bluuebunny/crossref_metadata_2025 huggingface dataset:
Developing Public–Private Partnerships in Plant Pathology Extension: Case Studies and Opportunities in the United States
Authors: Markell Samuel G. , Tylka Gregory L. , Anderson Edwin J. , van Esse H. Peter
Published: June 2020

Public–private partnerships (PPPs) can be an effective and advantageous way to accomplish extension and outreach objectives in plant pathology. The greatest opportunities for extension-focused PPPs may be in response to large-scale or emerging disease management concerns or in addressing complex issues that impact agriculture, such as climate change, digital technology, and public perception of science. The most fertile ground for forming PPPs is where the needs and strengths of the public and private sectors are complementary. Developing PPPs depends as much on professional relationships as on technical skills or contracts. Defining and making room for the success of all partners, identifying and addressing barriers to success, and earning and maintaining trust are components that contribute to the effectiveness of PPPs. Case studies in plant pathology demonstrate the positive impact PPPs can have on partners and stakeholders and provide guidance on the formation of PPPs in the future.
Antimicrobial Susceptibility Testing of Metronidazole and Clindamycin against Gardnerella vaginalis in Planktonic and Biofilm Formation
Authors: Li Ting , Zhang Zhan , Wang Fengjuan , He Yuanhui , Zong Xiaonan , Bai Huihui , Liu Zhaohui
Published: June 2020

Background. Bacterial vaginosis (BV), one of the most common vaginal ecosystem-related microbiologic syndromes, is the most common disorder in women of reproductive age. Gardnerella (G.) vaginalis is the predominant species causing this infection. Our aim was to compare the antimicrobial susceptibilities of metronidazole and clindamycin against G. vaginalis at planktonic and biofilm levels. Methods. From September 2019 to October 2019, we recruited a total of 10 patients with BV who underwent gynecological examinations at Beijing Obstetrics and Gynecology Hospital. G. vaginalis isolates were obtained from the vagina and identified using their characteristic colony morphology. Sequence data of clinical G. vaginalis isolates were confirmed by comparing 16S rDNA sequences. Subsequently, clinical isolates were evaluated for antimicrobial susceptibilities in vitro to metronidazole and clindamycin at planktonic and biofilm levels. The minimum inhibitory concentration (MIC) for metronidazole and clindamycin was evaluated by antimicrobial susceptibility testing. The minimum biofilm eradication concentration (MBEC) was evaluated by the biofilm inhibition assay. Results. Planktonic clinical isolates showed a significantly higher susceptibility rate (76.67%) and lower resistance rate (23.33%) to clindamycin than to metronidazole (susceptibility rate: 38.24%; resistance rate: 58.82%; P<0.05 for both). Furthermore, in comparison to planktonic isolates, the minimum inhibitory concentration (MIC) of metronidazole was significantly higher for biofilm-forming isolates (7.3 ± 2.6 μg/mL vs. 72.4 ± 18.3 μg/mL; P=0.005); the resistance rate was 27.3%, and the minimum biofilm eradication concentration (MBEC) was >128 μg/mL. Moreover, the MIC of clindamycin was higher too for biofilm-forming isolates (0.099 ± 0.041 μg/mL vs. 23.7 ± 9.49 μg/mL; P=0.034); the resistance rate was 27.3%, and the MBEC of clindamycin was 28.4 ± 6.50 μg/mL. Conclusion. Our results indicate that in comparison to metronidazole, clindamycin seems to be a better choice to tackle G. vaginalis as it exhibits a relatively higher susceptibility rate and lower resistance rate.
New Results on Stability of Delayed Cohen–Grossberg Neural Networks of Neutral Type
Authors: Faydasicok Ozlem
Published: June 2020

This research work conducts an investigation of the stability issues of neutral-type Cohen–Grossberg neural network models possessing discrete time delays in states and discrete neutral delays in time derivatives of neuron states. By setting a new generalized appropriate Lyapunov functional candidate, some novel sufficient conditions are proposed for global asymptotic stability for the considered neural networks of neutral type. This paper exploits some basic properties of matrices in the derivation of the results that establish a set of algebraic mathematical relationships between network parameters of this neural system. A key feature of the obtained stability criteria is to be independent from time and neutral delays. Therefore, the derived results can be easily tested. Moreover, a constructive numerical example is studied to check the verification of presented global stability conditions.
Scale Features of a Network Echo Mechanism: Case Study for the Different Internet Paths
Authors: Matcharashvili Teimuraz , Prangishvili Archil , Tsveraidze Zurab , Laliashvili Levan
Published: June 2020

We have investigated dynamics of the Internet performance through the assessment of scaling features of a network ICMP echo mechanism or pinging. Time series of round-trip times (RTT) from the host computer to 5 destination hosts and back, recorded during three consecutive days and nights, have been used. To assess correlation and scaling features of network echo mechanism, we used method of detrended fluctuation analysis (DFA) for RTT data sets. It was shown that for different, 10 minute long periods of day and night observations, RTT data sets mostly fluctuate within a narrow range, though sometimes we observe strong sharp spikes. RTT variations mostly reveal persistent behavior. DFA fluctuation curves often are characterized by crossovers indication stronger or lesser changes in the dynamics of network performance. Distribution function of DFA scaling exponents of considered RTT time series mostly was asymmetric with long tail on the right hand side. Dynamical changes occurring in the scaling features of Internet network as assessed by RTT fluctuations do not depend on the location of the host and destination nodes. Larger delays in round-trip time responses make the scaling behavior of the RTT series complicated and strongly influence their long range correlation features.
An Efficacy Predictive Method for Diabetic Ulcers Based on Higher‐Order Markov Chain‐Set Pair Analysis
Authors: Kuai Le , Fei Xiao-ya , Xing Jia-qi , Zhang Jing-ting , Zhao Ke-qin , Ze Kan , Li Xin , Li Bin
Published: June 2020

