bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive analysis of lymphocyte loss kinetics in patients treated with focal fractionated radiation therapy.
Authors: Yalamanchali Anirudh , Jin Jian-Yue , Zhang Hong , Grossman Stuart A. , Hobbs Robert F , Ellsworth Susannah G. 
Published: May 2019

e14191 Background: Radiation (RT)-induced lymphopenia (RIL) is associated with worse survival in patients with solid tumors as well as lower response rates to checkpoint inhibitors. This analysis aimed to model the kinetics of lymphocyte depletion during RT to assist in predicting RIL risk. Methods: This registry-based study included 419 patients who received either total body irradiation (TBI; n = 30), stereotactic body RT (SBRT; n = 73), or conventional chemoradiation (CRT; n = 316). For each patient, serial absolute lymphocyte counts (ALCs) were plotted against RT fraction number. The initial 3 weeks of treatment for conventionally irradiated patients and the entirety of treatment for SBRT and TBI patients were fit to exponential decay in the form ALC(x) = ae-bx. From those fits, percent per fraction loss in ALC (PFLAC) was calculated as PFLAC = (1 – e-b)*100, and multivariable regression was performed to find its significant predictors. Results: Curves were well fitted by exponential decay for all RT techniques (median linearized R2 0.98, 0.93, and 0.97 for patients treated with TBI, SBRT, and CRT, respectively). In CRT patients, apparent ALC loss rate slowed after week 3, potentially due to lymphocyte repopulation or other factors. TBI and SBRT patients completed RT before the end of the exponential decay phase, and their ALC loss rates remained unchanged throughout RT. Initial PFLAC varied significantly with treatment technique. Mean PFLAC was 35.5%, 24.3%, and 10.77% for patients treated with TBI, SBRT, and CRT, respectively (p < 0.001). Significant predictors of PFLAC varied by site and included field size, dose per fraction, mean spleen dose, chemotherapy backbone, and age. In pancreas cancer patients, gemcitabine was associated with a higher PFLAC (mean = 10.7) than 5-FU (mean = 8.3) after adjustment for covariates (p < 0.001). Finally, total % ALC loss during RT was highly correlated with PFLAC (p < 0.001). Conclusions: Lymphocyte depletion kinetics during the initial phase of fractionated RT are characterized by pure exponential decay. Initial PFLAC is strongly correlated with RT planning parameters and predicts total % ALC loss. The highest ALC loss rates were associated with RT-only regimens, implying that concurrent chemotherapy is not solely responsible for lymphopenia in patients receiving CRT. This work may also assist in selecting patients for adaptive RT approaches to mitigate RIL risk.
Precision probiotic therapy enhances immune checkpoint therapy efficacy in melanoma bearing mice.
Authors: Frankel Arthur E. , Honda Kenya , Roberts Bruce , Szabady Rose , Reddy Amit , Lightcap Johnny , McClellan Steve , Deshmukh Sachin Kumar , Koh Andrew Y. 
Published: May 2019

