bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 5031: Regulatory T cell ablation accelerates early stage breast cancer progression
Authors: Du Wei , Martinez Leandro , Robila Valentina , Clark Nicholas , Idowu Michael , Bos Paula , Bos Paula
Published: August 2019

Breast cancer is the most common malignancy in women worldwide. Early detection of pre-invasive breast tumor has dramatically improved due to the routine screening for women. Ductal carcinoma in situ is a non-obligate precursor of breast cancer, and it only progresses to invasive breast cancer in about 40% of patients. We have previously shown that transient ablation of regulatory T (Treg) cells in established breast tumors results in significant reduction of primary and lung metastatic tumor growth. In this study, we aim to investigate the specific role of Treg cells at the pre-malignant stages. Using a spontaneous, stage-wise MMTV-driven polyoma middle T (PyMT) model of murine mammary carcinogenesis, crossed to Foxp3DTR knock-in mice where injection of diphtheria toxin leads to a complete ablation of Treg cells for around 7 days, we found that ablation of Treg cells at the pre-invasive tumor stage resulted in a significant increase in the number of mammary glands developing tumors, as well as tumor growth compared to control mice. Histological examination of tissues revealed that the area of the incipient tumors was larger in Treg cell-ablated mice, and presented a more advanced tumor stage. In addition, Treg cell ablation resulted in a pronounced mammary inflammatory infiltrate, including an increase in tumor-associated macrophages and a soluble cytokine network conducive to tumor progression. Interestingly, Treg cell ablation increased the percentage of cancer stem/progenitor cells in the mammary compartment. Overall, our study demonstrates that unlike their role in established cancers, Treg cells ablation promotes breast cancer progression at early stages.

Citation Format: Wei Du, Leandro Martinez, Valentina Robila, Nicholas Clark, Michael Idowu, Paula Bos, Paula Bos. Regulatory T cell ablation accelerates early stage breast cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5031.
Abstract 504: Acarbose enhances intratumoral CD8 T cell responses in a pre-clinical model of kidney cancer
Authors: Orlandella Rachael M. , Smith Daniel L. , Norian Lyse A.
Published: August 2019

Metastatic renal cell carcinoma (RCC) exhibits high mortality rates and chemotherapeutic resistance. Treatment options include immune-stimulatory therapies, such as high-dose IL-2 and anti-PD-1; however, these agents only generate responses in 20-50% of patients. This illustrates the need to find ways to improve patient response rates. Long-term caloric restriction (CR) extends longevity and reduces cancer risk in animal studies. Caloric restriction mimetics (CRMs), which replicate the benefits of CR without reductions in calorie intake, were recently found to enhance chemotherapeutic efficacy by improving CD8 T cell mediated anti-tumor immunity. Here we examined acarbose, an FDA-approved anti-diabetic agent with CRM properties, in a preclinical model of kidney cancer. BALB/c mice were orthotopically tumor challenged with syngeneic luciferase-expressing Renca renal carcinoma cells, which spontaneously metastasize to the lungs. Mice were then randomized to either an acarbose-supplemented or control diet. Compared to mice on control diet, acarbose did not alter renal tumor progression at Day 28. Importantly, acarbose did not exacerbate weight loss associated with renal tumor growth. Flow cytometric analysis at Day 28 revealed increased frequencies of activated (CD44+CD62L-) intra-tumoral CD8 T cells in mice on acarbose (p=0.012). Additionally, renal tumors from mice on acarbose displayed increased frequencies of early effector (CD127-KLRG1-) CD8 T cells, in addition to heightened frequencies of PD-1+ CD8s. These findings suggest that acarbose exhibits immune-modulatory properties which could promote anti-tumor immunity. Future experiments will focus on elucidating mechanisms contributing to alterations in anti-tumor immunity. Importantly, these studies warrant investigating acarbose in combination with currently available treatments as a potentially novel therapeutic adjuvant.

Citation Format: Rachael M. Orlandella, Daniel L. Smith, Lyse A. Norian. Acarbose enhances intratumoral CD8 T cell responses in a pre-clinical model of kidney cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 504.
Abstract 5052: Immune profiles in the San Francisco Adult Glioma Study using Immunomethylomics
Authors: Wiencke John K. , Molinaro Annette , Gayathri Warrier , Clarke Jennifer , Taylor Jennie , Koestler Devin , Wiemels Joe , Hanson Helen , Sean Lee , Rice Terri , McCoy Lucie , Salas Lucas , Margaret Wrensch , Christensen Brock , Kelsey Karl T.
Published: August 2019

Glioma patients demonstrate abnormalities in peripheral blood leukocytes that have been associated with survival time. Here we assessed immune cell profiles in archival blood samples obtained 5-25 years ago using a novel epigenetic approach called immunomethylomics. We first validated the approach to measure the proportions of CD4 T, CD8 T cells, B cells, NK cells, neutrophils, and monocytes in archival blood using the new 850,000 feature EPIC Illumina methylation bead array. The immunomethylomic assay was shown to match the performance of multiparametric flow cytometry and thus is a highly accurate method for immune profiling. We next measured cell profiles in blood from 312 molecularly defined AGS subjects. In this cohort we enriched for patients with triple negative tumor subtypes (IDH wildtype, 1p19q negative, TERT non-mutant). Elevations in the neutrophil lymphocyte ratio (NLR) significantly increased with grade, whereas the proportions of T and B cells decreased with increasing grade. Using an established cut point of > 4.0 for the NLR revealed that this immune parameter was associated with shorter survival times in glioblastoma (median overall survival (mOS) 12.6 vs. 16.9 months) and non-glioblastoma (mOS 16.7 vs. 36 months) patients. Ongoing analyses of the cohort will be presented to evaluate the effects of age, gender, surgery, chemoradiation and tumor grade on the survival results. Because DNA based immune cell profiles do not require intact cells nor preserved proteins, they provide a powerful tool to glean potentially important immunologic information from historic stored samples that would otherwise be useless using current cytometry-based approaches.