Background. Clinical comprehensive decision‐making of diabetic ulcers includes curative effect evaluation and curative effect prediction. Nevertheless, there are few studies on the prediction of diabetic ulcers. Methods. Set pair analysis (SPA) was used to assess the curative effect evaluation, and therapeutic effect was evaluated by connection degree (CD). The higher‐order Markov chain‐SPA curative effect prediction model was established to predict the future curative effect development. The predicted results with higher‐order Markov chain‐SPA and traditional first‐order Markov‐SPA model were compared with the actual results of the patients to verify the effectiveness of prediction. Results. The connection degree of index levels I and II of 15 patients with diabetic ulcers after traditional Chinese medicine (TCM) treatment increased with time, while that of index levels IV and V decreased, indicating that the curative effect tends to improve. The higher‐order Markov chain‐SPA model was used to predict the curative effect. The results showed that the relative errors were fewer than the traditional first‐order Markov‐SPA model. Conclusions. The present study suggests that a method of SPA combined with higher‐order Markov‐SPA is relatively effective and can be applied to the clinical prediction of diabetic ulcers, which has higher accuracy than traditional first‐order curative effect prediction model.
INeo‐Epp: A Novel T‐Cell HLA Class‐I Immunogenicity or Neoantigenic Epitope Prediction Method Based on Sequence‐Related Amino Acid Features
Authors: Wang Guangzhi , Wan Huihui , Jian Xingxing , Li Yuyu , Ouyang Jian , Tan Xiaoxiu , Zhao Yong , Lin Yong , Xie Lu
Published: June 2020

In silico T‐cell epitope prediction plays an important role in immunization experimental design and vaccine preparation. Currently, most epitope prediction research focuses on peptide processing and presentation, e.g., proteasomal cleavage, transporter associated with antigen processing (TAP), and major histocompatibility complex (MHC) combination. To date, however, the mechanism for the immunogenicity of epitopes remains unclear. It is generally agreed upon that T‐cell immunogenicity may be influenced by the foreignness, accessibility, molecular weight, molecular structure, molecular conformation, chemical properties, and physical properties of target peptides to different degrees. In this work, we tried to combine these factors. Firstly, we collected significant experimental HLA‐I T‐cell immunogenic peptide data, as well as the potential immunogenic amino acid properties. Several characteristics were extracted, including the amino acid physicochemical property of the epitope sequence, peptide entropy, eluted ligand likelihood percentile rank (EL rank(%)) score, and frequency score for an immunogenic peptide. Subsequently, a random forest classifier for T‐cell immunogenic HLA‐I presenting antigen epitopes and neoantigens was constructed. The classification results for the antigen epitopes outperformed the previous research (the optimal AUC = 0.81, external validation data set AUC = 0.77). As mutational epitopes generated by the coding region contain only the alterations of one or two amino acids, we assume that these characteristics might also be applied to the classification of the endogenic mutational neoepitopes also called “neoantigens.” Based on mutation information and sequence‐related amino acid characteristics, a prediction model of a neoantigen was established as well (the optimal AUC = 0.78). Further, an easy‐to‐use web‐based tool “INeo‐Epp” was developed for the prediction of human immunogenic antigen epitopes and neoantigen epitopes.
A Support Vector Machine Model Predicting the Risk of Duodenal Cancer in Patients with Familial Adenomatous Polyposis at the Transcript Levels
Authors: Liu Weiqing , Dong Jian , Ma Shumin , Liang Lei , Yang Jun
Published: June 2020

Objective. Familial adenomatous polyposis (FAP) is one major type of inherited duodenal cancer. The estimate of duodenal cancer risk in patients with FAP is critical for selecting the optimal treatment strategy. Methods. Microarray datasets related with FAP were retrieved from the Gene Expression Omnibus (GEO) database. Differentially expressed genes were identified by FAP vs. normal samples and FAP and duodenal cancer vs. normal samples. Furthermore, functional enrichment analyses of these differentially expressed genes were performed. A support vector machine (SVM) was performed to train and validate cancer risk prediction model. Results. A total of 196 differentially expressed genes were identified between FAP compared with normal samples. 177 similarly expressed genes were identified both in FAP and duodenal cancer, which were mainly enriched in pathways in cancer and metabolic‐related pathway, indicating that these genes in patients with FAP could contribute to duodenal cancer. Among them, Cyclin D1, SDF‐1, AXIN, and TCF were significantly upregulated in FAP tissues using qRT‐PCR. Based on the 177 genes, an SVM model was constructed for prediction of the risk of cancer in patients with FAP. After validation, the model can accurately distinguish FAP patients with high risk from those with low risk for duodenal cancer. Conclusion. This study proposed a cancer risk prediction model based on an SVM at the transcript levels.
Acute Fatty Liver Disease of Pregnancy in the Second Trimester
Authors: Afridi Faraz , Feely Michael , Reddy Raju
Published: June 2020

