bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract B10: Feasibility of bronchial washing fluid-based approach to early-stage lung cancer diagnosis
Authors: Ryu Jeong Seon , Lee Myoung Kyu , Lee Seung Jae 
Published: June 2020

Abstract
Circulating tumor DNA has few applications for detecting early-stage lung cancers. Bronchial washing (BW) is minimally invasive, and BW fluids can contain tumor DNA. Thus, analysis of BW fluids could be used for precision medicine. Forty-eight paired specimens (primary tumor tissue, normal tissue, BW supernatant, and BW precipitate) from twelve patients with early-stage non-small cell lung cancer were analyzed using ultradeep next-generation sequencing with a custom panel containing 113 genes. In primary tumors, 130 missense mutations/indels (5–16 per patient) and 20 driver mutations (0–3) were found; 105 (80.8%) and 97 (74.6%) of these missense mutations/indels were identified in BW supernatants and precipitates, respectively, and 19 (95.0%) of the driver mutations in both BW supernatants and precipitates. Concordance between EGFR mutations in primary tumors, BW supernatants, and BW precipitates was 100%. The median allele frequencies (AFs) for missense mutations/indels in primary tumors, BW supernatants, and BW precipitates were 13.0%, 0.3%, and 0.1%, respectively. The AFs of missense mutations/indels in BW supernatants correlated with those in primary tumors and in BW precipitates (P&lt;0.001). In conclusion, this study provides evidence that the BW fluids, especially supernatants, can be an alternative to overcome the limitation that clinical utility of ctDNA is often not reliable in early-stage NSCLC.
Citation Format: Jeong Seon Ryu, Myoung Kyu Lee, Seung Jae Lee. Feasibility of bronchial washing fluid-based approach to early-stage lung cancer diagnosis [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 B10.
Abstract B15: Circulating tumor cells express tissue specific antigens in multiple cancers
Authors: Akolkar Dadasaheb , Patil Revati , Patil Darshana , Fulmali Pradip , Fulmali Pooja , Patel Shoeb , Devhare Pradip , Ainwale Akshay , Datta Vineet , Sims Cynthe , Srinivasan Ajay , Datar Rajan 
Published: June 2020

Abstract
Definitive diagnosis of solid organ cancers is based on histopathologic analysis of tumor tissue obtained by invasive biopsies. However, invasive biopsies are associated with procedural expenses, sequelae, and risks. Though immunocytochemistry (ICC) profiling of circulating tumor cells (CTCs) has been previously attempted for diagnosis in some cancers, they have been unviable due to limited yields of CTCs. We used a novel approach for enrichment of sufficient viable CTCs that permit meaningful ICC profiling for diagnosis of cancers in suspected cases. We obtained 15 mL of venous blood draw from 965 patients with confirmed diagnosis of various solid organ cancers. CTCs were enriched from PBMCs fraction using an epigenetically activated enrichment process that is lethal towards normal (nonmalignant) 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 for various organs such as lungs (TTF-1 or Napsin), breast (GCDFP15 or GATA3), ovarian (CA125 or WT-1), pancreatic (CK19 or CA19-9), cervical (P63), liver (Hep Par-1 or Glypican), colorectal (CK20 or CDX-2), head and neck (P63), kidney (Pax-8 or RCC), and prostate (PSMA or AMACR). CTCs (EpCAM+, pan-CK+) could be obtained from 94.4% of all samples. Organ-specific markers were positive in 100% of lung cancer, 79.3% of breast cancers, 70.0% of ovarian cancers, 93.3% of pancreatic cancers, 100% of cervical cancers, 61% of hepatocellular carcinomas, 92.6% ofcColorectal cancers, 98.8% of head and neck cancers, 100% of renal cancers, and 100% of prostate cancers. Our results show that deep ICC profiling of CTCs can determine tissue of origin in solid organ cancers noninvasively to substitute conventional procedures dependent on tissue extraction.
Citation Format: Dadasaheb Akolkar, Revati Patil, Darshana Patil, Pradip Fulmali, Pooja Fulmali, Shoeb Patel, Pradip Devhare, Akshay Ainwale, Vineet Datta, Cynthe Sims, Ajay Srinivasan, Rajan Datar. Circulating tumor cells express tissue specific antigens in multiple cancers [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 B15.
Abstract B26: A new way of fabricating high-porosity parylene membranes for high-throughput capturing of viable circulating and exfoliated tumor cells from large-volume bodily fluids
Authors: Gu Jian , Rabadi Inad , Zenhausern Frederic , Carpentieri David , Wang Jue 
Published: June 2020