Citation Format: John K. Wiencke, Annette Molinaro, Warrier Gayathri, Jennifer Clarke, Jennie Taylor, Devin Koestler, Joe Wiemels, Helen Hanson, Lee Sean, Terri Rice, Lucie McCoy, Lucas Salas, Wrensch Margaret, Brock Christensen, Karl T. Kelsey. Immune profiles in the San Francisco Adult Glioma Study using Immunomethylomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5052.
Abstract 5054: Are co-occurring structural birth defects associated with risk of acute lymphoblastic leukemia among children with Down syndrome
Authors: Schraw Jeremy M. , Chambers Tiffany M. , Woodhouse John P. , Langlois Peter H. , Canfield Mark A. , Scheuerle Angela E. , Scheurer Michael E. , Plon Sharon E. , Rabin Karen R. , Lupo Philip J.
Published: August 2019

Background: Children with Down syndrome (DS) have a 15- to 20-fold increased risk of developing acute leukemia (ALL). While children with DS typically also present with multiple co-occurring major and minor structural birth defects, very little is known about whether the number and type of these co-occurring birth defects in children with DS are associated with risk of ALL.

Methods: The Genetic Overlap Between Anomalies and Cancer in Kids (GOBACK) Study included linking data from population-based birth defects and cancer registries in Texas for the years 1999-2013. We performed a case-control analysis of ALL risk in participants diagnosed with DS. We evaluated the risk of ALL according to the presence of major birth defects in eight organ systems, as well as by the number of birth defects.

Results: We identified 7,684 children with DS (controls) and 81 children with DS-ALL (cases) from among 5.7 million live births. There was a high burden of co-occurring birth defects in both the DS and DS-ALL groups, with 97% compared to 98% being diagnosed with at least one co-occurring birth defect (p = 0.39), respectively, and 68% compared to 71% being diagnosed with at least one major birth defect (p = 0.33). Similar to what has been reported among the general population of ALL patients, children with DS and ALL had a significantly higher mean birthweight (3088 vs 2891 g, p <0.001) than children with DS overall, and were born to older parents (mean maternal age 33.7 vs. 31.7 yrs, p = 0.01; mean paternal age 36.6 vs. 33.8 yrs, p = 0.02). Although there were trends towards increased prevalences of major birth defects overall and in most organ systems among the DS-ALL group, none reached statistical significance. Similarly, we identified a non-significantly greater mean number of total birth defects in the DS-ALL group (p = 0.2). Neither number of total birth defects nor number of major birth defects were associated with ALL in multivariable Cox regression models.

Conclusions: In this population-based assessment, we did not find strong evidence that co-occurring structural birth defects were related to ALL risk among children with DS. However, the small numbers of children with DS-ALL make it difficult to draw definitive conclusions.

Citation Format: Jeremy M. Schraw, Tiffany M. Chambers, John P. Woodhouse, Peter H. Langlois, Mark A. Canfield, Angela E. Scheuerle, Michael E. Scheurer, Sharon E. Plon, Karen R. Rabin, Philip J. Lupo. Are co-occurring structural birth defects associated with risk of acute lymphoblastic leukemia among children with Down syndrome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5054.
Abstract 511: An assessment of pre-conditioning regimens for optimal hCD34+ hematopoietic stem cell humanization of NSGTMmice
Authors: Parello Caitlin S. , Cuiffo Benjamin G. , Kury Alexandria , Reardon Kasey , Dam Brett Van , Vu Sallyann , Costa Catarina , Ritchie Veronica , Gagnon Gavin , Bateson Timothy , Rogers Samantha , Lyng Gregory D. , Sonis Stephen T.
Published: August 2019

