bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract A10: Glioma cell-free DNA methylation marker for diagnosis and monitoring
Authors: Sabedot Thais , Malta Tathiane , Snyder James , Nelson Kevin , Wells Michael , deCarvalho Ana , Mukherjee Abir , Chitale Dhan , Mosella Maritza , Asmaro Karam , Robin Adam , Rosenblum Mark , Mikkelsen Tom , Rock Jack , Poisson Laila , Lee Ian , Walbert Tobias , Kalkanis Steven , Castro Ana Valeria , Noushmehr Houtan 
Published: June 2020

Abstract
Genome-wide DNA-methylation profiling has shown that epigenetic abnormalities are biologically and clinically important signs in glioma and can be used to classify these tumors into distinct prognostic groups. Thus far, DNA methylation profiling of gliomas has required surgically resected tissue. Because gliomas release tumoral material into biofluids, such as blood, we developed a method using a liquid biopsy (LB) for minimally invasive surveillance of the tumor. We performed a genome-wide CpG methylation profile of cell-free DNA extracted from serum of patients with primary glioma (N=48) and during clinical follow-up (N=33). We used a supervised machine learning (ML) approach to identify glioma-specific epigenetic signatures in the LB (eLB) (N=1000, false-discovery rate &lt; 0.003) to distinguish patients with glioma from those without glioma. The epigenetic profiles of matched tumor tissue showed that there was 67% concordance between the eLB signatures of the glioma in serum and tissue. Using these signatures as input for ML, we derived the glioma epigenetic liquid biopsy (GeLB) score. An independent validation study (68 gliomas and 65 nongliomas) showed that a GeLB score ≥ 50% could predict with 96% accuracy (sensitivity = 97.1% and specificity = 95.9%) whether a patient had glioma or not. Changes in GeLB score also reflected clinicopathologic changes observed during surveillance (e.g., progression, pseudoprogression, or response to a clinical trial drug). Our results suggest that the GeLB score could be used as a complementary approach to diagnose glioma and follow up patients postsurgically. Finally, we provide an online tool for predicting glioma based on the cell-free DNA methylome (hbtc.shinyapps.io/GeLB/).
Citation Format: Thais Sabedot, Tathiane Malta, James Snyder, Kevin Nelson, Michael Wells, Ana deCarvalho, Abir Mukherjee, Dhan Chitale, Maritza Mosella, Karam Asmaro, Adam Robin, Mark Rosenblum, Tom Mikkelsen, Jack Rock, Laila Poisson, Ian Lee, Tobias Walbert, Steven Kalkanis, Ana Valeria Castro, Houtan Noushmehr. Glioma cell-free DNA methylation marker for diagnosis and 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 A10.
Abstract A22: Simultaneous multiparametric profiling of cell-free RNA (cfRNA) and cell-free tumor DNA (ctDNA) in advanced-stage colorectal cancer
Authors: Feng Zheng , Wang Danyi , Merkle Dennis , Yu Jianjun , Jia Shidong , Scheuenpflug Juergen 
Published: June 2020

Abstract
Background: It has been recognized that intratumoral heterogeneity together with therapeutic intervention-associated multiple genomic alterations added complexity for precision therapy in late-stage colorectal cancer (CRC). The clinical utility/validity of ctDNA assays have been systematically analyzed and proved under clinical settings in select cancer types with demonstrated specificity and sensitivity. Notably, cfRNA sequencing confirmed and enhanced detection sensitivity for variants with low allele frequency. In this study, plasma-based ctDNA mutation and cfRNA gene expression in patients with advanced CRC were simultaneously tested using NGS liquid biopsy panels.
Methods: ctDNA and cfRNA were extracted from plasma of 25 treatment-naive patients with advanced CRC (stage III/IV), then were tested using the 600-gene PredicineATLAS ctDNA NGS assay and 180-gene PredicinePLUS cfRNA NGS assay, respectively. Various genomic alterations including single-nucleotide variation (SNV), Indel, copy number variation (CNV) and genome rearrangement are detected, along with tumor mutation burdens (TMB) evaluation/measurement. RNA-based variants and gene expression are also analyzed.
