bluuebunny/crossref_metadata_2025_split huggingface dataset:
Retrospective analysis of the role of CA 15-3 as a biomarker for breast cancer relapse.
Authors: Shaikh Marwan Elahi , Hall Samantha , Wen Sijin , Liu Hui , Miah Abdul , Salkeni Mohamad Adham 
Published: September 2018

e23051 Background: The latest ASCO guidelines regarding tumor markers in breast cancer do not recommend routine monitoring of serum CA 15-3 (CA) levels alone as a marker for relapse. They do, however, acknowledge their use in conjunction with a patient’s history, physical exam, and diagnostic imaging. The study objective is to evaluate CA as a marker for relapse and determine its continued use in our patient population. Methods: We performed a retrospective analysis on female stage I-III breast cancer patients with an elevated CA marker treated in our cancer center between 2009-2014. Patients with metachronous or synchronous malignancies were excluded. Patients were categorized into three groups: Group 1 (elevated CA at relapse), Group 2 (normal CA at relapse, with elevation post-relapse), Group 3 (elevated CA without relapse). Categorical variables were collected to fulfill our objectives and the Fisher’s exact test was used to assess the correlation between them. The incidence rate and its 95% confidence interval were estimated based on the binomial distribution. Results: Out of 340 initially screened patients, 92 met our inclusion criteria: Group 1 (n = 25), Group 2 (n = 23), Group 3 (n = 44). The PPV for an elevated CA as a marker for relapse was 36% (95% CI: 26-48%). On routine surveillance, patients with elevated CA levels were more likely to have relapse if they presented with nausea (p = 0.02), myalgia (p = 0.003), or axial bone pain (p = 0.04). At relapse, an elevated CA was associated with fatigue (p = 0.02), myalgia (p = 0.01), liver metastases (p = 0.01), axial bone metastases (p = 0.005), and peripheral bone metastases (p = 0.0002). In patients with an elevated CA, a BMI < 25 had a higher incidence of relapse in comparison to those with a BMI ≥ 25 (p = 0.01). Conclusions: Our study suggests that a patient’s history, physical, and symptom-dictated imaging should be the main way to screen for relapse in stage I-III breast cancer. Based on the higher incidence of relapse in patients with both an elevated CA and symptoms of nausea, myalgia, or axial bone pain, we conclude that serum CA levels may be used as an adjunctive test in symptomatic patients. Our data also suggests that elevated CA levels may be less useful in detecting relapse in patients with BMI ≥ 25.
Pharmacogenetic 3C interaction associated with the PDGFRA gene as a chromatin conformation marker for treatment with tyrosine kinase inhibitors.
Authors: Akoulitchev Alexandre , Ramadass Aroul , Green Jayne , Uzun Ulku , Mellor Jane , Hunter Ewan , Grand Francis 
Published: September 2018

e23054 Background: IDH1 mutations detected in glioma cells impair the insulator function between FIPL1L1 and PDGFRA at 4q12 ( Flavahan et al. 2016). We have used a high-resolution chromosome-conformation capture 3C analysis platform, EpiSwitch, and quantitative PCR, to map, evaluate, and quantify the TKI-sensitive conformational juxtaposition between FIP1L1 and PDGFRA. Loss of the insulator function in glioma prompted us to investigate the same interaction in the context of insulator loss with interstitial deletions at 4q12 in eosinophilic leukemias and AML. Methods: We tested a total of 72 primers in temperature gradient PCRs, with concentration matched negative controls, using the AML cell lines EOL-1 and HL-60. Products were sequenced in forward and reverse order. Dual label 5’FAM-BHQ1-3’hydrolysis probe assays, entirely specific for the PCR products, targeted the junction region of the 3C fragments. A reference 3C interaction was used as an internal copy number control for 3C library production. Results: EpiSwitch predicted and identified six 3C FIP1L1-PDGFRA interactions in different sequence orientations, within the 3D organization of the PDGFRA locus. The interaction D7 identified by the EpiSwitch qPCR assay was detected reproducibly in EOL-1 cells and glioblastoma tissue using both single step PCR and qPCR. An imatinib-sensitive AML cell line EOL-1 was used as a positive control for qPCR assays. Both AML and glioma cell lines tested positive using the assay as did glioma patient biopsies. The glioblastoma cell line DBTRG-05MG also tested positive for the D7 interaction at a maximum of 8.92 copies per 20 ng of the template. Conclusions: We confirmed and characterized, at high resolution, the conformational deregulation of FIP1L1 and PDGFRA in glioma. Additionally, our group detected the interaction in TKI-sensitive leukemia cell lines. The analysis of 3C microstructural alterations is consistent with latest insights into epigenetic regulation of PDGFRA. It provides a promising approach to the stratification of patients for tyrosine kinase inhibitor treatment, which could not be provided diagnostically with conventional sequencing approaches.
Characterization of circulating tumor cells in patients with localized high risk prostate cancer, post-prostatectomy.
Authors: Anantharaman Archana , Friedlander Terence W. , Welty Christopher J. , Zejnullahu Kreshnik , Hough Jeffrey , Edwards Matthew , Jendrisak Adam , Lee Jerry , Greene Stephanie , Ontiveros Priscilla , Graf Ryon , Rodriguez Angel , Suraneni Mahipal , Wang Yipeng , Landers Mark Andrew , Cooperberg Matthew R. , Carroll Peter , Dittamore Ryan Vance , Paris Pamela 
Published: September 2018