Humanized immune system (HIS) mice - immunocompromised Nod.Cg-Prkdcscid Il2rgtm1Wjl/SzJ animals in which the immune system has been humanized by the engraftment of CD34+ hematopoietic stem cells (HSC), peripheral blood mononuclear cells (PBMC), or other human cells/tissues - represent an important tool in pre-clinical oncology research. Here we investigated several pre-conditioning regimens (Busulfan pre-treatment or total body irradiation (TBI)) to determine which would yield maximum human leukocyte engraftment and lineage diversity. Animals were pre-treated either one or two doses of Busulfan (25 mg/kg) or varying doses of TBI (1.75, 2.0, or 2.5 Gy). One to two days later, animals received an adoptive transfer of native hCD34+ HSCs. Engraftment was monitored by flow cytometry assessment of peripheral blood four weeks after adoptive-transfer, and every four weeks thereafter through experiment termination at Week 16. Upon termination, spleen and bone-marrow were assessed for various leukocyte populations by flow cytometry. Animals undergoing pre-conditioning displayed increased human CD45+ cell engraftment at all timepoints as compared to animals without pre-conditioning, with animals treated with two doses of Busulfan demonstrating the greatest human CD45+ engraftment at all timepoints and reaching statistical significance at endpoint (vs no pre-conditioning; p<0.05). Diversity of leukocyte cell types (B cells, T cells, NK cells, and other hCD45+) in the bone-marrow was similar across pre-treatment paradigms, however for some lineages, representation in the bone-marrow was significantly altered between pre-conditioning type. The absolute number of T or B cells were increased in TBI and Busulfan treated groups, respectively, whereas NK cells as a percentage of singlets were increased in TBI treated groups. The diversity of leukocyte cell types in the spleen was likewise similar across groups, with B cells dominating. These data provide important insights into the utility of various pre-conditioning regimens for the humanization of NSG mice for pre-clinical oncology research, and demonstrate that the optimum pre-conditioning regimens should be selected based on treatment target.

Citation Format: Caitlin S. Parello, Benjamin G. Cuiffo, Alexandria Kury, Kasey Reardon, Brett Van Dam, Sallyann Vu, Catarina Costa, Veronica Ritchie, Gavin Gagnon, Timothy Bateson, Samantha Rogers, Gregory D. Lyng, Stephen T. Sonis. An assessment of pre-conditioning regimens for optimal hCD34+ hematopoietic stem cell humanization of NSGTMmice [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 511.
Abstract 5110: An online tool for summarizing and searching human cancer-genomic publications
Authors: Williams Kevin , Zhang Myron , Ramos Anayancy , Johnson Andrew , Stravoravdis Stefanos , Heenehan Megan , Dancik Garrett M.
Published: August 2019

PubMed catalogs over 33,000 articles published with the keywords “cancer” and “gene” in the past year alone. The large volume of cancer genomic publications necessitates the development of text-mining tools to help cancer researchers navigate and summarize articles efficiently. Here we present a Cancer Publication Portal (CPP) that allows a researcher to search and summarize cancer genomic literature based on a gene of interest. CPP integrates data from several sources, including PubTator, which uses robust text-mining tools to identify associations between articles and biological concepts; the Medical Subject Headings (MeSH) database; the HUGO Gene Nomenclature Committee human gene name database; PubMed, a database of biomedical literature citations; and the National Cancer Institute (NCI) Thesaurus. To begin a search, a user selects a gene of interest. CPP then summarizes the relevant cancer-related publications mentioning this gene through tabular and graphical summaries showing the frequency of articles stratified by references to any (1) cancer type, (2) pharmacological agent, (3) genomic mutation, and (4) additional human gene. Additionally, CPP catalogs and summarizes articles based on mentions of >30 additional cancer-related terms, based on an analysis of terms that are significantly more likely to occur in cancer-related abstracts. CPP allows users to quickly obtain statistics, e.g., to find the frequency of articles mentioning EGFR and Erlotinib across cancer types. Interactive summaries allow users to narrow in on a topic of interest by applying additional filters, in which case the summaries are updated and the process can be repeated. At any point, the user can browse through the current set of article abstracts and citation information to get more information about an article. Finally, we introduce a Citation Analysis module for helping users identify “important” articles. This module identifies articles which cite articles in a provided list. The module then generates an edge list that can be imported into network analysis tools such as Gephi for visualization and analysis. CPP currently includes information for ~1.1 million cancer-related publications associated with >19,000 human genes. The underlying data is stored in an MySQL database while R/Shiny is used to implement the web interface. CPP is available from the following link: https://gdancik.github.io/bioinformatics/CPP/

Citation Format: Kevin Williams, Myron Zhang, Anayancy Ramos, Andrew Johnson, Stefanos Stravoravdis, Megan Heenehan, Garrett M. Dancik. An online tool for summarizing and searching human cancer-genomic publications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5110.
Abstract 5128: Polyethnic-1000: Advancing cancer genomics by studying ethnically diverse, underserved patient populations in New York
Authors: Froeling Fieke E. , Robine Nicolas , Hubert Benjamin , Zody Michael , Oschwald Dayna , Varmus Harold E. , Sawyers Charles L. , Tuveson David A. ,   On behalf of the NYGC P1000 Consortium
Published: August 2019

Background and aims Recent advances in DNA sequencing technologies have revolutionized approaches to the prevention, risk assessment, early detection, diagnosis, and treatment of cancers. However, many ethnic groups, especially non-European populations, have been significantly under-represented in cancer research, including clinical trials, and have not received equal benefits in clinical practice. As a result, our current knowledge about tumor biology, cancer risk, and response to treatment has primarily been derived from patients of European descent. These inequities limit our understanding of the many types of cancer and may exacerbate health disparities in the United States. This multi-institutional study, named Polyethnic-1000, aims to address both the scientific and social issues by creating a dynamic research platform within the ethnically diverse greater New York City area.