Abstract
Liquid biopsy is a critical component in cancer precision medicine. The ability to capture rare cancer cells from liquid samples, such as circulating tumor cells (CTCs) from peripheral blood as well as exfoliated tumor cells (ETCs) from other body fluids, has shown great promises in cancer detection and prognosis, as well as understanding of cancer biology at different stages. Different ways have been developed for rare cancer cell capture, including biomarker-based immunocapture and capture through other physical processes, such as size, mechanical or dielectric properties, hydrodynamic fluids, etc. However, the throughputs of these techniques are limited to 0.2-2 mL/min. Recently, a high-porosity parylene membrane has been shown to be able to process sample at a fluid rate of &gt; 100 mL/min, which would greatly extend the capability of CTC and ETC-based liquid biopsy. The high porosity of the membrane can also dramatically reduce the shear stress the tumor cells encountered during capture, which has been shown to be critical to maintain cell viability. However, the current parylene membrane fabrication involves deep Si reactive ion etching, which is an expensive process and not widely available. The release of the parylene membrane can also be challenging. We report here a new method to fabricate the parylene membrane using simple photolithography and reactive ion etching techniques. The fabricated parylene membranes and their capability of processing large volume sample for viable cell capture will be presented.
Citation Format: Jian Gu, Inad Rabadi, Frederic Zenhausern, David Carpentieri, Jue Wang. A new way of fabricating high-porosity parylene membranes for high-throughput capturing of viable circulating and exfoliated tumor cells from large-volume bodily fluids [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 B26.
Abstract B37: Analysis of non-small cell lung cancer (NSCLC) circulating biomarkers for monitoring early response to radiation therapy
Authors: Purcell Emma , Niu Zeqi , Grzesik Madeline , Owen Sarah , Fairbairn Heather , Jolly Shruti , Nagrath Sunitha 
Published: June 2020

Abstract
Approximately 20% of non-small cell lung cancer (NSCLC) patients will be diagnosed with stage 3 cancer, with a predicted survival rate between 20-30%. Stage 3 NSCLC patients commonly undergo chemoradiation treatment, with imaging scans being the standard of care for determining tumor control or progression both during and after radiation treatment. Imaging technologies can only show progression after it has occurred, making treatment challenging. We suggest that the molecular characterization of biomarkers found in the bloodstream can identify or predict radiation treatment efficacy before progression becomes visible on a scan. In this study, patients undergo a response-driven adaptive radiation therapy (RDART) protocol: four weeks of chemoradiation followed by a set of imaging scans before an additional 2 weeks of adapted, personalized radiation with chemotherapy. In this work, we provide combined analysis of both circulating tumor cells (CTCs), a rare cell found in a patient’s peripheral blood, and exosomes, nanovesicles excreted from cells, for use in assessing radiation efficacy. Our initial cohort is 30 patients, and we aimed to collect six timepoints: one pretreatment, two during radiation treatment, and three after radiation treatment. In this study, we look at the changes in several characteristics: CTC counts, PD-L1 expression on CTCs, as well as gene expression changes of both CTCs and exosomes using Affymetrix microarrays. CTCs were isolated using a graphene oxide (GO)-based microfluidic device and were found to be present in all pretreatment samples and most following samples. Initial transcriptome profiling of 5 patients using microarrays highlighted clustered gene expression differences for both CTCs and exosomes when comparing pretreatment samples with those collected during radiation.
Citation Format: Emma Purcell, Zeqi Niu, Madeline Grzesik, Sarah Owen, Heather Fairbairn, Shruti Jolly, Sunitha Nagrath. Analysis of non-small cell lung cancer (NSCLC) circulating biomarkers for monitoring early response to radiation 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 B37.
Abstract B44: An optimized method of multimodal mRNA and gDNA isolation from low biomass input
Authors: van de Flierdt Jens , Sprenger-Haussels Markus , Otte Michael , Hauch Siegfried 
Published: June 2020