e23055 Background: Approximately 15% of men with newly diagnosed prostate cancer (PCa) have high-risk features, which increase the risk of recurrence. Better predictive biomarkers, such as circulating tumor cells (CTCs), could allow for earlier detection of biochemical recurrence. Here, we aim to evaluate the ability to detect CTCs using an enrichment free, unbiased CTC identification technology from men with high risk, localized PCa after radical prostatectomy (RP) and correlate their presence with prospective clinical data. Methods: Blood samples of 31 patients with high risk, localized PCa obtained 2-4 months post RP were shipped to Epic Sciences on an IRB approved protocol. All nucleated cells were subjected to immunofluorescent (IF) staining for cytokeratin (CK), CD45, and AR N terminus. CTCs were identified by fluorescent scanners using algorithmic analysis. CK expressing (CK+) CTCs were enumerated and analyzed for AR expression and individually sequenced for copy number variation (CNV) and large scale transition (LST, a surrogate of genomic instability). Patients were followed prospectively for biochemical recurrence, defined as detectable PSA. Progression free survival was calculated using Kaplan-Meier and Cox proportional hazards. Results: CTCs were detected in 87.1% (27/31) samples with an average of 5.6 CTCs/ml (range: 0 – 22.87) detected per patient. AR expression was detected in 12.9% (4/31) of patients. Ninety-nine CTCs from 14 patients were amenable to LST and CNV sequencing and analyses. 10.1% (10/99) CTCs from 7 patients exhibited higher ( > = 6) LSTs than control WBCs (95% WBCs had LST < 6). Copy number alterations were identified in CTCs in commonly mutated genes in PCa, including AR, MYC, and TP53 amplification and deletions in PTEN and RB1. Patients with higher CTC burdens exhibited a trend toward shorter PFS (hazard ratio: 1.65; 95% CI: 0.7-3.86; p: 0.13). Conclusions: There was a high incidence of CTC detection after RP in patients with high risk, localized PCa. We observed a trend toward shorter PFS in those with higher CTC burden and genomic alterations detectable in CTCs are consistent with established CNAs in PCa. Tissue genomic correlatives are under analysis.
The efficacy and safety of anti-PD-1/PD-L1 antibodies for treatment of advanced or refractory cancers: A meta-analysis.
Authors: Zhang Tengfei , Fan Ruitai , Shi Ni , Ma Wang 
Published: September 2018

e23075 Background: Immunotherapy based on anti-PD-1 (Programmed death 1)/PD-L1 (PD-1 Ligand 1) antibodies have achieved significant successes from bench to clinic. In this study, we systematically evaluate the overall efficacy and safety of current anti-PD-1/PD-L1 antibodies for treatment of patients with advanced or refractory cancer. Methods: Clinical trials reporting response or safety of anti-PD-1/PD-L1 antibodies for advanced or refractory cancer patients published were searched in PubMed and EMBASE database. Meta-analyses using random effects models were used to calculate the overall estimate. Results: Fifty-one trials including 6,800 patients were included. The overall response rates for melanoma, non-small cell lung cancer (NSCLC), and renal cell carcinoma (RCC) were 29% (95% CI: 1.53-2.41), 21% (95% CI: 17%-25%) and 21% (95% CI: 16%-27%) respectively. While the overall adverse effects rate for melanoma, NSCLC, RCC were 16% (95% CI: 6%-28%), 11% (95% CI: 8%-14%) and 20% (95% CI: 11%-32%) respectively. Tumor PD-L1 expression and patient smoking status might serve as biomarkers to predict response of anti-PD-1/PD-L1 antibody treatment. Compared to tumors with negative PD-L1 expression, tumors with positive PD-L1 expression had a significantly higher clinical response rate (41.4% versus 26.5%) with RR = 1.92 (95% CI: 1.53-2.41, P< 0.001). Smoker patients also showed a significantly higher response rate (33.7%) than patients who never smoked (4.2%) with RR = 6.02 (95% CI: 1.22-29.75, P= 0.028). Nivolumab and Pembrolizumab were associated with significantly increased response rate (RR = 2.89, 95% CI: 2.46-3.40, P< 0.001), reduced death risk (HR = 0.53; 95% CI: 0.48-0.57; P< 0.001), and decreased adverse effect rate (RR = 0.49, 95% CI: 0.30-0.80, P= 0.004) compared with other therapies. Conclusions: Anti-PD-1/PD-L1 antibodies have high response rates and low adverse effect rates for advanced or refractory cancers. PD-L1 expression was associated with better clinical response of anti-PD-1/PD-L1 antibody based immunotherapy.
Tumor mutation burden derived from large NGS panel as biomarker for immunotherapy response.
Authors: Vuzman Dana , Powers Winslow , Huang Xiu , Sun Ruobai , Eifert Cheryl , Cingolani Pablo , Bjonnes Andrew , Lyle Stephen , Protopopov Alexei 
Published: September 2018

