapy (immune deserts), and that “hot” tumor environments (TME) with the highest quartile of expression would be most likely to respond. Results: After six months of therapy, 13/40 (32.5%) patients with immune desert tumors responded to therapy, whereas 39/82 patients (47.6%) in the middle 50% of expression responded, and 33/62 (53.2%) of patients with “hot” TME responded to treatment. The two-tailed p-value of the null hypothesis, that TME status does not correlate with response, was 0.018 and could be rejected. After twelve months of observation, 9/40 (22.5%) immune desert patients were considered “responders”. 28/82 (34.2%) of the middle 50% of expression were classified as responders, and 29/62 (46.8%) of top quartile samples came from responders. The two-tailed p-value of the null hypothesis was 0.005 and could be rejected. Conclusions: Gene expression of CD8 as measured by RNA-seq from FFPE samples can be used to compare these samples versus a reference population to predict an increase or decrease in likelihood of response to CPIs. Patients in the lowest quartile of CD8 expression were the least likely to respond to these promising therapies.
The coupling of MDSCs with a computational analytic method to detect solid tumors.
Authors: Dominguez George , Sholevar Cyrus , Polo Alexander , Roop John , Campisi Anthony , Gabrilovich Dmitry , Rauscher Frank J. , Kumar Amit
Published: February 2018

24

Background: Myeloid-derived suppressor cells (MDSCs) are key contributors in supporting tumor progression and tumor escape through their ability to suppress anti-tumor responses mediated through T cell and natural killer (NK) cell activity. Several studies have demonstrated their utility as indicators of tumor progression and possible predictors of clinical outcomes, but there is significant overlap with healthy individuals preventing discrete and accurate calls. The objective of our study was to create a non-invasive cancer detection assay that analyzes flow cytometry data in an objective method using an artificial neural network (NN) to distinguish between cancer patients (CPs) and healthy donors (HDs) based upon the flow cytometry profiles of MDSCs and other leukocytes. Methods: We used standard multiparametric flow cytometry techniques to immunophenotype MDSCs and other leukocytes found in the peripheral blood of 52 biopsy-confirmed CPs with solid tumors and 70 HDs. A series of NNs utilizing pattern recognition computational algorithms are then created using three data sets: 1) the training set - this ‘teaches’ the two output categories of cancer and not cancer, 2) the validation set – this uses backpropagation to improve the accuracy of the trained networks, and 3) the testing set – this is used to rank the trained networks against each other. Finally, a naïve testing set is then used to determine the overall sensitivity and specificity for the top-ranking networks. Results: Using traditional flow cytometry gating methods to analyze MDSCs as a biomarker for cancer detection, it is difficult to achieve both high sensitivity and specificity due to the substantial overlap with healthy individuals. Here, we incorporated a standard 12 marker flow cytometry assay with NN technology to achieve a sensitivity of 92.3% and a specificity of 90.0% with an area under the ROC curve (AUC) of 0.9477. Conclusions: Pairing the advanced analytical capabilities of our NN with surface biomarker based analysis of MDSCs and certain leukocytes measured in peripheral blood has enabled us the ability to objectively identify patterns indicative for the existence of a solid tumor.
Characterization of biomarkers to immune checkpoint blockade therapy across solid tumors.
Authors: Russell Meaghan , Huang Xiu , Vuzman Dana , Lvova Maria , Pantazi Angeliki , Lyle Stephen , Tse Julie Y
Published: February 2018