Results: At ctDNA level, 96% (24/25) ctDNA samples were detected with at least 1 genomic alteration and total 265 SNV/Indels and 27 CNVs were identified across samples, including 180 genes with reported SNVs/indels and 23 genes with CNV. 20% (5/25) of the patients with RAS somatic mutations, 32% (8/25) with TP53 mutations, 8% (2/25) with APC mutations, and 8% (2/25) with PIK3CA mutations. TPM3-NTRK1 fusion was also detected in one patient. A subset of these variants detected at ctDNA level were also confirmed by cfRNA sequencing.
Conclusions: Our results demonstrated the clinical utility/feasibility of simultaneous multiparametric profiling of ctDNA and cfRNA for comprehensive molecular insight/characterization in advanced-stage cancer. cfRNA-derived variant detection confirms the variants originally detected in ctDNA test and further validates the high-specificity results for report interpretation. Further investigation of exploring concordance between temporally matched tissue and plasma samples is ongoing. The ctDNA and cfRNA-based combined liquid biopsy solution provides holistic molecular overview for detecting driver mutations, monitoring efficacy/disease burden, and identifying subclonal alterations that may related to drug resistance and tumor heterogeneity.
Citation Format: Zheng Feng, Danyi Wang, Dennis Merkle, Jianjun Yu, Shidong Jia, Juergen Scheuenpflug. Simultaneous multiparametric profiling of cell-free RNA (cfRNA) and cell-free tumor DNA (ctDNA) in advanced-stage colorectal 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 A22.
Abstract A23: Ultrasensitive mutation detection in FFPE tissues and circulating tumor DNA using SiMSen-Seq
Authors: Filges Stefan , Andersson Daniel , Kristiansson Helena , Vannas Christoffer , Johansson Gustav , Li Junrui , Godfrey Tony E. , Levin Max , Linderholm Barbro , Ståhlberg Anders 
Published: June 2020

Abstract
Novel diagnostic tools in oncology, prenatal diagnostics, and transplantation medicine depend on the detection of ultrarare variants. The analysis of cell-free DNA has the potential to revolutionize diagnosis, treatment monitoring, and recurrence and resistance of cancer. Yet these analysis remains challenging due to limited amounts of material and low allele frequencies of targeted variants. Simple, Multiplexed, PCR-based barcoding of DNA for Sensitive mutation detection using Sequencing (SiMSen-Seq) enables easy generation of libraries containing unique molecular identifiers (UMI) with minimal DNA input across several kilobases of DNA using two rounds of PCR and allows the detection of rare variants below 0.1% allele frequency. Clinical applications of ctDNA require highly optimized workflows to ensure high sensitivity and reproducibility. Here we present our state-of-the-art liquid biopsy workflow using SiMSen-Seq and simple quality control steps, applicable to almost any liquid biopsy protocol. In a series of case studies with melanoma patients we find that ctDNA mirrors the time-course of established protein markers such as S-100 and in some cases detects minimal residual months in advance of standard clinical diagnostics. SiMSen-Seq efficiently determined even rare mutations across multiple tumor forms in challenging sample types, such as FFPE tissue or cfDNA. We identified mutations in highly degraded FFPE tissue using a 60-plex SiMSen-Seq panel and then analyzed longitudinal cfDNA samples using patient-specific panels in a cohort of metastatic breast cancer patients. Our data indicate that ctDNA might be used as a biomarker for early detection of recurrence in these patients. We were able to detect treatment resistance variants as well as observe tumor recurrence well in advance of the onset of clinical symptoms. Thus, SiMSen-Seq offers an affordable, minimally invasive method for monitoring treatment efficiency and determination of drug resistance development in cancer.
Citation Format: Stefan Filges, Daniel Andersson, Helena Kristiansson, Christoffer Vannas, Gustav Johansson, Junrui Li, Tony E. Godfrey, Max Levin, Barbro Linderholm, Anders Ståhlberg. Ultrasensitive mutation detection in FFPE tissues and circulating tumor DNA using SiMSen-Seq [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 A23.
Abstract A31: Tracking the evolution of soft tissue sarcoma and GIST using liquid biopsies
Authors: Namløs Heidi M. , Boye Kjetil , Moosavi Seyed H , Vodak Daniel , Sharma Nitin , Lorenz Susanne , Bjerkehagen Bodil , Næss Stine , Hovig Eivind , Jebsen Nina , Ståhlberg Anders , Myklebost Ola , Meza-Zepeda Leonardo A. 