e14195 Background: Immune checkpoint inhibitor therapy, ICT, achieves remissions in melanoma patients but factors modulating response are not well defined. Our group (Frankel et al. Neoplasia 2017) and others have identified specific gut microbiota associated with improved ICT response. Recently, we identified specific gut microbiota that induce adaptive immune responses and potentiate ICT (Tanoue et al. Nature 2019). In this study, we determined whether this predefined consortia of gut microbiota augment ICT efficacy in melanoma bearing mice. Methods: Mice (C57BL/6, 6-8wk old, female, Jackson, n = 4-12 mice) received ± antibiotic water (penicillin G 1500U/mL + streptomycin 2mg/mL) for 6 d to deplete gut microbiota. Mice were then inoculated with 105 B16F10 melanoma cells SQ. At d 4, 8, 12 post-tumor inoculation, 0.2 mg anti-mCTLA4 + anti-mPD1 antibodies (Bio X Cell) were administered IP. Precision probiotic therapies included Vedanta Bioscience VE800 (Tanoue et al., Nature 2019), VE804 (same as VE800 without R. lactatiformans and F. ulcerans), VE411 (four Clostridial firmicutes) (Narushima, 2014), and Lactobacillus acidophilus (ATCC 4356) probiotics were given via gavage (1x109 cfu) starting day +1 after tumor inoculation and 3xwkly. Loss of survival was defined as death or tumor diameters ≥ 2 cm. Tumor growth inhibition, TGI = (1- mean treated tumor volume/mean control tumor volume) x 100%. Tumor mononuclear cells were isolated for flow cytometry for murine CD4, CD8, and CD11c. Results: TGI in mice with intact gut microbiota and treated with ICT was 84 ± 4% (SEM). Pre-treatment antibiotics reduced TGI to 38 ± 11%. Groups treated with Vedanta VE800, VE804, and VE411 exhibited TGIs of 77 ± 9, 61 ± 8, and 69%, respectively, whereas treatment with Lactobacillus acidophilus achieved TGIs 57%. VE800 treated mice had significantly increased length of survival compared to mice treated with antibiotics (p = 0.0008, log-rank test). Length of survival was not significantly different between groups with intact gut microbiota and those pretreated with antibiotics and dosed with VE800 (p = 0.52, log-rank test). ICT increased tumor CD4 cells to 11% from 2% and CD8 cells to 9% from 1%., however pre-treatment with antibiotics reduced CD4 cells to 4% and CD8 cells to 1%. Conclusions: Defined consortia of gut microbiota facilitate ICT efficacy. These preclinical studies lay the foundation for optimizing the host response to ICT.
Correlation of inflammation-related markers with MDSC and IL-17, and use as prognostic indicators in patients with advanced gastric and colorectal cancers.
Authors: Shibata Masahiko , Ujiie Daisuke , Ashizawa Mai , Kikuchi Tomohiro , Okayama Hirokazu , Fujita Shoutarou , Sakamoto Wataru , Nakajima Takahiro , Endo Hisahito , Saito Motonobu , Momma Tomoyuki , Shimura Tatsuo , Kono Koji , Takenoshita Seiichi 
Published: May 2019

e14204 Background: Although a causal relationship for inflammation and immunity of cancer is more widely accepted today, the precise cell mechanisms mediating this relationship have not been elucidated. Accumulating evidence suggests that myeloid-derived suppressor cells (MDSC), may contribute to the negative regulation of immune responses during cancer and inflammation. IL-17 is a pro-inflammatory cytokine that is primarily secreted by T helper (Th)17 cells and we have reported that IL-17 correlates with immunosuppressive conditions in patients with cancer. Methods: PBMC (peripheral blood mononuclear cells) were harvested from 106 patients including 43 with gastric and 63 with colorectal cancer. PBMC were stimulated with PHA (phytohemagglutinin) and the production of IL-17 was measured by ELISA. MDSC were detected by flow cytometry (CD11b+,CD14-,CD33+). The levels of CRP (C-reacting protein) and NLR (neutrophil to lymphocyte ratio) were used as inflammatory markers. Results: Both of MDSC and IL-17 production were increased in patients with advanced stages, and correlated with each other, inflammatory markers and immune suppression. The patients were divided with average levels of MDSC and IL-17 production and the prognosis were analyzed with Kaplan-Meier method. The overall survival of patients with high MDSC or high IL-17 production were significantly worse than those with low MDSC or low IL-17 production, respectively, in patients with stages III and IV, although the differences were not significant in patients with stages I and II. Conclusions: Thus these inflammatory markers are closely related with systemic inflammation involving IL-17 and with immunosuppression driven by MDSC, and are effective prognostic indicators in patients with stages III and IV gastric and colorectal cancer.
Microsatellite instability assessment of FFPE tumor samples through targeted next-generation sequencing.
Authors: Wong-Ho Elaine 
Published: May 2019

e14213 Background: Immunotherapies to treat malignancies have shown great promise, however, only a fraction of cancer patients respond to immunotherapy, making it imperative to identify biomarkers that predict response. Cancer-associated instabilities at microsatellite locations throughout the genome have been shown to be predictive of response to immunotherapy treatment. Here we determine the accuracy of determining the MSI status through targeted sequencing using Ion Torrent sequencing technology. Methods: We have identified optimal chemistry and developed a novel algorithm to assess MSI status of samples using a large number of markers on the Ion GeneStudio S5 Series sequencer. The diverse marker set includes monomers that vary in length between 10 BP and 40 BP in addition to di-and tri-nucleotide STR markers. Each sample is assigned an MSI score based on features that measure MSI response of markers in the assay. Results: We evaluated performance of the MSI markers in the context of a comprehensive targeted next generation sequencing assay with the MSI algorithm. A large set of FFPE tumor samples and MSI controls were evaluated. The resulting scores were in concordance with results from capillary electrophoresis studies. Conclusions: In summary, a next-generation sequencing based assay using multiple markers was developed to assign MSI status to FFPE tumor samples. The accuracy of the assay was validated using an orthogonal test. This allows us to use Ion Torrent sequencing technology to identify changes in complex repeat regions of the genome as part of a comprehensive genomic profiling approach.
Modified ketogenic diet in solid tumors: A Veteran Affairs Pittsburgh Healthcare System case series.
Authors: Tan Jocelyn Lai , Carrick Jennifer , Passero Vida Almario , Shields Jenna , Liman Andrew Dede , Rai Hema , Harrold Lauri 
Published: May 2019