26

Background: Immune checkpoint blockade (ICB) therapy has been effective patients with solid tumors. Currently, tumor expression of programmed death-ligand 1 (PD-L1) is clinically used as a biomarker of predicted response to ICBs in non-small cell lung cancer (NSCLC). However, across solid tumors, only a subset of patients benefit from ICBs, so there is need to identify other biomarkers to predict response to ICB. We investigated the use of large panel next generation sequencing (NGS) to characterize biomarkers to ICBs across solid tumors. Methods: NGS and PD-L1 immunohistochemistry (IHC) was performed on a series of solid tumors. NGS analysis included detection of single nucleotide polymorphisms (SNPs), insertions and deletions (indels), copy number variation (CNV), and gene-fusions in 435 cancer-related genes, microsatellite instability (MSI), tumor mutational burden (TMB) based on non-synonymous SNPs, and HPV16/18 and EBV viral status. Genomic alterations in previously reported biomarkers of response to ICBs were assessed. Results: 143 solid tumors were analyzed with NGS and PD-L1 IHC. The samples included 80 NSCLC, 15 colorectal carcinoma, 8 cutaneous melanoma, 6 breast carcinoma, and 34 other solid tumors. The mean TMB varied by tumor type, with the highest in melanoma. The frequency of PD-L1 expression was higher in NSCLC and melanoma compared to colorectal carcinoma. The relationship between PD-L1 expression and the other biomarkers varied by tumor type (Table 1). Positive association (+); Negative association (-): No association (None). Conclusions: We characterized biomarkers to ICBs across a range of solid tumors. We found tumor-specific differences in the mean TMB and frequency of PD-L1 expression. We also found tumor-specific differences in the associations between PD-L1 and other potential biomarkers, including KRAS, NRAs, HRAs, BRAF, and EGFR mutation status. We found no correlation between PD-L1 expression and MSI and viral status. NGS is an efficient platform for analysis of biomarkers in solid tumors.[Table: see text]
Predictive role of peritumoral CD3+ infiltration and neutrophil to lymphocyte ratio on overall survial in pateints affected by colorectal liver metastases treated with chemotherapy and surgery.
Authors: Cimino Matteo , Donadon Matteo , Mavilio Domenico , Di Tommaso Luca , Roncalli Massimo , Hudspeth Kelly , Sacerdote Carlotta , Torzilli Guido
Published: February 2018

27

Background: Systemic and local inflammation plays an important role in many cancers and colorectal liver metastases (CRLM). While the role of local immune response mediated by CD3+ tumour infiltrating lymphocyte is well established new evidence on systemic inflammation and cancer such as neutrophil–lymphocyte ratio (NLR) are emerging. The aim of the study is to associate these two markers of inflammation to predict overall survival (OS) in patients affected by CRLM. Methods: From January 2006 to January 2013 128 consecutive patients affected by CRLM treated with chemotherapy and surgery were included in the study. CD3+ peritumoral infiltration was defined as the ratio of intra-tumoural\invasive-margin CD3+ infiltration evaluated with immunohistochemistry on CRLM tumor slides. NLR was calculated as neutrophil absolute count divided by the absolute lymphocyte count on blood sample. ROC curves were used to calculate a cut-off for each bio-markers related to OS . Associating the bio-markers two risk groups were determined: low risk (LRG) two protective bio-markers; high risk (HRG) no protective bio-markers. Results: After a median follow-up of 45 months, median OS was 44 months.Twenty-nine patients (22.6%) belong to the LRG whereas 99 patients (77,4) belong to HRG. Adjusted Cox regression analysis showed a worse OS for HRG patients (HR 2.74 p = 0.003 95%CI 1.40-5.37). Median OS was 80.8 vs 42.5 months for LRG vs HRG respectively. Conclusions: High CD3+ peritumoural infiltration associated with low NRL are two protective factor on OS for patients affected by CRLM.
Estimating mutation load at 5% LOD from FFPE samples using a targeted next-generation sequencing assay.
Authors: Chaudhary Ruchi , Cyanam Dinesh , Mittal Vinay Kumar , Tom Warren , Au-Young Janice , Sadis Seth , Hyland Fiona
Published: February 2018

28

Background: High tumor mutation load is a biomarker which positively correlates with response to immune checkpoint inhibitors. Current methods to estimate tumor mutation load often require large amounts of DNA. Herein, we demonstrate the ability of a targeted panel to estimate mutation load from FFPE samples using low input amount of DNA. Methods: We developed a single-sample analysis workflow to estimate mutation load (somatic mutation count per Megabase (Mb)) from FFPE and fresh frozen tumor research samples. The assay utilizes a PCR-based target enrichment panel that covers ~1.7 Mb. Our workflow requires only 10 ng of input DNA, and enables a 2.5-day turn-around time from sample to the final report. The workflow enables < 60 minutes of hands-on time for automated library preparation and templating on a batch of 8 samples. Sequencing is performed using a high throughput semiconductor sequencing platform to achieve sufficient depth (~500x coverage) and accuracy. Our analysis pipeline calls variants with optimized parameters on the tumor sample only, with no matched normal sample required, and applies filters to remove germ-line. Results: An in-silico analysis using 21,000 exomes from COSMIC demonstrated the panel can achieve high sensitivity (>=93%) and specificity (>99%) necessary to stratify high and low mutation burden samples. Matched tumor-normal analyses on 14 lung and colorectal samples showed that our single tumor analysis workflow detects mutation load with strong correlation (r=0.8699) with tumor-normal analysis. Through dilution experiments on engineered control we learned that the workflow provides accurate estimates of mutation load, predicting ± 7% of expected mutation load on >=20% tumor content. To assess reproducibility, we compared mutation load in library replicates for a cohort of 8 samples (FFPE and fresh frozen tumors, engineered control, and NIST cell-lines) and observed high correlation (r=0.9906) among replicates. Conclusions: We developed a simple workflow on the Ion Torrent sequencing platform to estimate mutation load from FFPE and fresh frozen tumor research samples. This solution will advance research in immuno-oncology.
Use of cancer immunotherapies in the real-world in the setting of microsatellite instability.
Authors: Agarwala Vineeta , Gossai Anala , Singal Gaurav , O'Connell Claire , Li Gerald , Kao Ken , Bourque David , Feuchtbaum Dana , Cobb Garrett Alpha , Nunnally Allen , Frampton Garrett Michael , Ali Siraj Mahamed , Abernethy Amy Pickar , Kramarz Sarah , Trabucco Sally E.
Published: February 2018

