bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioinformatic profiling of tumor immunity from patient biopsies to predict survival and response to immunotherapy.
Authors: Mahmoud Yamil Damian , Veigas Florencia , Merlo Joaquin , Balzarini Monica , Rocha Dario , Rabinovich Gabriel Adrian , Fernandez Elmer , Girotti Maria Romina Romina 
Published: May 2020

e15198 Background: Immunotherapies have revolutionized cancer treatment, but responses are not universal and patients who initially respond to therapy develop resistance. The accurate quantification of tumor-infiltrating immune cells holds the promise to reveal the role of the immune system in human cancers and its involvement in tumor escape mechanisms and response to therapy. We present MIXTURE, a new algorithm for tumor immune cell-type proportions deconvolution from transcriptomic data that overcomes competitive methods and revealed novel associations of immune cell types with patient survival and immunotherapy response. Methods: We applied MIXTURE to transcriptomic data from BRCA (n = 1095), LUAD (n = 506), SKCM (n = 472), HNSC (n = 499) and COAD (n = 521) cohorts from TCGA and five published datasets of melanoma patients treated with anti-PD-1/anti-CLTA-4. Results: The analysis of TCGA breast cancer biopsies showed high proportions of M2-macrophages associated with poor patient survival (p < 0.001). In contrast, we found that proportions of follicular T helper cells were associated with better outcome (p < 0.001). We observed a differential immune composition in biopsies of lung adenocarcinoma patients with mutations in TP53 (WT; n = 247; Mut; n = 259) and EGFR (WT, n = 438; Mut, n = 68) related with their different response to immunotherapy (p < 0.05). We found correlations between immune cells proportions and current biomarkers of response to immunotherapy such as TMB, intratumoral heterogeneity, MSI and PD-L1 expression in the TCGA cohorts (p < 0.05). The meta-analysis of melanoma patients treated with immunotherapy showed a distinct immune infiltrate in patients who responded to anti-PD-1 with an increase of immune effector cells such as CD8, CD4 memory activated and gamma-delta T cells, and a decrease in immunosuppressive M2-macrophages (p < 0.05; R = 81; NR = 107). According with the latest findings, we observed higher presence of B cells in responders to anti-PD-1 on-treatment (p = 0.033; R = 31; NR = 23) and in baseline of responders to anti-CTLA-4 (p = 0.028; R = 14; NR = 26). Interestingly, patients that previously progressed to anti-CTLA-4 showed a differential immune profile that was associated with response to anti-PD-1 (p < 0.05; Ipi-Prog = 59; Ipi-Naïve = 102). Conclusions: We demonstrated the potential of MIXTURE to understand the tumor immune microenvironment and its relationship with patient survival and response to immunotherapies. MIXTURE is available for the wider scientific community as web application and as packages for R and Python.
targetSCAPE and ultraSCAPE: Simultaneous identification and deep profiling of human antigen-specific T cells and other immune cell subsets by mass cytometry.
Authors: Abel Brian , Kairi Faris , Nardin Alessandra , Newell Evan , Fehlings Michael 
Published: May 2020

e15204 Background: During clinical trial immune monitoring, especially in the field of immunotherapy, it is critical to collect in-depth phenotypic information from multiple immune cell populations in order to assess the biological activity of the immunotherapy, to identify biomarkers of response or disease progression, and/or to identify new drug targets. However, patient samples such as peripheral blood mononuclear cells or tissues, are often scarce and current methods face limitations in either achieving a sufficient depth of analysis and/or cell throughput. Methods: In order to identify therapy-relevant antigens and to facilitate a concurrent in-depth characterization of T cells directed towards these targets, immunoSCAPE leverages the high-dimensional immune profiling capabilities of mass cytometry and a unique methodology allowing the identification and characterization of rare antigen-specific T-cell subsets (targetSCAPE). By implementing a new cutting-edge technology that combines flow and mass cytometry in parallel with a combinatorial live cell barcoding strategy, we further increased the high-dimensional phenotyping capacities to over 100 different marker molecules on up to four different immune cell subsets simultaneously within the same sample. Results: We isolated 4 different immune cell populations from a single sample and combined 3 different phenotypic panels consisting of 35 makers each together with a combinatorial tetramer multiplex and phenotyping panel for deep profiling of myeloid cells, NK cells, B cells and T cells. We demonstrate the potential of this novel immuno-phenotyping method, by tracking virus-specific T cells while simultaneously characterizing 4 immune cell subsets with over 100 distinct phenotypic markers from a single sample, which is currently impossible employing modern flow cytometers or classical mass cytometry methods. Conclusions: With its ability to provide an unprecedented picture of the immune status within a single sample, including T cell specificity information and in-depth profiling of relevant immune cell subsets, ultraSCAPE in combination with targetSCAPE can provide detailed insights on the effects of immunotherapy on the immune cell population. Information learned from in-depth immune phenotyping of several immune cell subsets such as T, B, NK and myeloid cell subsets can be leveraged for the development of novel diagnostics, biomarker discovery and monitoring therapeutic strategies in immunotherapy clinical trials.
Balixafortide (a CXCR4 antagonist) plus eribulin in HER2 negative metastatic breast cancer: Dose-response analysis of efficacy from phase I single-arm trial.
Authors: Kaufman Peter A. , Pernas Simon Sonia , Martin Miguel , Gil-Martin Marta , Gomez Pardo Patricia , Lopez-Tarruella Sara , Manso Luis , Ciruelos Eva , Perez-Fidalgo Jose Alejandro , Hernando Cristina , Ademuyiwa Foluso Olabisi , Weilbaecher Katherine N. , Mayer Ingrid A. , Pluard Timothy J. , Martinez Garcia Maria , Vahdat Linda T. , Ringeisen Francois Philippe , Bobirca Alexandra , Cortes Javier 
Published: May 2020