Acute fatty liver of pregnancy (AFLP) is a rare disorder that typically presents in the third trimester. We report a case of a 21-year-old woman with a history of intrauterine fetal demise at 19 weeks’ gestation who developed fulminant liver failure 1 week after the fetal demise. She was diagnosed with AFLP as per the Swansea criteria. An orthotopic liver transplant was attempted but was unsuccessful. AFLP usually presents between the 30th to 38th weeks of gestation. However, it can occur in the postpartum period after only 19 weeks of gestation as highlighted in our case.
Antioxidant and Anti‐Inflammatory Activities of Agrimonia pilosa Ledeb. Extract
Authors: Kim Choon Young , Yu Qi-Ming , Kong Hyun-Joo , Lee Joo-Yeon , Yang Kyung-Mi , Seo Jung-Sook
Published: June 2020

The purpose of this study is to investigate the effect of Agrimonia pilosa Ledeb. extract (APLE) on lipopolysaccharide‐ (LPS‐) induced cell damage in hepatocytes with a focus on antioxidant and anti‐inflammatory activities. Total antioxidant and anti‐inflammatory activities of APLE itself were analyzed and phytochemical analysis was performed. Moreover, inhibitory effects of APLE on LPS‐induced oxidative stress and inflammation were assessed in human HepG2 hepatocytes. APLE was found to exert α,α‐diphenyl‐β‐picrylhydrazyl (DPPH), 2,2′‐azino‐bis(3‐ethylbenzothiazoline‐6‐sulphonic acid) (ABTS), and nitrite scavenging activities and reducing power in a dose‐dependent manner. The total phenolic and flavonoid contents of APLE were 44.30 ± 1.61 mg GAE/g and 29.65 ± 1.81 mg QE/g, respectively. HPLC analysis revealed that gallic acid is the major phenolic compound in APLE, followed by rutin, genistein, taxifolin, quercetin, luteolin, and apigenin, in descending order. Treatment of 100 and 200 μg/mL APLE significantly reduced LPS‐stimulated intracellular reactive oxygen species production to the basal level without any cytotoxicity. Oppositely, APLE reversed LPS‐suppressed expression of glutathione peroxidase gene and protein. Consistent with this result, APLE suppressed LPS‐triggered expression of proinflammatory cytokine genes in a dose‐dependent manner. These results reinforce the fact that the antioxidant and anti‐inflammatory activity of APLE helps protect hepatocytes from LPS. Thus, APLE may be utilized as a bioactive ingredient in functional foods.
Field Tests of Super‐Long and Large‐Diameter Drilled Shaft Pile Foundations
Authors: Wang Peisen , Ding Hongyan , Zhou Jialin , Hu Wenjun , Gu Xuechen , Oh Erwin
Published: June 2020

This study investigated the compressive behaviour of super‐long pile foundations with large diameters. Three 52 m, 73 m, and 83 m long piles with a diameter of 1500 mm, 1500 mm, and 1800 mm were cast and tested, respectively. Given that large loading was required, an improved compressive static load test was introduced, and the load transfer mechanism, shaft resistance development, and distribution were analysed. This study found that the transferred load decreased along the pile during each applied load, but the gradients were different. For most layers, when increasing the load, the shaft resistance developed in the upper layers first, while the shaft resistance from the lower part did not always fully develop. Moreover, the “mutual compensation” phenomenon was discovered, which was when the shaft softening occurred from one soil layer, the shaft hardening of the other soil would occur simultaneously. Under consideration of the soil layer differences around these piles, it was recommended that shaft and base grouting should be applied on 52 m and 73 m piles, while only shaft grouting should be applied on the 83 m pile. For this longest pile design, whose toe resistance was discovered to be very small, increasing the pile length was not appropriate; thus, it was preferable to increase the pile diameter to increase the ultimate bearing capacity.
Preoperative Altered Spontaneous Brain Activity and Functional Connectivity Were Independent Risk Factors for Delayed Neurocognitive Recovery in Older Adults Undergoing Noncardiac Surgery
Authors: Jiang Zhaoshun , Zhang Xixue , Lv Yating , Zheng Xiaodong , Zhang Huibiao , Zhang Xuelin , Jiang Chongyi , Lin Guangwu , Gu Weidong
Published: June 2020

