bluuebunny/crossref_metadata_2025_split huggingface dataset:
Peripheral blood TCRB chain convergence and clonal expansion following cytomegalovirus infection: Implications for the biomarker use of TCR-seq.
Authors: Looney Timothy , Zheng Jianping , Topacio-Hall Denise , Lowman Geoffrey , Hyland Fiona 
Published: July 2019

134 Background: Human cytomegalovirus (CMV) is a common immune-evasive herpes family virus leading to lifelong asymptomatic infection in 50 to 80% of humans. The effect of CMV infection on the T cell repertoire may be relevant given interest in identifying T cell repertoire features predictive of response to checkpoint blockade immunotherapy (CPI) for cancer. Here we sought to identify features of CMV infection using TCRB profiling of peripheral blood (PBL) total RNA. Methods: Total RNA from PBL was obtained from 35 blood donors of known CMV status, then used for TCRB sequencing via the Oncomine TCRB-LR assay (amplicon spanning CDR1, 2 and 3) and the Ion Torrent S5. In parallel, we prepared libraries via the Oncomine TCRB-SR assay (CDR3 only). Data were used to identify TCRB repertoire features correlated with CMV status and compare repertoire features across the two assays. Results: T cell clone evenness was reduced in CMV positive individuals irrespective of age, predictive of CMV status (AUC = .86, p = 2E-4, Wilcoxon), and strongly correlated between LR and SR assays (Spearman cor = .96). TCR convergence was elevated in CMV positive individuals and uncorrelated with evenness (Spearman cor = -.03) such that the combination of convergence and evenness improved the performance of a logistic regression classifier (AUC = .93). Conclusions: We identify reduced T cell evenness and elevated TCR convergence as features of chronic CMV infection. CMV infection appears to significantly alter the T cell repertoire, suggesting that CMV status may be required for proper interpretation of T cell expansion in the context of CPI for cancer.
Chemo-immunotherapy combination after PD-1 inhibitor failure improves clinical outcomes in metastatic melanoma patients.
Authors: Vera Aguilera Jesus , Paludo Jonas , Failing Jarrett , McWilliams Robert R. , Kottschade Lisa A. , Block Matthew Stephen , Markovic Svetomir , Dronca Roxana Stefania , Yan Yiyi 
Published: July 2019

138 Background: Clinical management of metastatic melanoma (MM) after PD-1 blockade failure remains challenging and lacks a standard of care. Chemo-immunotherapy (CIT) combinations have demonstrated favorable efficacy and safety profiles in lung cancer patients. In this study, we compared the clinical outcomes of CIT with immunotherapy or chemotherapy alone after PD-1 blockade failure. Methods: We reviewed MM patients seen at Mayo Clinic between Jan, 2012 and Jun, 2018 who failed anti-PD1 therapy and received subsequent CIT, or immune checkpoint inhibitors (ICI) or chemotherapy alone. A total of 60 patients were analyzed, the CIT cohort [n=33 (55%)] treatment consisted of carboplatin/paclitaxel (n=29), nab-paclitaxel (n=2), paclitaxel (n=1), and temozolomide (n=1). In the ICI (n=9) or chemotherapy alone cohort (n=18) [n=27 (45%)], treatment consisted of carboplatin/paclitaxel (n=11), temozolomide (n=4), nab-paclitaxel (n=3), ipilimumab/nivolumab (n=4), pembrolizumab (n=4), or nivolumab (n=1). Results: Patients in the CIT cohort had a median OS of 3.5 years (95% CI: 1.7-NR) compared to 1.8 years (95% CI: 0.9-2) in the ICI or chemotherapy alone cohort, p=0.02. The median EFS following CIT was 7.6 months (95% CI: 6-10) compared to 3.4 months (95% CI: 2.8-4.1) following either ICI or chemotherapy alone, p=0.0005. A trend towards longer median EFS with use of CIT was seen in patients with BRAF wild-type [median 9 months (95% CI: 6-12)] compared to those harboring a BRAF mutation [median 6.5 months (95% CI: 1.8-9.1), p=0.29]. Side effects were similar among both groups. Conclusions: In MM patients who have failed anti-PD-1 therapy, the CIT combination showed favorable clinical outcomes and acceptable safety profile. This regimen should be considered for MM pts in this setting who have limited treatment options. [Table: see text]
The outcome and toxicity profile of checkpoint inhibitor immunotherapy subsequent to high-dose IL-2 in the treatment of metastatic melanoma and renal cell carcinoma.
Authors: Berg Stephanie A. , Clark Joseph I. , Henry Elizabeth , Wagner Courtney Regan , Flanigan Robert Charles , Mai Hanh P. 
Published: July 2019