e23077 Background: Tumor mutation burden (TMB) is an informative biomarker for predicting response to immunotherapy in a growing number of malignancies. The TMB clinical applicability is limited due to cost and bioinformatics requirements of sequencing and analyis of whole exome/gemone. Here, we demonstrate that a large next generation sequencing (NGS) panel can accurately identify hypermutation status. Methods: A novel algorithmic approach to derive the predicted total mutation load (PTML) described in J Roszik et al, BMC Med, 2016, was applied to our large NGS panel, CANCERPLEX. Statistical weights were calculated for each of the genes using publically available TCGA database. The algorithm was tested using CANCERPLEX data of stomach adenocarcinoma (199), colorectal cancer (59), and lung cancer (60) cohorts (n = 318). The correlation of PTML status with mismatch repair (MMR) status (n = 11) was also tested. The correlation of PTML status with clinical outcome was assessed using WES data following distinct immunotherapies (n = 16). The actual total mutation load (ATML) was compared to PTML by downsampling the WES data to our region of interest. Results: The mean values of PTML were evaluated for stomach adenocarcinoma (199), colorectal cancer (59), and lung cancer (60) cohorts. The PTML results for these 3 cancer types were statistically similar, and therefore the cohorts were combined into one dataset (n = 318). The hypermutation threshold was calculated from the PTML distribution of the three cancer types. This hypermutation threshold was in high concordance with our MMR validation set (n = 11), and also correlated (0.86) with an independent validation set of clinical outcome data from WES, which had undergone treatment with distinct immunotherapies (n = 16). This threshold predicts response to immunotherapy with 90% accuracy. Conclusions: NGS across a large gene panel captures sufficient information to predict tumor mutation burden with a single threshold for hypermutation status for stomach adenocarcinoma, colorectal, and lung cancers. This threshold highly correlates with MMR status and clinical outcome for immunotherapy response. Additional cancer types are currently being tested for inclusion in this study.
Influence of a STAT3 inhibitor on tumor infiltrating lymphocytes in malignant pleural mesothelioma.
Authors: Matsumoto Seiji , Takuwa Teruhisa , Kondo Nobuyuki , Hasegawa Seiki 
Published: September 2018

e23078 Background: Patients with malignant pleural mesothelioma have elevated IL-6 levels in their blood and pleural fluid. IL-6 activates the JAK-STAT pathway and promotes transcriptional activation. Our previous work on a STAT3 inhibitor (BBI-608: napabucasin) as a molecular target drug for malignant pleural mesothelioma confirmed its antitumor effect. In this study, the effect of napabucasin on tumor immunity, specifically on tumor infiltrating lymphocytes, was evaluated. Methods: A mouse-derived malignant pleural mesothelioma cell line (AB22; 1.0 × 105 cells) was subcutaneously injected into BALB/cAJcl mice. When the tumors grew to 250 mm3, the mice were divided into three groups (five mice per group): untreated control, 5 mg/kg napabucasin, and 20 mg/kg napabucasin groups. The drug was orally administered twice daily. Tumor volumes were measured twice weekly, and the subcutaneous tumors were removed 15 days after treatment initiation. Tumor infiltrating lymphocytes were extracted from the tumors, and the CD8+ cell percentage was measured using FACS. Results: The subcutaneous tumors of the mice in the untreated control, 5 mg/kg napabucasin, and 20 mg/kg napabucasin groups grew to 2318 mm3, 1764 mm3, and 1383 mm3, respectively, after 15 days of treatment. Suppression of subcutaneous tumor growth was observed, and the inhibitory effect was greater in the 20 mg/kg than in the 5 mg/kg napabucasin groups. The CD8+ cell percentage of tumor infiltrating lymphocytes for the untreated control, 5 mg/kg napabucasin, and 20 mg/kg napabucasin groups was 8.6%, 6.9%, and 19.0%, respectively. The CD8+ cell percentage increased with the increase in drug dosage. Conclusions: We had previously confirmed the antitumor effect of napabucasin by STAT3 inhibition in malignant pleural mesothelioma. In this study, 20 mg/kg napabucasin increased the CD8+ cell percentage of tumor infiltrating lymphocytes, indicating that the drug appears to enhance tumor immunity and that it may be used in combination with an antitumor immune antibody.
Effect of CA125/MUC16 on complement-dependent cytotoxicity (CDC) of farletuzumab and other CDC-mediating antibodies via inhibition of antibody-C1q binding.
Authors: Kline J Bradford , Fernando Shawn , Harley Stephen , Grasso Luigi , Nicolaides Nicholas C 
Published: September 2018