Objectives. Recently, it has been demonstrated that patients with subtle preexisting cognitive impairment were susceptible to delayed neurocognitive recovery (DNR). This present study investigated whether preoperative alterations in gray matter volume, spontaneous activity, or functional connectivity (FC) were associated with DNR. Methods. This was a nested case-control study of older adults (≥60 years) undergoing noncardiac surgery. All patients received MRI scan at least 1 day prior to surgery. Cognitive function was assessed prior to surgery and at 7-14 days postsurgery. Preoperative gray matter volume, amplitude of low-frequency fluctuation (ALFF), and FC were compared between the DNR patients and non-DNR patients. The independent risk factors associated with DNR were identified using a multivariate logistic regression model. Results. Of the 74 patients who completed assessments, 16/74 (21.6%) had DNR following surgery. There were no differences in gray matter volume between the two groups. However, the DNR patients exhibited higher preoperative ALFF in the bilateral middle cingulate cortex (MCC) and left fusiform gyrus and lower preoperative FC between the bilateral MCC and left calcarine than the non-DNR patients. The multivariate logistic regression analysis showed that higher preoperative spontaneous activity in the bilateral MCC was independently associated with a higher risk of DNR (OR=3.11, 95% CI, 1.30-7.45; P=0.011). A longer education duration (OR=0.57, 95% CI, 0.41-0.81; P=0.001) and higher preoperative FC between the bilateral MCC and left calcarine (OR=0.40, 95% CI, 0.18-0.92; P=0.031) were independently correlated with a lower risk of DNR. Conclusions. Preoperative higher ALFF in the bilateral MCC and lower FC between the bilateral MCC and left calcarine were independently associated with the occurrence of DNR. The present fMRI study identified possible preoperative neuroimaging risk factors for DNR. This trial is registered with Chinese Clinical Trial Registry ChiCTR-DCD-15006096.
Abstract B07: Potential clinical value of methylated microRNAs in saliva-liquid biopsy for surveillance of head and neck squamous cell carcinoma
Authors: Lv Ling , Quattlebaum Steve , Gao Dexiang , Cao Yu , Milam Ben , Hall Francis , Smith Derek , Handley Elyse , Bornstein Sophia , Gross Neil , Song John , Lu Shi-Long
Published: June 2020

Head and neck squamous cell carcinoma (HNSCC) is a biologically aggressive cancer in which high rates of recurrence (local, locoregional, or distant) contribute significantly to poor patient survival. One of the primary goals for current clinical practice of HNSCC surveillance is to detect recurrence at an early stage. However, current methods are either subjective, invasive, hard to access, not able to detect recurrence in a timely manner, or expensive. Saliva, given its directly adjacence to the anatomic location of HNSCC, may represent an opportunity to monitor HNSCC progression in a completely noninvasive, easy-to-access, and cost-effective method for HNSCC surveillance in a timely manner. We have developed a panel of seven biomarkers through screening of methylated microRNA loci (i.e., 9-1, 124-1, 124-2, 124-3, 129-2, 137, and 148) for HNSCC, and hereafter referred to as HNKlear. HNKlear demonstrated 92.1% sensitivity and 97.8% specificity in 189 HNSCC and 92 control tissue samples and 84.9% sensitivity and 95.4% in 86 pretreatment HNSCC and 108 control saliva samples. HNKlear is able to detect 93.5% T1 tumor and 91.2% stage I tumor in tissue, and 85.0% or 80.0% of HNSCC saliva when tumor is at T1 or stage I, respectively. In our prospective study, the value of HNKlear in patients’ saliva correlates with the tumor burden in 42 patients’ saliva before and after surgery within 3 months. HNKlear value is associated with progression-free survival in 57 primary tumor tissues and 38 treatment-naïve saliva. More importantly, HNKlear in saliva was shown to detect recurrence ranging from 90-337 days ahead of clinical detection of recurrence in the longitudinal follow-up of 43 HNSCC patients. Although these findings need to be validated in a large clinical trial, they suggest that analysis of certain methylated mciroRNA in saliva could have clinical significance for surveillance of HNSCC patients.

Citation Format: Ling Lv, Steve Quattlebaum, Dexiang Gao, Yu Cao, Ben Milam, Francis Hall, Derek Smith, Elyse Handley, Sophia Bornstein, Neil Gross, John Song, Shi-Long Lu. Potential clinical value of methylated microRNAs in saliva-liquid biopsy for surveillance of head and neck squamous cell carcinoma [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr B07.
Abstract B25: Isolation and engraftment of circulating tumor cells into zebrafish embryos to predict tumor response of ovarian cancer patients
Authors: Fieuws Charlotte , Vierstraete Jeroen , Van De Vijver Koen , Denys Hannelore , Claes Kathleen BM
Published: June 2020

Ovarian cancer is characterized by poor prognosis and high relapse rate, unfortunately accompanied with resistance to previously used therapy. Currently, resistance is defined by the time between treatment and progression of the disease. A better model to test resistance is to make patient-derived xenografts (PDX). We propose here the development of a PDX platform in zebrafish. This model allows testing of both previously used treatment and possible other treatment strategies. The fast readout of less than 15 days and the limited amount of material required (few 100s of cells) allow implementation in clinical practice. In a first phase, a correlation study will be performed to establish that zebrafish PDX models mimic the response of the patient to adjuvant chemotherapy by using primary tumor tissue. In the second phase of this project, circulating tumor cells will be isolated at different time points during treatment and follow-up. The objective of this part of the study is to isolate and cultivate CTCs for engraftment. For this we will apply a recently introduced size-based separation method (MetaCell®). The viable cells will undergo a short in vitro culture to expand and to get rid of remaining lymphocytes. Possible changes in mesenchymal-to-epithelial transition are picked up by single-cell sequencing (10xGenomics®) of the cells prior and post culturing. After culturing the CTCs are fluorescently labeled and engrafted into two-day-old zebrafish embryos. Tumors are formed the following day and treated with different treatment options for three executive days. Tumor proliferation and growth is observed in vivo through fluorescence microscopy. Post-mortem readouts are based on immunohistochemistry profiles. Resistance is defined by high proliferation rate (Ki-67) and mitotic index and low apoptosis rate (Caspase-3). Comparative morphology with primary tissue and CTC-PDX is evaluated by hematoxylin and eosin staining on FFPE-slices. This methodology may provide an opportunity for more personalized medicine in which treatment for OC may be guided by information from an individual’s zebrafish PDX response to therapy.