30

Background: In May 2017, the FDA approved for the first time a cancer therapy (pembrolizumab) for use in patients based on the presence of a genomic marker (microsatellite instability, or MSI) rather than anatomical tumor type. Real-world data on the rates and clinical impact of MSI on treatment selection and response are scant, especially outside of colorectal cancer. Methods: We performed a retrospective study of all patients treated in the Flatiron Health network (>265 oncology practices across the U.S.) between January 2011 and June 2017, and who underwent FoundationOne tumor sequencing as part of routine clinical care. Tumor type was determined by pathologist review of specimens submitted to Foundation Medicine. Data on therapy use was sourced from electronic health records (EHRs). Assessment of MSI was performed from DNA sequencing across the coding regions of >300 genes. Results: Our overall cohort included n=16,020 patients. Among patients in whom MSI status could be assessed (n=12,411), 207 patients had MSI-high tumors. The observed rate of MSI-high was 1.7% across all tumor types combined; tumor-specific rates varied significantly, from 4.9% in colorectal adenocarcinoma to 0.3% in breast and non-small cell lung cancer. The rate of MSI-high was 2.4% in patients with an unknown primary based on specimen review. A total of 1,329 patients received common checkpoint inhibitors (nivolumab, pembrolizumab, atezolizumab). Among the checkpoint-inhibitor treated patients with known MSI status (n=1,175), 14 (1.2%) had MSI-high tumors, and the majority of these patients (n=8) had colorectal cancer. Conclusions: Evidence of MSI-high is rare in real world cancer care settings. Early identification of patients with this biomarker is important in order to efficiently match them to treatment. Further evaluation of the real-world effectiveness of immune checkpoint inhibitors in the MSI-high population is still needed. Because most patients receiving these therapies today do not have high MSI, exploration of additional biomarkers for immunotherapy response is also critical.
Effect of dual PI3K-δ,γ inhibitor duvelisib on immunosuppressive Tregs and myeloid cells to enhance efficacy of checkpoint and co-stimulatory antibodies in a B cell lymphoma model.
Authors: Pachter Jonathan A , Weaver David T.
Published: February 2018

33

Background: Duvelisib is a dual inhibitor of PI3K-δ and PI3K-γ which has shown clinical activity as monotherapy in CLL/SLL, FL and T cell lymphoma (O’Brien; Flinn; Horwitz, ASH 2014). Recent publications have demonstrated that PI3K-δ inhibition reduces immunosuppressive Tregs (Ali, Nature, 2014) whereas PI3K-γ inhibition reduces immunosuppressive myeloid cells (Kaneda, Nature, 2016; De Henau, Nature, 2016). Hence, we postulated that duvelisib may augment the efficacy of immune checkpoint or co-stimulatory antibodies. Methods: Mice bearing syngeneic A20 B cell lymphoma tumors (60-90 mm3) were treated with vehicle, duvelisib, anti-PD1, anti-PD1 + duvelisib, anti-OX40, or anti-OX40 + duvelisib. Tumor volumes were measured by caliper. Tregs, macrophages and MDSCs were quantified by flow cytometry from mice bearing A20 tumors after 8 days of treatment. Results: In the A20 model, duvelisib, anti-PD-1 and anti-OX40 treatments each induced tumor growth delay. When duvelisib and anti-PD-1 were combined in mice with pre-existing A20 tumors, strong anti-tumor synergy was observed. When anti-OX40 and duvelisib were combined, tumor regression was observed which correlated with strong reduction of tumor Tregs, M2 macrophages and MDSCs. To assess immune memory, tumor-free mice following anti-OX40 alone or anti-OX40 + duvelisib were injected with A20 cells in the contralateral flank with no further treatment. Whereas mice that had received anti-OX40 alone grew new tumors upon A20 re-challenge, all tumor-free mice that had received anti-OX40 + duvelisib did not grow tumors upon re-challenge and showed elevated memory T cells in blood and spleen. These findings indicate that anti-OX40 + duvelisib treatment established immune memory. Conclusions: The dual inhibition of PI3K-δ and PI3K-γ appears to make duvelisib especially effective in reducing both lymphoid and myeloid immuno-suppressive populations, enhancing the anti-tumor efficacy of immune checkpoint and co-stimulatory antibodies. These data support potential clinical exploration of duvelisib in combination with checkpoint or co-stimulatory antibodies.
Multi-institutional report on toxicities from combined radiation and nivolumab.
Authors: Parker Sean Medard , Zainib Maliha , Mattes Malcolm , Amin Neha
Published: February 2018