e23082 Background: Human cancers employ a number of mechanisms to evade host immune responses. Here we report the effects of the tumor-shed antigen CA125 on suppressing complement-dependent cellular cytotoxicity (CDC). This finding relates to a prespecified subgroup analysis of an 1100 patient Ph3 clinical trial testing the investigational agent farletuzumab, a monoclonal antibody (mAb) to folate receptor alpha, plus standard-of-care chemotherapy in patients with recurrent ovarian cancer. In this study, patients with low levels of CA125 (no greater than 3X the upper limit of normal) treated with farletuzumab compared to placebo demonstrated improvements in both progression free survival (HR 0.49, p = 0.0028) and overall survival (HR 0.44, p = 0.0108). Farletuzumab’s pharmacologic activity is mediated in part through antibody dependent cellular cytotoxicity (ADCC) and CDC. Here we show that CA125 inhibits IgG1- and IgM-mediated CDC by suppressing antibody interaction with the C1q complement-initiating protein. Methods: Functional assays employing cell lines expressing antibody-specific antigens were used to measure CDC activity. CA125 isolates from various patients and cell lines were used to monitor CA125 effects on complement function. ELISA assays were used to measure the effects of CA125 inhibition on C1q-antibody interaction. Results: Functional assays showed that CA125 suppressed antibody-mediated CDC in a dose dependent fashion. Molecular studies revealed that this suppression is caused by CA125 binding to antibody, leading to suppression of antibody-C1q interaction. Conclusions: Here we demonstrate that CA125 can elicit immunosuppression by perturbing the interaction of tumor targeting antibodies and the C1q complement-initiating protein. This effect is through a direct binding of CA125 to antibody. These findings provide new insights into the potential biological mechanisms by which tumors produce tumor shed antigens like CA125 to suppress host immune responses such as CDC. This finding has important clinical applications for the development of therapeutics utilizing complement-mediated mechanisms.
Anti-PD1 treatment to induce M1 polarization of tumor infiltrating macrophages in a 3D ex vivo system of lung cancer patients.
Authors: Mediavilla-Varela Melanie , Page Melba Marie , Kreahling Jenny , Antonia Scott Joseph , Altiok Soner 
Published: September 2018

e23090 Background: Nivolumab and pembrolizumab treatment targeting the PD1/PD-L1 axis has demonstrated increased survival benefit in subpopulations of patients with advanced non-small cell lung cancer (NSCLC). The impact of these therapeutics on tumor immune microenvironment is not fully understood. Classical M1 macrophages are critical components involved in the inflammatory response and antitumor immunity. In this study, we evaluated the effect of PD1/PD-L1 blockade on M1 polarization of tumor-associated macrophages (TAMs) and activation of cytotoxic T-cells in a 3D ex vivo system of NSCLC. Methods: Fresh tumor tissues obtained from consented patients with NSCLC at the time of surgical resection were utilized in a 3D ex vivo tumor miscrosphere assay. 3D tumor microspheres were treated with nivolumab or pembrolizumab at 10 mg/ml for 36 hours within an intact tumor microenvironment. Flow cytometry analysis was performed to evaluate treatment-mediated TAM polarization, activation of T-cells and changes in CD4 and CD8 subpopulations. A multiplex human cytokine assay was used to simultaneously analyze the differential secretion of cytokines. Additionally, a NanoString platform containing probes to quantitate 770 immune function genes was used to determine potential positive or negative associations between expression of immune function genes and TIL activation by ex vivo treatment. Results: Both nivolumab and pembrolizumab treatment increased population of M1 macrophages (CD68+, CD80+, CD163-) and simultaneous release of MIP1b, IFN-ɣ, TNF-a, and GM-CSF cytokines as well as expression of genes related to the M1 phenotype that was accompanied by activation of CD8 cells assessed by Ki67 and CD107a expression and increased expression of genes involved in the IFNg pathway. Conclusions: Our studies showed that anti PD1/PD-L1 treatment leads to M1 macrophage polarization and T-cell activation in subgroups of NSCLC patients emphasizing the importance of comprehensive analysis of tumor immune microenvironment for a better understanding of the mechanism of action of immuno-oncology drugs that may help developing rationale combination treatments in NSCLC.
Endoscopic molecular imaging of early gastric cancer targeting transferrin receptor 1.
Authors: Tian Jie , Du Yang 
Published: September 2018