e15209 Background: Balixafortide (B) is a potent, selective antagonist of the chemokine receptor CXCR4. High CXCR4 levels correlate with aggressive metastatic phenotypes and poor prognosis in metastatic breast cancer (MBC). Efficacy and safety data were published recently from the Phase 1 trial investigating B + eribulin (E) in patients with HER2 negative MBC1. We report the final efficacy analyses from this trial, including assessment of dose-response. Methods: In this single-arm, dose escalation trial, patients (pts) received E + increasing doses of B using a 3+3 design in 3 parts: Part I (cohorts received low E doses); Part II (dose-escalation cohort for B [1−5.5mg/kg] + 1.4mg/m2 E); Expanded Cohort (EC; 5.5mg/kg B + 1.4mg/m2 E) to confirm safety and efficacy. Results: At entry, all 56 women (age range 33−82 years) were HER2-negative (IHC and/or FISH), CXCR4 positive. The majority were Caucasian. Most pts were heavily pre-treated in the metastatic setting (line of chemotherapy on study: 29% 2nd line, 50% 3rd line, 21% 4th line). 75% were hormone receptor positive and 23% had triple negative breast cancer. Conclusions: A consistent dose response effect for B + E was suggested in heavily pretreated pts with HER2 negative MBC across all efficacy endpoints. A comparison of these efficacy results, and particularly response data, with single agent data for E in similar populations2, 3 showed that pts in the EC had a more profound benefit observed consistently throughout all efficacy endpoints. Further data and analysis will be forthcoming for presentation. 1. 3 patients from Part II also included in EC because they received the B dose selected for EC (5.5mg/kg). 2. Part I was an initial safety run-in with lower E doses, and so is not included in the table. 1. Pernas S et al. Lancet Oncol. 2018; 19: 812−24 2. Cortes J et al. Lancet. 2011; 377: 914−923 3. Kaufman PA et al. J Clin Oncol. 2015; 33: 594−601. Clinical trial information: NCT01837095 . [Table: see text]
The landscape of chromosome 11q13 amplification in Chinese solid tumor patients and hyperprogressive disease (HPD) clinical example.
Authors: Yu Jieli , Wang Minghui , Song RongFeng , Li Shuben , Wang Hongbiao , Xie Jianjiang , Zhou Chengzhi , Li Kunsong , Chi Liangjie , Huang Jian , Shen Zhuojian , Gu Weiguang , Li Yun , LU Zhen-hai , Xue FangQin , Liu Dan , Shi Xiaoliang , Liu Angen , Zhang Lin 
Published: May 2020