39

Background: Indications for Nivolumab (NIVO), a checkpoint inhibitor immunotherapy drug, in treating a variety of metastatic malignancies has markedly increased. Radiation therapy (RT) is also commonly used in this patient population, however, there are limited data on the safety profile of combined RT-NIVO. We reviewed our experience to assess the acute toxicity profile of concurrent RT-NIVO. Methods: All consecutive patients who received NIVO from 1/2015 to 5/2017 at 4 centers across 2 institutions were retrospectively reviewed. Those patients who completed a course of RT from 1 day prior to initial NIVO infusion through 1 month after last NIVO infusion were considered to have received concurrent therapy and included in the subsequent analysis. Descriptive statistics are reported for patient/tumor/treatment characteristics and observed acute toxicities within 3 months of RT completion. Results: Among 261 patients who received NIVO, 46 (17.6%) received concurrent RT to 67 different sites. The median f/u was 3.3 (.1-19.8) months and 11/46 (24%) were still alive at last analysis. The most common histology, RT prescription, and treatment site included non-small cell lung cancer (23/46, 50%), 30 Gy in 10 fractions (16/67, 24%), and central thorax/abdomen (26/67, 39%), respectively. 79% (53/67) of irradiated sites were treated with 3D-conformal technique and palliative dose-fractionation. Grade 3, 4, and 5 toxicities were experienced by 11, 1, and 2 patients, respectively. However all grade 4 and 5 toxicities were outside of the irradiated area and attributed to the NIVO alone, and only 4/11 (36%) of the grade 3 toxicities were attributed to the RT-NIVO. The irradiated site in these cases included the brain [2/10 (20%)] and central thorax/abdomen [2/19 (10.5%)], including one unexpected grade 3 pancreatitis following stereotactic body RT to the left adrenal gland. Conclusions: Concurrent RT-NIVO is generally well tolerated, though with potentially increased rates of severe toxicity when irradiating the lung, abdomen, or brain. Pending more definitive data, we recommend counseling patients on the potentially increased rates of side effects from combined immunotherapy and radiotherapy to these locations.
Analysis of over 100,000 patients with cancer for CD274 (PD-L1) amplification: Implications for treatment with immune checkpoint blockade.
Authors: Goodman Aaron , Piccioni David Eric , Kato Shumei , Boichard Amelie , Walavalkar Vighnesh , Frampton Garrett Michael , Connelly Caitlin , Fabrizio David , Miller Vincent A. , Sicklick Jason K. , Kurzrock Razelle
Published: February 2018

47

Background: The majority of patients with Hodgkin lymphoma have copy number alterations in the genes CD274 (PD-L1), PDCD1LG2 ( PD-L2) and JAK2 (chromosome 9p24.1) resulting in high response rates to PD-1/PD-L1 blockade, even in refractory disease. The prevalence and importance of this biomarker as a predictor of response to PD-1 blockade is unknown across all solid tumors. Methods: We analyzed > 100,000 de-identified patient samples from the Foundation Medicine database and 2,039 clinically annotated patients from UCSD. CD274 amplification was called for copy number alterations (CNAs) ≥ 6. PFS was calculated by KM analysis. Results: Altogether, 0.7% of all tumors types had ≥ 6 CNAs in CD274 (Table). CD274 CNAs were identified in 121 tumor histologies. 13 patients at UCSD were found to have CD274 amplification of which nine were treated with PD-1/PD-L1 blockade (either alone or in combination with another immunotherapeutic or targeted therapy) after a median of four prior systemic therapies. The response rate to PD-1/PD-L1 blockade was 67% (6 of 9 patients); median PFS = 15.1 (range, 1.6-21.8+) months (includes 3 objective responses ongoing for 15+ months as well as a glioblastoma with a PR for 4.4+ months). Conclusions: CD274 amplification is rare in most malignancies; however, testing for this alteration is warranted given the frequent and durable responses to PD-1/PD-L1 blockade. [Table: see text]
Phase I study of E7046, a novel PGE2 receptor type 4 inhibitor, in patients with advanced solid tumors: Clinical results and effects on myeloid- and T-lymphoid cell-mediated immunosuppression.
Authors: Hong David S. , Parikh Aparna , Shapiro Geoffrey , Varga Andrea , Naing Aung , Meric-Bernstam Funda , Reyderman Larisa , Bao Xingfeng , Binder Terri A. , Ren Min , Siu Amy , Xu Lu , Liu Mingjie , Dayal Satish , Bhagawati-Prasad Vijay , Tchakov Ilian , Owa Takashi , Ooi Chean Eng , Marabelle Aurelien
Published: February 2018

