bluuebunny/crossref_metadata_2025_split huggingface dataset:
Total number of circulating tumor DNA (ctDNA) genomic alterations and outcome after checkpoint inhibitor-based immunotherapy.
Authors: Khagi Yulian , Goodman Aaron , Daniels Gregory A. , Patel Sandip Pravin , Bazhenova Lyudmila , Kurzrock Razelle 
Published: September 2018

e14504 Background: High tumor mutational burden on tissue biopsy correlates with efficacy of checkpoint immunotherapy in cancers, such as non-small cell lung cancer and melanoma. However, the relationship between mutational burden detected in non-invasive surrogates, such as blood-derived ctDNA genomic alterations, and outcome after immunotherapy, has not been evaluated. Methods: We analyzed 69 patients with diverse malignancies whose plasma-derived ctDNA had undergone next generation sequencing (NGS) (54 to 70 genes: Guardant Health) and who had received checkpoint inhibitor-based immunotherapy. Data was assessed to correlate total number of alterations (characterized alterations and variants of unknown significance, VUS) in ctDNA and outcome: stable disease (SD) >6 months, complete or partial remission (CR or PR), progression-free and overall survival (PFS and OS), from date of immunotherapy initiation. Results: The69 patients had 23 different diagnoses. All individuals received checkpoint inhibitor-based immunotherapy, with the majority receiving anti-PD1/PD-L1 monotherapy. Evaluable patients with ≥6 vs. <6 total ctDNA alterations had significantly higher rates of SD≥6 months/CR/PR: 40.9% (9/22) vs. 15.9% (7/44) (p=0.035) (Table). Median PFS was 2.85 months vs. 2.1 months (p=0.046). OS was not statistically different. A landmark analysis at 2 months showed that median PFS in the ≥6 alterations group was 23.2 months for responders (CR/PR) vs. 2.3 months for non-responders (p=0.0006); for the group with <6 alterations, the median PFS was 12.6 vs. 3.3 months (p = 0.0006). Conclusions: Total number of ctDNA genomic alterations merits further exploration as a potential predictive biomarker for outcome with checkpoint inhibitor-based immunotherapy. Achieving response to checkpoint-based immunotherapy strongly predicts PFS from the 2-month mark. [Table: see text]
Relationship between lymphopenia and objective response rate with programmed death-1 (PD-1) inhibitor therapy: A single-center retrospective analysis.
Authors: Yarchoan Mark , Diehl Adam , Johnson Burles Avner , Scott Blake , Hopkins Alexander , Azad Nilofer Saba , Jaffee Elizabeth M. , Grossman Stuart A. 
Published: September 2018

e14512 Background: Lymphopenia is frequent in advanced cancers, but the impact of absolute lymphocyte count (ALC) on clinical responses with PD-1 immune checkpoint inhibitors is unknown. Methods: We performed a retrospective chart review of adult solid tumor patients treated with a PD-1 inhibitor (nivolumab or pembrolizumab) at Johns Hopkins from 2015-2016. Patients receiving PD-1 inhibitors concurrently with investigational immunotherapies, on unreported clinical trials or for cancers in which the activity of immune checkpoint inhibitors is unclear, or for whom response information is not available, were excluded. Data were collected on patient treatment history, objective response to PD-1 therapy by RECIST 1.1, and ALC at treatment initiation and one and three months after treatment initiation. Results: 172 patients met the inclusion criteria (lung n = 54; melanoma n = 61; kidney n = 25; other tumors n = 32). Lymphopenia (ALC < 1000) was present in 30.2%, 26.7%, and 34.3%, at 0, 1, and 3 months after treatment initiation. In a multiple regression analysis that adjusted for age, sex, ethnicity, tumor type, number of prior therapies, and concurrent ipilimumab usage, lymphopenia at baseline was not predictive of response to an immune checkpoint inhibitor. However, in this same model, lymphopenia at 1 and 3 months after treatment initiation was inversely related to response rate (p < 0.01). Of patients with lymphopenia at baseline, 37 patients (71.2%) had persistent lymphopenia (ALC < 1000 at baseline persisting to month 3) whereas 15 patients (28.8%) had normalized lymphocyte counts by month 3. In a univariate analysis, patients with persistent lymphopenia had decreased response rates as compared to patients who were not lymphopenic at baseline (21.6% vs. 47.5%, p < 0.01). However, patients with lymphopenia at baseline who had normalized lymphocyte counts at month 3 responded similarly as patients who were not lymphopenic at baseline (46.7% vs. 47.5%). Conclusions: Patients on anti–PD-1 therapy with persistent lymphopenia may have a reduced likelihood of responding to these agents. This association requires further validation in additional patient cohorts.