e15222 Background: Multiple biomarkers are thought to be effective guides in selecting immune checkpoint inhibitors, such as Tumor mutational burden (TMB), PD-L1 and MSI/dMMR. Immunotherapy may be miraculous effective in some patients but many other patients experienced poor prognosis and even tumor overgrowth after immunotherapy in real practice. Previous studies have reported that 11q13 (CCND1, FGF3, FGF4, and FGF19) amplifications were associated with HPD. However, the characterization of chromosome 11q13 amplification in Chinese solid tumor patients are not clear. Methods: A total of 10167 Chinese solid tumor patients’ FFPE and matching blood samples sequenced by next-generation sequencing (NGS) targeting 450 cancer genes were included in this study. Genomic alterations including single nucleotide variants (SNV), insertions and deletions, copy number variations and fusions were assessed. The testing was carried out by a College of American Pathologists (CAP) accredited and Clinical Laboratory Improvement Amendments (CLIA) certified laboratory. Results: Chromosome 11q13 amplifications were identified in 679 (6.7%) Chinese solid tumor patients. The top six tumor types with 11q13 amplification were esophageal carcinoma 43.8%, melanoma 17%, urothelial carcinoma 16%, breast carcinoma 13.4%, head and neck carcinoma 13.1% and hepatocellular carcinoma 9.4%. In 2257 patients with TMB-H (10muts/Mb) / PD-L1 expression / MSI samples, chromosome 11q13 copy number gain were identified in 184 (8.2%) patients. Chromosome 11q13 amplification and MSI were independent events and didn't occur simultaneously. In TMB-H patients, the detection rate of 11q13 amplification was 8.5%, while in PD-L1 positive patients, the amplification rate of 11q13 was 7.4%. In patients with TMB-H and PD-L1 positive, the detection rate of 11q13 amplification was 9.4%. In our clinical practice, we saw example of HPD exist in a lung squamous cell carcinoma patient who was treated with multiple lines of therapy and then used the Nivolumab. The patient underwent genetic testing and was found to be chromosome 11q13 amplified. Conclusions: The proportion of 11q13 amplification was different in different types of solid tumor. Esophageal carcinoma, melanoma and urothelial carcinoma were top three types of solid tumors with 11q13 amplification. The 11q13 amplification did not coincide with MSI but it overlapped with PD-L1 expression or TMB-H. Together, these results may provide immunotherapy guidance in clinical practice.
Efficacy and hepatotoxicity of Infliximab in resolving steroid-refractory immune-related adverse events (irAEs) in a real-world setting.
Authors: Pimentel Muniz Thiago , Araujo Daniel Vilarim , Yang Anjie , Sorotsky Hadas , Keshavarzi Sareh , Butler Marcus O. , Saibil Samuel , Spreafico Anna , Hogg David 
Published: May 2020

e15227 Background: Infliximab is used to treat steroid-refractory immune-related adverse events (irAEs) induced by immune checkpoint inhibitors (ICI). Current dogma holds that infliximab is contraindicated in immune hepatitis; steroid refractory disease should be managed with mycophenolate mofetil (MMF). This is based on anecdotal reports of infliximab-induced hepatotoxicity in patients with rheumatologic diseases who received multiple infusions of the drug. In this series of 56 consecutive cases of infliximab-treated patients, we assessed the efficacy of infliximab in resolving specific steroid-refractory irAEs and evaluated the risk of hepatotoxicity from this drug. Methods: We reviewed consecutive patients treated with infliximab for steroid-refractory irAE at a tertiary cancer center between January 2010 and February 2019. To judge hepatotoxicity, we used the Wilcoxon signed rank test to compare the mean value of ALT, AST and total bilirubin (BT) between 0-4 weeks before and after infliximab therapy. We compared factors associated with infliximab efficacy by logistic regression. A p value < 0.05 was considered statistically significant. Results: Mean age was 61.9 years. The majority had a diagnosis of melanoma (62%); 45% had a combination of two ICI before toxicity onset, of whom 73% received an anti-PD1 and an anti-CTLA-4. Colitis was the most common toxicity (66%), followed by pneumonitis (11%). Infliximab was used to treat immune related hepatitis (ir-hepatitis) in 1 patient (2%). Median number of infliximab doses was 1 (1-3), with resolution of toxicity in 76% of patients. Colitis was likely to resolve with infliximab in comparison to other irAE [OR 0.2(95% CI 0.05-0.73)]. Univariate logistic regression did not demonstrate statistical difference in toxicity outcome when ICI were given either as monotherapy (p = 0.3) or combination (p = 0.97). Mean BT, ALT and AST levels before and after infliximab were not statistically different (see table), with no evidence of infliximab-induced hepatotoxicity. The patient treated for ir-hepatitis had a complete recovery, with no further hepatotoxicity. Conclusions: Infliximab was effective in treating irAE and was not associated with hepatotoxicity in this dose-limited setting. Infliximab may be an alternative to MMF in steroid-refractory ir-hepatitis and should be tested prospectively in a randomized trial. [Table: see text]
Key issues in the development and approval of new anti-cancer immune therapies.
Authors: Blunt Al , Gyorffy Steve , Messerschmidt Gerald L. 
Published: May 2020