Abstract
Background: In cell-based applications in liquid biopsy research (circulating tumor cells [CTC], fetal cells, endothelial cells), often transcriptomes get analyzed. Here and in single-cell research there is a requirement to also investigate genomic variants. Therefore, a multimodal sample preparation for both gDNA and RNA (preferably mRNA) is increasingly needed in the market. There are several combined RNA/DNA preparation solutions already available with the following caveats: Optimizing DNA yield and quality is often achieved under the compromise of accepting losses in RNA yield and/or quality or vice versa. This may be acceptable for larger sample inputs but is critical for low-biomass samples. The goal of this project, therefore, was to develop an optimized AllPrep solution for low-biomass samples that provides both highest mRNA and gDNA quality and yield without any compromises.
Material and Methods: As starting material for the mRNA purification from low-biomass input samples, the AdnaTest EMT 2/StemCell Select/Detect procedure was used. The procedure has already been tested widely to get highest yields of mRNA from as few as 2 cells spiked into 5 mL of blood. Cells captured with immunomagnetic beads as provided in the AdnaTest CTC-Select procedure were lysed using the AdnaTest Lysis/Binding Buffer and mRNA was purified using Oligo(dT)25 beads. After mRNA depletion cell lysates still contained gDNA, which can be isolated using magnetic affinity binding beads in an optimized workflow. mRNA recovery was demonstrated by reverse transcription and subsequent endpoint PCR. gDNA was analyzed using PCR and pyrosequencing as downstream applications.
Results: It has been shown that the optimized workflow combination allowed the isolation of mRNA and gDNA from as few as 5 tumor cells spiked into 5 mL of blood. Tumor cell-related gene expression profiles can be analyzed after reverse transcription of mRNA and multiplex PCR. In parallel, the recovered gDNA was successfully used in PCR assays as well as for detection of known gene variants by means of pyrosequencing. Furthermore, gel electrophoretic analysis of the gDNA eluates showed good gDNA integrity with mean molecular weight values of &gt;60 kbp.
Citation Format: Jens van de Flierdt, Markus Sprenger-Haussels, Michael Otte, Siegfried Hauch. An optimized method of multimodal mRNA and gDNA isolation from low biomass input [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 B44.
Abstract B48: Minimally invasive classification of pediatric solid tumors using reduced representation bisulfite sequencing of cell-free DNA
Authors: Van Paemel Ruben , De Koker Andries , Vandeputte Charlotte , Van Zogchel Lieke , Lammens Tim , Laureys Geneviève , Vandesompele Jo , Schleiermacher Gudrun , Chicard Matthieu , Van Roy Nadine , Vicha Ales , Tytgat Godelieve A. M. , Callewaert Nico , De Wilde Bram , De Preter Katleen 
Published: June 2020