Methods and results Polyethnic-1000 is a collaborative effort organized by the New York Genome Center (NYGC), involving staff and patients at academic centers and partnering hospitals in the New York City region. The genomics and informatics capabilities of the NYGC will be used to determine how inherited and somatically acquired genetic variations affect the behavior of cancers occurring in ethnically diverse populations. In a first, retrospective stage we are establishing the necessary infrastructure and workflow from sample acquisition to whole-exome and RNA sequencing, data analysis and data sharing within the consortium. Then we will start a prospective study enabling the formation of cohorts of interest for particular cancer types and particular ethnicities, with uniform consent allowing germline and somatic sequencing with broad data sharing of the somatic variants identified.

Conclusion By establishing a collaborative network, Polyethnic-1000 will deepen our understanding of the contributions that ethnicities make to the incidence and biology of cancers, potentially improving outcomes for patients who currently lack access to the most recent advances in medical science.

Citation Format: Fieke E. Froeling, Nicolas Robine, Benjamin Hubert, Michael Zody, Dayna Oschwald, Harold E. Varmus, Charles L. Sawyers, David A. Tuveson, On behalf of the NYGC P1000 Consortium. Polyethnic-1000: Advancing cancer genomics by studying ethnically diverse, underserved patient populations in New York [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5128.
Abstract 5129: Actionable activating oncogenic HER2 transmembrane and juxtamembrane domain mutations
Authors: Bajaj Kanika
Published: August 2019

Deregulated HER2 is a target of many approved cancer drugs. We analyzed 111,176 patient tumors and identified recurrent mutations in HER2 transmembrane domain (TMD) and juxtamembrane domain (JMD) including G660D, R678Q, E693K and Q709L. Using a saturation mutagenesis screen and testing of patient-derived mutations we found several activating TMD and JMD mutations. Structural modeling and analysis showed that the TMD/JMD mutations function by improving the active dimer interface or stabilizing an activating conformation. Further, we found that HER2 G660D employed asymmetric kinase dimerization for activation and signaling. Importantly, anti-HER2 antibodies and small molecule kinase inhibitors blocked the activity of TMD/JMD mutants. Consistent with this, a G660D germline mutant lung cancer patient showed remarkable clinical response to HER2 blockade.

Citation Format: Kanika Bajaj. Actionable activating oncogenic HER2 transmembrane and juxtamembrane domain mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5129.
Abstract 5137: Comprehensive analysis of POLE and POLD1 mutation in 9322 Chinese cancer patients
Authors: Dong Hua , Bai Yuezong , Cao Xinkai , Wang Yanyan , Shi Lin , Li Fugen , Ye Yizhou , Sun Shuyang
Published: August 2019

POLE and POLD1 proofreading mutations can cause ultra-hypermutant-phenotype in cancer, but the distribution of POLE and POLD1 mutation frequency in Chinese population are not clear compared to microsatellite instability (MSI) and tumor mutation burden(TMB). Herein, we examined mutation profiles of POLE and POLD1 in 9322 Chinese cancer patients by two target sequencing panels including POLE and POLD1 gene. Tissue samples from 5866 patients were sequencing with a lab validated CP381 gene panel while plasma samples from 3155 patients were sequencing with a lab validated CT150 gene panel in a CAP certified lab 3DMed. Wet lab experiments and dry lab bioinformatics analysis were done by standard FFPE and ctDNA sample processing and analysis pipeline. POLE and POLD1 pathogenic mutation was defined by published research evidence. Of the 9322 cancer patients, 23 cases showed POLE and POLD1 pathogenic mutations (20 POLE and 3 POLD1), with the total mutation frequency 0.25% (0.35% for tumor sample and 0.006% for plasma sample). However, except for two Intrahepatic cholangiocarcinoma, one melanoma and one endometrial cancer patients, all the left mutation were from colon and rector cancer (CRC), account for a total mutation frequency 1.4% in CRC (19/1335). Although Endometrial cancer is reported with high POLE/POLD1 mutation, there were only 49 endometrial cancer patients in our cohort with mutation frequency 2%(1/49). POLE/POLD1 pathogenic mutations are micro satellite stable (MSS) in 20 cases while the left 3 were MSI-H. Eight cases have co-occurrence with MMR pathway gene loss of function mutation (any one of MSH2/MSH6/MLH1/PMS2), we infer those MMR gene mutations are not driver mutation but passenger mutation induced by POLE and POLD1 proofreading mutations as those eight cases are mostly MSS. Two patients with POLE pathogenic mutation with immune checkpoint inhibitor treatment were followed up for further response evaluation. POLE-and POLD1 pathogenic mutation are very rare in Chinese cancer patients, enrich in CRC type with 2.9% mutation frequency. POLE/POLD1 pathogenic mutations are usually exclusive to MSI-H patients, thus could expand the patient population in colon cancer which have potential to benefit from immune-therapy.

Citation Format: Hua Dong, Yuezong Bai, Xinkai Cao, Yanyan Wang, Lin Shi, Fugen Li, Yizhou Ye, Shuyang Sun. Comprehensive analysis of POLE and POLD1 mutation in 9322 Chinese cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5137.
Abstract 5140: Discovery of biomarkers predicting response to radiation and anti PD1 therapy in head and neck squamous cell cancer
Authors: Lee Joon Sang , Sanicola-Nadel Michele , Protopopov Alexei , Wang Emma , Theilhaber Joachim , Lin Tun Tun , Korrer Michael , Roy Sohini , Kim Young Jun , Pollard Jack
Published: August 2019

Introduction: Treatment of head and neck squamous cell cancer (HNSCC) frequently includes surgery, radiation, chemotherapy, targeted agents, and increasingly combination of the former with immune checkpoint inhibition. An understanding of the mechanisms mediating response to these therapies as well as biomarkers that can better tailor therapy on an individualized basis and reduce treatment-related toxicity would benefit patients.