Citation Format: Charlotte Fieuws, Jeroen Vierstraete, Koen Van De Vijver, Hannelore Denys, Kathleen BM Claes. Isolation and engraftment of circulating tumor cells into zebrafish embryos to predict tumor response of ovarian cancer patients [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr B25.
Abstract B29: Development of CTC-derived xenograft (CDX) mouse models from early-stage non-small cell lung cancer patients
Authors: Nagaraj Suvilesh Kanve , Manjunath Yariswamy , Radhakrishnan Vijay , Avella Diego , Kimchi Eric , Staveley-O'Carroll Kevin , Li Guangfu , Kaifi Jussuf
Published: June 2020

Introduction: Circulating tumor cells (CTCs) are liquid biomarkers with high potential for application in precision medicine cancer care. However, no robust methods have been developed to culture CTCs from early-stage cancer patients owing to their rarity from limited disease burden and instability. Here, we describe a successful protocol to establish CTC culturing and CTC-derived xenograft (CDX) mouse models from early-stage non-small cell lung cancer (NSCLC) patients.

Methods: Surgically resected primary tumor fragments from patients with early-stage I NSCLCs were subcutaneously (s.c.) implanted to immunodeficient NOD SCID gamma (NSG) mice to generate patient-derived xenograft (PDX) models. Once palpable tumor reached a diameter of 1.5 cm, animals were euthanized and blood was collected via retro-orbital vein puncture. CTCs were enriched with OncoQuick® and cultured in vitro. These patient-derived CTCs were further characterized by immunostaining with antihuman antibodies against CK 8/18/19, Napsin, TTF-1, and CD45. Once human CTCs were confirmed, we then injected expanded CTCs s.c. and intravenous (i.v.) into naïve NSG mice to establish CDX models. Tumor growth and metastatic potential in CDX models were measured by MRI, autopsy, and histopathology.

Results: Human NSCLC primary tumor fragments implanted in NSG mice were tumorigenic at the s.c. implantation site, metastatic to distant organs, and passaged successfully to naïve NSG generations to maintain the PDX colonies. CTCs enriched from the PDX models were successfully cultured in vitro and positive for human NSCLC-specific markers (CK 8/18/19, Napsin, and TTF-1), but negative for human leukocyte marker CD45. Cultured PDX-derived CTCs that were xenografted into naïve NSG mice by s.c. and i.v. implantation demonstrated tumorigenicity and metastatic potential in CDX models.

Conclusion and Future Perspectives: This approach establishes CDX models from early-stage NSCLC patients at a high rate for personalized precision medicine. Models provide a unique opportunity to characterize rare patient-derived CTCs from curable, nonmetastatic NSCLC patients towards understanding CTC tumor biology and developing effective anticancer therapeutic strategies. Further, combined genetic and proteomic characterization of primary, PDX, and CDX tumors will be highly useful in discovering novel diagnostic/therapeutic target(s) specific to NSCLC.

Citation Format: Suvilesh Kanve Nagaraj, Yariswamy Manjunath, Vijay Radhakrishnan, Diego Avella, Eric Kimchi, Kevin Staveley-O'Carroll, Guangfu Li, Jussuf Kaifi. Development of CTC-derived xenograft (CDX) mouse models from early-stage non-small cell lung cancer patients [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr B29.
Abstract B41: Piritramide analgesia reduces CEA mRNA-positive circulating tumor cells’ presence compared to morphine and epidural analgesia following radical colon cancer surgery
Authors: Srovnal Josef , Berta Emil , Rehulkova Alona , Vidlarova Monika , Prasil Petr , Vecera Lubomir , Stourac Petr , Kourilova Pavla , Hajduch Marian
Published: June 2020

Purpose: Piritramide is a strong opioid widely used for postoperative analgesia (PA) in Europe while morphine and epidural PA are well established worldwide. Our retrospective analysis revealed that compared to morphine, piritramide improved cancer-specific survival in patients undergoing radical colon cancer surgery. Since circulating tumor cells’ (CTCs) presence has negative effect on colon cancer survival, we hypothesized that different types of PA could affect postoperative CTCs levels.

Patients and Methods: In total, 60 patients undergoing radical colon cancer surgery were enrolled in this prospective, randomized, two-center pilot study. Patients were randomized to receive either piritramide, morphine, or epidural PA. The presence of carcinoembryonic antigen (CEA) and cytokeratin 20 (CK-20) mRNA positive CTCs in peripheral blood was measured at four points (before and immediately after surgery, on postoperative day 2, and one month after surgery) using quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR). Perioperative treatment was standardized.

Results: In piritramide-treated patients, the levels of CEA mRNA positive cells were significantly lower on postoperative day 2 compared to other patients (p=0.04). CK-20 mRNA positive cells levels remained similar. In all groups, CTCs levels returned to preoperative baseline one month after surgery. Groups were similar regarding age, sex, ASA status, TNM, and grading.

Conclusion: Compared to morphine and epidural analgesia, piritramide reduces postoperative CEA mRNA-positive circulating tumor cells’ presence following radical colon cancer surgery. Further trials enrolling larger numbers of patients are needed.

Acknowledgments: This study was supported by Ministry of Health of the Czech Republic (NV18-03-00470), Ministry of Education, Youth and Sport of the Czech Republic (LO1304, LM2015089), European Regional Development Fund (ENOCH CZ.02.1.01/0.0/0.0/16_019/0000868) and Cancer Research Czech Republic.