49

Background: E7046 is a selective inhibitor of the prostaglandin E2 (PGE2) receptor EP4, which transduces potent immunosuppressive activity of PGE2 in myeloid and T-lymphoid cells. In preclinical studies, E7046 reversed PGE2-mediated activities and facilitated activation of cytotoxic T-cells. Here, we present initial clinical, PK and PD results from a first-in-human study of E7046 in patients (pts) with cancers having high myeloid cell infiltration. Methods: E7046 was given orally, once-daily, in 21-day cycles in sequential dose-escalating cohorts (125, 250, 500 and 750mg). Tumor responses were evaluated by irRECIST and metabolic responses by 18FDG-PET. Immune response modulation was assessed in tumors and peripheral blood. Results: Thirty pts were treated, with no dose-limiting toxicities observed. The most common adverse events were fatigue (37%), diarrhea (33%), and nausea (30%). Grade 3/4 AEs in > 1 pt were abdominal pain (3 pts) and vomiting (2 pts). Grade 3/4 treatment-related AEs occurred in 4 pts (rash in 2 pts, and diarrhea, allergic reaction, anaphylaxis, hypersensitivity, and hyperuricemia, in 1 pt each). Four pts discontinued E7046 due to an AE (bowel obstruction, allergic reaction, abdominal pain, acute renal failure). No objective tumor responses were reported. Treatment duration of ≥20 wks with best response of stable disease (SD) was observed in 5 pts, 3 of whom had partial metabolic responses. E7046 exposure was dose-proportional up to 500 mg. Elimination half-life (12 hr) justified once-daily dosing. E7046 treatment significantly increased tumor CD3+ and CD8+ T-cell infiltration, and blood levels of the T-cell-recruiting chemokine CXCL10. E7046 also modulated blood expression of EP4 signaling genes (IDO1, EOMES, PD-L1). Longer duration of therapy with SD was associated with higher baseline tumor infiltrate of CD8+ T-cells and CD163+ macrophages. Conclusions: E7046 demonstrated favorable tolerability with preliminary evidence of anti-tumor activity and immune modulation in tumor and peripheral blood. MTD was not reached. Further studies of E7046 in combination with other agents are planned. Clinical trial information: NCT02540291.
Capturing the complexity of the immune microenvironment of acute myeloid leukemia with 3D biology technology.
Authors: Rutella Sergio , Vadakekolathu Jayakumar , Altmann Heidi , Patel Tasleema , Reeder Stephen , Liang Yan , Schmitz Marc , Hood Tressa , Danaher Patrick , Warren Sarah , Cesano Alessandra , Beechem Joseph M , Pockley A. Graham , Tasian Sarah K. , Bornhäuser Martin
Published: February 2018

