bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 565: A single institutional experience with droplet digital polymerase chain reaction (ddPCR) liquid biopsy for therapeutic decision in avanced solid tumors
Authors: Murad Andre Marcio 
Published: July 2021

Abstract
Droplet digital polymerase chain reaction (ddPCR) is a promising method for analyzing minor amounts of cell-free circulating free nucleic acid (DNA and RNA) due to its high sensitivity, low cost, and fast reading, since it dispenses bioinformatics, making it an appropriate alternative to new generation sequencing (NGS) for the detection of biomarkers to guide molecularly targeted cancer therapy. The assay covers main actionable hotspot alterations across many actionable genes: EGFR(mutations), ALK (fusion, mutations), ROS1(fusion), BRAF(mutations), KRAS (mutations), NRAS(mutations), PIK3CA (mutations), ERBB2(CNV- copy number variation), ESR1(mutations), KIT(CNV) and PDGFRA(CNV). Therefore, our genes can be used in panels, both in therapeutically applied genotyping and in detecting molecular responses as well as in secondary resistance to tumors such as NSCLC, breast, cervix. rectal, GIST, melanoma and pancreas. METHODS: dd-PCR was performed using the QX200 system (BIO-RAD®, Hercules). The extraction of DNA and RNA was done using the magnetic beads technique of Thermofisher's MagMAX Kit. All samples were tested in duplicate. Up to now, 108 metastatic cancer patients were tested: NSCLC - 28 (26%), breast - 22 (20%), colorectal - 22(20%), melanoma - 18(17%), pancreas - 8(7%), ovarian - 6(6%), salivary glands - 2 (4%) and GIST 2(4%). RESULTS: Significant genomic alterations were detected in 38(35%) patients: 10 (9%) mutations in the KRAS G12V gene (all in colorectal cancer), 10 (9%) ERBB2 amplification (breast cancer), 4 (3.65%) EGFR L858R mutations (NSCLC), 4 (3.5%) EGFR del19 mutations (NSLC), 4 (3.5%) EGFR T790M mutations (NSCLC), 4 (3.5%) BRAF-V600E mutations (colon and melanoma), 2 (1.8%) ALK-EML4 fusion (NSCLC). The MAF (Mutant Allele Fraction) ranged from 0.9% to 24%. In all cases, the results were decisive for the indication or change of a targeted therapy. Median turnaround time was 36 hours and the average cost of the panels was around 500 USD (median of 4 genes per panel). CONCLUSION: Our results suggest that dd-PCR is a highly sensitive method and could be used for a routine laboratory detection of the important genomic variations to determine the targeted therapy in patients with varied advanced solid tumors.
Citation Format: Andre Marcio Murad. A single institutional experience with droplet digital polymerase chain reaction (ddPCR) liquid biopsy for therapeutic decision in avanced solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 565.
Abstract 570: Detecting cancer using genome-wide cfDNA nucleosomal fragmentation in a prospective multi cancer cohort
Authors: Carey Jacob , Leal Alessandro , Chesnick Bryan , Butler Denise , Rongione Michael , Jones Sian , Scharpf Rob , Villadsen Mette , Bojesen Stig E. , Johansen Julia S. , Feltoft Claus L. , Velculescu Victor E. , Dracopoli Nicholas C. 
Published: July 2021

Abstract
Genome-wide cfDNA fragmentation patterns have previously been demonstrated to distinguish with high sensitivity and specificity between plasma samples from individuals with and without cancer. To further evaluate cfDNA fragmentation as a blood-based screening test for cancer, we have used low coverage whole genome sequencing to analyze plasma samples from 280 patients referred to an advanced diagnostic center due to non-organ specific signs and symptoms of cancer. Within three months of inclusion, 74 of these patients were diagnosed with one of 16 different solid cancers while 206 patients did not have cancer. Using an improved version of our genome-wide cfDNA fragmentation analyses, we observed high performance in distinguishing cancer and non-cancer samples (AUC=0.92, 95% CI 0.88-0.96), including lung cancer (n=12, AUC=0.91, 95% CI 0.80-1.00) and colorectal cancer (n=12, AUC=0.94, 95% CI 0.89-0.99). Although many of the patients in this cohort had other common illnesses including cardiovascular, autoimmune, and inflammatory diseases, the machine learning models of cfDNA fragmentation were able to detect cancer with high sensitivity and specificity. These data support the development of genome-wide cfDNA fragmentation analyses as a non-invasive detection screening approach for both single and multiple cancers.
Citation Format: Jacob Carey, Alessandro Leal, Bryan Chesnick, Denise Butler, Michael Rongione, Sian Jones, Rob Scharpf, Mette Villadsen, Stig E. Bojesen, Julia S. Johansen, Claus L. Feltoft, Victor E. Velculescu, Nicholas C. Dracopoli. Detecting cancer using genome-wide cfDNA nucleosomal fragmentation in a prospective multi cancer cohort [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 570.
Abstract 585: A robust method for expanding patient-derived circulating tumor cells ex vivo
Authors: Xiao Jerry , Kassner Joshua D. , Stanton Kelly , Schlegel Richard , Pohlmann Paula R. , Agarwal Seema 
Published: July 2021