Methods: To uncover these mechanisms and biomarkers, we analyzed whole transcriptome RNA-Seq data of two different cohorts of head and neck squamous cell cancer patients: pre and post-treatment samples from radiation therapy and pre-treatment samples from anti-PD1 therapy. We evaluated the abundance of eight immune and two stromal cell populations and pathway activity changes by using Gene Set Variation Analysis (GSVA).

Results and Conclusions: Following radiation genes involved in epithelial to mesenchymal transition, extracellular matrix remodeling, and wound healing are upregulated. Additionally, there is evidence of tumor microenvironment remodeling post-radiation consistent with increased fibroblast abundance and decreased immune cell infiltration. Furthermore, innately resistant tumors to anti-PD1 also display similar signatures of gene regulation, suggesting a common mechanism mediating response to both types of treatment. Notably, these signatures are strongly correlated to activation of the transforming growth factor (TGF-β) signaling pathway and suggest that attenuating its signaling may improve anti-PD-1 response and also response to radiation treatment in head and neck squamous cell cancer.

Citation Format: Joon Sang Lee, Michele Sanicola-Nadel, Alexei Protopopov, Emma Wang, Joachim Theilhaber, Tun Tun Lin, Michael Korrer, Sohini Roy, Young Jun Kim, Jack Pollard. Discovery of biomarkers predicting response to radiation and anti PD1 therapy in head and neck squamous cell cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5140.
Abstract 5155: Increased longevity of continuous bone marrow cultures and radioresistance of bone marrow stromal cells from SOD193A ALS (Amyotrophic Lateral Sclerosis) mice
Authors: Henderson Andrew , Epperly Michael W. , Fisher Renee , Shields Donna , Rigatti Lora , Donnelly Christopher , Watkins Simon , Greenberger Joel S.
Published: August 2019

Introduction: The SOD1G93A mouse model of ALS, demonstrates hind limb paralysis beginning at 90 - 100 days of age with stage 4 paralysis at 125 days of age and progressive neuromuscular loss.

Materials and Methods: To determine whether deficiency of functional SOD1 influenced parameters of hematopoiesis, long-term bone marrow cultures were established from ALS and control mice. Bone marrow stromal cell lines derived from LTBMCs were tested for clonogenic radiation survival. We tested the effect of bone marrow transplant after total body irradiation on delay of paralysis.

Results: SOD1G93A marrow cultures demonstrated significant increase in production of hematopoietic progenitor cells (p < 0.0001) and overall longevity of production of hematopoietic cells (p = 0.0354), and bone marrow stromal cell lines were significantly radioresistant (D0 = 1.33 ± 0.09, and ñ = 8.57 ± 1.8) compared to control C57BL/6J mice (D0 = 1.59 ± 0.11, p = 0.117; and ñ = 3.4 ± 0.4, p= 0.0466). Total body irradiation and bone marrow transplantation with GFP+ donor marrow demonstrated a significant increase in paralysis free interval from 129.2 ± 3.0 to 240.7 ± 21.1 days (p = 0.0010), normalization of blood/brain barrier permeability, and increase in M2 marrow origin microglial cells in proximity to degenerating anterior horn cell/motor neurons. Isolated brain and spinal cord irradiation did not prolong the paralysis free interval (129.0 ± 2.7 days, p = 0.7748).

Conclusions: The results of hematopoiesis in LTBMCs in the absence of functional SOD1 showed improved LTBMC longevity and radioresistance of marrow stromal cells both unexpected pleiotropic effects of the SOD1G93A genotype. Marrow transplant after TBI prolonged the paralysis free interval in ALS mice.

Citation Format: Andrew Henderson, Michael W. Epperly, Renee Fisher, Donna Shields, Lora Rigatti, Christopher Donnelly, Simon Watkins, Joel S. Greenberger. Increased longevity of continuous bone marrow cultures and radioresistance of bone marrow stromal cells from SOD193A ALS (Amyotrophic Lateral Sclerosis) mice [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5155.
Abstract 5165: Secreted CCDC80 from hepatic stellate cells promote metastasis of hepatocellular carcinoma
Authors: Kim Kwang-Suck , Lee SaeHwan , Jun Nayoung , Kwon Hyog Young
Published: August 2019