Circulating immune-profile as predictor of outcome in advanced NSCLC patients treated with nivolumab.
Authors: Tiseo Marcello , Veneziani Michele , Gelsomino Francesco , Buti Sebastiano , Facchinetti Francesco , Squadrilli Anna , Bordi Paola , Bersanelli Melissa , Cosenza Agnese , Ferri Leonarda , Rapacchi Elena , Mazzaschi Giulia , Leonardi Francesco , Quaini Federico , Ardizzoni Andrea , Missale Gabriele 
Published: September 2018

e14514 Background: Detection of predictive markers of anti-PD-1/PD-L1 antibodies activity is of pivotal interest in non-small cell lung cancer (NSCLC). This study aimed to identify a circulating immuno-profile as predictor of outcome in NSCLC patients treated with nivolumab Methods: A peripheral blood immuno-profile evaluation was performed at baseline (T0), after 2 (T1) and 4 cycles (T2) of bi-weekly nivolumab in advanced pre-treated NSCLC patients from two Italian Institutions. First tumor assessment was performed after 4 cycles and then every 2 months. FACS analysis of lymphocyte subpopulations [CD3, CD4, CD8, NK (CD56), Treg (FOXP3) and MDSC] was performed. Absolute and % changes of lymphocyte subsets together with their functional and proliferative activity were assessed. Quali-quantitative leucocyte composition at baseline and its variation during therapy were correlated with tumor response and survival. Results: In the overall population of 54 treated patients, baseline Neutrophil-to-Lymphocyte ratio and NK count, lymphocyte count and CD4 variations during therapy showed a statistically significant prognostic role (p < 0.001; p = 0.012; p < 0.001; p = 0.010, respectively). Among 31 patients (squamous carcinoma, n = 17; adenocarcinoma, n = 14) in which all 3 time-points samples were available, 19 were responders (response and stable disease) and 12 non-responders. In responders, absolute numbers of total NK and NKCD56dim subset were higher at baseline and their increase between T0 and T1 was statistically significant (p < 0.05). Responders also displayed increased cytotoxic capability as shown by a higher baseline expression of CD3ζ, perforin and granzyme in NKCD56dim subset. No significant variation was documented in absolute number and functional activity of CD4+ and CD8+ lymphocytes. A higher percentage of CD8+PD-1+ cells at baseline was observed in responders, while non-responders showed a statistically significant increase in the absolute number of MDSC during therapy (p < 0.05). Conclusions: The number and function of NKs and the frequency of PD-1 expression in CD8+ cells could represent predictive peripheral immuno-biomarkers for nivolumab treatment in advanced NSCLC.
Heterogeneity assessment of two PD-L1 clones: 22C3 and SP142 in patients with non-small cell lung cancer (NSCLC).