Abstract
In the United States, an estimated 280,000 people will be diagnosed with invasive breast cancer, which has a 5-year survival rate of 27% and 22% in females and males, respectively. Despite the clinical burden of metastasis, the underlying machinery of metastasis remains unclear. This is largely due to a lack of available technologies that can robustly expand patient-derived metastatic cell populations for study ex vivo. One such population is circulating tumor cells (CTCs), which are cells that escape from the primary tumor, intravasate through blood vessel endothelium, and circulate throughout the body. Eventually, CTCs will extravasate at the metastatic site and become the seeds for metastatic colonization. Based on their role in metastasis, CTCs yield great promise for identifying key mechanistic drivers of metastasis. Unfortunately, CTCs exist in low levels within the blood (typically &lt; 100 cells/10mL of blood). Previous methods for culturing CTCs ex vivo have reported low success rates (~ 20%), and often depend on the presence of a high number of CTCs for success. To better interrogate the mechanisms of metastasis, robust methods to propagate CTCs for study are needed. Recently, our lab developed a method using an unbiased selection criterion for isolating and propagating CTCs derived from metastatic breast cancer, yielding 100% success in twelve distinct individuals. This method, based on a density gradient centrifugation, extracts not only CTCs from blood plasma, but also includes potential cancer-associated neutrophils and macrophages. All cultures under our conditions demonstrated growth for &gt; 30 days and were confirmed to have an epithelial and breast phenotype. Notably, 6/12 samples grew longer and were associated with increased CD45 expression using qRT-PCR. We have also recently demonstrated further success in culturing CTCs derived from a variety of other cancers, including colorectal, lung, and pancreatic cancers. This study therefore not only defines a novel technology for expanding CTCs, but also suggests a deficiency in modern isolation methods, which rely on CD45 exclusion, that is limiting culture success in previous methods.
Citation Format: Jerry Xiao, Joshua D. Kassner, Kelly Stanton, Richard Schlegel, Paula R. Pohlmann, Seema Agarwal. A robust method for expanding patient-derived circulating tumor cells ex vivo [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 585.
Abstract 629: Flavonoids are NR4A1 antagonists and target PAX3-FOXO1 and G9a in alveolar rhabdomyosarcoma cells
Authors: Shrestha Rupesh , Mohankumar Kumaravel , Martin Gregory , Safe Stephen 
Published: July 2021