e23093 Background: Gastric cancer is primarily managed endoscopically by white light gastroscope with suboptimal diagnostic accuracy. Emerging optical imaging technologies possess great potential for improving diagnostic accuracy but currently lack imaging agents for molecular specificity. In this study, a novel ligand of transferrin receptor 1 (TfR1), human H-ferritin (HFn), was labeled with fluorescent agents to enable in vivo real-time imaging by confocal laser endomicroscopy (CLE). Methods: In vivo fluorescence imaging was performed in tumor-bearing mice from human gastric cancer cell lines using fluorescently labeled HFn nanoprobe. The HFn-FITC as molecular imaging agent was applied to the gastric cancer with confocal laser endomicroscopy (CLE) in fresh endoscopic submucosal dissection (ESD) of early gastric cancer. Results: Intravital imaging of gastric xenograft tumors revealed a specific tumor targeting effects of HFn-IRDye800CW, whereas no specific signal was observed in mice injected with free dye. An ex vivo experiment on human specimens using a rigid confocal probe showed positive fluorescent staining in ESD samples diagnosed as early gastric cancers. Our CLE evaluation correlated well with immunohistochemical findings. Conclusions: CLE can be used for in vivo, molecular analysis of early gastric cancer and to identify TfR1 expression in xenografts and human tissue samples. HFn-targeted molecular imaging could improve early detection of gastric cancer.
Assessment of EGFR mutations in plasma from advanced NSCLC patients by modified cell-free DNA extraction method and blocker PCR assays.
Authors: Zhang Meiling , Gong Ziying , Li Chun , Hu Jie , Hong Qunying , Hou Yingyong , Zhang Daoyun , Zhang Xin 
Published: September 2018

e23115 Background: Epidermal growth factor receptor (EGFR) mutation testing in plasma cell-free DNA (cfDNA) for lung cancer patients is an emerging clinical tool.However,the sensitivity of plasma testing,compared with tissue testing, is not high enough. We aimed to investigate the likelihood of improving the plasma testing sensitivity by increase the cell-free DNA(cfDNA )yields using a modified extraction method and blocker PCR. Methods: Blood samples were collected from 106 patients without EGFR-TKI treatment and 127 patients with acquired EGFR-TKI resistance.CfDNA was extracted from plasma by the modified extraction method and mutations were identified by blocker PCR.The yields of circulating tumor DNA (ctDNA) and cfDNA from 106 patients were quantified by standard curve.Next generation sequencing (NGS)was employed to verify the reliability of blocker PCR. Meanwhile,paired tumor tissues were examined by amplification refractory mutation system (ARMS). Results: The novel extraction method can extract small fragment less than 100bp.The yield of total cfDNA of 106 plasma was mostly between4 000and 200,000 copies per milliliter.With regard to exon 19 deletions(E19-DELs) , the ctDNA proportion of 85% samples (17/20)was from 0.1% to 5% . As for L858R mutations, the fraction of ctDNA of 84.6%(11/13)cases was calculated with the range of 0.01% to 0.1%.For 106 patients,the overall concordance rate,sensitivity and specificity between plasma and tumor tissue was 99.06%[k = 0.97; 95% confidence interval (CI), 0.87-0.99; P < 0.0001],94.87%(95% CI, 83.11%-98.58%) and 100 % (95% CI,94.58%-100%).Among the 127patients,40.16%(51/127)T790M was detected in the plasma, 78.44%(40/51) of which coexists with an EGFR activating mutation. Conclusions: The modified extraction method can improve ctDNA yields and thus improve the sensitivity of liquid biopsy.The blocker PCR offers the possibility of detecting mutations in cfDNA with high concordance with tumor tissues.