Liver cirrhosis is the most important risk factor for hepatocellular carcinoma (HCC) and hepatic stellate cell (HSC) has pivotal role in developing cirrhosis by producing various extracellular matrix (ECM). HSC are essential mediators of tumor microenvironment of HCC through remodeling of ECM and angiogenesis. We found that CCDC80 expression is upregulated in activated HSCs from RNA-sequencing with human fetal stellate cell. However, the role of CCDC80 was not well known in hepatocarcinogenesis. First, we validated mRNA expression of CCDC80 was increased in activated HSC lines and protein expression was also increased in cultured media. Functional analysis of knockdown and over expression CCDC80 was investigated in both HCC and HSC cell lines, and HCC cell lines were analyzed for proliferation (MTT assay), migration (using transwell), invasion (using Matrigel-coated transwell), and wound healing assay with condition media of CCDC80 knockdown HSCs. Expression of epithelial-mesenchymal transition (EMT) markers in HCC was evaluated with conditioned media. Knockdown of CCDC80 resulted in significantly reduced invasion, migration and wound healing behaviors of HCC cell lines. Overexpression of CCDC80 was increased invasion and migration. Expression of E-cadherin was increased and snail and vimentin expression were decreased in HCC cell lines cultured with conditioned media of CCDC80 knockdown HSCs. The associations between CCDC80 and EMT markers were validated in CCDC80 transfected HSC cell line compared with control. The mouse xenograft model also has shown the lower tumor growth, tumor weight and metastatic tumor nodule number in CCDC80 knockdown HSC with HCC co-injection compared with normal HSC and HCC co-injected mouse. Taken together, secreted CCDC80 from HSCs affected the aggressiveness and EMT of HCC cell lines. CCDC80 might be a novel biomarker and therapeutic target for patients with HCC.

Citation Format: Kwang-Suck Kim, SaeHwan Lee, Nayoung Jun, Hyog Young Kwon. Secreted CCDC80 from hepatic stellate cells promote metastasis of hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5165.
Abstract 5166: Extracellular matrix protein tenascin C increases phagocytosis mediated by CD47 loss-of-function in glioblastoma
Authors: Ma Ding , Liu Senquan , Lal Bachchu , Laterra John , Wilson Mary Ann , Xia Shuli
Published: August 2019

Glioblastomas (GBMs) are highly infiltrated by myeloid-derived innate immune cells that contribute to an immunosuppressive nature of the brain tumor microenvironment (TME). CD47 has been shown to mediate immune evasion as the CD47-SIRPα axis prevents phagocytosis of tumor cells by macrophages and other myeloid cells. In this study, we established CD47 homozygous deletion (CD47-/-) in human and mouse GBM cells by genome editing to investigate the impact of eliminating the “don’t eat me” signal on tumor growth and tumor-TME interactions. CD47 knockout (KO) did not significantly alter tumor cell proliferation in vitro, but significantly increased phagocytosis of tumor cells by macrophages in co-cultures. Compared with CD47 wild type xenografts, orthotopic xenografts derived from CD47-/- tumor cells grew much slower with enhanced tumor cell phagocytosis and increased recruitment of M2-like tumor associated microglia/macrophages (TAMs). CD47 KO increased tumor-associated extracellular matrix protein tenascin C (TNC) in xenografts, which was further examined in vitro. CD47 loss-of-function upregulated TNC expression in tumor cells via a Notch pathway mediated mechanism. ShRNA-based TNC knockdown in tumor cells enhanced the growth of CD47-/-xenografts in vivo, and decrease the number of TAMs. TNC knockdown inhibited phagocytosis of CD47-/- tumor cells in co-cultures. Furthermore, TNC stimulated release of pro-inflammatory factors including TNF-α via a toll-like receptor 4 (TLR4) and STAT3-dependent mechanism in human macrophage cells. These results reveal a vital immunomodulation role of TNC in brain tumor biology and demonstrate the prominence of the TME extracellular matrix in affecting the anti-tumor function of brain innate immune cells.

Citation Format: Ding Ma, Senquan Liu, Bachchu Lal, John Laterra, Mary Ann Wilson, Shuli Xia. Extracellular matrix protein tenascin C increases phagocytosis mediated by CD47 loss-of-function in glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5166.
Abstract 5181: Global alteration of CTCF binding in the cancer genome
Authors: Fang Celestia , Wang Zhenjia , Martinez Carlos A. , Ntziachristos Panagiotis , Zang Chongzhi
Published: August 2019

The goal of this study is to understand the functions of altered CTCF binding in the cancer genome and its role in tumorigenesis. CTCF is a zinc finger protein that binds to DNA and functions as a transcriptional factor (TF) or a chromatin insulator. Disruption of individual CTCF bindings have been reported in several systems that associate with DNA methylation changes and result in aberrant chromatin interaction and differential expression of genes associated with the topological associated domains (TADs). We systematically analyzed over 500 CTCF ChIP-seq datasets across different human tissues and identified cancer-specific aberrant (gained) and disrupted (lost) CTCF binding sites in several cancer types. Through integrative analysis with other genomic data including RNA-seq, hi-C and DNA methylation profiles, we found that CTCF binding alterations correlate with differential chromatin interaction in the TADs, but most altered binding sites do not have DNA methylation changes. Instead, lost CTCF bindings at gene promoter regions associate with transcriptional repression, while gained bindings primarily occur in the distal enhancer regions bound by oncogenic transcription factors inducing gene expression. We validated these findings in T-cell acute lymphoblastic leukemia (T-ALL) using patient derived samples and identified NOTCH1 among oncogenic TFs bound at enhancers co-occupied with T-ALL-specific gained CTCF binding. These findings indicate that alteration of CTCF binding is an epigenomic signature of cancer cells, and our approach demonstrates a framework of integrating existing multi-omics data for mechanistic studies of cancer gene regulation.