e14217 Background: Cancers prefer glucose due to mitochondrial dysfunction. Ketogenic diets fuel normal cells while starving cancer. Sparse data exists on ketogenic diets in solid tumors. Methods: Studied 5 advanced solid tumor patients on a modified ketogenic diet plus standard of care chemotherapy. Daily carbohydrate limited to 20-40 grams, no sweets or starch. Histories and clinical courses are presented. Results: Case 1: 70 year old male, medically inoperable Stage IIIA poorly differentiated squamous cell lung cancer and non-hodgkins lymphoma. Treated with radiation and paclitaxel/carboplatin. After 5 months, lung cancer relapsed in a neck mass, treated with chemoradiation plus the diet. At 46 months, scans and blood counts were normal. Case 2: 42 year old, 417 lb. male diabetic stage IV colon cancer, spread to lungs and liver. Progressed on 5FU/bevacizumab/oxaliplatin, irinotecan, tipiracil/trifluridine, regorafenib but responded to 5FU/irinotecan rechallenge plus liver chemoembolization. Dieted, mild ketosis but lost 64 lbs, stable disease at 6.5 years. Case 3: 42 year old male, Stage III BRAF V600 E melanoma, Vemurafenib intolerant. Bulky axillary nodes resected plus diet for 3 years. Complete remission at 7 yrs 9 months. Case 4: 57 year old male, medically inoperable liver cancer, normal AFP values and normal scans after 5 months of sorafenib. AFP later increased to 690 ng/ml. Advised to change treatment but he refused and started the ketogenic diet with the sorafenib. After 5 months, AFP improved to 445 ng/ml. Sorafenib and diet interrupted for 3 months, AFP rose to 1017. At 7 yrs, 4 months, back on sorafenib and diet, AFP 1520 mg/ml, negative scans. Case 5: 49 year old male, aggressive digital papillary skin adenocarcinoma, multi-organ metastases. Had side-effects with many chemotherapies (paclitaxel/bevacizumab/carboplatin, sorafenib, gemcitabine, oxaliplatin/5FU, cyclophosphamide) Stable disease on diet despite multiple therapy changes. At 34 months, he was off the diet, tumors grew plus new brain lesions (resected). Alive on atezolizumab at 36 months. Conclusions: Ketogenic diets in human solid tumors seem well tolerated and may improve response and survival after standard therapy.
Spatially-resolved, multiplexed quantification of protein and mRNA distribution and abundance in colorectal cancer tumor microenvironment with multiple modalities of NanoString GeoMx Digital Spatial Profiler.
Authors: Demirkan Gokhan , Merritt Chris , Hinerfeld Douglas , Ong Giang , Sorg Kristina , Balasundaram Gayathri , Dunaway Dwayne , Geiss Gary K , Beechem Joseph M 
Published: May 2019

e14218 Background: Characterization of the spatial distribution and abundance of proteins and mRNAs with morphological context within tissues enables a better understanding of biological systems in many research areas, including immunology and oncology. However, it has proven difficult to perform such studies in a highly multiplexed manner. To address this unmet need, we have developed a novel optical-barcode based microscope and tissue-sampling platform designed to simultaneously analyze hundreds of proteins or mRNAs on a single FFPE section from distinct tissue spatial regions. Methods: Using colorectal cancer FFPE sections we spatially resolve protein and mRNA expression of immune-oncology targets and present a series of modalities and associated applications for the GeoMx Digital Spatial Profiler platform. Results: Microsatellite stable (MSS) or instable (MSI) colorectal tumors will be characterized to evaluate active and suppressive immune mechanisms in both immune dense regions and tumor versus stroma by utilizing segment profiling. Regions from the invasive margins and tumor centers will be investigated with contour profiling to define different immunosuppressive and activated immune phenotypes. Evaluation of tumor versus stroma will also identify pathways related to each compartment that are different between MSI and MSS tumors. These techniques can be used to discover drug mechanism of action or immune activation status, as well as to facilitate prediction of treatment response and disease progression or investigation of specific rare cell populations’ molecular profiles. Conclusions: This study will demonstrate multiplexed pathway-level protein and gene expression analysis from discrete regions within a colorectal tumor (tumor center and immune invasive margin), enabling systematic interrogation of immune activity in FFPE samples. Further studies could eventually lead to the identification of unique localized immune characteristics to guide combination therapeutic approaches.
Applying machine learning strategy for microsatellite status detection in plasma sample type.
Authors: Zhao Lili , Han Wenbo , Zhou Wei , Fang Lu , Hong Yuanyuan , Tian Chen , Chen Weizhi , He Ji 
Published: May 2019