Abstract
Rhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma that is primarily observed in children and adolescent, and accounts for 50% of soft tissue sarcomas in children. There are two major forms of RMS, namely embryonal RMS (ERMS) and alveolar RMS (ARMS) and these tumors are readily distinguished by their histological and genomic characteristics. ERMS patients have a better prognosis than ARMS patients and both groups undergo radiation, surgical and chemotherapeutic regiments. Many ARMS patients express different oncogenes including the histone methyltransferase G9a and the PAX3-FOXO1 fusion gene that contribute to ARMS cell growth, survival and migration/invasion. Studies in this laboratory have demonstrated that both G9a and PAX3-FOXO1 are regulated by the orphan nuclear receptor 4A1 (NR4A1) and can be targeted by bis-indole derived (CDIMs) NR4A1 antagonists. A recent study showed that the flavonoid kaempferol decreased G9a expression in gastric cancer cells and we hypothesized that kaempferol may be an NR4A1 ligand. Kamepferol and quercetin were used as models and both compounds bound NR4A1 at low μM concentrations and decreased NR4A1-dependent transactivation in ARMS cells. Functional studies showed that like CDIM/NR4A1 ligands, kaempferol and quercetin decrease ARMS cell growth, survival and migration/invasion, consistent with their activity as antagonists and inhibitors of NR4A1 regulated pro-oncogenic functions. In addition, kaempferol and quercetin also decreased expression of G9a, PAX3-FOXO1 and downstream genes regulated by them in ARMS cells further demonstrating their activity as NR4A1 antagonists. These results suggest that NR4A1-active flavonoids could be readily incorporated into chemotherapies used for treatment of ARMS patients to improve their efficacy and decrease the toxic side-effects of currently used cytotoxic drugs.
Citation Format: Rupesh Shrestha, Kumaravel Mohankumar, Gregory Martin, Stephen Safe. Flavonoids are NR4A1 antagonists and target PAX3-FOXO1 and G9a in alveolar rhabdomyosarcoma cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 629.
Abstract 649: Classics to diagnostics: Assessing EMT biomarkers in colorectal cancer prognosis
Authors: Patel Rohin , Robertson Angelique , Saxena Anjana , Patel Mintoo 
Published: July 2021

Abstract
Colorectal cancer (CRC) is a second most common cause of cancer death in the United States and exhibits disparities among racial and ethnic minorities. Colon polyps are abnormal growth in the epithelium that can rapidly invade surrounding mesenchyme and metastasize to form multiple secondary tumor sites. Such Epithelial-Mesenchymal Transition (EMT) is the fundamental event that results in lower survival rate for CRC patients. Altered EMT processes are also indicative of health disparity as observed for aggressive nature of prostate cancer in African Americans. In search of potential diagnostic markers that enable us to capture this transition in situ in CRC, we focused on two major biomarkers, E-Cadherin, an epithelial specific surface protein, and Vimentin, a mesenchymal specific cellular filament component. We obtained de-identified biopsy tissues samples of different stages in CRC, classified as precancerous and cancerous, along with the normal tissues, that were collected during colonoscopies for routine histopathological evaluation. In parallel, these formalin fixed paraffin embedded tissues were immunostained for the expression of E-Cadherin and Vimentin. As expected, normal tissue specimens expressed E-Cadherin exclusively in the mucosal epithelial cells while mesenchymal cells in the stroma specifically stained for vimentin expression. Interestingly, in some precancerous and cancerous specimens, we observed vimentin-positive foci within epithelial cells that lack E-Cadherin expression. This suggests a proof-of principal that an initiation of epithelial to mesenchymal transition can be detected at the clinics by performing selective immunofluorescence staining of these markers. More importantly, such detection can be correlated with the stage of the CRC that can be very insightful for the progression of the disease. Early detection in CRC through these biomarkers to supplement histopathological evaluation is promising and would provide more predictive and detailed analysis of cancer progression in tissue samples to aid in the choice of appropriate treatment plan. The accurate pre-treatment patient evaluation is pivotal to the modern push for personalized therapy. The array of early detection biomarkers will also enhance our understanding in health disparity in CRC when a large set of samples are analyzed for these markers.
Citation Format: Rohin Patel, Angelique Robertson, Anjana Saxena, Mintoo Patel. Classics to diagnostics: Assessing EMT biomarkers in colorectal cancer prognosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 649.
Abstract 66: BCG can subvert patients antitumor immune response by downregulating HLA-I expression on cancer cells
Authors: Rouanne Mathieu , Adam Julien , Radulescu Camélia , Mouraud Séverine , Bredel Delphine , Letourneur Diane , Tan Tuan Zea , Signolle Nicolas , Bigorgne Amélie , Dussiot Michael , Susini Sandrine , Tselikas Lambros , Danlos François-Xavier , Chabanon Roman , Schneider Anna K. , Vacher Sophie , Lebret Thierry , Bièche Ivan , Allory Yves , Soria Jean-Charles , Thiery Jean Paul , Zitvogel Laurence , Marabelle Aurélien 
Published: July 2021