Citation Format: Josef Srovnal, Emil Berta, Alona Rehulkova, Monika Vidlarova, Petr Prasil, Lubomir Vecera, Petr Stourac, Pavla Kourilova, Marian Hajduch. Piritramide analgesia reduces CEA mRNA-positive circulating tumor cells’ presence compared to morphine and epidural analgesia following radical colon cancer surgery [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr B41.
Abstract B45: High-throughput label-free isolation and expansion of circulating tumor cells (CTCs) from non-small cell lung cancer (NSCLC) patients for personalized treatments
Authors: Zeinali Mina , Huang Wei , Lee Maggie , Nadhan Arthi , Mathur Anvya , Hedman Casey , Lin Eric , Harouaka Ramdane , Wicha Max S. , Zhao Lili , Palanisamy Nallasivam , Hafner Mathias , Reddy Rishindra , Kalemkerian Gregory P. , Schneider Bryan J. , Hassan Khaled A. , Ramnath Nithya , Nagrath Sunitha
Published: June 2020

Background: Circulating tumor cell (CTC) clusters are emerging as clinically significant harbingers of metastases in solid organ cancers. Prior to engaging these CTC clusters in animal models of metastases, it is imperative for technology to identify them with high sensitivity. These clusters often present heterogeneous surface markers, and current methods for isolation of clusters may fall short.

Methods: We have applied the inertial microfluidic Labyrinth device for high-throughput, biomarker-independent, size-based isolation of CTCs and CTC clusters from patients with metastatic non-small cell lung cancer (NSCLC).

Results: Using the Labyrinth device, CTCs (PanCK+/DAPI+/CD45-) were isolated from metastatic NSCLC patients (n=25). Heterogeneous CTC populations were detected, including CTCs expressing epithelial (EpCAM), mesenchymal (vimentin), or both markers. CTCs were isolated from 100% of patients (417±1023 CTCs/mL), and CTCs that were EpCAM negative were significantly higher in numbers than EpCAM+ CTCs. Cell clusters of ≥2 CTCs were observed in 96% of patients, of which 75% were negative for EpCAM. Patients with higher number of CTC clusters than single CTCs had worse progression-free survival (PFS) (p=0.05). Recovered CTCs from patients with RET, ROS1, and ALK-rearranged tumors revealed identical genetic aberrations as the primary tumor for each gene using FISH analysis. We have successfully expanded the recovered CTCs from 2 patients and screened for therapeutic targeting. We have found that TPX-0005 might be effective in these patients and would direct them to a clinical trial using this compound.

Conclusions: The label-free Labyrinth device demonstrated the capability of collecting recovered CTCs from the device using a continuous processing technique while in a suspension state. This advantage opens the opportunities not only for CTC expansion off-chip, but also for ex vivo drug testing to direct patient-specific therapies.

Citation Format: Mina Zeinali, Wei Huang, Maggie Lee, Arthi Nadhan, Anvya Mathur, Casey Hedman, Eric Lin, Ramdane Harouaka, Max S. Wicha, Lili Zhao, Nallasivam Palanisamy, Mathias Hafner, Rishindra Reddy, Gregory P. Kalemkerian, Bryan J. Schneider, Khaled A. Hassan, Nithya Ramnath, Sunitha Nagrath. High-throughput label-free isolation and expansion of circulating tumor cells (CTCs) from non-small cell lung cancer (NSCLC) patients for personalized treatments [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr B45.
Abstract B52: Standardized exosome isolation and profiling for biomarker discovery
Authors: Fadiel Ahmed , Sharma Nirmal , Anderson Matthew L.
Published: June 2020

The discovery of an early detection biomarker for advancing disease like cancer is one of the major diagnostic challenges in medicine. Exosomes are microvesicles that are secreted by almost all cells and contain a cargo of DNA, RNA, and/or protein that is not only characteristic of their cell of origin but also capable of functionally impacting target cells and tissues. In this study, we utilized two sources of liquid biopsy to isolate and profile exosomes and perform molecular profiling potential relevant to cancer diagnostics. Using differential immuno-electron and atomic force microscopy, we have identified multiple structurally distinct subtypes of microvesicles and exosomes present in bronchial washings. We have also characterized the patterns of protein contained biomarkers associated with the unique class of exosomes identified in pulmonary washings. We have been able to identify at least three potential biomarkers potentially diagnostic of lung cancer from exosomes obtained with bronchial lavage. Lastly, we have used a bioinformatic approach to simulate potential functional networks of protein-protein interactions and determine how these protein cargoes of pulmonary exosomes impact adjacent pulmonary tissues and determine whether protein expression in specific subtypes of exosomes provides a predictive model of the current cancer state, remotely. Our results led us to conclude that the isolation of exosomes from liquid biopsy offers enormous potential to improve the diagnostic and prognostic capacity of liquid biopsy and their promise to revolutionize diagnostic medicine.