14 Background: Approved treatments for metastatic melanoma (MM) and metastatic renal cell carcinoma (mRCC) include targeted agents, high dose interleukin-2 (HD IL-2) and checkpoint inhibitors (CI). A subset of responders to HD-IL2 can achieve long term durable remissions (7-10%). Recently, data suggests that durable remissions are possible with CI. Thus, despite increased toxicity, first-line immunotherapy with HD-IL2 is a reasonable consideration in carefully selected patients with clear cell mRCC and MM followed by CI upon relapse. Our study explores the utility and safety of CI subsequent to HD-IL2 in patients (pts) in this population. Methods: We conducted a single institution retrospective analysis of pts with MM or mRCC who received HD-IL2 and subsequent CI from 2008-2017. Pts treated with prior targeted therapy were included. Statistical analysis was performed using Fischer's exact tests, log-rank test for KM analysis and non-parametric Wilcoxon Rank Sum tests to compare the groups. Results: We identified 34 unique pts (19 MM, 15 mRCC) from our pre-specified cohort. Pts were male (73%), Caucasian (88%), and median age=53. mRCC pts received more cancer related treatments than MM prior to CIs after HD-IL2 was given (2 vs. 1, p=0.002), had more total CI cycles administered (12 vs. 7, p=0.10) but less IL-2 doses than MM pts (20 vs. 24, p=0.26). mRCC pts tended to record higher HD-IL2 toxicity grade compared to MM pts (exact =0.04). 26% (9/34) of pts experienced a grade 2 or higher CI toxicity. Pts had higher HD IL-2 toxicities than CI toxicities during therapy but these two measures were not significantly correlated (r=0.07, p=0.73); furthermore, there was no survival difference between pts with reported grade 2 or higher CI toxicity compared to pts without any CI toxicity ( p=0.14). Conclusions: Our study suggests that CI therapy after HD-IL2 is feasible and not associated with more frequent toxicity or less clinical efficacy in pts with MM or mRCC.
Effect of radiofrequency ablation (RFA) combined with anti-CTLA-4 and anti-PD1 in a preclinical melanoma model.
Authors: Franco-Mahecha Olga L. , Christou Anna , Mauda-Havakuk Michal , Katti Prateek , Pritchard William F. , Karanian John W. , Wood Bradford J. 
Published: July 2019

143 Background: The aim is to characterize the effect of Radiofrequency Ablation (RFA) with anti-CTLA-4 and anti-PD1 checkpoint inhibitors, on tumor growth and immune responses against B16-OVA melanoma tumors implanted in a syngeneic mouse model. Methods: Adult c57BL/6J female mice were distributed among a non-tumor placebo group (n=5) and four experimental tumor groups: no RFA (n=10); RFA alone (n=5); CPI post-RFA (n=5); and CPI pre-and-post-RFA (n=5). On day 0, mice were inoculated SQ with 2.5x105 B16-OVA cells. RFA was performed at day 15. Three doses of anti-mouse CTLA-4 and anti-mouse PD-1 (200 µg/dose each, every 24 h) were given IP to the appropriate groups. To evaluate the effect of the therapy on a distant tumor, each tumor group was re-inoculated SQ at day 20 with 2.5x105 B16-OVA cells. Serum samples were collected to measure concentration of cytokines. Mice were euthanized at day 36. T-cell and non-T cell fractions were collected from splenocytes for co-culture and evaluation of killing in vitro. Results: Mice that received RFA alone or RFA plus CPI showed significantly smaller primary tumors and minimal growth of secondary tumors compared to untreated mice, suggesting that these therapies may have an abscopal effect. Based on the cytokine profile in serum, mice treated with CPI pre-and-post-RFA showed balanced and sustained concentrations of IFNγ and IL-2 (T cell activation) and controlled inflammatory responses. In vitro experiments showed that T cells from mice treated with CPI pre-and-post-RFA produced significantly more IFNγ when co-cultured with B16-OVA cells. However, these T cells did not demonstrate a high killing activity on the tumor cells. The killing capacity of T cells from mice treated with RFA alone or with CPI pre-and-post-RFA increased significantly when the non-T cell fraction (dendritic cells, macrophages, NK cells, and B cells) was added to the co-culture. Conclusions: RFA therapy combined with CPI given to mice bearing B16-OVA tumors may induce systemic immune responses capable of improving control of distant tumor growth. In culture, primed T cells are not able to kill B16-OVA by themselves, but the addition of the non-T cell fraction may improve T cell killing capacity.
Survey of the immunogenomic landscape of solid tumors through clinical DNA and RNA sequencing.
Authors: Lau Denise , Chang Alan , Perera Jason , Lozac'hmeur Ariane , Bobe Alexandria , Khan Aly 
Published: July 2019