e14219 Background: Microsatellite(MS) status is an important biomarker in cancer diagnosis . Most of available detection algorithms were based on figuring out number of validated allele types from control and cases, then determine the MS status by identify the difference. That would be suitable for tissue like samples due to their clear and sufficient tumor nucleic acid content. But for liquid biopsy such as plasma, lower ctDNA concentration and higher background ratio induced from laboratory and sequencing procedure make it necessary to develop novo method for plasma MS status detection. Methods: We developed an machine learning based approach to detect the MS status by using NGS sequencing data from plasma sample. 98 blood cell , 12 tumor tissue samples with PCR confirmed MSS status and 87 plasma samples from 134 patients were used to build normal baseline, and check the sequencing stability and population polymorphism of 207 candidate SSR locus in our panel. 97 locus then passed and were chosen as original biomarkers for model construction. For each coming sample, the allele probability distribution were obtained for each locus. Followed by calculating the Kullback–Leibler Divergence (KLD) value between target and baseline samples for each locus, the KLD value was used as input for feature selection and machine learning model fitting. Finally a leave one out strategy was used for model performance evaluation. Results: We obtained 17 most relevant SSR locus with suitable for MS status analysis of plasma sample. By using a SVM model fitted with 49 real patients sample data (21 MSI and 28 MSS) , The MS status prediction of plasma sample was of high sensitivity and specificity which were 90.47% and 96.42% respectively. Conclusions: Our results suggest that our MSI calculation model by using KLD value and SVM method is appropriate for the plasma sample. Further large-scale prospective studies are needed to validate our model.
MDNA109: Effect of an interleukin-2 superkine on CD8 T-cell properties in the tumor microenvironment.
Authors: Rafei Moutih , Fidai Shafique , Merchant Rosemina , Merchant Fahar 
Published: May 2019

e14220 Background: Proleukin (a cysteine-modified variant of interleukin (IL)-2) is the only common-γc cytokine approved for the treatment of metastatic melanoma and renal cell carcinoma. Its therapeutic use is however hampered by its short half-life and severe toxicity. At low doses, Proleukin administration leads to preferential activation of regulatory T cells (Tregs) due to their expression of the high affinity trimeric IL-2 receptor (IL-2R) consisting of CD25, CD122 and CD132 instead of cytotoxic CD8 T cells expressing the intermediate affinity IL-2R (CD122 and CD132). Methods: To bypass these limitations, we evaluated engineered variants of IL-2 (MDNA109 superkine) exhibiting enhanced affinity towards CD122 including their long-acting and bispecific superkine fusions. This approach allows preferential activation of CD8 T cells while displaying reduced adverse effects in vivo. Results: Both Biacore analysis and signaling studies on human peripheral blood mononuclear cells confirmed enhanced binding of MDNA109 to CD122 and STAT5 activation, respectively. When tested in vivo, MDNA109 co-administration with the immune-checkpoint blockers anti-programmed cell death (PD)-1 or anti-cytotoxic T-Lymphocyte-Associated Protein (CTLA)4 cured mice with pre-established MC38 or CT26 colon cancers respectively. In addition, bi-weekly administration of the long-acting MDNA109-Fc fusion led to similar therapeutic outcomes in the B16F10 model when compared to MDNA109 administered daily. Finally, in vitro and in-vivo results using (a) MDNA109 muteins with completely impaired CD25 binding activity and (b) novel bispecific superkine fusions consisting of MDNA109 and a dual IL-4/IL-13 super-antagonist capable of selective CD8 T-cell activation while mitigating the suppressive functions of myeloid-derived suppressor cells and tumor-associated macrophages will be presented. Conclusions: Altogether, these data demonstrate that both MDNA109 and MDNA109-Fc are therapeutically superior to Proleukin. Furthermore, use of MDNA109-based strategies will not only ensure complete abrogation of adverse effects, but will in addition eliminate immunosuppression caused by both Tregs and myeloid cells.
An umbrella for the cytokine storm: Enabling precision detection of CRS in CAR-T therapy.
Authors: Quan Qimin 
Published: May 2019