Abstract
Patients with high-risk non muscle-invasive bladder cancer (NMIBC) frequently relapse after standard BCG immunotherapy and have a dismal outcome after progression to muscle-invasive bladder cancer (MIBC). The mechanisms of tumor resistance to such immunotherapy remain elusive. We performed functional assays of fresh bladder tumors mixed with BCG, reinforced with in vitro experiments and in situ immune profiling of a cohort of MIBC pre- and post BCG therapy. Here, we demonstrate two distinct patterns of BCG-induced immune subversion. In the first pattern, intracellular BCG infection was associated with HLA-I loss and epithelial-to- mesenchymal transition (EMT) characteristics. HLA-I deficient tumors displayed a myeloid immunosuppressive microenvironment and dismal outcomes. Conversely, HLA-I+ BCG-treated tumors generated a Th1 type of immune response associated with an upregulation of exhaustion markers. Such patients had a very favorable outcome upon radical surgery. We surmise that HLA-I expression in bladder cancers does not result from immunoediting but rather from a BCG-induced EMT process that predicts dismal prognosis. Cancer cells HLA-I scoring by immunohistochemistry (IHC) staining can be easily implemented by pathologists in routine practice in order to stratify future urothelial cancer patient treatment strategies.
Citation Format: Mathieu Rouanne, Julien Adam, Camélia Radulescu, Séverine Mouraud, Delphine Bredel, Diane Letourneur, Tuan Zea Tan, Nicolas Signolle, Amélie Bigorgne, Michael Dussiot, Sandrine Susini, Lambros Tselikas, François-Xavier Danlos, Roman Chabanon, Anna K. Schneider, Sophie Vacher, Thierry Lebret, Ivan Bièche, Yves Allory, Jean-Charles Soria, Jean Paul Thiery, Laurence Zitvogel, Aurélien Marabelle. BCG can subvert patients antitumor immune response by downregulating HLA-I expression on cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 66.
Abstract 7: Modeling cell-cell crosstalk in TNBC brain metastasis
Authors: Zhao Hong , Wang Xin , Liu Nikola , Sheng Jianting , Wong Stephen 
Published: July 2021

Abstract
Brain metastasis (BrM) is a difficult clinical problem in triple-negative breast cancer (TNBC) patients: it occurs in 25% to 40% of metastatic patients while two-year survival rate stubbornly remains a single digit. TNBC usually spreads to the brain rapidly at earlier stages or before the diagnosis of primary cancer. The shorter development time of BrM in TNBC and shorter survival time after BrM diagnosis may indicate a unique innate ability of TNBC tumor cells in adapting to the brain. Indeed, emerging data including ours indicates that TNBC tumor cells have intrinsic brain-like traits resulting in brain-tropism metastasis. Our preliminary studies identified enriched and diverse expressions of receptors and transporters of various neuro-active substances in brain metastatic TNBC cells, including neurotransmitters, gliotransmitters, neurotrophic factors and neural cytokines. By immunopanning astrocytes and microglia/macrophages from mouse brains bearing TNBC brain metastatic tumors at day 3 post tumor cell injection through left cardiac ventricle, and use the CCCExplorer software in modeling the interactions among tumor cells, astrocytes, and microglia/macrophage with cell-type specific RNAseq data, we identified several novel crosstalk signaling, including tumor autocrine TPH1-HTR2, astrocyte→tumor PCDH7-EGFR, IL6-IL6R, CCL5-CCR5 and VGF-C3AR1, and microglia/macrophage→tumor ARTN-GFAR3. Functional experiments demonstrated that cell type-specific depletion of the secreted neuro-active substances deactivated the activities of corresponding receptor and downstream signaling in co-cultured BrM tumor cells. Given that more complex paracrine/autocrine signaling network may dynamically evolve during BrM development, we are characterizing the spatiotemporal cell-cell crosstalk in the BrM metastatic niche that will have important implications for novel therapeutics development.
Citation Format: Hong Zhao, Xin Wang, Nikola Liu, Jianting Sheng, Stephen Wong. Modeling cell-cell crosstalk in TNBC brain metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 7.
Abstract 70: Obesity-induced impairment of antitumor immunity is associated with an immunosuppressive tumor immune landscape
Authors: Pazdrak Barbara , Mak Duncan , Damsky William , Bosenberg Marcus , Lochmann Brooklyn , Gubin Matthew , McQuade Jennifer 
Published: July 2021