e15232 Background: Immunotherapy (IT) is now an established treatment option for a select group of cancer patients, and holds great promise for broader application. However, the number of new IT drug approvals has remained low, despite hundreds of new immune therapies entering clinical trials. Methods: We examined both successes and failures of immune-therapeutics (small molecules, large molecules and cellular therapies) to develop insight into this trend. We searched multiple public data sources including clinicaltrials.gov, PubMed, and other large data bases to identify informative trials and primary endpoints. A key area of our research focus was the rate of objective tumor responses following treatment with the immunotherapy agents. Results: Our main observation was that most clinical trials in solid tumors were characterized by a low rate of objective response. Tumor shrinkage is known to be the final manifestation of a multi-step process that begins with the therapeutic product’s ability to bind to its target, and the subsequent engagement of pathways that result in tumor infiltration and tumor cell destruction. A critical step is a sustained immune effector cell attack on the tumor cells. However, a growing body of evidence supports the concept that both non-cellular and cellular immune therapies are active primarily in the setting of a “very warm” or “hot” tumor microenvironment (TME). We found evidence of a positive correlation between objective responses and the degree of ‘hotness’ of the TME. Importantly, our research indicates that study drugs were typically successful in precisely engaging their targets in the associated pathway. High response appears to require selection of appropriate populations with respect to tissue/organism level pathways that lead to successful tumor destruction. Conclusions: The success of IT drugs requires clinical trial designs based on insight into both the study drug’s target pathway, and the impact of key organism level physiologic processes, (e.g., TME) that interfere with optimal anti-tumor activity. [Table: see text]
Lack of association of immune checkpoint protein expression with T stage or stage grouping in colorectal cancer (CRC): A tissue microarray (TMA) based analysis of clinical data.
Authors: Levy Rachel , Acuna-Villaorduna Ana , Maitra Radhashree , Goel Sanjay 
Published: May 2020

e15241 Background: Immunotherapy is a valuable therapeutic intervention in multiple cancer types. In CRC, it is currently limited to those with microsatellite instability–high expression. Thus, immunotyping of CRC patients is critical to identifying potential targets for drug development. In this study, we profiled 171 CRC patient tumor samples to assess the expression of three immune check-point regulators (HHLA2, B7H3, and PD-L1), and 3 clinically useful biomarkers (CK7, CK20, and CDX2) and their association with T stage and stage grouping. Methods: TMA was created from 171 samples of CRC diagnosed between 2000 and 2016 in a major urban cancer center. Formalin fixed paraffin embedded (FFPE) tissues were used for immunohistochemistry (IHC). Antibodies specific for IHC staining were used for HHLA2, B7H3, PD-L1, CK7, CK20, and CDX2. Each specimen was scored from 4-12, based on multiplication of tumor tissue staining value (1 if 1-25%, 2 if 26-50%, 3 if 51-75%, and 4 if 76-100% of area visualized) by the intensity (1-3X). Expression of the proteins was sub divided into two or three groups, depending on the mean expression. Association between the six proteins and pathologic features including T stage and stage grouping (based on the AJCC stage at time of diagnosis) was assessed using chi-square or Fisher Exact tests. Results: Of the 171 patients, 62 (36.3%) presented with a primary cancer that recurred at a later date, and 109 (63.7%) had metastatic disease at presentation. Twenty patients were excluded from statistical analysis due to lack of staging data. The % of tumors with positive expression was 38.1 (HHLA), 37.6 (B7H3), 54.7 (PD-L1), 20.9 (CK7), 52.5 (CK20), and 58.2 (CDX2). There was no significant association between expression of each of the 6 proteins (HHLA2, B7H3, PD-L1, CK7, CK20, and CDX2) and the T stage (T1-2, T3 or T4) or stage grouping (stage 1-2 or stage 3). Consistent with clinical expectation, the expression of CK20 was higher than CK7 (p < 0.05). Conclusions: Expression of HHLA2, B7H3, PD-L1, CK7, CK20, and CDX2 were not associated with T stage or stage grouping of CRC samples in our study. These data suggest that these proteins are expressed early in the onset of CRC. Studies to determine their predictive and prognostic implications are underway.
Single cell dissociation from mouse tumor samples and analysis on BD FACSLyric Flow Cytometer.
Authors: Huang Wei , Pereira Nate , Neuhoefer Patrick Thomas , Middlebrook Aaron , Ghanekar Smita 
Published: May 2020