50

Background: Tumor phenotypes are dictated not only by the neoplastic cell component, but also by the tumor microenvironment (TME), which includes immune and inflammatory cells. We characterized the immune ecosystem of the bone marrow (BM) TME in patients with acute myeloid leukemia (AML) to correlate transcriptomic and proteomic profiles with patient outcome. Methods: We used the nCounter system (NanoString Technologies) to characterize BM specimens from 42 children and 28 adults with AML. Ninety BM samples (63 from de novo AML, 18 from AML in complete remission [CR] and 9 from relapsed AML) were analyzed using the RNA Pan-Cancer Immune Profiling Panel. In situ leukemia-immune system interactions were visualized using Digital Spatial Profiling (DSP). Results: Hierarchical clustering identified subgroups with heightened expression of lymphocyte-associated genes, including NK cell and cytotoxicity genes (“immune-enriched” samples). They also expressed CD8A, IFNG, FOXP3, the cell chemoattractants CXCL9, CXCL10, and inhibitory molecules including IDO1 and the immune checkpoints LAG3, CTLA4 and PD-L1. Conversely, ‘immune-depleted’ samples over-expressed genes associated with mast cell functions and CD8 T-cell exhaustion and showed low expression of T-cell and B-cell genes. Importantly, relapse-free survival (RFS) and overall survival (OS) were significantly shorter in patients with “immune-enriched” compared with “immune-depleted” AMLs (2.2 vs. 18.3 months, p = 0.0064, and 6.3 vs. 22.4 months, p = 0.017, respectively). DSP of the BM TME showed the co-localization of CD8 T cells with FoxP3 Treg cells and PD-L1- and VISTA-expressing cell types, an immune landscape which is consistent with the establishment of adaptive immune resistance mechanisms of immune escape. Conclusions: Our study has identified heterogeneous immune profiles in children and adults with AML. From a clinical standpoint, ‘immune enriched’ AMLs might be amenable to immunotherapy approaches tailored to the BM microenvironment, including blockade of co-inhibitory molecules and/or small-molecule IDO1 inhibitors. Grant support: Roger Counter Foundation, UK; Qatar National Research Fund (#NPRP8-2297-3-494).
Identification of novel liquid biopsy biomarker for monitoring the immune set point in both solid tumor and hematological malignancy patients.
Authors: King David John , Adams Ryan , Nangle Leslie , Mertsching Elisabeth , Ogilvie Kathy , Cubitt Andrea , Mendlein John
Published: February 2018

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Background: We identified an extracellular pathway that plays a role in modulating T cell activity in vivo, which we call the Resokine Pathway. The pathway specifically involves a 60 amino acid domain of the tRNA Synthetase for Histidine, which is an essential gene in all cells, including tumor cells, vis-a-vis protein synthesis. Methods: Circulating Resokine levels were measured in 466 plasma samples from patients bearing a number of different tumor types, as well as healthy individuals, using an ECLIA format with sensitivity to 5pM. Serum Resokine levels were also measured in tumor-bearing mice. Results: Low, Circulating Resokine Levels in Cancer Patients are Negligible Compared to Healthy Individuals: Resokine levels in healthy volunteers (n = 148) ranged from 8pM - > 2333pM with 18% of the individuals possessing a level below 30pM. In contrast, levels measured across patients with all tumor types tested ranged from 20pM to > 2333pM (above the upper limit of quantification) with only 4% of the patients possessing low levels, defined as < 30pM; (P < 0.0001). Tumors in Mice Induce Higher Circulating Resokine Levels: Resokine levels in serum from normal C57Bl6 mice ranged from 70 to 250pM (n = 10). Significantly higher levels (450-3000pM) were found in the serum of B16F10 tumor-bearing mice with up to a 10-fold increase in the mean serum level compared to healthy mice (p < 0.001). Resokine levels were correlated with tumor size. Conclusions: Resokine levels correlate with tumor size in mice, and are elevated in human cancer patients. This is consistent with the hypothesis that tumors secrete Resokine, to avoid detection by the immune system. Measurement of levels of the Resokine protein may offer a new liquid biopsy biomarker for tracking immune cell activity in cancer patients. It may also be a target for therapeutic intervention but the pathway may be challenging to inhibit given the presumably higher levels at the tumor and that there are many splice variants of HARS with potential activity (Lo et al. Science 2014, 345:328-32). Acknowledgements: We would like to thank Jedd Wolchok and Phil Wong of MSKCC, New York for access to patient samples.
T cell receptor activation status as biological context for interpreting PD1/PDL1 biomarker measurements.
Authors: Parchment Ralph E. , Navas Tony , Fino Kristin , Fung Andy , Cutuli Facundo , Wang Lihua , Kinders Robert J. , Doroshow James H.
Published: February 2018

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Background: Direct cytolysis of tumor cells by CD8+ T cells results from the net effect of at least two biochemical pathways: (1) stimulatory signaling from the activated T cell receptor (TCR) complex in response to its recognition of a tumor neoantigen presented in the context of autologous MHC class I, and (2) suppressive signaling from immune checkpoints, such as the response of PD1 to binding its ligand, PDL1. Because the PD1:PDL1 immune checkpoint is significant for therapy only when there is tumor cell-specific TCR activation and signaling, it is not surprising that simple measurements of either PD1 or PDL1 in tumor biopsies are, at best, imperfect predictive biomarkers. Instead, a more precise test that quantifies PD1 signaling due to PDL1 binding only in the subset of CD8+ T cells exhibiting activated TCR signaling should provide a more accurate assessment of the extent of immune checkpoint suppression of tumor immunity and therefore be a more predictive biomarker of response to PD1/PDL1-targeted immunotherapy. Methods: We have developed a multiplexed immunofluorescence microscopy test capable of simultaneous quantitation of TCR activation (phospho-CD3zeta), immune checkpoint signaling via PD1 (phospho-SHP1 and -SHP2), and the net stimulation or inhibition resulting from the integration of these two pathways (phospho-ZAP70). Results: Specific antibodies to these biomarkers have been qualified, including peptide inhibition studies to establish antibody specificity, and their performance established by fit-for-purpose studies of in vitro models of CD8+ T cell activation. This multiplex biomarker panel is suitable for clinical use with formalin-fixed, paraffin embedded core needle biopsies of tumor and quantitative immunofluorescence microscopy (qIFA). Conclusions: The additional biomarkers of tumor immunity are expected to add an important context for interpreting PD1/PDL1 measurements. Funded by NCI Contract No. HHSN261200800001E.
Immune dysregulation in peripheral blood mononuclear cells from patients with liver cancer.
Authors: Zhou Juhua
Published: February 2018