153 Background: In the past decade, immunotherapy has emerged as an important new modality in cancer treatment. However, studies have shown that only a fraction of patients will experience any clinical benefit when treated with immune checkpoint blockade drugs. Given the cost and potent adverse events associated with immunotherapy, the need for effective biomarkers is clear. We sought to understand the role of key immunotherapy biomarkers, like tumor mutational burden (TMB), microsatellite instability (MSI), and PD-L1 immunohistochemistry (IHC), in the context of the greater immunogenomic landscape of solid tumors in patients. Methods: We analyzed data from a cohort of 500 patients across 10 cancer types who received the Tempus xT 595 gene targeted DNA sequencing assay and whole transcriptome sequencing assay as part of their clinical care. We determined the TMB, MSI status, and neoantigen load for each sample using the DNA sequencing data. We used the RNA expression data to evaluate immune activation and tumor infiltration by determining the expression of inflammatory gene signatures and estimating the relative proportion of key immune cell types. Results: Integrative analysis of the DNA and RNA sequencing data showed that the immunogenicity of the tumor, as measured by TMB or neoantigen load, correlates with levels of immune activation and tumor infiltration. Inflammatory immune cells, like CD8 T cells and M1 polarized macrophages, were significantly higher in TMB-high samples; while non-inflammatory immune cells, like monocytes, were significantly lower in TMB-high samples. Additionally, samples could be clustered into immunologically active “hot” tumors or immunologically silent “cold” tumors based on gene expression. The immunologically “hot” population was enriched for samples that were TMB-high, MSI-high or PD-L1 IHC positive. Conclusions: Paired next generation DNA and RNA sequencing assays allows for the identification of patients that have immunologically active tumors that lack traditional immunotherapy biomarkers. These patients represent an interesting new population who may potentially benefit from immunotherapy.
Low-dose IL-12 preconditions the tumor microenvironment to enhance the efficacy of PD-1 blockade.
Authors: Diaz-Montero C. Marcela , Ravichandran Sairekha , Pavicic Paul G. , Rayman Patricia A. , Tannenbaum Charles , Finke James , Ko Jennifer S. , Funchain Pauline , Tarhini Ahmad A. 
Published: July 2019

20 Background: The immunomodulatory effects of IL-12 are well known to result in potent anti-tumor responses. However its therapeutic development has been hindered by its potential toxicity. Here we explored the impact of systemic low dose IL-12 administration as a strategy to enhance the efficacy of PD-1 blockade. Methods: Mice bearing D4M melanoma tumors were treated with anti PD-1 antibody alone or in combination with low dose IL-12 (100ng twice a week). Tumor progression was monitored, and characterization of immune cell types was performed by flow cytometry and gene expression analysis. Results: A significant reduction in tumor progression after combinatorial treatment with low dose IL-12 and anti PD-1 was observed. This synergistic effect was associated with elevated levels of intratumoral IFN-γ, iNOS, CXCL9, CXCL10, CXCL11, and perforin. Single treatment with low dose IL-12 induced a decrease in the levels of circulating neutrophils and an increase in the levels of circulating CD8+ T cells. Within the TME, low dose IL-12 treatment was associated with an increase in the frequencies of tumor infiltrating M-MDSCs expressing high levels of CXCL9. Elevated levels of CD8+ TILs were also found, which were characterized by their increased expression of PD-1 and PD-L1, as well as CD107a, CXCR3 and CD103. No signs of toxicity were noted. Conclusions: Low dose IL-12 synergizes with anti PD-1 to induce superior regression of D4M melanoma tumors. This effect was associated with an increase in the levels of molecules involved in the recruitment and effector function of CD8+ T cells. Analysis of tissues from animals treated with low dose IL-12 alone showed significant changes in the composition and phenotype of myeloid and T cells in both the tumor and blood. Expression of CXCL9 on tumor infiltrating MDSCs suggested a reversal of their immunosuppressive function to an immunopromoting one, and could explain the elevated accumulation of CD8+ TILs via enhanced CXCR3-dependent recruitment. These findings suggest that low dose IL-12 is sufficient to induce changes in the TME, with minimal toxicity,that enhance the anti-tumor effects of PD-1 blockade. A clinical study testing the safety of this combination is currently underway.
Automated flow cytometric profiling of tumor heterogeneity, tumor-infiltrating leukocyte (TIL) exhaustion, and coexpression of checkpoint receptors/ligands in patient-derived carcinomas.
Authors: Salojin Konstantin , Hauther Christine , Liu Dai , Putta Santosh , Purvis Norman , Westfall Matt 
Published: July 2019