Citation Format: Ahmed Fadiel, Nirmal Sharma, Matthew L. Anderson. Standardized exosome isolation and profiling for biomarker discovery [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr B52.
Abstract B59: Validation of an exosomal osteosarcoma-associated gene signature in dogs with osteosarcoma
Authors: Makielski Kelly M. , Donnelly Alicia J. , Scott Milcah C. , Tomiyasu Hirotaka , Khammanivong Ali , Kisseberth William C. , Modiano Jaime F.
Published: June 2020

Introduction: Osteosarcoma, the most common primary bone tumor in dogs, has a guarded prognosis. A major hurdle in developing more effective therapies is the lack of osteosarcoma-specific biomarkers to predict risk, prognosis, or therapeutic response. Exosomes are secreted microvesicles emerging as powerful diagnostic tools. However, wide clinical use of exosomes is precluded by the difficulty in identifying diseased cargo from the vastly larger background of normal cargo. We developed a method to distinguish tumor-derived exosome cargo from normal background, allowing for identification of an osteosarcoma-specific gene signature.

Methods: Serum exosomes were enriched from osteosarcoma xenografts and control mice. Enriched genes associated with canine osteosarcoma were identified with RNA-sequencing. From identified candidates, we defined an osteosarcoma-associated gene signature. qRT-PCR amplification validated the gene signature in serum exosomes from clinical canine cases. Machine learning algorithms classified patients into disease groups based on this gene signature.

Results: We identified an osteosarcoma-associated signature consisting of five mRNAs (SKA2, NEU1, PAF1, PSMG2, and NOB1). Serum exosomes were isolated from dogs in clinical groups, including “healthy,” “osteosarcoma,” “other bone tumor,” or “non-neoplastic disease.” Machine learning classified samples, with 82% and 86% of untrained samples predicted as osteosarcoma by CN2 and RF models, respectively. Post-treatment samples “misclassified” as non-osteosarcoma were associated with longer remissions, potentially from a lack of remaining osteosarcoma cells.

Conclusions: We identified a gene signature associated with canine osteosarcoma. This gene signature was validated by qRT-PCR with serum exosomes from patients with osteosarcoma, as well as used to train artificial intelligence to correctly classify canine patients according to disease group with up to 93.8% accuracy.

Clinical Significance: This study combines a bioinformatics approach to biomarker discovery with machine learning to correctly identify osteosarcoma in canine patients. These results set the stage for future discoveries to inform cancer risk, diagnosis, prognosis, and response to therapy.

Citation Format: Kelly M. Makielski, Alicia J. Donnelly, Milcah C. Scott, Hirotaka Tomiyasu, Ali Khammanivong, William C. Kisseberth, Jaime F. Modiano. Validation of an exosomal osteosarcoma-associated gene signature in dogs with osteosarcoma [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr B59.
Abstract B62: Wholesome non-invasive liquid biopsies for pharmacodiagnostic work-up in breast cancer
Authors: Akolkar Dadasaheb
Published: June 2020

Background: Diagnosis and treatment of breast cancers is based on histopathological analysis of tumor tissue obtained by invasive biopsies. However invasive biopsies cause pain, anxiety and carry the risk of needle seeding. Though Immunocytochemistry (ICC) profiling of Circulating Tumor Cells (CTCs, defined as EpCAM+, panCK+, CD45-) has been previously attempted for diagnosis, these efforts have been unsuccessful. We used an epigenetically modified medium for enrichment of sufficient viable CTCs. These CTCs were used for diagnosis and characterization.

Methods: We obtained 15 ml of venous blood draw from 2500 patients with confirmed diagnosis of breast cancer. CTCs were enriched from PBMCs fraction using an epigenetically acting enrichment process that is lethal towards normal (non-malignant) cells, but confers survival privilege on apoptosis-resistant CTCs. Harvested CTCs were confirmed by immunostaining for EpCAM and pan-CK. Deep ICC profiling of these CTCs was performed with organ specific marker GCDFP15. Theranostic ICC Profiling was performed with ER and Her2.

Results: CTCs could be obtained from 2232 samples (89.3%) out of 2500. A subset of 100 samples were characterised by deep ICC profiling, among which 80% of samples were positive for GCDFP15. 14 and 17 samples out of 100 were positive for ER and Her2 respectively.

Conclusions: Our results show that ICC based characterization of CTCs can provide necessary diagnostic information non-invasively to substitute conventional procedures dependent on tissue extraction.

Citation Format: Dadasaheb Akolkar. Wholesome non-invasive liquid biopsies for pharmacodiagnostic work-up in breast cancer [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr B62.
Abstract IA17: Comprehensive genomic profiling of cell-free DNA enables treatment response monitoring
Authors: Adalsteinsson Viktor
Published: June 2020

Liquid biopsies have advanced significantly over the past decade but are still not routinely used to guide patient care. Part of the reason is that prospective clinical trials will be needed to demonstrate clinical utility, but detection sensitivity also needs to improve. For instance, liquid biopsies are not yet capable of discerning which patients need surgery after neoadjuvant treatment or which patients need adjuvant treatment right after surgery. They are also not yet sensitive enough to determine whether it is safe to stop therapy, as BCR-ABL testing has shown for patients with CML. We reason that 1,000-fold higher detection sensitivity (10−6) will be required to provide sufficient dynamic range to guide treatment decisions in most patients.

One way to improve detection sensitivity is to track more mutations per patient. This is because when tumor fraction is low in the bloodstream, only some mutations will be drawn in a blood tube, and the sampling of mutations will be random. Yet, each patient’s cancer is unique, with mutations scattered throughout the genome, and existing technologies are not well suited for tracking large numbers of distinct mutations. Conventional sequencing has an error rate of 10−3 and methods that repeatedly sequence each fragment, or model noise in normal samples, can achieve 10−4 to 10−5 but are not robust to spontaneous errors. Duplex sequencing is the most accurate method for mutation detection (10−6) but requires extremely deep sequencing to form a consensus of sense strands of each cfDNA duplex, which makes it highly inefficient and costly.