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Background: Immune regulation may play an important role in cancer development. The immune dysregulation and underlying mechanisms in patients with liver cancer have not fully understood. Methods: Peripheral blood mononuclear cells (PBMC) were isolated from patients with liver cancer. Deep-sequencing, FACS analysis, ELISA and real-time PCR were used to analyze the immune dysregulation and underlying mechanisms in patients with liver cancer. Results: Our analysis discovered that the percentages of immune cell populations in PBMC from patients with liver cancer were significantly different from those in normal controls. Specifically, the percents of B cells and regulatory T cells were high in PBMC from patients with liver cancer. Expression of 161 genes such as EGF, IRF3, CD177, MAP2K2 and MMP9 was found to be significantly inhibited, but 66 genes including CD19, CD70, FOXP1 and IL-32 were significantly up-regulated in PBMC from patients with liver cancer. Further analysis showed that 190 long non-coding RNAs (lncRNAs) were significantly down-regulated; whereas150 lncRNAs were significantly up-regulated in PBMC from patients with liver cancer. Dysregulated lncRNAs were involved in the control of immune cell signaling, cell division and differentiation. Conclusions: The results suggest that the immune dysregulation may play a critical role in the pathogenesis of liver cancer. It also has a great implication in the development of immune therapeutic methods for patients with liver cancer.
Kinetics of intratumoral T-cell activation during chemoradiation for cervical cancer.
Authors: Dorta-Estremera Stephanie , Nookala Sita Mahalakshmi Krishna , Yanamandra Ananta V , Colbert Lauren Elizabeth , Yang Guojun , Eifel Patricia J. , Jhingran Anuja , Ramondetta Lois M. , Jazaeri Amir A. , Frumovitz Michael M. , Klopp Ann , Sastry Jagannadha
Published: February 2018

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Background: Limited data in cancer patients have suggested that chemotherapy and radiation impact local and systemic immune cell populations. Radiation therapy (RT) is known to deplete circulating lymphocytes but is thought to increase local antigen presentation. The dynamics of these competing effects on the kinetics of intratumoral infiltration and expansion of activated and immunoregulatory T cells are unknown. Methods: We prospectively evaluated intratumoral immune infiltration during fractionated RT using multi-spectral flow cytometry. Cervical brushings were obtained from 14 patients before (baseline) and during RT (week 1, 3 and 5). Cells collected from the cervical brushings were stained with a 16-color panel of antibodies that included markers to identify T cell and dendritic cell subsets with activation and suppressor molecules. Changes in immune cell subsets at different time points were evaluated and calculated using matched-pair analysis with Wilcoxon rank sum test. Results: CD3+ T cells declined over the first week of treatment (28% of CD3 at baseline, vs. 14.8% at week 1, p = 0.0273). The percentage of CD3+ cells subsequently increased at 3 weeks (25.6%) and 5 weeks (37.8%). Both CD8+ and CD4+ T cells underwent a decline at week 1 followed by expansion at week 3 and 5. Percentages of regulatory T cells (CD4+Foxp3+) showed a similar trend of reduction and further expansion but did not reach significance. The percentage of CD8+ T cells expressing the T cell activation marker CD69 and the cytotoxic protease Granzyme B (GrzB) continuously increased over time (CD69+: 11.8%, 27.7%, 38.7%, 57.5%, and GrzB+: 23.9%, 53.2%, 48.1%, 58.2%). While the percentage of dendritic cells (CD11c+ CD11b+) was stable during treatment, the subset of activated dendritic cells expressing CD86 increased at week 1 and subsequently declined (week 1, 19.1% vs week 5, 9.8%, p = 0.0642). Conclusions: Activated CD8+ effector T cells expand in the cervix during radiation therapy. Moreover, in the first week of treatment, CD8+ T cells contract while dendritic cells undergo activation suggesting this may be a critical time to intervene to maximize anti-tumor immunity.
Obesity results in higher PD-1-mediated T-cell suppression but greater T-cell effector functions following blockade.
Authors: Canter Robert J. , Aguilar Ethan , Wang Ziming , Le Catherine , Khuat Lam , Dunai Cordelia , Rebhun Robert , Tarantal Alice , Blazar Bruce R. , Monjazeb Arta , Murphy William J
Published: February 2018