Citation Format: Celestia Fang, Zhenjia Wang, Carlos A. Martinez, Panagiotis Ntziachristos, Chongzhi Zang. Global alteration of CTCF binding in the cancer genome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5181.
Abstract 5188: Epigenetic changes mediated by polycomb repressive complex 2 are associated with cisplatin acquired resistance in testicular germ cell tumor
Authors: Singh Ratnakar , Fazal Zeeshan , Bikorimana Emmanuel , Corbet Andrea , Rodriguez Jennifer , Steege Alyssa , Freemantle Sarah J. , Spinella Michael J.
Published: August 2019

Testicular germ cell tumors (TGCTs) represent the most common carcinoma affecting young men. TGCTs serve as a paradigm of chemo-sensitive tumors as more than 80% of metastatic disease can be cured with cisplatin-based chemotherapy. However, therapy resistance can occur, which results in poor patient outcomes. The mechanisms of cisplatin resistant in these tumors remain largely undefined. To study the mechanism of cisplatin acquired resistance we generated several independent, acquired resistant clones of parental NT2/D1, 833K and 2102EP testicular cancer cells employing an in vitro protocol designed to mimic the standard-of-care cisplatin regimen used to treat TGCT patients. We further characterized 10 of these clonal lines and confirmed stable cisplatin resistance ranging from 5- to 30-fold. After confirming the cisplatin resistance, we performed RNA seq transcriptomic profiling, differential gene expression analysis, DAVID and GSEA. Remarkably, RNA-seq based transcriptional profiling revealed highly significant alterations shared between the majority of the resistant cells regardless of their parental cell of origin. This includes apparent amplification of chromosomal region 17q21-25 in 8 of 10 lines. Unexpectedly, 7 of 10 lines had a highly significant enrichment of genes regulated by H3K27 methylation and polycomb repressive complex 2 (PRC2). Transcription factor prediction analysis of genes differentially expressed between resistant and parental cells revealed that polycomb complex members were among the most highly ranked predicted transcription factors responsible for the gene expression changes. These include EZH2, SUZ12, JARID2 and BMI1. We will present our ongoing studies investigating the role of PRC2 and H3K27 methylation in mediating cisplatin resistance in these cells and in patient samples. Together our data suggests that repression of H3K27 methylation may be a mechanism of cisplatin acquired resistance in TGCTs and that restoration of PRC2 function could be a viable approach to overcome treatment failure.

Citation Format: Ratnakar Singh, Zeeshan Fazal, Emmanuel Bikorimana, Andrea Corbet, Jennifer Rodriguez, Alyssa Steege, Sarah J. Freemantle, Michael J. Spinella. Epigenetic changes mediated by polycomb repressive complex 2 are associated with cisplatin acquired resistance in testicular germ cell tumor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5188.
Abstract 5194: Epigenomic and transcriptional profiling of CRC cell lines with distinct response patterns to the BET inhibitor BI 894999
Authors: Savarese Fabio , Gerlach Daniel , Koller Larissa , Straubinger Susy , Träxler Paula Elena , Kaya Onur , Schweifer Norbert , Tontsch-Grunt Ulrike , Kraut Norbert
Published: August 2019

The bromodomain and extra-terminal (BET) protein BRD4 is a “reader” of epigenetic information and binds to acetylated chromatin. BRD4 acts as key regulator of transcriptional elongation by activating P-TEFb at distinct genes. It is via this specific activation of potentially oncogenic transcripts, e.g. MYC, that BRD4 is thought to contribute to tumorigenesis. Inhibition, via so-called BET inhibitors, has indeed proven to be a novel and attractive treatment option tested in ongoing clinical trials for both hematological as well as solid cancers. While BET inhibition shows good efficacy in pre-clinical models of hematological indications, solid tumors show much more heterogeneous responses to monotherapy. Consequently, biomarkers predicting response to treatment with BET inhibitors are of high interest. Colorectal cancer (CRC) is a heterogeneous disease in which novel treatment options are urgently needed. Our pre-clinical studies show that the BET inhibitor BI 894999 is highly active in a fraction of cell lines tested. H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq) and transcriptional profiling of sensitive and resistant cell lines identified a small set of H3K27ac peaks associated with sensitivity to BET inhibition. Much of the transcriptional response in CRC cell lines however was cell line specific, leading to only few commonly regulated genes within sensitive versus resistant cell lines. Regarding pharmacodynamic biomarkers in CRC, we could confirm modulation of HEXIM1 after treatment in both sensitive and resistant cell lines. In agreement with previous results (Cohen et al, Nature Comm. 2017), we identified AP1 binding sites in BRD4-bound regulatory regions, which indicates that BRD4 may regulate expression of these genes cooperatively with the transcription factor AP1. Furthermore, the transcription factor TCF4 showed enrichment, suggesting possible interactions between BRD4 and the WNT pathway in a subset of CRC cell lines. The AXIN1, a core WNT pathway component, e.g. is down-regulated in 5/9 cell lines, which however does not track with overall BI 894999 sensitivity. These results, further supporting heterogeneous responses to single-agent BETi treatment, will be discussed. These studies support the further evaluation of BI 894999 as a therapeutic option for colorectal cancer therapy.