Abstract
In the clinical management of pediatric solid tumors, histologic examination of tumor tissue obtained by an invasive biopsy remains the gold standard to establish a conclusive pathologic diagnosis. However, correct diagnosis in pediatric oncology can be challenging in some tumor types, especially in renal tumors or central nervous system tumors. The DNA methylation pattern of a tumor is known to correlate with the histopathologic diagnosis across cancer types and is showing promise in the diagnostic workup of tumor samples. It has previously been shown that this methylation pattern can be detected in the cell-free circulating DNA isolated from blood plasma of cancer patients. Here, we provide proof of concept of histopathologic classification of pediatric tumors using cell-free reduced representation bisulfite sequencing (cf-RRBS) from retrospectively collected plasma and cerebrospinal fluid samples. Using computational deconvolution of the DNA methylation profiles, we were able to obtain the correct tumor type in 49 out of 60 (81.6%) samples starting from minute amounts (less than 10 ng) of cell-free circulating DNA. We could demonstrate that the majority of misclassifications were associated with bad sample quality, evidenced by an increase of the test accuracy to 94.3% when only including good-quality samples. Misclassifications were not associated with the extent of the disease. Furthermore, we were able to derive the copy number profile or tumor subtype from the same assay. Our findings show the potential of the approach to tackle some of the remaining diagnostic challenges in pediatric oncology in a cost-effective and minimally invasive manner. Given the fact that primary tumor material might be difficult to obtain, in particular in critically ill children or depending on the tumor location, and might be limited in terms of quantity or quality, our assay could become complementary to the classical tissue biopsy in these difficult cases. A preprint of the study manuscript is already available at bioRxiv: https://doi.org/10.1101/795047.
Citation Format: Ruben Van Paemel, Andries De Koker, Charlotte Vandeputte, Lieke Van Zogchel, Tim Lammens, Geneviève Laureys, Jo Vandesompele, Gudrun Schleiermacher, Matthieu Chicard, Nadine Van Roy, Ales Vicha, Godelieve A. M. Tytgat, Nico Callewaert, Bram De Wilde, Katleen De Preter. Minimally invasive classification of pediatric solid tumors using reduced representation bisulfite sequencing of cell-free DNA [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 B48.
Abstract B58: Detection of ESR1 gene fusions in breast cancer cell-derived exosomal RNA
Authors: Liu Tiantong , Hooda Jagmohan , Ludwig Nils , Whiteside Theresa , Atkinson Jennifer M. , Oesterreich Steffi , Lee Adrian 
Published: June 2020

Abstract
Background: Estrogen receptor-positive (ER+) breast cancer is often intractable due to endocrine therapy resistance. Although ER basepair hotspot mutations have been well characterized in ~20-30% of endocrine-resistant disease, accumulating evidence from our group and others suggests that other genetic alterations such as ER fusions (e.g., ESR1-DAB2) could also play a role. As an important component of liquid biopsies, exosomes have recently gained much attention in the field of clinical oncology. It is well established that some species of RNA, typically microRNA and mRNA, are packaged into these small membrane-enclosed structures, which could potentially serve as a noninvasive biomarker to constantly and comprehensively monitor tumor progression and tumor cell evolution. We tested whether ESR1 fusions could be detected in exosomal RNA (exoRNA) produced by breast cancer cell lines.
Methods: Multiple methods were used to characterize exosomes isolated from cell culture media: 1) Nanoparticle tracking analysis (NTA) confirmed concentration and size of exosomes, 2) immunoblotting identified protein markers that are enriched or lacking in exosomes, 3) transmission electron microscopy validated the size and shape of exosomes. During exoRNA extraction, DNA contamination was removed by DNase treatment. Fusion-specific regions in exoRNA were amplified by standard PCR.
Results: We used breast cancer cell lines stably infected with cDNA encoding ESR1 fusions ESR1-DAB2 and ESR1-SOX9. NTA shows that our isolated exosomes had a size ranging from 30-150 nm, with the peak at 80 nm. Immunoblotting showed TSG101 and CD81 as positive markers of our exosomes, while Grp94 was negative. By RT-PCR, we identified a fusion-specific region amplified for both ESR1-SOX9 and ESR1-LPP from exoRNA for the fusion cell lines.
Conclusions: Collectively, these data indicate that multiple ESR1 fusions are detectable in breast cancer cell line-derived exoRNA.
Citation Format: Tiantong Liu, Jagmohan Hooda, Nils Ludwig, Theresa Whiteside, Jennifer M. Atkinson, Steffi Oesterreich, Adrian Lee. Detection of ESR1 gene fusions in breast cancer cell-derived exosomal RNA [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 B58.
Abstract IA08: Use of liquid biopsy to facilitate drug development in early-stage disease—FDA perspective
Authors: Beaver Julia A. 
Published: June 2020