Published: June 2020

Abstract
Molecular analysis of circulating tumor DNA (ctDNA) has a large potential for clinical application by capturing mutations and heterogeneity through noninvasive sampling. The CircSarc studies aims to provide new insights into the clinical utility of liquid biopsies in soft tissue sarcomas (CircSarc STS) and gastrointestinal stromal tumors (CircSarc GIST). In CircSarc STS, we have enrolled 35 high-grade soft-tissue sarcoma patients with localized disease. Plasma from each patient has been collected longitudinally throughout the course of their disease, with a follow-up of up to 5 years. To identify patient-specific somatic mutations, the patients’ tumor and germline DNA have been exome sequenced. Somatic mutations in cfDNA are being identified using ultra-low-pass WGS or targeted NGS. At time of surgery and/or progression, we detect ctDNA in 30% of the first soft-tissue sarcoma samples with higher levels in larger or metastatic tumors. In a proof-of-concept study, we have shown that that levels of tumor-specific mutations in plasma correlated to clinical manifestation of metastatic disease. In CircSarc GIST, plasma has been collected for a cohort of 30 metastatic GISTs and at time of diagnosis for 50 GISTs. Somatic mutations in the tumor have been determined by targeted sequencing or whole-exome sequencing. Somatic mutations in ctDNA are identified using targeted NGS. The levels of somatic mutations in ctDNA are being correlated with clinicopathologic features. ctDNA was detected in 36% of treatment-naïve GIST patients, including all patients with metastatic disease, and the tumor burden was the most important detection determinant. Analysis of metastatic GISTs is ongoing, but repeated plasma samples in a progressing patient have demonstrated that clonal evolution can be monitored over time. ctDNA analysis of the patient revealed multiple resistance mutations, and these were spatially distributed in the primary tumor. Our work shows that detection of mutations in plasma is particularly feasible for patients with high tumor burden. Mutational analysis by use of liquid biopsies can capture the molecular heterogeneity of the tumor and guide treatment decisions during progression.
Citation Format: Heidi M. Namløs, Kjetil Boye, Seyed H Moosavi, Daniel Vodak, Nitin Sharma, Susanne Lorenz, Bodil Bjerkehagen, Stine Næss, Eivind Hovig, Nina Jebsen, Anders Ståhlberg, Ola Myklebost, Leonardo A. Meza-Zepeda. Tracking the evolution of soft tissue sarcoma and GIST using liquid biopsies [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 A31.
Abstract A33: Impact of tumor-derived exosomes on CD28 expression in T cells
Authors: Schulte Ashley J. , Mills Lauren J. , Makielski Kelly M. , DePauw Taylor A. , Modiano Jaime F. 
Published: June 2020

Abstract
Osteosarcoma is a rare disease with a disproportionate impact, as it is seen mostly in children and adolescents. Despite aggressive treatment, more than 50% of patients succumb to their disease within 10 years of diagnosis, making safe and effective treatments a huge unmet need. Immunotherapy, including immune checkpoint blockade, is drastically changing cancer treatment by increasing the antitumor immune response. Mechanisms of resistance to immune checkpoint blockade are incompletely understood; therefore, there is currently no available method to specifically identify patients who will respond favorably to immunotherapy. Exosomes are extracellular vesicles that can carry proteins, lipids, mRNA, microRNA, and DNA and play a role in extracellular communication. Exosomes can be found in circulation, making them an attractive tool for diagnostic testing. One potential mechanism of immunotherapy resistance could be destabilization of the CD28 coreceptor in T cells by microRNAs secreted in tumor-derived exosomes. Utilizing next-generation RNA-sequencing, we previously identified 2 microRNAs in dogs and 2 microRNAs in humans that were inversely correlated with CD28 expression in 44 human and 39 canine osteosarcoma tissues. Current work entails isolating exosomes from canine and human osteosarcoma tumor cell lines. Using a species mismatched approach, we can identify canine microRNAs in human T cells that were treated with canine exosomes, and vice versa, to verify delivery of microRNAs to T cells via tumor-derived exosomes. We are also using the CRISPR-Cas system to genetically engineer a human osteosarcoma cell line (HOS) that expresses the exosome marker CD63 linked to GFP so we can track exosome uptake by T cells by flow cytometry and determine the effect on CD28 expression levels. Identifying mechanisms of resistance will lead to improved patient selection and identification of therapeutic targets to combat this resistance.