e14223 Background: Cytokine release syndrome (CRS), a systemic inflammatory response observed with monoclonal antibody drugs and adoptive T cell treatments, has become a major issue for CAR-T therapy. CRS can present as a mild reaction requiring minimally invasive supportive care up to a severe systemic response resulting in patient death. Monitoring this response during these therapeutic treatments is non-trivial due the wide range of biomarker concentrations, small sample volumes, and long assay times. Current analytical methods are unable to address these needs, limiting the precision of CAR-T therapy and effective management of its side effects. Methods: Emerging studies in this area have focused in establishing a panel of predictive biomarkers to manage dosing and early interventions, among them, IFNγ, IL6, TNFα, MIP1 have shown predicative powers in pediatric patients. Nevertheless, a significant improvement (100x) on the detection sensitivity is required to predict the CRS response with currently available methods. In addition, CRS-associated biomarkers including CRP and ferritin vary from 10ng/mL-10mg/mL while other predictive biomarkers (eg, IL6, IFNγ, etc.) vary from 1pg/mL-100ng/mL. At present, no analytical tool, known to us, can provide this large dynamic range ( > 9 logs), with the requisite lower limit of detection, in a rapid single test to predict and differentiate low, medium or high grade responses. Results: We present the NanoMosaic platform, the technology that has requisite sensitivity and breadth of dynamic range to enable precision detection based on precise quantitation of CRS-relevant biomarkers. NanoMosaic technology is enabled by single molecule nanoneedle sensors that are densely integrated on a silicon chip and manufactured with a CMOS-compatible process. Absolute quantitation is achieved by imaging the spectrum of nanoneedles, corresponding directly to the number of molecules. Conclusions: Direct comparison of different protein biomarkers with orders of magnitude concentration variations becomes possible in one platform and small sample sizes. We envision NanoMosaic technology will not only drive biomarker discovery, but also enable precise dosing management for CAR-T therapy.
Collagen affinity improves efficacy and safety of antibody and cytokine cancer immunotherapy.
Authors: Ishihara Ako , Ishihara Jun , Hubbell Jeffrey A , Swartz Melody A 
Published: May 2019

e14232 Background: Cancer immunotherapy with immune checkpoint inhibitors (CPI) and interleukin (IL)-2 have demonstrated clinical antitumor efficacy but is frequently accompanied with severe side-effects caused by excessive and systemic immune system activation. Methods: We addressed this need by targeting both the CPI antibodies anti-CTLA4 (aCTLA4) + anti-PD-L1 (aPD-L1) and the cytokine IL-2 to tumors via conjugation (for the antibodies) or recombinant fusion (for the cytokine) to a collagen-binding domain (CBD) derived from the blood protein von Willebrand factor (VWF) A3 domain. This approach harnesses the exposure of tumor stroma collagen to blood components due to the leakiness of the tumor vasculature. Results: We show that intravenously (i.v.) administered CBD protein accumulated in tumors in an orthotopic MMTV-PyMT breast tumor model. CBD conjugation or fusion decreased the systemic toxicity of both aCTLA4+aPD-L1 combination therapy and IL-2. CBD-conjugation to CPI abolished T cell infiltration into the liver and eliminated hepatotoxicity as well as decreased systemic cytokine release in the blood serum. CBD-fusion to IL-2 ameliorated capillary leak syndrome and pulmonary edema. These side-effects have been reported in the clinic. CBD-CPI and CBD-IL-2 significantly suppressed tumor growth compared to their unmodified forms in B16F10 melanoma, CT26 colon carcinoma and MMTV-PyMT slow growing breast cancer models, and both CBD-CPI and CBD-IL-2 increased tumor-infiltrating CD8+ T cells; increases in the ratio of effector CD8+T cells to T regulatory cells were observed. In an orthotopic breast tumor model, combination treatment with CPI and IL-2 eradicated tumors in 9/13 animals with the CBD-modified drugs, whereas it did so in only 1/13 animals with the unmodified drugs. Conclusions: Our data suggest that the A3 domain of VWF can be used to engineer immunotherapies (e.g. CPI and cytokine) with high translational promise as systemically-administered tumor targeting drugs with improved safety and efficacy compared to their native forms.