In my talk, I will first describe our team’s efforts to thoroughly optimize duplex sequencing for accurate tracking of large mutation fingerprints. I will show that detection limits up to 100-fold better than ddPCR can be achieved in serial dilution series, and that this enables treatment response monitoring in patients treated for early-stage breast cancer. I will then describe a new method to improve the efficiency of duplex sequencing using mutation enrichment. I will show that it is possible to track tens of thousands of distinct mutations in cfDNA using up to 1000-fold less sequencing, and that this enables 1000-fold better detection limit than ddPCR. In all, we believe that the improved dynamic range, afforded by the higher accuracy and efficiency in cfDNA sequencing, could make treatment response monitoring feasible for more cancer patients.

Citation Format: Viktor Adalsteinsson. Comprehensive genomic profiling of cell-free DNA enables treatment response monitoring [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr IA17.
Abstract PR09: Frequency and etiology of ctDNA-positive metastatic prostate cancer with BRCA2, ATM, or CDK12 mutations
Authors: Warner Evan , Yip Steven , Annala Matti , Wang Gang , Angeles Arkhjamil , Beigi Arshia , Schönlau Elena , Wong Amanda , Taavitsainen Sinja , Vandekerkhove Gillian , Beja Kevin , Nykter Matti , Khalaf Daniel , Chi Kim , Wyatt Alexander
Published: June 2020

Recent sequencing efforts have shown that genomic alterations within DNA damage repair (DDR) pathways are relatively common in metastatic prostate cancer (mPCa). Patients harboring DDR gene aberrations can respond poorly to standard-of-care androgen receptor (AR)-targeted therapy, potentially because defective DNA repair enables rapid tumor evolution. Research has shown that DDR-deficient mPCa is often genetically unstable due to its high mutation frequency; however, the specific differences in mutations and copy number alterations between DDR mutant and nonmutant tumors have not been established. We performed targeted next-generation sequencing on 1,214 cell-free DNA samples from 718 patients with mPCa. In 30 patients with disruption of BRCA2, ATM, or CDK12, we also sequenced archival primary tumor tissue. 118 patients had a deleterious germline or somatic mutation in at least one of the 22 DDR genes on our targeted panel. The most commonly altered were BRCA2 (n=41), ATM (n=20), and CDK12 (n=21), together present in ~14% of patients. Disruption of the intact second allele was detected in 96%, 82%, and 84% of patients with mutations in BRCA2, ATM, and CDK12, respectively. Patients with a mutation in any one of these genes had fewer mutations in TP53 than a control cohort of DDR-intact patients (p<0.05). However, BRCA2-defective patients had frequent compound deletions of tumor-suppressor genes (TP53, PTEN, RB1). In patients with CDK12 mutations, PTEN or RB1 deletion was rare and samples instead exhibited copy number gains of MDM2 and/or CCND1. ATM-deficient cases did not demonstrate the same degree of genomic instability as either BRCA2- or CDK12-defective disease. In summary, patients with BRCA2, ATM, or CDK12 gene disruption possess distinct patterns of genomic alterations. These findings might help clarify why some DDR-deficient mPCa cases represent a more aggressive disease subtype with a poor response to AR-targeted therapy.

This abstract is also being presented as Poster A36.

Citation Format: Evan Warner, Steven Yip, Matti Annala, Gang Wang, Arkhjamil Angeles, Arshia Beigi, Elena Schönlau, Amanda Wong, Sinja Taavitsainen, Gillian Vandekerkhove, Kevin Beja, Matti Nykter, Daniel Khalaf, Kim Chi, Alexander Wyatt. Frequency and etiology of ctDNA-positive metastatic prostate cancer with BRCA2, ATM, or CDK12 mutations [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr PR09.
A Biobank of Stem Cells of Human Exfoliated Deciduous Teeth: Overview of Applications and Developments in Brazil
Authors: Zalaf Bianca Rapini , Bringel Mayara , Jorge Paula Karine , de Oliveira Bárbara , Tanabe Kim , Santos Carlos Ferreira , Oliveira Rodrigo Cardoso , Rios Daniela , Cruvinel Thiago , Lourenço Neto Natalino , Oliveira Thais Marchini  , Machado Maria Aparecida Andrade Moreira
Published: June 2020

A biobank is an organized collection of biological human material and its associated information stored for research according to regulations under institutional responsibility, without commercial purposes, being a mandatory and strategical activity for research, regenerative medicine, and innovation. Stem cells have largely been employed in research and frequently stored in biobanks, which have been used as an essential source of biological materials. Stem cells of human exfoliated deciduous teeth (SHED) are stem cells which have a high multipotency and can be easily obtained. Besides, this extremely accessible tissue has advantages with respect to storage, as the SHED obtained in childhood can be used in later life, which implies the necessity for the creation and regulation of biobanks. The proper planning for the creation of a biobank includes knowledge of the material types to be stored, requirements regarding handling and storage conditions, storage time, and room for the number of samples. Thus, this study aimed to establish an overview of the development of a SHED biobank. Ethical and legal standardization, current applications, specific orientations, and challenges for the implementation of a SHED biobank were discussed. Through this overview, we hope to encourage further studies to use SHED biobanks.