bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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 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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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&lt;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.
Late Gadolinium Enhancement–Dispersion Mapping
Authors: Aquaro Giovanni Donato , Grigoratos Chrysanthos , Bracco Antonio , Proclemer Alberto , Todiere Giancarlo , Martini Nicola , Habtemicael Yacob Ghebru , Carerj Scipione , Sinagra Gianfranco , Di Bella Gianluca 
Published: June 2020

Background:
Late gadolinium enhancement (LGE) is an important prognostic marker in hypertrophic cardiomyopathy and an extent >15% it is associated with high risk of sudden cardiac death. We proposed a novel method, the LGE-dispersion mapping, to assess heterogeneity of scar, and evaluated its prognostic role in patients with hypertrophic cardiomyopathy.

Methods:
One hundred eighty-three patients with hypertrophic cardiomyopathy and a low- or intermediate 5-year risk of sudden cardiac death underwent cardiac magnetic resonance imaging. A parametric map was generated from each LGE image. A score from 0 to 8 was assigned at every pixel of these maps, indicating the number of the surrounding pixels having different quality (nonenhancement, mild-enhancement, or hyperenhancement) from the central pixel. The Global Dispersion Score (GDS) was calculated as the average score of all the pixels of the images.

Results:

During a median follow-up time of 6 (25th–75th, 4–10) years, 22 patients had hard cardiac events (sudden cardiac death, appropriate implantable cardioverter-defibrillator therapy, resuscitated cardiac arrest, and sustained ventricular tachycardia). Kaplan-Meier analysis showed that patients with GDS>0.86 had worse prognosis than those with lower GDS (
P
<0.0001). GDS>0.86 was the only independent predictor of cardiac events (hazard ratio, 9.9 [95% CI, 2.9–34.6],
P
=0.0003). When compared with LGE extent >15%, GDS improved the classification of risk in these patients (net reclassification improvement, 0.39 [95% CI, 0.11–0.72],
P
<0.019).

Conclusions:
LGE-dispersion mapping is a marker of scar heterogeneity and provides a better risk stratification than LGE presence and its extent in patients with hypertrophic cardiomyopathy and a low-intermediate 5-year risk of sudden cardiac death.