28 Background: Clinical benefits of immune checkpoint receptor (ICP-R) blockade in cancer patients can be predicted using various biomarkers such as Immune Index. However, traditional IHC approaches are lacking in sensitivity and in addressing the heterogeneity of the tumor microenvironment (TME), TIL functional status, expression of targetable ICP-R and their ligands (ICP-L), and detection of rare immune subsets within the TME. Methods: We developed a flow cytometry platform (ImmunoINTEL™) that delivers quantitative, clinically relevant information by merging these aspects of tumor biology into a single automated HTP assay comprised of multi-parameter Ab panels and automated sample/data processing procedures for immunophenotyping of blood and tissue specimens from patients with lung, breast, renal, and colorectal carcinomas. Results: Analysis of tumor specimens revealed distinct immune profiles characterized by variations in TIL makeup, differential expression of ICP-R and ICP-L (PD1/PDL1, TIGIT/CD112&CD155, Tim-3/Galectin-9, SIRPa/CD47), and changes in the functional/exhaustion status of TILs. We observed several discrete carcinoma profiles characterized by (1) an elevated Treg : CD8+GZMB+ T cell ratio, (2) high expression of ICP-L on epithelial cells and myeloid TILs, (3) enrichment for M1 macrophages (Mφ), M2 Mφ, and mixed M1/M2 phenotype Mφ (4) elevated levels of myeloid cells with suppressive phenotypes (MDSCs), (5) significant presence of myeloid and plasmacytoid dendritic cells, and (6) enrichment for mesenchymal cells. The elevated expression of several ICP-Ls on TILs and ICPs on epithelial cells suggested tumor- and TIL-intrinsic mechanisms modulating checkpoint interactions. Conclusions: The heterogeneity of TILs and ICP-R/ICP-L expression profiles across cell and tumor types can be explored in proof-of-mechanism studies and clinical trials to provide a rational for targeting distinct ICP-R/ICP-L interactions and TIL exhaustion mechanisms with immunotherapeutics, and for more refined selection of potential responders to ICP inhibitors.
Anti-PD-1 antibody cetrelimab (JNJ-63723283) in patients with advanced cancers: Updated phase I/II study results.
Authors: Rutkowski Piotr , Felip Enriqueta , Moreno Victor , Trigo Perez Jose Manuel , Calvo Aitana , Kowalski Dariusz , Cortinovis Diego , Lee James J. , Manikhas George , Plummer Elizabeth Ruth , Maio Michele , Ascierto Paolo Antonio , Vladimirov Vladimir Ivanovich , Gaffney Dana , Li Lilian Y. , Bae Kyounghwa , Greger James G. , Shin Chu Ri , Xie Hong , Calvo Emiliano 
Published: July 2019