Abstract
Background: With advances in precision oncology, liquid biopsies have shown promise as a minimally invasive means to potentially diagnose cancer, detect resistance mutations and monitor tumor evolution, predict relapse, provide prognosis, and guide treatment decisions. One unique setting for the use of liquid biopsy to facilitate drug development is in early-stage disease where there is the potential for use in patient selection, prognostication, and drug activity demonstration.
Discussion: From the regulatory and clinical trial perspective, liquid biopsies can be used as prognostic biomarkers to identify the likelihood of disease recurrence in early-stage cancer. For example, circulating cell-free tumor DNA (ctDNA) in an adjuvant cancer setting affords the potential to select a high-risk population that could be utilized as a stratification factor, or selection of an enriched high-risk population in which specific drug development could be pursued. Use of liquid biopsy as a putative surrogate endpoint or efficacy-response biomarker, in this setting, would require a large body of evidence demonstrating biologic plausibility, demonstration of studies of prognostic value of the surrogate endpoint for the clinical outcome, and evidence from clinical trials (or meta-analysis) that the treatment effects on the biomarker correlate to the long-term outcome. Another use of liquid biopsy as an efficacy-response biomarker could allow for go or no-go decision making earlier on in drug development, which could also be applied in the adjuvant setting.
Conclusions: Liquid biopsies will continue to play a role in the clinical management of malignancies and have the potential to support drug approval and become more broadly incorporated and utilized in early-stage clinical trials.
Citation Format: Julia A. Beaver. Use of liquid biopsy to facilitate drug development in early-stage disease—FDA perspective [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 IA08.
Abstract IA20: Circulating tumor cells: Biology and clinical applications as liquid biopsy
Authors: Pantel Klaus 
Published: June 2020

Abstract
The analysis of circulating tumor cells (CTCs) in blood may provide clinically relevant information as “liquid biopsy” and provide new insights into tumor biology (Alix-Panabieres, Pantel, Nature Rev Cancer 2014; Keller, Pantel, Nature Rev Cancer 2019). Various technologies have been developed over the past 10 years, which include label-dependent assays based on the expression of tumor-associated cell surface antigens and label-independent assays based on physical properties of tumors cells distinct from the surrounding leukocytes (Pantel, Alix-Panabieres, Nature Rev Cancer 2019). After detection, CTCs can be further analyzed at the DNA, RNA, and protein level to obtain global information on tumor biology and targets relevant to cancer therapy (Pantel, Alix-Panabieres, Nature Rev Clin Oncol 2019). Liquid biopsy analyses with validated platforms provide reliable information on prognosis and may serve to identify therapeutic targets or mechanisms of resistance on metastatic cells. Metastatic cells might have unique characteristics that can differ from the bulk of cancer cells in the primary tumor currently used for stratification of patients to systemic therapy. Moreover, monitoring of blood samples before, during, and after systemic therapy (e.g., chemotherapy or targeted therapy) provides unique information for the future clinical management of the individual cancer patient and serves as surrogate marker for response to therapy (Alix-Panabieres, Pantel, Cancer Discovery 2016; Bardelli, Pantel, Cancer Cell 2017).
Citation Format: Klaus Pantel. Circulating tumor cells: Biology and clinical applications as liquid biopsy [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 IA20.
Abstract IA21: Exploiting the biology of exosomes for diagnosis and treatment of cancer
Authors: Kalluri Raghu 
Published: June 2020

Abstract
Humans circulate trillions of exosomes at all times. Exosomes are extracellular vesicles with a size range of 40-150 nm and a lipid bilayer membrane and are released by all cell types. Normal exosomes contain DNA, RNA, and proteins. Some proteins such as CD9, CD63, and flotillin are often detected on the surface of exosomes and serve as markers. Exosomes likely remove excess and/or unnecessary constituents from the cells, functioning like garbage bags. Although their precise physiologic role remains largely unknown, is it suggested that exosomes may mediate specific cell-cell communication and activate signaling pathways in cells they fuse or interact with. Exosomes are detected in the tumor microenvironment, and emerging evidence suggests that they play a role in facilitating tumorigenesis by regulating angiogenesis, immunity, and metastasis. Circulating exosomes could be used as liquid biopsies and noninvasive biomarkers to potentially inform on early detection and diagnosis of cancer patients. Exosomes can be used for the treatment of cancer. This lecture will highlight some of the recent advances in the area of exosomes’ biology and their utility in the diagnosis and treatment of cancer. Additionally, the use of exosomes in personalized therapy for cancer patients will be discussed.
Citation Format: Raghu Kalluri. Exploiting the biology of exosomes for diagnosis and treatment of 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 IA21.