Authors: Xu Haipeng , Li Chao , Gen Lin , Fang Rong Xi , Lin Dong xian , Huang Yunjian , Zhuang Wu , Miao Qian , Jiang Kan , Huang Cheng 
Published: September 2018

e14515 Background: Pembrolizumab proves to be effective for clinical treatment of non-small cell lung cancer (NSCLC). The clinical application of pembrolizumab should be hinged on the magnitude of PDL1 expression justified by 22C3 assay on Dako platform. However, whether another diagnostic assay, SP142, can replace 22C3 in pembrolizumab-based immunotherapy thus far remains largely unknown. Methods: Forty-nine cases were randomly collected from 207 NSCLC patients with known PD-L1 expression detected by 22C3. Each case was stained with SP142 on ventana platform. The scores obtained with SP142 were compared with 22C3 , according to the interpretation of 22C3 standard. The concordance of PD-L1 expression between 22C3 and SP142 were assessed by weighted Kappa Coefficient and McNemar-Bowker test, respectively. Results: Based on Dako 22C3-IHC platform, 5 (10.2%), 9 (18.4%) and 35 (71.4%) of 49 cases were classified into groups of strongly positive, weakly positive, and negative for PD-L1, respectively. Yet, 37 (75.5%) of 49 cases had the same results with SP142 protocol (Kappa value: 0.472, p < 0.001). Six cases with weakly positive PD-L1, 3 cases with strongly positive PD-L1 and 1 case with negative PD-L1 according to the 22C3 were misdiagnosed as negative, weak positive and weak positive PD-L1 by SP142, respectively (McNemar-Bowker analysis: p = 0.037). When using the 50% tumor cell PD-L1 expression as the cut-off point, overall sensitivity and specificity of SP142 were 40% (95% [CI], 5.3%-85.3%) and 100% (95% CI, 87.1%-100%), respectively (Kappa value: 0.545, p = 0.009; McNemar-Bowker analysis: p = 0.125). When using the 1% tumor cell PD-L1 expression as the cut-off point, adoption of SP142 yielded the sensitivity of 57.1% (95% CI, 28.9%-82.3%) and the specificity of 97.1% (95% CI, 83.3%-99.9%), respectively (Kappa value: 0.608, p < 0.001; McNemar-Bowker analysis: p = 0.063). Conclusions: Compared with 22C3 assay, PD-L1 expression scores were usually underestimated by the SP142, and it has a higher specificity but lower sensitivity. Our findings collectively suggest that it is not applicable to adopt the SP142-PD-L1 IHC Ventana platform to stratify NSCLC patients for pembrolizumab-based immunotherapy.
Estimating tumor mutation burden using next-generation sequencing assay.
Authors: Chaudhary Ruchi , Bishop John , Broomer Adam , Cyanam Dinesh , Mandelman David , Nistala Goutam , Hyland Fiona , Sadis Seth 
Published: September 2018

e14529 Background: High tumor mutation burden is a promising biomarker shown in some cancer types to predict positive response to immune checkpoint inhibitors. We show the ability of a targeted cancer research panel to estimate tumor mutation burden per megabase. Methods: We present a single sample analysis workflow for estimating tumor mutation burden from FFPE research samples. Our assay utilizes a PCR-based target enrichment panel that interrogates 409 known key cancer genes covering ~1.7 megabase of genomic space. Our customized workflow requires only 20 ng of input DNA, and enables a 2 day turn-around time from sample to the result. The ease of our workflow enables less than 60 minutes of hands-on time for automated library preparation and templating on a batch of 8 samples. Next-generation Sequencing is performed using high throughput semiconductor sequencing platform to achieve sufficient depth (~500x coverage) and accuracy. Our custom 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 variants and background noise. Results: Through in silico analysis performed on The Cancer Genome Atlas (TCGA) data we demonstrate that the panel achieves high sensitivity ( > 90%) and specificity ( > 95%) necessary to separate high and low mutation burden samples. Our workflow provides clear separation between allele ratio of somatic and germ-line variants. Our filters consistently eliminate ~98% of germ-line variants from the set of all variants called in single sample analysis workflow. Evidence from tumor-normal analyses on matched tumor and normal samples suggests that our single sample analysis, on the tumor sample only, detects somatic mutations with high sensitivity and specificity with residual of < 3% germ-line variants. Our pipeline identifies mutational signatures consistent with specific mechanisms such as spontaneous deamination of 5-methyl-cytosine, as well as base-damage from FFPE processing. Conclusions: A simple workflow has been developed on the Ion Torrent sequencing platform to estimate per megabase somatic mutational burden from a single tumor FFPE sample. This solution can help advance research in immuno-oncology.