Citation Format: Ashley J. Schulte, Lauren J. Mills, Kelly M. Makielski, Taylor A. DePauw, Jaime F. Modiano. Impact of tumor-derived exosomes on CD28 expression in T cells [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 A33.
Abstract A35: Cell-free tumor DNA profiling of colon cancer patients: Searching for mechanisms of chemoresistance
Authors: Vymetalkova Veronika , Pardini Barbara , Urbanova Marketa , Cervena Klara , Vodicka Pavel , Naccarati Alessio 
Published: June 2020

Abstract
Colorectal cancer (CRC) is a worldwide health burden, with nearly 1.2 million new cases expected each year. Significant efforts are currently being employed to find patients who will benefit from chemotherapy. In fact, drug resistance is a limiting factor for the efficacy of chemotherapy in CRC treatment. In the present work, we aimed at identifying molecular markers in plasma cell-free DNA that could be associated with good/poor response and chemoresistance, comparing good responders (i.e., benefitting from chemotherapy, not having side effects like toxicity, no relapses, and having a complete response with no residual cancer) from non-/poor responders (patients with chemoresistance and lacking any response, or developing toxicity). Paired plasma samples from 10 colon cancer patients collected before and after adjuvant 5-fluorouracil (5-FU)-based therapy were profiled by a whole-exome sequencing (WES) approach in order to identify mutations associated with therapy response. In concomitance, DNA from tumor tissue from the same patients was also profiled by WES for mutation burden concordance. Analyses were performed on colon cancer patients treated with the same 5-FU-based therapy. The first sampling was performed at the time of the diagnosis (i.e., active disease), and the second after 6-9 months depending on patients’ conditions (i.e., covering the tumor resection, administration of adjuvant chemotherapy, etc.). After follow-up, 3 patients were clinically classified as “good responders” and 7 as “non-/poor responders.” All prepared libraries passed the quality control checkpoints and were sequenced. The number of total reads exceeds 2,57 × 109. Mean read length is about 100 nt. Alignment to human reference genome (hg38) is &gt; 99.8%. The bioinformatics analyses are currently ongoing to profile the two different groups over time. Detailed results of the study will be presented during the meeting. The significance of the project lies in the improvement of the diagnosis and therapy efficacy in colon cancer patients. Supported by grant AZV MZ 17-30920A.
Citation Format: Veronika Vymetalkova, Barbara Pardini, Marketa Urbanova, Klara Cervena, Pavel Vodicka, Alessio Naccarati. Cell-free tumor DNA profiling of colon cancer patients: Searching for mechanisms of chemoresistance [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 A35.
Abstract A47: Circulating tumor cell-defined minimal residual disease in locally advanced rectal cancer treated with multimodality therapy
Authors: Lee Lucas , Hall Carol , Lucci Antony , Bednarski Brian , Rodriguez-Bigas Miguel , Chang George , You Y. Nancy 
Published: June 2020

Abstract
Background: Current treatment for locally advanced rectal cancer (LARC) includes multimodality therapy in the neoadjuvant and adjuvant settings. Response to neoadjuvant therapy (NT) is prognostic of long-term outcomes. While long-course chemoradiation (CRT) had been the traditional NT regimen, novel regimens adding systemic therapy and/or eliminating radiation have been introduced. We examined if circulating tumor cells provide prognostic information independent of the specific treatment regimen utilized. Specifically, we aimed to define the significance of CTC-defined minimal residual disease (MRD) in LARC.
Methods: A prospective longitudinal protocol enrolled LARC patients (N=100; clinical stage II=4; stage III=96) undergoing NT. Peripheral blood was collected at baseline (t1, treatment-naive), after NT (t2, intraoperatively before tumor manipulation), after resection (t3, 2-8 weeks postoperatively), and after completion of adjuvant therapy (t4, 2-12 weeks after completion). CTC was enumerated by the CellSearch® platform within 72 hours of collection. Patients were followed for disease-free survival (DFS).