Abstract
Obesity is associated with an increased risk and progression in a variety of cancers. In melanoma, obesity is associated with an increased risk of recurrence following surgical resection which may reflect immune escape of cancer surveillance. We sought to examine the impact of obesity on antitumor immunity in an immunogenic preclinical melanoma model.Male C57/Bl6 mice were fed a 45% fat diet or 10% fat diet for 12 months resulting in obese (body weight 52.8g ±1.3) vs control mice (body weight 38.8g ±2.2). For these studies, we utilized the YUMMER cell line, a C57BL/6J syngeneic melanoma cell line with three driver mutation/deletions (BrafV600E, Pten-/-, Cdkn2a-/-), irradiated to mimic the high mutation burden of human melanoma. 0.5x106 YUMMER cells were subcutaneously injected into the flank of aged (13 month old) control and obese mice. After 14 days post injection, tumors in control mice either had growth arrest or regression. In contrast, all obese mice exhibited progressively growing tumors with 6-fold greater tumor weights after 21 days as compared to control (1.3g ±0.4 vs 0.23g ±0.06). CyTOF analysis of tumor-infiltrating immune cells at day 21 showed 2-fold decrease in the percentage of CD4 T cells in tumors from obese mice (9.8% vs 21.1% of CD45). In addition, obesity resulted in 4-fold increase in the frequency of intratumoral Treg (26.1% vs 8.3% of CD3CD4 cells) and CD8/Treg ratio was 2-fold reduced in obese mice. In contrast to prior findings in obese mice bearing B16 melanomas, the percentage of CD8 T cells expressing PD1 was similar (80.4% vs 74.3%), but we found 2-fold higher frequency of CD8PD1 T cells co-expressing TIM3 and LAG3 in tumors from obese mice (43.3% vs 23.0%). Moreover, obesity also attenuated the frequency of tumor-infiltrating cDC2 (1.4% vs 3.5% of CD45) but did not affect NK cells or B cell proportions. Furthermore, the ratio of tumor infiltrating myeloid cells to T cells was higher in obese mice (1.94:1 vs 0.82:1). Moreover, myeloid cells from obese mouse tumors had higher expression of PDL1, CD206, and CD38 markers.Our findings provide evidence that obesity impairs antitumor immunity by modulating the relative abundance of intratumoral immune cell populations and their phenotypes to promote immunosuppressive microenvironment. These findings will be validated in subsequent studies and examined in human specimens.
Citation Format: Barbara Pazdrak, Duncan Mak, William Damsky, Marcus Bosenberg, Brooklyn Lochmann, Matthew Gubin, Jennifer McQuade. Obesity-induced impairment of antitumor immunity is associated with an immunosuppressive tumor immune landscape [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 70.
Abstract 700: CellSig: A data-driven model of cytokine activity identifies therapeutic targets for severe COVID-19 and cancer immunotherapy-induced colitis
Authors: Jiang Peng , Zhang Yu , Ru Beibei , Ruppin Eytan , Wucherpfennig Kai 
Published: July 2021

Abstract
Studies of cytokine activity are foundational to immunology research. However, the complexity and redundancy of cytokine functions have prevented systematic profiling of signaling activities in biological samples. To address these issues, we developed Cell Signaling Analyzer (CellSig, https://cellsig.ccr.cancer.gov), a data-driven infrastructure to model how cytokines cooperate with and antagonize each other in inflammation processes. We manually curated 20,591 transcriptomic profiles related to human cytokine, chemokine, and growth-factor response. CellSig revealed two main cytokine groups typified by NFKB and interferon-associated signals, respectively. The primary pro-inflammatory members of each group induce a distinct set of secondary signals and are repressed by different anti-inflammatory cytokines. CellSig can reliably predict target activities of 43 cytokines using the transcriptomic data from severe COVID-19 cases, cancer immunotherapy-induced colitis, and immune checkpoint blockade response. Among these clinical applications, the differential activities of the NFKB and interferon cytokine groups revealed potential therapeutic targets for alleviating adverse inflammation without compromising viral clearance or cancer treatment.
Citation Format: Peng Jiang, Yu Zhang, Beibei Ru, Eytan Ruppin, Kai Wucherpfennig. CellSig: A data-driven model of cytokine activity identifies therapeutic targets for severe COVID-19 and cancer immunotherapy-induced colitis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 700.