Neutrophil to lymphocyte ratio as predictive of prolonged progression free survival (PFS) and overall survival (OS) in patients with metastatic non-small cell lung cancer (NSCLC) treated with second-line PD-1 immune checkpoint inhibitors.
Authors: Labomascus Stephanie , Fughhi Ibtihaj , Bonomi Philip , Fidler Mary J. , Borgia Jeffrey Allen , Basu Sanjib , Hoch Matthew A , Batus Marta 
Published: September 2018

e14530 Background: Baselinehigh neutrophil to lymphocyte ratio (NLR) has been associated with inferior overall survival in patients with stage III/IV NSCLC. Inflammation and neutrophilic infiltrates in the tumor microenvironment appear to inhibit anti-tumor immune response. We suspect that NLR might reflect the level of inflammation in tumor microenvironment. The objectives of this study were to evaluate potential relationships between pretreatment NLR and and PFS and OS in advanced NSCLC patients treated with second-line nivolumab or pembrolizumab. Methods: Patients with stage IV NSCLC who received at least one cycle of nivolumab or pembrolizumab after first-line treatment with a platinum doublet between January 2015 and December 2016 were included. Patient demographics including NLR at baseline, date of starting immunotherapy, and date of progression were recorded. The association between NLR and duration of response was assessed using a Mann-Whitney-Wilcoxon test. A cutoff of NLR of 3.5 and 5.0 based on published data (ref) were analyzed for differences in median overall survival and progression free survival. Results: 113 patients were analyzed: median age 68, male/female 38.9%/61.1%, 15% never smoked. The median PFS for patients with NLR < 5 was 4.14 months vs. 2.27 months in those with NLR > 5 (p = 0.031). Overall survival was also impacted by NLR. There were a total of 29 deaths in the cohort, 24 of these occurred in patients with NLR > 3.5 and 5 were in patients with NLR < 3.5. A lower NLR at baseline was significantly associated with improved overall survival (p = 0.036). Conclusions: A low baseline NLR is associated with superior progression free survival and overall survival in metastatic non-small cell lung cancer patients treated with nivolumab or pembrolizumab. These findings suggest that evaluating mediators of inflammation might help to identify potential therapeutic targets which could enhance effectiveness of PD-1 immune check point inhibitors in advanced NSCLC.
Serial genome-wide sequencing of cell-free DNA (cfDNA) by assays used in non-invasive prenatal testing (NIPT) to identify copy number alterations (CNAs) associated with immunotherapy response.
Authors: Goodman Aaron , Jensen Taylor , Kato Shumei , Ellison Christopher , Tran Lisa , Mazloom Amin , Grosu Daniel S. , Ehrich Mathias , Kurzrock Razelle 
Published: September 2018

e14533 Background: cfDNA derived from tumor cells can be detected in the plasma of many cancer patients. Noninvasive methods to detect CNAs have been developed to detect chromosomal abnormalities in the setting of prenatal screening. We hypothesized that similar methods can be used to enable quantitative detection of CNAs in cfDNA, as represented by a genome instability number (GIN), in patients with cancer and used to monitor response to immunotherapy. Methods: Peripheral blood for CNA analysis was collected from patients with diverse cancers for whom immunotherapy was planned. Plasma was separated from peripheral blood using centrifugation. cfDNA was collected and subjected to low-coverage, genome-wide sequencing. CNAs were detected using methods developed for noninvasive prenatal testing. GIN was calculated as the cumulative sum of the deviation from baseline for all detected autosomal CNAs. The current analysis focused on patients with a complete or partial response (CR/PR) or progressive disease (PD). Results: Of 48 patients, 11 (23%) attained CR/PR; 17 (35%), PD; 20, stable disease. Twelve of the 28 patients (43%) with CR/PR (5 (42%)) or PD (7 (58%)) had a GIN value consistent with the presence of CNAs at treatment initiation and ≥ 1 additional sample for comparison. Four of the 5 patients with CR/PR had a decrease in their GIN from their baseline while all 7 patients with PD had a sustained increase in their GIN. The mean (standard error of the mean (SEM)) change in GIN from maximum to minimum for responders was –2753.8 (+/-1643); mean (SEM) change in GIN from minimum to maximum for progressors was 1373.76 (+/-576) (p = 0.0221). Interestingly, 3 of the 5 responders had an initial increase in their GIN after 2-3 weeks of treatment followed by a decline, while all 7 progressors had a continuous increase in their GIN. Conclusions: GIN can be used to monitor response to immune checkpoint inhibitors in cancer patients. Serial evaluation shows an initial GIN increase followed by decline in patients who eventually attain CR/PR, but a sustained increase in patients with progression.