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Background: Obesity is increasingly prevalent and viewed as a critical co-factor in many pathologic conditions due to metabolic, inflammatory and immune perturbations. We performed a multi-species evaluation of the impact of obesity T cell effector functions and markers of immune exhaustion. Methods: We examined the impact of obesity on PD-1 and T cell-mediated responses across different pre-clinical models (tumor, infection, and autoimmune encephalomyelitis [EAE]) and species (mouse, dog, non-human primate, and human). Results: CD4 and CD8 T cells from obese mice, dogs, non-human primates and humans displayed increases in memory T cells and PD-1 expression, as well as impaired proliferative responses compared to lean controls, indicating a greater degree of T cell exhaustion at baseline. Following immunization with myelin oligodendrocyte glycoprotein, obese mice were resistant to induction of EAE, correlating with reduced antigen-specific CD4 T cells in the central nervous system. Administration of anti-PD-1 resulted in restoration of EAE and increased antigen-specific T cell numbers in obese mice. Tumors in obese mice exhibited accelerated growth compared to lean mice, and T cells displayed higher PD-1 expression correlating with RNAseq/molecular signatures of exhaustion compared to tumor-bearing lean mice. PD-1 blockade resulted in marked anti-tumor effects only in obese mice, and not lean. Impaired viral resistance to murine cytomegalovirus (MCMV) resulted was seen in obese mice, associated with increased PD-1/PD-L1 expression, which was reversible by PD-1/PD-L1 blockade. Conclusions: Obesity results in an increase in PD-1/PD-L1 expression and inhibition of T cell responses across species, and blockade not only reverses this inhibition but also leads to markedly augmented T cell effector responses compared to lean counterparts where no effects were observed. These results highlight how the immune system has evolved to control T cell responses using checkpoints contingent on dynamic host conditions and have translational relevance for predicting both efficacy and toxicity in clinical immuno-oncology.
Developing a screening platform for genetic and small molecule targets of cancer immunotherapy.
Authors: Upadhyay Ranjan , Wroblewska Aleksandra , Koo Clara , Brown Brian , Brody Joshua
Published: February 2018

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Background: The success of checkpoint blockade therapy is often dependent on CD8 T cell activation against tumor antigens. However, clinical benefit is only seen in a subset of patients, suggesting that there are other possibly targetable immunosuppressive pathways that are allowing the tumor to escape immune surveillance. Methods: A CD8 T cell that recognizes the EGFP200-208 peptide epitope allowed for the use of EGFP as a model tumor antigen while monitoring expression levels at the single cell resolution. Using a lymphoma line expressing EGFP or mCherry as our antigen-positive and -negative cancer models, we employed 3 screening strategies: 1) a forward genetics approach in which we selected for tumor cells that had naturally developed resistance to killing by CD8 T cells; 2) a reverse genetics approach that involved the use of pooled CRISPR libraries to identify knockout clones with a selection advantage or disadvantage when pressured by activated T cells; and 3) small molecule libraries, including FDA-approved drugs, to identify compounds that increased antigen-specific CD8 T cell killing. Results: Despite antigen recognition and early activation in response to the resistant tumor line, T cells failed to produce effector cytokines and underwent apoptosis in a PD-L1 and CTLA-4 independent manner. Candidate genes mediating this phenotype were derived from expression differences between the original susceptible tumor line and the immunoedited resistant tumor line. The pooled CRISPR approach was validated in a curated library by identifying genes with known roles in T cell-mediated killing and antigen presentation, such as Fas, B2m, and Tap1, as well as known suppressive molecules such as BTLA and PD-L1. LDL receptor expressed on the cancer cell emerged as a possible novel suppressor of T cells. Decitabine and 4-cinnolinethiol, among other small molecules, emerged as possible enhancers of CD8 T cell activity. Conclusions: We have identified several gene candidates as potentially novel and targetable checkpoint-like molecules, as well as small molecule compounds that may be able to enhance the anti-tumor activity of CD8 T cells. Efforts are ongoing in order to validate these targets and to screen larger libraries.