e15245 Background: Single cell multiomics analysis of tumor cells and tumor infiltrating immune cells using high parameter flow cytometry and single cell genomics technologies is a powerful approach in the investigation of tumor biology and in the discovery of new drug targets and biomarkers. The preparation of single cells from solid tumor samples often involves a physical dissociation step in combination with an enzymatic digestion step. Methods: The effect of the tumor cell dissociation process on the phenotypic properties of single cells isolated from solid tumor samples were analyzed using a 12-color reagent panel on the BD FACSLyric flow cytometer. Specifically, spontaneous pancreatic tumor samples from genetically modified mice were processed using a manual dissociation process with a scalpel blade as well as an integrated tumor sample dissociation process with the prototype Singulator instrument with various protocol settings. The BD Horizon Dri Tumor & Tissue Dissociation Reagent (TTDR) reagent was used for the enzymatic step in all sample preparations. The yield, viability, and frequency of tumor cells and different subsets of leukocytes were measured for each tumor-derived single cell sample preparation. On the Singulator system, cell yield reached a plateau with highest viability at the 30-min process time and a higher percentage of tumor cells was obtained compared to the manual sample processing method. Results: The relative frequencies of T cells, B cells, myeloid cells and macrophages also changed in different sample preparation methods. However, the spatial heterogeneity in the tumor section and cell composition may contribute to these differences and would require more in-depth analysis. In summary, these results suggest that there are many variables in the tumor sample single cell dissociation process that could impact the downstream study results, particularly for multiomics studies. Conclusions: This study highlights the need for optimization and standardization of the sample processing methodologies for downstream analysis. Disclaimers: For Research Use Only. Not for use in diagnostic or therapeutic procedures. Class 1 Laser Product. BD, the BD Logo, FACSLyric, and Horizon are trademarks of Becton, Dickinson and Company. © 2020 BD and its subsidiaries. All rights reserved.
Identifying biomarkers to guide immunotherapy treatment of cancer of unknown primary.
Authors: Mileshkin Linda R. , Posner Atara , Pattison Andrew , Balachander Shiva , Etemadmoghadam Dariush , Fellowes Andrew , Wong Hui Li , Dow Eryn , deFazio Anna , Gao Bo , Karapetis Christos Stelios , Singh Madhu Sudan , Collins Ian M. , Steer Christopher , Warren Mark Andrew , Karanth Narayan , Bowtell David , Prall Owen W.J. , Tothill Richard 
Published: May 2020

e15252 Background: Cancer of unknown primary (CUP) is a metastatic cancer where the primary tissue of origin (ToO) evades detection despite extensive clinical investigation. Recent approaches to the management of CUP have involved gene-expression profiling to resolve the likely ToO and mutational profiling to identify targeted treatments. Current evidence is that both of these methods can have some clinical benefit but only in a minority of cases. Immunotherapy may also be effective in CUP, but clinical trials looking at this are yet to report and the best way to select patients who may benefit is uncertain. Methods: Through a national cohort study called Solving Unknown Primary Cancer (SUPER), 245 CUP patients had molecular profiling performed and clinical follow-up. Variant detection from DNA sequencing using a targeted panel of 386 genes (SureSelect Agilent) was used to calculate tumour mutation burden (TMB). Additionally, a custom gene expression assay including 225 genes associated with ToO and 35 immune genes (SUPERDx, nCounter NanoString) was used to classify the likely ToO and immune profile the tumours. We used the genomic data from 217 of these patients to explore interdependencies between immune gene-expression patterns and TMB. We also retrospectively reviewed the outcomes of patients treated with anti-PD1/PD-L1 immune checkpoint inhibition (ICI) therapy in whom genomic data was available. Results: TMB was weakly correlated with a gene-expression score for immune response (IR) based on averaged z-score values of six genes (CD8A, IFNG, PRF1, PD-L1, GZMA, GZMB) (Spearman rho = 0.21) with many outliers exhibiting low TMB but high IR scores. Among twenty patients treated with ICIs, with both molecular data and response data available, 6 had a partial response (PR), 5 had stable disease (SD) and 9 had progressive disease (PD). We found that an elevated IR score was more predictive of ICI response than TMB. Most patients with either PR or SD to ICI treatment had a high IR score (9/10), and most patients with PD had low IR scores. However, only 3/10 patients with TMB available and a PR or SD had a high TMB ( > 10). Conclusions: Our results demonstrate that ICI therapy may benefit some CUP patients and that an immune response gene-expression scoremay predict ICI treatment response.