31 Background: Cetrelimab (JNJ-63723283) is an IgG4, anti-programmed cell death protein-1 (PD-1) antibody. Here we present updated results from an ongoing phase 1/2 study of cetrelimab in patients (pts) with advanced or refractory solid cancers. Methods: Part 2 of the study evaluated safety and efficacy of cetrelimab at 240 mg Q2W, a recommended phase 2 dose selected in Part 1 (Calvo JCO 2018; 36 suppl 5:58). Tumor types for Part 2 included non-small cell lung cancer (NSCLC), melanoma (MEL), bladder, renal cell, small cell lung cancer (SCLC), microsatellite-high (MSI-H)/DNA mismatch repair deficient (dMMR; locally or centrally tested) colorectal cancer (CRC) and gastric/esophageal cancer (GCA/EC). Tumor response was assessed by the investigator following RECIST v1.1. Results: As of 3 Sep 2018, 192 pts have been treated with cetrelimab from 80–800 mg Q2W and 480 mg Q4W. Median age was 60 years (23–86), and median prior regimens was 2 (1–12). Median duration of treatment was 85 days (1–561); 82 pts remain on treatment. Full receptor occupancy was maintained throughout dosing interval. Most common adverse events (AEs) were asthenia (19%), fatigue (19%), dyspnea (16%) and diarrhea (16%). Grade ≥3 AEs, regardless of causality, were reported in 45% of pts; most common were anemia (6%), dyspnea (4%), increased ALT (3%) and increased AST (3%). Observed serious AEs were dyspnea (4%), pleural effusion and intestinal obstruction (3% each). All grade and grade ≥3 immune-related AEs were reported in 30% and 7% of pts, respectively. Among response-evaluable pts (n = 156) from Parts 1 and 2, overall response rate (ORR) was 15%, with 2 complete and 22 partial responses. Half of pts had stable disease or better. ORR was 26% (7/27) in NSCLC (42% [5/12] in PD-L1+ NSCLC [≥50% by IHC]), 25% (12/49) in MEL (28% [12/43] in non-uveal MEL), 50% (1/2) in renal cancer, 8% (2/26) in MSI-H/dMMR CRC (recruited later per amendment) and 14% (2/14) in GCA/EC. No responses were observed in bladder cancer (n = 4) or SCLC (n = 10). Conclusions: The safety profile and preliminary activity of cetrelimab in immune-sensitive advanced cancers is consistent with known PD-1 inhibitors. The study is ongoing and analysis by PD-L1 status will be reported later. Clinical trial information: NCT02908906.
Tumor mutational burden (TMB) may be a promising predictive biomarker of response to PD-1/PD-L1 targeting in MSI-H colorectal cancer.
Authors: Fakih Marwan , Sandhu Jaideep Singh , Ouyang Ching , Sokol Ethan , Ross Jeffrey S. , Miller Vincent A. , Lim Dean , Chao Joseph , Catenacci Daniel V.T. , Cho May Thet , Braiteh Fadi S. , Maron Steven Brad , Chase Leah , Klempner Samuel Jacob , Ali Siraj Mahamed , Schrock Alexa Betzig 
Published: July 2019

43 Background: PD-1 targeting with pembrolizumab or nivolumab leads to durable clinical benefits in patients (pts) with microsatellite instability-high (MSI-H) tumors. However, 30-35% of mCRC pts with MSI-H tumors will experience progressive disease (PD) as a best response when treated with anti-PD1 agents, highlighting the need of additional predictive biomarkers. Methods: We performed a retrospective multi-center clinical investigation to evaluate the impact of TMB, age, gender, stage at initial presentation, pattern of metastatic disease, tumor grade, and RAS/RAF status on response to anti-PD1/PD-L1 in MSI-H mCRC. TMB and MSI status were determined by hybrid capture-based next-generation sequencing (Foundation Medicine [FM]). The TMB distribution in MSI-H CRC was estimated from a large data set from FM. Results: 22 eligible MSI-H mCRC pts were identified across 5 cancer centers: 19 pts received pembrolizumab, 1 pt received nivolumab, 1 pt received nivolumab + ipilimumab, and 1 pt received durvalumab + tremelimumab. Among tested variables, TMB (as a continuous variable) showed the strongest association with an objective response (OR; p < 0.001). Also, both univariate and multivariate analyses supported that TMB serves as an independent prognostic variable in predicting progression-free survival (PFS; p < 0.001 and p < 0.01, respectively). Using log-rank statistics, the optimal predictive cut-point for TMB was estimated between 37-41 mutations/Mb to dichotomize pts into TMBhigh and TMBlow groups. All 13 pts (100%) with TMBhigh had an OR, while only 2/9 (22%) pts with TMBlow had an OR and 6/9 had PD. The median PFS for TMBhigh pts has not been reached (no progressors, median follow-up > 18 mos), while the median PFS for TMBlow pts was 2 mos. Amongst 821 MSI-H CRC cases tested at FM, the 25th, 35th, 50th and 75th percentile TMB cutoffs were 33.1, 37.4, 46.1, and 61.8 mutations/Mb, respectively. Our optimal TMB cut-point range suggests that MSI-H mCRC with the lowest 35th percentile of TMB have a low likelihood of benefit from anti-PD1. Conclusions: These TMB findings require validation in prospective trials and may guide the sequencing of PD-1 inhibitor monotherapy in MSI-H mCRC.