Results: At t1, CTCs were detected in 28/90 (31.1%) patients with available samples with a median CTC count of 1.5 [IQR: 1.0, 2.75]. NT consisted of long-course pelvic CRT (65%), extended NT with systemic chemotherapy and long- or short-course pelvic CRT (22%), and a radiation-sparing regimen with systemic chemotherapy only (13%). At t2, CTCs were detected in 34/75 (45.3%) patients with a median CTC count of 1 [IQR: 1, 1]. Type of NAT did not correlate with CTC positivity (p=0.637). Ten (9.4%) patients declined surgery, while cPR occurred in 12/93 (12.9%) surgical patients. Postoperatively (t3), CTC was detected in 12/47 (25.5%) patients, with a median count of 1.5 (IQR: 1.0-3.0). After completing adjuvant chemotherapy (t4), only 3/29 (10.3%) patients had detectable CTC. With a median follow-up of 47.50 months from diagnosis for the entire cohort, CTC positivity at t4 significantly stratified DFS (p=0.035).
Conclusions: One third of locally advanced RC patients harbored detectable CTCs at baseline. CTC detection after completion of curative-intent multimodality therapy (i.e., MRD) correlated with long-term DFS.
Citation Format: Lucas Lee, Carol Hall, Antony Lucci, Brian Bednarski, Miguel Rodriguez-Bigas, George Chang, Y. Nancy You. Circulating tumor cell-defined minimal residual disease in locally advanced rectal cancer treated with multimodality therapy [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 A47.
Abstract A49: Viable circulating ensembles of tumor-associated cells persist in pretreated patients with solid organ cancers showing no radiologically detectable disease
Authors: Limaye Sewanti A. , Crook Timothy , Akolkar Dadasaheb , Patil Darshana , Devhare Pradip , Patil Revati , Patel Shoeb , Khan Shabista , Dhasarathan Raja , Datta Vineet , Sims Cynthe , Srinivasan Ajay , Datar Rajan 
Published: June 2020

Abstract
The success of treatment in solid organ cancers is ascertained by radiologic imaging as per standard-of-care protocol, with PET-CT being the modality of choice. However, even in cases where complete resolution of the disease is noted radiologically, recurrence or emergence of new metastases is not uncommon. To explore the underlying cause of such recurrence, we hypothesized that circulating metastatic disease (CMD) in the nature of viable tumor cells or clusters would be a persistent systemic feature of solid organ cancers, although there may be no overt evidence of disease. We identified 1,217 patients with known and previously treated cases of various solid organ cancers (metastatic and nonmetastatic), where a recent PET-CT scan showed no radiologic evidence of disease. 15 mL peripheral blood was collected from these patients. Peripheral blood mononuclear cells (PBMCs) were harvested by centrifugation. Circulating ensembles of tumor-associated cells (C-ETACs) were enriched from PBMCs using an epigenetically acting stabilization process, which is cytotoxic towards nonmalignant cells but confers survival privilege on apoptosis-resistant cells of tumorigenic origin as well as their heterotypic clusters (C-ETACs). C-ETACs were characterized by immunostaining for EpCAM, pan-CK, and CD45 as well as for organ-specific markers. Among the 1,217 patients with no radiologic evidence of disease, C-ETACs were detected in 1,118 (91.9%) and were confirmed by immunostaining. In a subset analysis, C-ETACs from 80 samples were immunostained for organ- or subtype-specific antigens including those from head and neck (P63), breast (GCDFP15), colorectum (CDX2), liver (Hep Par-1), ovary (CA125), prostate (PSMA), cervical (P63), and lung (TTF-1/Napsin-A). Circulating metastatic disease (CMD) in the form of viable C-ETACs is a potent threat in patients with solid organ cancers despite complete radiologic response to treatment.
Citation Format: Sewanti A. Limaye, Timothy Crook, Dadasaheb Akolkar, Darshana Patil, Pradip Devhare, Revati Patil, Shoeb Patel, Shabista Khan, Raja Dhasarathan, Vineet Datta, Cynthe Sims, Ajay Srinivasan, Rajan Datar. Viable circulating ensembles of tumor-associated cells persist in pretreated patients with solid organ cancers showing no radiologically detectable disease [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 A49.