The anti-tumour immune response after radiofrequency ablation of colorectal cancer.
Authors: Lemdani Katia , Capron Claude , Seguin Johanne , Mignet Nathalie , Boudy Vincent , Peschaud Frederique , Emile Jean Francois , Malafosse Robert 
Published: September 2018

e14540 Background: Results of radiofrequency ablation (RFA), increasingly used to treat liver tumors, are compromised by local and systemic relapse. Hyperthermia related cancer cells death, release of tumor antigens and expression of danger signals activate a tumor-specific T-cells response. This effect remains ineffective to avoid recurrence. Therefore we propose to combine RFA with an activation of a solid immune antitumor response as curative treatment of a colorectal (CRC) metastatic disease in immunocompetent mouse. Methods: RFA was used to treat a CT26- luc tumor. In two distinct clinical situations, distant macroscopic or microscopic tumors were established as metastases before or at the time of RFA. Immune response was modulated by an injection in situof a thermo-reversible hydrogel loaded by GM-CSF and BCG, targeting dendritic cells. In the group of mice with large far lesions this strategy was combined with immune checkpoint inhibition. The efficiency was assessed on survival, evolution of distant lesions, characterization of lymphocyte infiltration in tumors and systemic immunity through specific TNF- α and IFN-y expression in spleen and draining lymph nodes. Results: The in situ immunogel injection after RFA resulted in a prolonged survival of mice. Regression of distant lesions was related to a strong systemic antitumor immune response and a great improvement of tumor infiltration by specific cytotoxic lymphocytes. In adjuvant situation, the use of immunogel induced a complete cure of microscopic secondary lesions without any treatment. Immune escape of large secondary lesions was reversed by association of RFA-immunogel vaccination with a systemic check point blockade, separately ineffective. Conclusions: Validation of this strategy, combining RFA of liver metastases and activation of a strong immune response controlling the residual disease, could result in a clinical assay including this approach within the standard treatment of CRC. Furthermorethe powerful synergy between RFA-in situ immunomodulation as a starter treatment and checkpoint blockade ineffective alone in CRC or after single RFA, allows reconsidering the use of immune checkpoint inhibitors in metastatic microsatellite stable CRC.
Preclinical development of tumor-infiltrating lymphocyte (TIL) based adoptive cell transfer (ACT) immunotherapy for patients with sarcoma and the potential benefit of anti-CD137 stimulation.