Citation Format: Fabio Savarese, Daniel Gerlach, Larissa Koller, Susy Straubinger, Paula Elena Träxler, Onur Kaya, Norbert Schweifer, Ulrike Tontsch-Grunt, Norbert Kraut. Epigenomic and transcriptional profiling of CRC cell lines with distinct response patterns to the BET inhibitor BI 894999 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5194.
Abstract 5196: Vorinostat exhibits anticancer effects through modulation of nuclear receptors and tumor suppressor genes in sub-types of triple negative breast cancer cells
Authors: NouriEmamzadeh Fatemeh , Word Beverly , Cotton Ebony , Littlejohn Kai , Miranda-Carboni Gustavo , Lyn-Cook Beverly
Published: August 2019

Aberrantly expression of histone deacetylases (HDAC) play a critical role in tumorigenesis. The expression of individual HDACs has been shown to correlate to decreases in both, disease-free and overall survival, thus targeting HDACs is emerging as a new therapy for cancer. Histone acetylation is associated with elevated transcription, while deacetylation is associated with gene repression. Emerging evidence suggests their role in triple negative breast cancer (TNBC) progression. TNBC is an aggressive type of cancer that has poor prognosis and molecular studies have shown several subtypes within TNBC. These cancers lack targeted treatments and several options used such as, PARP inhibitors, angiogenesis inhibitors, androgen receptor inhibitors and others have shown limited efficacy, however histone deacetylase inhibitors are showing promising results in clinical trials. Vorinostat, a histone deacetylase inhibitor, also known as suberanilohydroxane acid (SAHA) was approved by the FDA for treatment of cutaneous T cell lymphoma. In this study, vorinostat was investigated in subtypes of TNBC cell lines, MB231(MSL) and two basal-like 2 TNBC cell lines, HCC70 and HCC1806. Cells were treated with vorinostat for 24 hrs. Vorinostat significantly up-regulated the tumor suppressor gene NR4A1 by 20 fold, NR4A3 by 10 fold and AR5A by 5 fold. RORα gene had the highest up-regulation, 60 fold, whereas PPARγ 4.5 fold. Estrogen related receptor A, ESRRA was also up-regulated in HCC70 cells. A decrease in expression was noted in DDX5, which is known to be elevated in basal-like tumors. A different profile was noted in the MB231 TNBC cells. Vorinostat also decreased growth and cell invasion, which shows its functional effects on these aggressive TNBC cell lines These changes suggest that vorinostat, which is currently in clinical trials for TNBC may be exerting its effect through modulation of orphan nuclear receptors and reactivation of tumor suppressor genes through epigenetic mechanisms. Further studies are needed to determine other signaling pathways modulated by this HDAC inhibitor.

Citation Format: Fatemeh NouriEmamzadeh, Beverly Word, Ebony Cotton, Kai Littlejohn, Gustavo Miranda-Carboni, Beverly Lyn-Cook. Vorinostat exhibits anticancer effects through modulation of nuclear receptors and tumor suppressor genes in sub-types of triple negative breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5196.
Abstract 5205: EWS-FLI1 activates HOXD13 expression through enhancer reprogramming
Authors: Apfelbaum April Ann , Svoboda Laurie , Magnuson Brian , Ljungman Mats , Lawlor Elizabeth
Published: August 2019

Ewing sarcomas (ES) are bone tumors of mesenchymal stem cell (MSC) origin. ES is defined by EWS-FLI1 fusions, which initiate tumorigenesis via enhancer reprogramming. Posterior homeobox D (HOXD) genes, in particular HOXD13, are over-expressed by ES, where they function as obligate, cooperative oncogenes. These genes play crucial roles in limb development and spatiotemporal control of HOXD13 expression depends on long-range enhancers that flank the HOXD locus. We hypothesize that HOXD13 is aberrantly activated in the ES cell of origin as a result of EWS-FLI1-dependent hijacking of developmental enhancers.

We interrogated ChIP-seq and RNA-seq data to identify EWS-FLI1 binding sites and HOXD13 activation states in ES cells. These analyses revealed an EWS-FLI1 binding site within the developmentally conserved posterior HOXD enhancer region, which we will refer to as Desert Enhancer 268 (DE268). These sites were also marked with the active enhancer marks, H3K27Ac and H3K4me1. EWS-FLI1 knockdown was associated with loss of EWS-FLI1 binding, loss of H3K27Ac and H3K4me1, and loss of HOXD13 expression. Findings were independently validated by ChIP-qPCR and RT-qPCR. Through BruUV-seq we also identified that DE268 has eRNA expression that is lost upon EWS-FLI1 knockdown. Thus, HOXD13 expression in ES cells is maintained by EWS-FLI1-mediated enhancer activation. To address whether hijacking of HOXD13 enhancers is an initiating event in tumorigenesis, we evaluated enhancer profiles in MSCs ± EWS-FLI1. Whereas DE268 was not active in parent MSC, EWS-FLI1 binding and enhancer activation were evident in EWS-FLI1+ MSC. However, although EWS-FLI1 reproducibly binds and activates DE268, expression of HOXD13 is limited to discrete conditions. Together, these results suggest that EWS-FLI1 is necessary for enhancer activation, but that the fusion is alone is insufficient for induction of HOXD13 expression. Ongoing studies will utilize CRISPRi technologies to determine the contribution of DE268 on HOXD13 gene expression.

Citation Format: April Ann Apfelbaum, Laurie Svoboda, Brian Magnuson, Mats Ljungman, Elizabeth Lawlor. EWS-FLI1 activates HOXD13 expression through enhancer reprogramming [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5205.