Authors: Nielsen Morten , Krarup-Hansen Anders , Hovgaard Dorrit , Petersen Michael Mørk , Loya Anand Chainsukh , Westergaard Marie Christine Wulff , Svane Inge Marie , Junker Niels 
Published: September 2018

e14545 Background: Tumor specific TILs can be in vitro expanded and have the ability to induce complete and durable tumor regression in some patients following ACT. In this preclinical study we investigated the feasibility of expanding TILs from sarcomas, as well as performing functional in vitro analyses on these. Methods: Fresh tumor samples from sarcoma patients were obtained, and TILs were isolated and expanded in growth medium containing IL-2. In a sub study, we investigated the effect of adding an agonistic CD137 antibody (Urelumab, BMS) and/or an anti-CD3 antibody (OKT3) to the medium. Phenotype and functional analyses was performed using flow cytometry and IFNγ-Elispot. Results: Tumor samples from 30 patients with various types of sarcomas were obtained, and we were able to expand a minimum of 40 million TILs from 27 of these. Mean expansion times were 32 days (14 - 61). 87,7 % (36,4 – 99,1) of these cells were CD3+, and of these, 66,7 % (16,3 – 99,1) were CD4+, and 21,8 % (0,1 – 50,6) were CD8+. A sub study revealed that adding anti-CD137 and/or OKT3 increased total yield of TILs; anti-CD137 skewed the phenotype significantly towards more CD8+ TILs and in some cases NK cells and γδ T cells. TILs from 8 of 17 tested tumor samples from four different sarcoma subtypes (undifferentiated pleomorphic sarcoma, myxofibrosarcoma, myxoid liposarcoma and osteosarcoma) demonstrated reactivity against autologous tumor cells using IFNγ-Elispot (40 – 500 spots per 100.000 TILs). In TILs stimulated with anti-CD137 the reactivity increased. Conclusions: We were able to expand TILs from 90 % of the acquired tumor samples to numbers needed for possible future clinical ACT implementation. Expanded TILs were a mix of CD4+ and CD8+ with CD4+ being predominant. Approximately half of the TIL cultures showed some degree of in vitro tumor reactivity as determined by Elispot. Early analyses suggest that addition of anti-CD137 could influence expansion time, phenotype, and functional capacity of the expanded TILs. Based on these results, we conclude that it is feasible to translate TIL based ACT into clinical testing in sarcoma patients.
The status of PD-L1 expression and TILs among ESCC patients in China and changes after radiation and chemotherapy.
Authors: Wen Song , Huang Dingzhi , Ba Yi , Li Hongli , Liu Rui 
Published: September 2018

e14567 Background: The status of PD-L1 expression and TILs (tumor infiltrating lymphocytes) is suggested as a predictive biomarker for the clinical effect of PD-1/PD-L1 inhibitors. In our study, weevaluate the status of PD-L1 expression and TILs in ESCC (esophageal squamous cell carcinoma), especially in CD8+ T cells. We also evaluate the changes in PD-L1 expression after chemotherapy or radiation. Then, we analyze the significance of these profiles. Methods: We retrospectively collected a total of 240 patients with histologically confirmed ESCC who underwent a radical operation between May 2009 and January 2015 at TianJin Medical University Cancer Institute & Hospital. Of these 240 patients, 104 patients received neoadjuvant therapy, including chemotherapy, radiotherapy or CCRT. We then examined the expression of PD-L1, CD8 and PD-1 in every patient. Results: We find a significant association between the PD-L1 expression and CD8+ T cell status (P = 0.044), while there is a negative relationship between the PD-L1 expression and PD-1+ T cell status (P = 0.048). Compared with the surgery-only group, there is an increase in the PD-L1 expression in NACRT and NCT (≥3 cycles) groups (P = 0.001 and 0.025). The PD-L1 expression non-significantly decreases in the NCT ( < 3 cycles) group (P = 0.197). We also observe an increase in CD8+ T lymphocytes in the NACRT and NCT ( < 3 cycles) groups (P = 0.116 and 0.036). Conclusions: We find a relatively high expression of PD-L1 and TILs in Chinese ESCC, indicating that PD-1/PD-L1 inhibitors may have a role in treatment. Additionally, there is an increase in PD-L1 and TILs after radiation or chemotherapy. As a result, combining PD-1/PD-L1 inhibitors with traditional cytotoxic therapy is a promising direction.